,Genome ID,Additional Metadata,Altitude,AntiMicrobial Resistance,AntiMicrobial Resistance Evidence,Assembly Accession,Assembly Method,BRC1 CDS,BioProject Accession,BioSample Accession,Biovar,Body Sample Site,Body Sample Subsite,Cell Shape,Chromosomes,Collection Date,Comments,Completion Date,Contigs,Culture Collection,Date Inserted,Date Modified,Depth,Disease,GC Content,GenBank Accessions,Genome Length,Genome Name,Genome Status,Genus,Geographic Location,Gram Stain,Habitat,Host Age,Host Gender,Host Health,Host Name,Isolation Comments,Isolation Country,Isolation Site,Isolation Source,Latitude,Longitude,MLST,Motility,NCBI Taxon ID,Optimal Temperature,Organism Name,Other Clinical,Other Environmental,Other Typing,Oxygen Requirement,PATRIC CDS,Pathovar,Plasmids,Publication,RefSeq Accessions,RefSeq CDS,Salinity,Sequences,Sequencing Centers,Sequencing Depth,Sequencing Platform,Sequencing Status,Serovar,Sporulation,Strain,Temperature Range,Type Strain,QC/QA
0,1042876.5,,,,,GCA_000219705.1,,,PRJNA67881,SAMN02603862,,,,,1,,-,2011-06-30T00:00:00Z,,,2014-12-08T22:12:39.139Z,2015-03-16T03:17:09.594Z,,,62.32,CP002870,5984790,Pseudomonas putida S16,Complete,Pseudomonas,,,,,,,,,,,,,,,,1042876,-,Pseudomonas putida S16,,,,,5373,,,21914868,NC_015733,5218,,1,Shanghai Jiao Tong University|Chinese National Human Genome Center|Helmoholtz Center for Infection Research,,,complete,,,S16,,,"Included in the study, passed QC/QA"
1,1089456.3,,,,,GCA_000284555.1,GS De Novo Assembler v. 2.3,,PRJNA162173,,,,,,1,,"The MDR P. aeruginosa strain NCGM2.S1 caused an outbreak of urinary tract infection at a hospital in Miyagi Prefecture, northern Japan",2011-09-30T00:00:00Z,,,2014-12-08T22:12:37.664Z,2015-03-16T03:17:09.594Z,,Urinary tract infection,0.661,AP012280.1,6764661,Pseudomonas aeruginosa NCGM2.S1,Complete,Pseudomonas,Japan: Miyagi Prefecture,,,,,,"Human, Homo sapiens",,Japan,,Homo sapiens; urinary tract,,,MLST.Pseudomonas_aeruginosa.235,,1089456,,Pseudomonas aeruginosa NCGM2.S1,,,,,6325,,,22123763,NC_017549.1,6269,,1,,29x,ABI3730xl; 454,assembly,,,NCGM2.S1,,,"Included in the study, passed QC/QA"
2,1093787.3,,,,,GCA_000271365.1,,,PRJNA73815,SAMN02603895,,,,,1,,Complete genome of Pseudomonas aeruginosa DK2 strain isolated from a cystic fibrosis patient.,2012-06-20T00:00:00Z,,,2014-12-08T22:12:37.204Z,2015-03-16T03:17:09.594Z,,Commensal (plant),66.3,CP003149.1,6402658,Pseudomonas aeruginosa DK2,Complete,Pseudomonas,,Negative,Multiple,,,cystic fibrosis,"Human, Homo sapiens",isolated from a cystic fibrosis patient,,,cystic fibrosis patient,,,MLST.Pseudomonas_aeruginosa.386,,1093787,,Pseudomonas aeruginosa DK2,,,,,5984,,,,NC_018080.1,5884,,1,Technical University of Denmark,,,complete,,,DK2,,,"Included in the study, passed QC/QA"
3,1123015.3,,,,,GCF_001045685.1,HGAP3 v. 2.3.0,,PRJNA285827,SAMN03761153,,,,,1,,Complete Genome sequencing of Pseudomonas aeruginosa,2015-08-27T00:00:00Z,,DSM:50071,2016-01-17T16:11:29.561Z,2016-01-17T16:11:29.561Z,,,66.52,CP012001,6317050,Pseudomonas aeruginosa DSM 50071,Complete,Pseudomonas,,,,,,,,,,,,,,,,1123015,C,,,,,Aerobic,5946,,,26294631,NZ_CP012001.1,5710,,1,Okinawa Institute of Advanced Sciences,843x,PacBio,,,,DSM 50071,,,"Included in the study, passed QC/QA"
4,1147787.3,,,,,GCA_000714515.1,Cofactor Genomics' reference-guided,,PRJNA83447,SAMN02740985,,,,Bacilli,1,2011,"P. aeruginosa PAO1 was inoculated in water and isolated after 1 year. This strain, designated PAO1H2O was sequenced and characterized.",2014-06-27T00:00:00Z,1,,2014-12-09T00:32:52.969Z,2015-03-16T03:17:09.594Z,,,66.3,CP008749.1,6264400,Pseudomonas aeruginosa PAO1H2O,Complete,Pseudomonas,"USA: Bluefield, West Virginia",Negative,Multiple,,,,,isolated after 1 year,United States,,water,,,,Yes,1147787,,,,,,Facultative,5738,,,-,-,5544,,1,University of Virginia,370x,Illumina GA IIx,,,,PAO1H2O,Mesophilic,,"Excluded from the study, failed QC/QA."
5,1150601.3,"sample_type:cell culture;biomaterial_provider:Ondrej Uhlik (ondrej.uhlik@vscht.cz), Laboratory of Applied Microbial Ecology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technicka 3 (building B) 166 28 Praha 6 - Dejvice, Czech republic;collected_by:Martina Mackova;identified_by:Ondrej Uhlik",,,,GCF_001767335.1,Newbler v. 2.8,,PRJNA84349,SAMN05290347,,,,Bacilli,1,2000,An environmental isolate capable of growth on several different chlorobenzoates.,2016-10-18T00:00:00Z,,,2016-11-17T08:17:41.736Z,2016-11-17T08:17:41.736Z,,,61.81,CP016212,5846746,Pseudomonas putida JB,Complete,Pseudomonas,Czech Republic: dumpsite Lhenice,Negative,Terrestrial,,,,,,Czech Republic,,PCB contaminated soil,,,,Yes,1150601,30C,,,,,Aerobic,5453,,,,NZ_CP016212.1,5215,,1,Institute of Molecular Genetics of the ASCR,50,454,,,,JB,Mesophilic,,"Included in the study, passed QC/QA"
6,1196325.3,,,,,GCA_000281215.1,,,PRJNA167844,SAMN02603217,,,,,1,,"'Complete genome of the aromatic hydrocarbon-degrading and solvent-tolerant, Pseudomonas putida DOT-T1E.'",2012-07-24T00:00:00Z,,,2014-12-08T22:12:38.983Z,2015-03-16T03:17:09.594Z,,,61.4,CP003734.1,6260702,Pseudomonas putida DOT-T1E,Complete,Pseudomonas,,Negative,,,,,,,,,,,,,,1196325,,Pseudomonas putida DOT-T1E,,,,,5704,,,20139187,NC_018220.1,5721,,1,EEZ-CSIC,,,complete,,,DOT-T1E,,,"Included in the study, passed QC/QA"
7,1211579.3,,,,,GCA_000412675.1,Newbler v. 2.6,,PRJDB191,,,,,Bacilli,1,,Comparative genomics of clinical and environmental Pseudomonas isolates,2013-06-15T00:00:00Z,,,2014-12-08T22:12:39.082Z,2015-03-16T03:17:09.594Z,,,62.3,AP013070.1,6156701,Pseudomonas putida NBRC 14164,Complete,Pseudomonas,,Negative,,,,,,,,,,,,,Yes,1211579,25-30,Pseudomonas putida NBRC 14164,,,,Aerobic,5448,,,,NC_021505.1,5449,,1,National Institute of Technology and Evaluation,0.6x ABI3730; 17.6x GS-FLX Titanium; 94.3x,ABI3730; GS-FLX Titanium; Illumina HiSeq,complete,,No,NBRC 14164,Mesophilic,,"Included in the study, passed QC/QA"
8,1215087.7,,,,,GCF_000495455.2,CLC Genomics Workbench v. 6.5.1,,PRJNA222630,SAMN02470872,,,,Cocci,1,1989,Draft genome sequence of the solvent-tolerant Pseudomonas putida S12 including megaplasmid pTTS12,2015-04-13T00:00:00Z,,ATCC:700801,2016-01-17T15:33:43.931Z,2016-01-17T15:33:43.931Z,,,61.44,AYKV01000000,6382434,Pseudomonas putida S12,Complete,Pseudomonas,Netherlands,Negative,,,,,,,Netherlands,,soil,,,,Yes,1215087,,,,,,,5990,,1,,"NZ_CP009974.1,NZ_CP009975.1",5616,,2,RWTH Aachen University,,Sanger dideoxy sequencing; Illumina;,,,,S12,,,"Included in the study, passed QC/QA"
9,1215088.3,,,,,GCA_000325725.1,1,,PRJNA171349,SAMN02604102,,,,,1,,Multi-Drug resistant,2012-12-19T00:00:00Z,,,2014-12-08T22:12:39.022Z,2015-03-16T03:17:09.594Z,,,62.6,CP003738.1,5875750,Pseudomonas putida HB3267,Complete,Pseudomonas,,,,,,,"Human, Homo sapiens",,,,,,,,,1215088,,Pseudomonas putida HB3267,,,,,5321,,,,NC_019905.1,5292,,1,Universidad de Huelva,,,complete,,,HB3267,,,"Included in the study, passed QC/QA"
10,1279007.3,,,,,GCA_000496605.1,Assembler v. 2.3,,PRJNA185335,SAMN02603191,,,,Bacilli,1,,"We have completed the sequencing of Pseudomonas aeruginosa PA1, which belongs to the Pseudomonadaceae.",2013-11-12T00:00:00Z,, ,2014-12-08T22:12:37.683Z,2015-03-16T03:17:09.594Z,,,66.3,CP004054.1,6528877,Pseudomonas aeruginosa PA1,Complete,Pseudomonas,,Negative,,,,,,,,,,,,MLST.Pseudomonas_aeruginosa.782,,1279007,,Pseudomonas aeruginosa PA1,,,,,6117,,,,NC_022808.1,5799,,1,"Department of Microbiology, The Third Military Medical University",,454,complete,,,PA1,,,"Included in the study, passed QC/QA"
11,1279008.3,,,,,GCA_000496645.1,Assembler v. 2.3,,PRJNA185336,SAMN02603192,,,,Bacilli,1,,"We have been completed the sequencing of Pseudomonas aeruginosa PA1R, which belongs to the Pseudomonadaceae.",2013-11-12T00:00:00Z,, ,2014-12-08T22:12:37.702Z,2015-03-16T03:17:09.594Z,,,66.3,CP004055.1,6309305,Pseudomonas aeruginosa PA1R,Complete,Pseudomonas,,Negative,,,,,,,,,,,,MLST.Pseudomonas_aeruginosa.782,,1279008,,Pseudomonas aeruginosa PA1R,,,,,5916,,,,NC_022806.1,5612,,1,"Department of Microbiology, The Third Military Medical University",,454,complete,,,PA1R,,,"Included in the study, passed QC/QA"
12,1280938.3,,,,,GCA_000359505.1,"ABySS v. July, 2011; Roche Newbler",,PRJNA185969,SAMN02603669,,,,,1,,Characterization of a Psedomonas aeruginosa isolate from an infant with community-acquired diarrhea.,2013-04-09T00:00:00Z,,,2014-12-08T22:12:36.399Z,2015-03-16T03:17:09.594Z,,,66.4,CP004061.1,6421010,Pseudomonas aeruginosa B136-33,Complete,Pseudomonas,,,,,,,"Human, Homo sapiens",isolate from an infant with community-acquired diarrhea,,,infant with community-acquired diarrhea,,,MLST.Pseudomonas_aeruginosa.1024,,1280938,,Pseudomonas aeruginosa B136-33,,,,,5952,,,,NC_020912.1,5828,,1,National Tsing Hua University,,Sanger dideoxy sequencing; 454; Illumina;,complete,,,B136-33,,,"Included in the study, passed QC/QA"
13,1331671.3,,,,,GCA_000410575.1,BLASTN v. actual,,PRJNA202087,SAMN02604103,,,,Bacilli,1,,Sequencing of a Pseudomonas putida clinical isolate.,2013-06-11T00:00:00Z,,,2014-12-08T22:12:39.011Z,2015-03-16T03:17:09.594Z,,,61.6,CP005976.1,6870827,Pseudomonas putida H8234,Complete,Pseudomonas,,Negative,HostAssociated,,,,,,,,,,,,Yes,1331671,,Pseudomonas putida H8234,,,,,6307,,,,NC_021491.1,6357,,1,Universidad de Huelva,25X,454,complete,,,H8234,,,"Included in the study, passed QC/QA"
14,1340851.3,,,,,GCA_000414035.1,Newbler-gsAssembler module v.  2.5.3;,,PRJNA206088,SAMN02603771,,,,,1,,"Complete genome sequence of Pseudomonas aeruginosa RP73, a persistent isolate from a patient with Cystic Fibrosis.",2013-06-24T00:00:00Z,,,2014-12-08T22:12:37.904Z,2015-03-16T03:17:09.594Z,,,66.5,CP006245.1,6342034,Pseudomonas aeruginosa RP73,Complete,Pseudomonas,,,,,,Cystic Fibrosis,"Human, Homo sapiens",isolate from a patient with Cystic Fibrosis,,,patient with Cystic Fibrosis,,,MLST.Pseudomonas_aeruginosa.198,,1340851,,Pseudomonas aeruginosa RP73,,,,,5940,,,,NC_021577.1,5762,,1,"San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Diseases, Milano, Italy",50X,454,complete,,,RP73,,,"Included in the study, passed QC/QA"
15,1352354.3,,,,,GCA_000468555.1,,,PRJNA209856,SAMN02603587,,,,Bacilli,1,,Mucoid variant of P. aeruginosa is associated with chronic lung infection in patients with cystic fibrosis.,2013-09-16T00:00:00Z,, ,2014-12-08T22:12:37.825Z,2015-03-16T03:17:09.594Z,,Cystic fibrosis,66.4,CP006705.1,6043974,Pseudomonas aeruginosa PAO581,Complete,Pseudomonas,,Negative,Multiple,,,,,,,,,,,MLST.Pseudomonas_aeruginosa.549,Yes,1352354,25-37C,Pseudomonas aeruginosa PAO581,,,,Facultative,5655,,,18599839,-,5500,Mesophilic,1,Marshall University School of Medicine,,,complete,,No,PAO581,Mesophilic,,"Included in the study, passed QC/QA"
16,1352355.3,,,,,GCA_000468935.1,Illumina Pipeline v. SCS 2.8.0;,,PRJNA209859,SAMN02603588,,,,Bacilli,1,,Mucoid isolate from a patient with a chronic lung infection with P. aeruginosa.,2013-09-16T00:00:00Z,, ,2014-12-08T22:12:38.118Z,2015-03-16T03:17:09.594Z,,,66.5,CP006728.1,6262305,Pseudomonas aeruginosa c7447m,Complete,Pseudomonas,,Negative,HostAssociated,,,chronic lung infection with P. aeruginosa,"Human, Homo sapiens",isolate from a patient with a chronic lung infection with P. aeruginosa,,,patient with a chronic lung infection with P,,,,Yes,1352355,37C,Pseudomonas aeruginosa c7447m,,,,Facultative,5805,,,24115552,-,5657,Unknown,1,Marshall University School of Medicine,224X,Illumina GAIIX,complete,,No,c7447m,Mesophilic,,"Included in the study, passed QC/QA"
17,1356855.3,,,Susceptible,Computational Prediction,,,,PRJEB9823,SAMEA3484633,,,,,1,1997,"Pseudomonas aeruginosa is an important opportunistic pathogen associated with chronic pulmonary infections and mortality in cystic fibrosis (CF) patients. Here, we present the complete genome sequence of stable mucoid P. aeruginosa strain DK1-NH57388A, a CF isolate which has previously been used to establish chronic lung infections in an animal model.",2015-11-03T00:00:00Z,,,2017-07-23T07:40:40.496Z,2017-07-23T07:40:40.496Z,,,66.57,LN870292,6212531,Pseudomonas aeruginosa DK1 strain DK1,Complete,Pseudomonas,Denmark,,,,,,"Human, Homo sapiens",,,,sputum,,,,,1356855,,,,,,,5813,,,,,5640,,1,DTU Systems Biology,,,,,,DK1,,,"Included in the study, passed QC/QA"
18,1367493.3,,,,,GCA_000484495.1,Novocraft novoalign v. 2.07.13,,PRJNA212861,SAMN02603589,,,,Bacilli,1,,Understand the mechanism of mucoid biofilm formation in Cystic Fibrosis,2013-10-28T00:00:00Z,, ,2014-12-08T22:12:37.806Z,2015-03-16T03:17:09.594Z,,Cystic fibrosis,66.6,CP006831.1,6265484,Pseudomonas aeruginosa PAO1-VE2,Complete,Pseudomonas,,Negative,HostAssociated,,,,,,,,,,,MLST.Pseudomonas_aeruginosa.549,Yes,1367493,37C,Pseudomonas aeruginosa PAO1-VE2,,,,Aerobic,5837,,,24336371,-,5670,Mesophilic,1,Marshall University School of Medicine,375.56x,Illumina,complete,,No,PAO1-VE2,Mesophilic,,"Included in the study, passed QC/QA"
19,1367494.3,,,,,GCA_000484545.1,Novocraft novoalign v. 2.07.13,,PRJNA212862,SAMN02603590,,,,Bacilli,1,,Understand the mechanism of mucoid biofilm formation in Cystic Fibrosis.,2013-10-28T00:00:00Z,, ,2014-12-08T22:12:37.796Z,2015-03-16T03:17:09.594Z,,Cystic fibrosis,66.6,CP006832.1,6265484,Pseudomonas aeruginosa PAO1-VE13,Complete,Pseudomonas,,Negative,HostAssociated,,,,,,,,,,,MLST.Pseudomonas_aeruginosa.549,Yes,1367494,37C,Pseudomonas aeruginosa PAO1-VE13,,,,Aerobic,5833,,,24336371,-,5671,Mesophilic,1,Marshall University School of Medicine,356.67x,Illumina,complete,,No,PAO1-VE13,Mesophilic,,"Included in the study, passed QC/QA"
20,1407059.3,,,,,GCA_000531435.1,,,PRJEB4573,SAMEA3138907,,,,,1,,"A series of extensively drug-resistant (XDR) isolates of Pseudomonas aeruginosa from two outbreaks in UK hospitals were characterized by whole genome sequencing (WGS). Although these isolates were resistant to antibiotics other than colistin, we confirmed that they are still sensitive to disinfectants. The sequencing confirmed that isolates in the larger outbreak were serotype O12 and further revealed that they belonged to the ST111 sequence type which is a major epidemic strain of P. aeruginosa throughout Europe. As this is the first reported sequence of an ST111 strain, the genome was examined in depth, focusing particularly on antibiotic resistance and potential virulence genes, and on the reported regions of genome plasticity. High degrees of sequence similarity were discovered between outbreak isolates collected from recently infected patients, sinks, an isolate from the sewer and an historical isolate, suggesting that the ST111 strain has been endemic in the hospital for many years. The ability to translate easily from outbreak investigation to detailed genome biology using the same data demonstrates the flexibility of WGS application in a clinical setting.",2014-01-23T00:00:00Z,1,,2014-12-08T22:42:01.328Z,2015-03-16T03:17:09.594Z,,,64.9,HG530068.1,7586150,Pseudomonas aeruginosa PA38182,Complete,Pseudomonas,,,,,,,"Human, Homo sapiens","isolate from the sewer and an historical isolate, suggesting that the ST111 strain has been endemic in the hospital for many years",,,"the sewer and an historical isolate, suggesting that the ST111 strain has been endemic",,,,,1407059,,,,,,,7206,,,-,NZ_HG530068.1,7279,,1,BUGS,,,,serovar O12,,PA38182,,,"Excluded from the study, failed QC/QA."
21,1408271.3,,,,,GCA_000583935.1,GS De novo assembler v. 2.6; Consed v.,,PRJNA222517,SAMN03081517,,,,,1,,The aim of this study was to generate high-quality genome sequences for 7 isolates of the Liverpool epidemic strain (LES) from both the UK and Canada representing different virulence characteristics,2014-03-03T00:00:00Z,, ,2014-12-08T22:12:37.463Z,2015-03-16T03:17:09.594Z,,,66.3,CP006982.1,6591121,Pseudomonas aeruginosa LES400,Complete,Pseudomonas,,,,,,,,7 isolates of the Liverpool epidemic strain (LES) from the UK and Canada,,,,,,MLST.Pseudomonas_aeruginosa.146,,1408271,,Pseudomonas aeruginosa LES400,,,,,6183,,,,-,6015,,1,"'IBIS, University Laval'",19.0x,Sanger dideoxy sequencing; 454,complete,,,LES400,,,"Included in the study, passed QC/QA"
22,1408272.3,,,,,GCA_000508765.1,GS De novo Assembler v. 2.6; Consed v.,,PRJNA222518,SAMN02641592,,,,,1,,The aim of this study was to generate high-quality genome sequences for 7 isolates of the Liverpool epidemic strain (LES) from the UK and Canada representing different virulence characteristics,2013-12-17T00:00:00Z,, ,2014-12-08T22:12:37.472Z,2015-03-16T03:17:09.594Z,,,66.3,CP006937.1,6550070,Pseudomonas aeruginosa LES431,Complete,Pseudomonas,,,,,,,,,,,,,,MLST.Pseudomonas_aeruginosa.146,,1408272,,Pseudomonas aeruginosa LES431,,,,,6135,,,,NC_023066.1,5964,,1,"IBIS, University Laval",50X,Sanger dideoxy sequencing; 454,complete,,,LES431,,,"Included in the study, passed QC/QA"
23,1408273.3,,,,,GCA_000583955.1,GS De novo assembler v. 2.6; Consed v.,,PRJNA222519,SAMN03081518,,,,,1,,The aim of this study was to generate high-quality genome sequences for 7 isolates of the Liverpool epidemic strain (LES) from the UK and Canada representing different virulence characteristics,2014-03-03T00:00:00Z,, ,2014-12-08T22:12:37.492Z,2015-03-16T03:17:09.594Z,,,66.4,CP006983.1,6527005,Pseudomonas aeruginosa LESB65,Complete,Pseudomonas,,,,,,,,7 isolates of the Liverpool epidemic strain (LES) from the UK and Canada,,,,,,MLST.Pseudomonas_aeruginosa.146,,1408273,,Pseudomonas aeruginosa LESB65,,,,,6136,,,,-,5952,,1,"'IBIS, University Laval'",30.0x,Sanger dideoxy sequencing; 454,complete,,,LESB65,,,"Included in the study, passed QC/QA"
24,1408274.3,,,,,GCA_000583975.1,GS De novo assembler v. 2.6; Consed v.,,PRJNA222520,SAMN03081519,,,,,1,,The aim of this study was to generate high-quality genome sequences for 7 isolates of the Liverpool epidemic strain (LES) from the UK and Canada representing different virulence characteristics,2014-03-03T00:00:00Z,, ,2014-12-08T22:12:37.500Z,2015-03-16T03:17:09.594Z,,,66.4,CP006984.1,6509070,Pseudomonas aeruginosa LESlike1,Complete,Pseudomonas,,,,,,,,7 isolates of the Liverpool epidemic strain (LES) from the UK and Canada,,,,,,MLST.Pseudomonas_aeruginosa.146,,1408274,,Pseudomonas aeruginosa LESlike1,,,,,6113,,,,-,5927,,1,"'IBIS, University Laval'",18.0x,Sanger dideoxy sequencing; 454,complete,,,LESlike1,,,"Included in the study, passed QC/QA"
25,1408275.3,,,,,GCA_000583995.1,GS de novo assembler v. 2.6; Consed v.,,PRJNA222521,SAMN03081520,,,,,1,,The aim of this study was to generate high-quality genome sequences for 7 isolates of the Liverpool epidemic strain (LES) from the UK and Canada representing different virulence characteristics,2014-03-03T00:00:00Z,, ,2014-12-08T22:12:37.509Z,2015-03-16T03:17:09.594Z,,,66.4,CP006985.1,6524053,Pseudomonas aeruginosa LESlike4,Complete,Pseudomonas,,,,,,,,7 isolates of the Liverpool epidemic strain (LES) from the UK and Canada,,,,,,MLST.Pseudomonas_aeruginosa.683,,1408275,,Pseudomonas aeruginosa LESlike4,,,,,6112,,,,-,5952,,1,"'IBIS, University Laval'",30.0x,Sanger dideoxy sequencing; 454,complete,,,LESlike4,,,"Included in the study, passed QC/QA"
26,1408276.3,,,,,GCA_000583895.1,GS De novo assembler v. 2.6; Consed v.,,PRJNA222522,SAMN03081515,,,,,1,,The aim of this study was to generate high-quality genome sequences for 7 isolates of the Liverpool epidemic strain (LES) from the UK and Canada representing different virulence characteristics,2014-03-03T00:00:00Z,, ,2014-12-08T22:12:37.518Z,2015-03-16T03:17:09.594Z,,,66.4,CP006980.1,6543350,Pseudomonas aeruginosa LESlike5,Complete,Pseudomonas,,,,,,,,7 isolates of the Liverpool epidemic strain (LES) from the UK and Canada,,,,,,MLST.Pseudomonas_aeruginosa.146,,1408276,,Pseudomonas aeruginosa LESlike5,,,,,6141,,,,-,5955,,1,"'IBIS, University Laval'",26.0x,Sanger dideoxy sequencing; 454,complete,,,LESlike5,,,"Included in the study, passed QC/QA"
27,1408277.3,,,,,GCA_000583915.1,GS De novo assembler v. 2.6; Consed v.,,PRJNA222523,SAMN03081516,,,,,1,,The aim of this study was to generate high-quality genome sequences for 7 isolates of the Liverpool epidemic strain (LES) from the UK and Canada representing different virulence characteristics,2014-03-03T00:00:00Z,, ,2014-12-08T22:12:37.527Z,2015-03-16T03:17:09.594Z,,,66.5,CP006981.1,6467914,Pseudomonas aeruginosa LESlike7,Complete,Pseudomonas,,,,,,,,7 isolates of the Liverpool epidemic strain (LES) from the UK and Canada,,,,,,MLST.Pseudomonas_aeruginosa.146,,1408277,,Pseudomonas aeruginosa LESlike7,,,,,6063,,,,-,5873,,1,"'IBIS, University Laval'",23.0x,Sanger dideoxy sequencing; 454,complete,,,LESlike7,,,"Included in the study, passed QC/QA"
28,1415629.8,,,,,GCF_000504045.1,Newbler v. 2.8,,PRJNA225944,SAMN02389526,,,,,1,,Complete genome sequencing to gain insight into the bacterial community that can degrade man-made chemicals.,2014-03-04T00:00:00Z,,,2016-01-17T15:33:54.718Z,2016-01-17T15:33:54.718Z,,,66.24,CP006853,6580038,Pseudomonas aeruginosa MTB-1,Complete,Pseudomonas,India,,,,,,,,India,,t-HCH contaminated soil,,,,,1415629,,,,,,,6284,,,24459257,NC_023019.1,6078,,1,Tohoku University,120x,454; Illumina,,,,MTB-1,,,"Included in the study, passed QC/QA"
29,1427342.3,,,,,GCA_000510305.1,HGAP SMRTPortal v. 2.0.1,,PRJNA229445,SAMN02415141,,,,,1,,Complete genome sequence of highly adherent P.aeruginosa small-colony variant SCV20265,2013-12-18T00:00:00Z,, ,2014-12-08T22:12:37.932Z,2015-03-16T03:17:09.594Z,,Cystic fibrosis,66.3,CP006931.1,6725183,Pseudomonas aeruginosa SCV20265,Complete,Pseudomonas,,Negative,HostAssociated,,,,"Human, Homo sapiens",,,,,,,MLST.Pseudomonas_aeruginosa.299,Yes,1427342,,Pseudomonas aeruginosa SCV20265,,,,,6312,,,,NC_023149.1,6299,,1,Helmholtz Center for Infection Research,135x,PacBio; Illumina GAIIx,complete,,,SCV20265,,,"Included in the study, passed QC/QA"
30,1448140.3,,,,,GCA_000524595.1,HGAP v. unknown,,PRJNA234476,SAMN02641599,,,,,1,,to perform whole genome sequencing of the QS bacteria isolates.,2014-01-30T00:00:00Z,, ,2014-12-08T22:12:38.102Z,2015-03-16T03:17:09.594Z,,,66.4,CP007147.1,6433441,Pseudomonas aeruginosa YL84,Complete,Pseudomonas,Malaysia,,,,,,,,Malaysia,,compost,,,,,1448140,,Pseudomonas aeruginosa YL84,,,,,5992,,,24699957,NZ_CP007147.1,5821,,1,UNIVERSITY OF MALAYA,210.43x,Pacific Biosciences RS II,complete,,,YL84,,,"Included in the study, passed QC/QA"
31,1457392.3,,,,,GCA_000626655.2,Newbler v. 2.1.1; MapSolver v. 2.1.1,,PRJNA237015,SAMN03081533,,,,Bacilli,1,,"clinical isolate, host of plasmid pOZ176",2014-04-11T00:00:00Z,2,,2014-12-09T00:46:20.094Z,2015-03-16T03:17:09.594Z,,,65.6726,CP007224.1,6944930,Pseudomonas aeruginosa PA96,Complete,Pseudomonas,,Negative,,,,,,,,,,,,,Yes,1457392,,,,,,,5963,,,23716048,-,5837,,1,Universite Laval,26x,454/GS FLX Titanium Chemistry,,,No,PA96,,,"Included in the study, passed QC/QA"
32,160488.4,,,,,GCA_000007565.1,,,PRJNA267,SAMN02603999,,,,Rod,1,," Pseudomonas putida strain KT2440. This strain was derived from a toluene-degrading isolate, Pseudomonas arvilla strain mt-2 (renamed Pseudomonas putida mt-2), by loss of its plasmid. It is the best characterized saprophytic bacteria, and the choice for cloning and gene expression in Gram-negative bacteria and can survive in the general environment (outside the laboratory). It is used in the development of biopesticides and is the first Gram-negative soil bacterium to be certified as a safety strain by the Recombinant DNA Advisory Committee.",2003-01-22T00:00:00Z,,,2014-12-08T22:12:39.036Z,2015-03-16T03:17:09.594Z,,,61.5,AE015451,6181863,Pseudomonas putida KT2440,Complete,Pseudomonas,,-,Multiple,,,,,"derived from a toluene-degrading isolate, Pseudomonas arvilla strain mt-2 (renamed Pseudomonas putida mt-2), by loss of its plasmid",,,"toluene-degrading isolate, Pseudomonas arvilla strain mt-2 (renamed Pseudomonas putida mt-2),",,,,Yes,160488,-,Pseudomonas putida KT2440,,,,Aerobic,5777,,,12534463,NC_002947,5350,,1,TIGR,,,complete,,,KT2440,Mesophilic,,"Included in the study, passed QC/QA"
33,208963.12,,,,,GCA_000014625.1,,,PRJNA386,SAMN02603591,,,,Rod,1,," Pseudomonas aeruginosa strain UCBPP-PA14. This strain is a human clinical isolate from a human burn patient. It is infectious in mice, Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana. It is an excellent model for the study of pathogenesis and biofilm formation.",2006-10-06T00:00:00Z,,,2014-12-08T22:12:37.968Z,2015-03-16T03:17:09.594Z,,,66.3,CP000438,6537648,Pseudomonas aeruginosa UCBPP-PA14,Complete,Pseudomonas,,-,Multiple,,,,"Human, Homo sapiens",isolate from a human burn patient,,,human burn patient,,,MLST.Pseudomonas_aeruginosa.253,Yes,208963,25-30,Pseudomonas aeruginosa UCBPP-PA14,,,,Aerobic,6022,,,17038190,NC_008463,5892,,1,Massachusetts General Hospital|Harvard Medical School Partners Healthcare Center for Genetics and Genomics,,,complete,,,UCBPP-PA14,Mesophilic,,"Included in the study, passed QC/QA"
34,208964.12,,,,,GCA_000006765.1,,,PRJNA331,,,,,Rod,1,," Pseudomonas aeruginosa strain PA01. This strain contains one of the largest bacterial genomes ever sequenced which consists of a circular chromosome of 6,264,403 bp. It is the most widely used Pseudomonas aeruginosa laboratory strain.",2000-09-13T00:00:00Z,,,2014-12-08T22:12:37.777Z,2015-03-16T03:17:09.594Z,,,66.6,AE004091,6264404,Pseudomonas aeruginosa PAO1,Complete,Pseudomonas,,-,Multiple,,,,,,,,,,,MLST.Pseudomonas_aeruginosa.549,Yes,208964,25-30,Pseudomonas aeruginosa PAO1,,,,Aerobic,5836,,,"10984043,15608211,18978025",NC_002516,5566,,1,PathoGenesis Corporation,,,complete,,,PAO1,Mesophilic,,"Included in the study, passed QC/QA"
35,231023.4,,,,,GCA_000264665.1,,,PRJNA162897,SAMN02603188,,,,,1,,Complete nucleotide sequence of plasmid pND6-2 from Pseudomonas putida ND6 and characterization of conjugative genes.,2012-05-29T00:00:00Z,,,2014-12-08T22:12:39.092Z,2015-03-16T03:17:09.594Z,,,15.9055,"CP003588.1,CP003589.1",6202452,Pseudomonas putida ND6,Complete,Pseudomonas,,,,,,,,,,,,,,,,231023,,Pseudomonas putida ND6,,,,,5558,,1,,NC_017986.1,6289,,2,Department of Microbiology of Nankai University,,,complete,,,ND6,,,"Included in the study, passed QC/QA"
36,287.1306,,,,,GCA_000816985.1,HGAP v. 2,,PRJNA237986,SAMN026733269,,,,,1,,Pseudomonas aeruginosa isolate from infected cancer patients,2015-01-09T00:00:00Z,1,,2015-03-12T13:51:22.729Z,2015-03-16T03:17:09.594Z,,,66.22,CP007399.1,6603099,Pseudomonas aeruginosa F22031,Complete,Pseudomonas,,,,,,,,,,,,,,,,287,,,,,,,6114,,,-,NZ_CP007399.1,6077,,1,MSKCC,111x,PacBio,,,,F22031,,,"Included in the study, passed QC/QA"
37,287.1307,,,,,GCA_000829255.1,Minimus2 v. 3.1.0,,PRJDB3032,SAMD00019082,,,,,1,,"Multidrug-resistant Pseudomonas aeruginosa has become a threating nosocomial pathogen worldwide. P. aeruginosa NCGM1984 clinical isolate harbors a metallo-beta-lactamase gene blaIMP-41 and aminoglycoside 6'-N-acetyltransferase gene aac(6') gene, which are associated with highly multidrug-resistance. In order to clarify the mechanism of the acquisition of drug-resistant genes, the complete genome sequence of the NCGM1984 was determined.",2014-09-18T00:00:00Z,1,,2015-03-12T13:51:23.601Z,2015-03-16T03:17:09.594Z,,,65.96,AP014646.1,6850954,Pseudomonas aeruginosa NCGM 1984,Complete,Pseudomonas,,,,,,,,,,,,,,,,287,,,,,,,6388,,,-,NZ_AP014646.1,6282,,1,National Center for Global Health and Medicine,533x,PacBio RSII,,,,NCGM1984,,,"Included in the study, passed QC/QA"
38,287.1308,,,,,GCA_000829275.1,Minimus2 v.3.1.0,,PRJDB2972,SAMD00018700,,,,,1,,"Multidrug-resistant Pseudomonas aeruginosa has become a threating nosocomial pathogen worldwide. P. aeruginosa NCGM1900 clinical isolate harbors a metallo-beta-lactamase gene blaIMP-34 and aminoglycoside 6'-N-acetyltransferase gene aac(6')-Ib, which are associated with highly multidrug-resistance. In order to clarify the mechanism of the acquisition of drug-resistant genes, the complete genome sequence of the NCGM1900 was determined.",2014-08-01T00:00:00Z,1,,2015-03-12T13:51:24.487Z,2015-03-16T03:17:09.594Z,,,65.98,AP014622.1,6814936,Pseudomonas aeruginosa NCGM 1900,Complete,Pseudomonas,,,,,,,,,,,,,,,,287,,,,,,,6353,,,-,NZ_AP014622.1,6358,,1,"Department of Infectious Diseases, National Center for Global Health and Medicine",554x,PacBio RSII,,,,NCGM1900,,,"Included in the study, passed QC/QA"
39,287.1309,,,,,GCA_000829885.1,BioNumerics v. 6.6,,PRJNA245215,SAMN02732380,,,,,1,1979,Complete Genome Sequence of Pseudomonas aeruginosa mucoid strain FRD1 isolated from a cystic fibrosis patient,2015-01-29T00:00:00Z,1,,2015-03-12T13:51:24.806Z,2015-03-16T03:17:09.594Z,,,66.09,CP010555.1,6712339,Pseudomonas aeruginosa FRD1,Complete,Pseudomonas,USA: Oregon,,,,,,"Human, Homo sapiens",,United States,,the sputum of a cystic fibrosispatient,,,,,287,,,,,,,6314,,,"3102460,2160929,8444793,7686997,8394313,7928961,8932318,9171421,9457868,9473053,10383954,11208804,12003941,12426404,12581364,16177314,16267280,16585775,18524916,21358759",NZ_CP010555.1,5852,,1,Mercer University,353,Illumina,,,,FRD1,,,"Included in the study, passed QC/QA"
40,287.1484,biomaterial_provider:USAMRIID,,,,GCF_000743405.1,Newbler v. 2.6; Velvet v. 1.2.08; AllPaths,,PRJNA244576,SAMN02870863,,,,,,,Genome sequencing of Pseudomonas aeruginosa PAG,2014-08-25T00:00:00Z,1,,2016-01-17T15:38:58.902Z,2016-01-17T15:38:58.902Z,,,66.11,JOVK01000000,6820284,Pseudomonas aeruginosa strain PAG,Complete,Pseudomonas,,,,,,,,,,,,,,,,287,,,,,,,6504,,,,,6295,,1,Los Alamos National Laboratory,163.0x,454; Illumina,,,,PAG,,,"Included in the study, passed QC/QA"
41,287.1485,,,,,GCF_000750905.1,,,PRJEB5488,SAMEA3139100,,,,,,,"Bacterial infections causing mastitis in sheep can result in severe economic losses for farmers. A large survey of milk samples from ewes with mastitis in Sardinia, Italy, indicated an increasing prevalence of Pseudomonas aeruginosa infections. Using quantitative PCR to determine the expression of P. aeruginosa genes directly in mastitis-associated ovine milk samples, we found that gene expression profiles resembled those obtained for strain PAO1 grown as a biofilm, rather than grown to exponential or stationary phase. Furthermore, we report the phenotypic and genomic characterisation of two clonal P. aeruginosa isolates (PSE305 and PSE306) from a mastitis infection outbreak, representing distinct colony morphology variants. In addition to pigment production, PSE305 and PSE306 differed in phenotypic characteristics including biofilm formation, utilisation of various carbon and nitrogen sources, twitching motility. We found higher levels of expression of genes associated with biofilm formation (pelB) and twitching motility (flgD) in PSE305, compared to the biofilm and twitching-defective PSE306. Comparative genomics analysis revealed single nucleotide polymorphisms (SNPs) and minor insertion / deletion variations between PSE305 and PSE306, including a SNP mutation in the pilP gene of PSE306. By introducing a wild-type pilP gene we were able to partially complement the defective twitching motility of PSE306. There were also three larger regions of difference between the two genomes, indicating genomic instability. Hence, we have demonstrated that P. aeruginosa population divergence can occur during an outbreak of mastitis, leading to significant variations in phenotype and genotype, and resembling the behaviour of P. aeruginosa during some chronic respiratory infections.",2015-02-13T00:00:00Z,1,,2016-01-17T15:39:24.900Z,2016-01-17T15:39:24.900Z,,,65.31,HG974234,6762448,Pseudomonas aeruginosa strain PSE305,Complete,Pseudomonas,,,,,,,,,,,,,,,,287,,,,,,,6557,,,25475851,,6463,,1,IGH,,,,,,PSE305,,,"Excluded from the study, failed QC/QA."
42,287.1491,,,,,GCF_000981825.1,CLC NGS Cell v. 6.5.1,,PRJNA281807,SAMN03389320,,,,,1,2012-04-16,"In the recent years, the blaVIM+ P. aeruginosa strains reoccurred multiple times at different locations and patients in and around the hospital. To investigate these specific strains, two genome sequencing projects were performed on P. aeruginosa isolates to determine antibiotic resistance and specific phenotypical reoccurrence in combination with biofilm formation. The genomes sequenced in this project differ from previously described projects by their genome size and complexity.",2015-04-29T00:00:00Z,,,2016-01-17T15:55:31.615Z,2016-01-17T15:55:31.615Z,,,65.6,CP011317,7497593,Pseudomonas aeruginosa strain Carb01 63,Complete,Pseudomonas,Netherlands:Rotterdam,,,,,,,,Netherlands,,Microbial feature,,,,,287,C,,,,,,7347,,,,NZ_CP011317.1,6900,,1,Maasstad Hospital,98.0x,PacBio,,,,Carb01 63,,,"Included in the study, passed QC/QA"
43,287.1494,,,,,GCF_000988505.1,CLC NGS Cell v. 6.5.1,,PRJNA277811,SAMN03396926,,,,,,2013-11-06,"In the recent years, the blaVIM+ P. aeruginosa strains reoccurred multiple times at different locations and patients in and around the hospital. To investigate these specific strains, two genome sequencing projects were performed on P. aeruginosa isolates to determine antibiotic resistance and specific phenotypical reoccurrence in combination with biofilm formation. The genomes sequenced in this project differ from previously described projects by their genome size and complexity.",2015-05-06T00:00:00Z,1,,2016-01-17T15:57:01.861Z,2016-01-17T15:57:01.861Z,,,65.83,"CP011369,CP011370",7259150,Pseudomonas aeruginosa strain S04 90,Complete,Pseudomonas,Netherlands: Rotterdam,,,,,,"Human, Homo sapiens",,Netherlands,,Microbial mat material,,,,,287,,,,,,,7136,,1,,,6720,,2,Maasstad Hospital,98.0x,PacBio,,,,S04 90,,,"Included in the study, passed QC/QA"
44,287.1773,"collected_by:Mayo Clinic Department of Laboratory Medicne and Pathology, Division of Clinical Microbiology",,,,GCF_001086805.1,Spades v. 3.1.0; Velvet v. 1.2.10,,PRJNA287647,SAMN03787337,,,,,,13-Apr-2014,"Pseudomonas aeruginosa (class: gamma-proteobacteria) is an important opportunistic pathogen in the immunocompromised, classically associated with outbreaks in hospital burn units. The complete genome sequences of 8 clinical isolates, from a single care facility, were obtained for epidemiological studies of relatedness (i.e. clonality).",2015-07-17T00:00:00Z,1,,2016-01-17T16:22:58.140Z,2016-01-17T16:22:58.140Z,,,65.98,LFMT01000000,6879005,Pseudomonas aeruginosa strain BTP036,Complete,Pseudomonas,"USA: Rochester, Minnesota",,,,,Not Collected,"Human, Homo sapiens",,United States,,Associated Infection,,,,,287,C,,,,,,6518,,,,,,,1,The Mayo Clinic,75x,Illumina MiSeq,,,,BTP036,,,"Included in the study, passed QC/QA"
45,287.1866,"sample_type:cell culture;biomaterial_provider:Department of Microbiology, Third Military Medical University, 30# Gaotanyan St., Shapingba District, Chongqing, China;collected_by:Shuguang Lu;identified_by:Shuguang Lu;lab_host:not applicable;mating_type:not applicable;passage_history:3 passages, LB medium;specimen_voucher:not applicable",not applicable,,,GCF_001293085.1,RS_HGAP_Assembly v. 2.0,,PRJNA295473,SAMN04074798,,,,,1,15-May-2014,Pseudomonas aeruginosa PA1RG is a phage-resistant mutant of Pseudomonas aeruginosa PA1 (NC_022808). The goal of this study is to reveal the phage-resistant mechanisms.,2015-09-17T00:00:00Z,,not applicable,2016-01-17T17:09:32.480Z,2016-01-17T17:09:32.480Z,sediment,,66.34,CP012679,6500439,Pseudomonas aeruginosa strain PA1RG,Complete,Pseudomonas,China: Chongqing,,,,,,,,China,,,,,,,287,37 C,,,,genotype:not applicable,,6186,,,,NZ_CP012679.1,5910,,1,Third Military Medical University,320,PacBio,,not applicable,,PA1RG,,,"Included in the study, passed QC/QA"
46,287.1997,,,,,GCA_001447845.1,BGI Hybrid Assembler v. SEP-2015,,PRJNA302926,SAMN04284690,,,,,1,,Genome sequence of a highly virulent Pseudomonas aeruginosa strain VA-134 isolated from burn patient,2015-11-24T00:00:00Z,,,2016-01-17T17:49:04.280Z,2016-01-17T17:49:04.280Z,,Skin wound infection of burn patient,66.42,CP013245,6400418,Pseudomonas aeruginosa strain VA-134,Complete,Pseudomonas,,,HostAssociated,,,,"Human, Homo sapiens",,,,Skin wound of burn human patient,,,,,287,C,,,,,Aerobic,6020,,,,NZ_CP013245.1,5729,,1,The Forsyth Institute,200x,PacBio; Illumina HiSeq,,,,VA-134,Mesophilic,,"Included in the study, passed QC/QA"
47,287.2005,sample_type:Cell culture,,,,GCF_001077475.1,HGAP v. 3,,PRJNA289296,SAMN03852256,,,,,1,2009,"Pseudomonas aeruginosa is the one of the most well studied human pathogens, strain F9676 was isolated from a diseased rice sample in 2009.",2015-07-13T00:00:00Z,,,2016-01-17T16:20:39.419Z,2016-01-17T16:20:39.419Z,,,66.47,CP012066,6368008,Pseudomonas aeruginosa strain F9676,Complete,Pseudomonas,China: Hangzhou,,,,,,"Rice, Oryza sativa",isolated from a diseased rice sample in 2009,China,,diseased rice sample,,,,,287,C,,,,,,5974,,,,NZ_CP012066.1,5721,,1,China National Rice Research Institute,100,PacBio,,,,F9676,,,"Included in the study, passed QC/QA"
48,287.2537,,,,,GCF_001457615.1,,,PRJEB6403,SAMEA2479570,,,,,1,1963,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,2015-05-09T00:00:00Z,,,2016-01-30T13:26:38.601Z,2016-01-30T13:26:38.601Z,,,66.52,LN831024,6316979,Pseudomonas aeruginosa strain NCTC10332,Complete,Pseudomonas,Czech Republic: Prague,,,,,,,,Czech Republic,,not known,,,,,287,,,host_health_state:not known,,,,5978,,,,NZ_LN831024.1,5760,,1,SC,,,,not known,,NCTC10332,,,"Included in the study, passed QC/QA"
49,287.2538,,,,,GCA_001465155.1,velvet v. 1.2.01,,PRJNA296749,SAMN04102969,,,,,1,2014,help with disposal of industrial waste water,2015-12-10T00:00:00Z,,,2016-01-31T00:15:21.372Z,2016-01-31T00:15:21.372Z,,,66.65,CP013144,6123018,Pseudomonas aeruginosa strain Cu1510,Complete,Pseudomonas,China,,Aquatic,,,,,,China,,water,,,MLST.Pseudomonas_aeruginosa.137,,287,30 C,,,,,,5959,,,,,5310,,1,njut,199x,Illumina,,,,Cu1510,,,"Included in the study, passed QC/QA"
50,287.2542,,,,,GCF_001482325.1,BGI Hybrid Assembler v. SEP-2015,,PRJNA306518,SAMN04351367,,,,,1,,"Pseudomonas aeruginosa is an opportunistic pathogen that frequently infects wounds, significantly impairs wound healing, and causes mortality in burn patients. Here we report the genome sequence of a virulent strain of P. aeruginosa, 12-4-4(59), isolated from the blood culture of a burn patient.",2015-12-24T00:00:00Z,,,2016-01-31T21:04:06.159Z,2016-01-31T21:04:06.159Z,,septicemia,66.35,CP013696,6431911,Pseudomonas aeruginosa strain 12-4-4(59),Complete,Pseudomonas,,,HostAssociated,,,,"Human, Homo sapiens",isolated from the blood culture of a burn patient,,,Blood culture of burn human patient,,,MLST.Pseudomonas_aeruginosa.152,,287,C,,,,,Aerobic,6099,,,,NZ_CP013696.1,5813,,1,The Forsyth Institute,200x,PacBio; Illumina HiSeq,,,,12-4-4(59),Mesophilic,,"Included in the study, passed QC/QA"
51,287.2548,isolate:S86968;collected_by:Memorial Hospital,,,,GCF_001515845.1,HGAP v. 3,,PRJNA253624,SAMN02894350,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:05:40.170Z,2016-02-02T21:05:40.170Z,,,66.04,CP008865,6951288,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.155,,287,,,,,,,6624,,,,,6218,,1,MSKCC,64.94x,PacBio,,,,,,,"Included in the study, passed QC/QA"
52,287.2549,isolate:T38079;collected_by:Memorial Hospital,,,,GCF_001515915.1,HGAP v. 3,,PRJNA253624,SAMN02894349,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:05:46.203Z,2016-02-02T21:05:46.203Z,,,66.15,CP008866,6809437,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.155,,287,,,,,,,6469,,,,,5996,,1,MSKCC,79.71x,PacBio,,,,,,,"Included in the study, passed QC/QA"
53,287.255,isolate:T52373;collected_by:Memorial Hospital,,,,GCF_001516005.1,HGAP v. 3,,PRJNA253624,SAMN02894348,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:05:59.874Z,2016-02-02T21:05:59.874Z,,,66.51,CP008867,6322459,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,,,287,,,,,,,5938,,,,NZ_CP008867.1,5517,,1,MSKCC,77.25x,PacBio,,,,,,,"Included in the study, passed QC/QA"
54,287.2551,isolate:T63266;collected_by:Memorial Hospital,,,,GCF_001516105.1,HGAP v. 3,,PRJNA253624,SAMN02894347,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:05:55.162Z,2016-02-02T21:05:55.162Z,,,66.33,CP008868,6456866,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.132,,287,,,,,,,6148,,,,NZ_CP008868.1,5749,,1,MSKCC,62.19x,PacBio,,,,,,,"Included in the study, passed QC/QA"
55,287.2552,isolate:W16407;collected_by:Memorial Hospital,,,,GCF_001516165.1,HGAP v. 3,,PRJNA253624,SAMN02894346,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:06:13.094Z,2016-02-02T21:06:13.094Z,,,65.93,CP008869,6829406,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.244,,287,,,,,,,6567,,,,,6034,,1,MSKCC,75x,PacBio,,,,,,,"Included in the study, passed QC/QA"
56,287.2553,isolate:W36662;collected_by:Memorial Hospital,,,,GCF_001516185.1,HGAP v. 3,,PRJNA253624,SAMN02894345,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:06:18.140Z,2016-02-02T21:06:18.140Z,,,66.17,CP008870,6804266,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.17,,287,,,,,,,6479,,,,,6095,,1,MSKCC,82.86x,PacBio,,,,,,,"Included in the study, passed QC/QA"
57,287.2554,isolate:W45909;collected_by:Memorial Hospital,,,,GCF_001516205.1,HGAP v. 3,,PRJNA253624,SAMN02894344,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:06:22.977Z,2016-02-02T21:06:22.977Z,,,66.25,CP008871,6803881,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.27,,287,,,,,,,6506,,,,,6099,,1,MSKCC,79.21x,PacBio,,,,,,,"Included in the study, passed QC/QA"
58,287.2555,isolate:W60856;collected_by:Memorial Hospital,,,,GCF_001516225.1,HGAP v. 3,,PRJNA253624,SAMN02894343,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:06:37.521Z,2016-02-02T21:06:37.521Z,,,66.18,CP008864,6907606,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.959,,287,,,,,,,6557,,,,,6195,,1,MSKCC,86.31x,PacBio,,,,,,,"Included in the study, passed QC/QA"
59,287.2556,isolate:F23197;collected_by:Memorial Hospital,,,,GCF_001516245.1,HGAP v. 3,,PRJNA253624,SAMN02894358,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:06:48.816Z,2016-02-02T21:06:48.816Z,,,66.21,CP008856,6535112,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.1295,,287,,,,,,,6149,,,,,5775,,1,MSKCC,83.61x,PacBio,,,,,,,"Included in the study, passed QC/QA"
60,287.2557,isolate:F30658;collected_by:Memorial Hospital,,,,GCF_001516265.1,HGAP v. 3,,PRJNA253624,SAMN02894357,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:06:55.581Z,2016-02-02T21:06:55.581Z,,,65.76,CP008857,7273258,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.111,,287,,,,,,,6984,,,,NZ_CP008857.1,6469,,1,MSKCC,80.91x,PacBio,,,,,,,"Included in the study, passed QC/QA"
61,287.2558,isolate:H5708;collected_by:Memorial Hospital,,,,GCF_001516305.1,HGAP v. 3,,PRJNA253624,SAMN02894355,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:07:22.056Z,2016-02-02T21:07:22.056Z,,,66.5,CP008859,6351710,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,,,287,,,,,,,5971,,,,,5675,,1,MSKCC,72.02x,PacBio,,,,,,,"Included in the study, passed QC/QA"
62,287.2559,isolate:H27930;collected_by:Memorial Hospital,,,,GCF_001516325.1,HGAP v. 3,,PRJNA253624,SAMN02894354,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:07:31.066Z,2016-02-02T21:07:31.066Z,,,66.23,CP008860,6598021,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.389,,287,,,,,,,6226,,,,,5828,,1,MSKCC,64.87x,PacBio,,,,,,,"Included in the study, passed QC/QA"
63,287.256,isolate:H47921;collected_by:Memorial Hospital,,,,GCF_001516345.1,HGAP v. 3,,PRJNA253624,SAMN02894353,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:07:11.369Z,2016-02-02T21:07:11.369Z,,,66.07,CP008861,6836415,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.1105,,287,,,,,,,6539,,,,NZ_CP008861.1,6113,,1,MSKCC,87.35x,PacBio,,,,,,,"Included in the study, passed QC/QA"
64,287.2561,isolate:M1608;collected_by:Memorial Hospital,,,,GCF_001516365.1,HGAP v. 3,,PRJNA253624,SAMN02894352,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:07:03.095Z,2016-02-02T21:07:03.095Z,,,65.96,CP008862,6475385,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.253,,287,,,,,,,6152,,,,,5744,,1,MSKCC,x,PacBio,,,,,,,"Included in the study, passed QC/QA"
65,287.2562,isolate:M37351;collected_by:Memorial Hospital,,,,GCF_001516385.1,HGAP v. 3,,PRJNA253624,SAMN02894351,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-02-02T21:07:17.592Z,2016-02-02T21:07:17.592Z,,,65.97,CP008863,6897231,Pseudomonas aeruginosa,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.253,,287,,,,,,,6615,,,,NZ_CP008863.1,6164,,1,MSKCC,89.18x,PacBio,,,,,,,"Included in the study, passed QC/QA"
66,287.2563,,,,AMR Panel,GCF_001518975.1,HGAP3 v. 2.3.0,,PRJNA281531,SAMN04158502,,,,,1,2013-09-25,"Commingling and transportation of cattle is common within the North American beef production system as is the use of macrolide antibiotics to treat or control bovine respiratory disease complex (BRDC). Therefore, the purpose of this project was to evaluate the effects of commingling, transportation, and antibiotic treatment for the control of bovine respiratory disease complex on the diversity and dynamics of nasopharyngeal and rectoanal mucosal bacterial populations in beef calves.  Three groups of 60 commercial 5-7-month-old male beef calves were used in this study, each originating either from Missouri, Kentucky or Tennessee and were transported to a backgrounding facility in Kansas in late September 2013. On arrival at the facility, calves from within each source were randomly assigned to receive either a macrolide antibiotic or saline injection and assigned to separate pens according to treatment within source for a total of 6 pens; for the duration of the trial, each pen was prevented from nose-to-nose contact with any other pen. Nasopharyngeal samples from these calves were collected at four time points: at the sale barn before transport (day 0), at the backgrounding facility upon arrival (day 1), and 9 and 28 days later. Additionally, calves were monitored daily for signs of BRDC using a clinical illness scoring (CIS) system and rectal temperature cutoff as described in (DeDonder et al., 2015). If a calf met the case definition for BRDC, they were treated with a macrolide antibiotic, and additional nasopharyngeal samples were obtained at the time of classification of onset of BRDC morbidity.  These samples were processed using classical microbiological techniques for bacterial isolation, and some isolates were selected for species identification, antimicrobial resistance testing, and whole genome sequencing. The selection criteria for the nasopharyngeal isolates were either that the bacterial species was not represented by a closed genome in GenBank or that the species was known to be associated with respiratory disease in other mammals.",2016-01-20T00:00:00Z,,,2016-02-02T21:12:51.948Z,2016-02-02T21:12:51.948Z,,,66.39,CP013989,6364583,Pseudomonas aeruginosa strain USDA-ARS-USMARC-41639,Complete,Pseudomonas,USA:Kansas,,,5-7 months,,,Bos taurus,,United States,,nasopharynx,,,,,287,,,host_subject_id:150,,,,5994,,,,NZ_CP013989.1,5758,,1,USDA-ARS-USMARC,69x,PacBio P5,,,,USDA-ARS-USMARC-41639,,,"Included in the study, passed QC/QA"
67,287.257,collected_by:Memorial Hospital,,,,GCF_001542795.1,HGAP v. 3,,PRJNA253624,SAMN02894342,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-29T00:00:00Z,,,2016-02-29T21:19:10.801Z,2016-02-29T21:19:10.801Z,,,66.42,CP008872,6371121,Pseudomonas aeruginosa strain X78812,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.257,,287,,,,,,,5992,,,,,5652,,1,MSKCC,84.18x,PacBio,,,,X78812,,,"Included in the study, passed QC/QA"
68,287.2571,collected_by:Memorial Hospital,,,,GCF_001542835.1,HGAP v. 3,,PRJNA253624,SAMN02894359,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-29T00:00:00Z,,,2016-02-29T21:22:02.475Z,2016-02-29T21:22:02.475Z,,,66.15,CP008873,6794354,Pseudomonas aeruginosa strain F9670,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,MLST.Pseudomonas_aeruginosa.155,,287,,,,,,,6526,,,,NZ_CP008873.1,5846,,1,MSKCC,29.84x,PacBio,,,,F9670,,,"Included in the study, passed QC/QA"
69,287.2578,,,,,GCF_001547955.1,The SMRT Analysis HGAP v. 2.1.1,,PRJDB3186,SAMD00020552,,,,,1,2004-11,"Pseudomonas aeruginosa is one of the causative agents of nosocomial infection. In this study, risk factors including patients factors, care and medication associated with nosocomial infection of P. aeruginosa were evaluated to elucidate the critical factors to cause spread of particular P. aeruginosa strains based on whole genome sequencing.",2015-02-27T00:00:00Z,,,2016-03-01T06:57:01.412Z,2016-03-01T06:57:01.412Z,,,65.91,AP014651,7090694,Pseudomonas aeruginosa strain NCGM257,Complete,Pseudomonas,Tokyo,,,,,,"Human, Homo sapiens",,Japan,,,,,MLST.Pseudomonas_aeruginosa.357,,287,,,,,,,6892,,,,NZ_AP014651.1,6892,,1,National Center for Global Health and Medicine,,PacBio,,,,NCGM257,,,"Included in the study, passed QC/QA"
70,287.2579,,,,,GCF_001548135.1,HGAP3 v. 2.2,,PRJDB3600,SAMD00027370,,,,,1,1989-11-22,"We determined complete genome sequences of a clinical isolated strain, Pseudomonas aeruginosa 8380. It was reported that three types of multi-drug-resistant mutants, NalB, NfxB and NfxC-type mutants, were isolated from 8380 strain.",2015-08-12T00:00:00Z,,,2016-03-01T07:14:36.399Z,2016-03-01T07:14:36.399Z,,,66.23,AP014839,6613260,Pseudomonas aeruginosa strain 8380,Complete,Pseudomonas,Japan,,,,,,"Human, Homo sapiens","isolated strain, Pseudomonas aeruginosa 8380",Japan,,,,,,,287,,,,,,,6280,,,25999558,NZ_AP014839.1,6196,,1,Tokushima University,80x,PacBio RSII,,,,8380,,,"Included in the study, passed QC/QA"
71,287.258,,,,,GCF_001548335.1,Minimus2 v. 3.1.0,,PRJDB4304,SAMD00042491,,,,,1,2012,"Multidrug-resistant Pseudomonas aeruginosa has become a threating nosocomial pathogen worldwide. P. aeruginosa IOMTU133 clinical isolate harbors a metallo-beta-lactamase encoding gene DIM-1 and a novel 16S rRNA methylase encoding gene rmtF2, which are associated with highly multidrug-resistance. In order to clarify the mechanism of the acquisition of drug-resistant genes, the complete genome sequence of the IOMTU133 was determined.",2015-11-26T00:00:00Z,,,2016-03-01T07:56:07.016Z,2016-03-01T07:56:07.016Z,,,65.98,AP017302,6897018,Pseudomonas aeruginosa strain IOMTU 133,Complete,Pseudomonas,Nepal: Kathmandu,,,,,,"Human, Homo sapiens",,Nepal,,,,,MLST.Pseudomonas_aeruginosa.1047,,287,,,,,,,6555,,,,NZ_AP017302.1,6433,,1,"Department of Infectious Diseases, National Center for Global Health and Medicine",283X,PacBio RSII,,,,IOMTU 133,,,"Included in the study, passed QC/QA"
72,287.2658,collected_by:Memorial Hospital,,,,GCF_001594325.1,HGAP v. 3,,PRJNA253624,SAMN02894356,,,,,1,2012,29 Pseudomonas aeruginosa clinical isolates for GWAS study,2016-01-15T00:00:00Z,,,2016-04-27T17:49:04.265Z,2016-04-27T17:49:04.265Z,,,66.23,CP008858,6641519,Pseudomonas aeruginosa strain F63912,Complete,Pseudomonas,"New York, NY, USA",,,,,Cancer,"Human, Homo sapiens",,United States,,"Joao Xavier, MSKCC",,,,,287,,,,,,,6385,,,,,6027,,1,MSKCC,91.34x,PacBio,,,,F63912,,,"Included in the study, passed QC/QA"
73,287.2664,,,,,GCF_001606045.1,SOAPdenovo v. 2.04,,PRJNA265138,SAMN03145716,,,,,,15-Jun-2013,Aflatoxin B1 degradation by a Pseudomonas Strain,2016-04-04T00:00:00Z,1,CGMCC:8511,2016-04-28T01:05:59.854Z,2016-04-28T01:05:59.854Z,subsurface,,66.41,CP014948,6370730,Pseudomonas aeruginosa strain N17-1,Complete,Pseudomonas,"China: Haidian, Beijing",,,,,,,,China,,soil,,,,,287,,,,,,,6003,,,,NZ_CP014948.1,5763,,1,"Institute of Agro-products Processing Science and Technology, Chinese Academy of Agricultural Sciences",200X,Illumina,,,,N17-1,,,"Included in the study, passed QC/QA"
74,287.2665,collected_by:Yanfang Feng,,,,GCF_001618925.1,ABySS v. 1.5.1; SSPACE-LongRead scaffolder,,PRJNA316664,SAMN04589231,,,,,1,01-May-2014,Pseudomonas aeruginosa rapidly develops resistance against five medically relevant antibiotics upon exposure to non-lethal concentrations. Whole genome sequencing of the culture during the acquisition of resistance indicates that specific mutations accompany the increase of MIC against tobramycin and ciprofloxacin.,2016-04-12T00:00:00Z,,ATCC:27853,2016-04-28T10:37:43.909Z,2016-04-28T10:37:43.909Z,,,66.11,CP015117,6827737,Pseudomonas aeruginosa strain ATCC 27853,Complete,Pseudomonas,Netherlands,,,,,nosocomial infections,"Human, Homo sapiens",,Netherlands,,,,,MLST.Pseudomonas_aeruginosa.155,,287,,,,,,,6542,,,,NZ_CP015117.1,6273,,1,Universiteit van Amsterdam,95x,Illumina HiSeq; PacBio,,,,ATCC 27853,,,"Included in the study, passed QC/QA"
75,287.267,,,,,GCA_900070375.1,,,PRJEB9838,SAMEA3485223,,,,,1,,"To resist virulent bacteriophages, bacteria develop different strategies which can have transient or permanent effect on their genome or result in long-term co-evolution between the host and the prey. We investigated the frequency and characteristics of P. aeruginosa strain PAO1 variants resisting infection by different combinations of virulent phages belonging to four genera.",2015-09-08T00:00:00Z,,,2016-04-28T20:22:59.201Z,2016-04-28T20:22:59.201Z,,,66.54,LN871187,6276469,Pseudomonas aeruginosa strain PAO1_Orsay,Complete,Pseudomonas,,,,,,,,,,,,,,,,287,,,,,,,5882,,,,NZ_LN871187.1,5589,,1,INSTITUT DE GENETIQUE ET MICROBIOLOGIE,,,,,,PAO1_Orsay,,,"Included in the study, passed QC/QA"
76,287.2692,,,,,GCF_001632245.1,BGI Hybrid Assembler v. SEP-2015,,PRJNA319532,SAMN04893615,,,,,1,not collected,"Pseudomonas aeruginosa is an opportunistic pathogen that frequently infects wounds, significantly impairs wound healing, and causes mortality in burn patients. Here we report whole genome sequence of a multidrug-resistant strain of Pseudomonas aeruginosa, BAMCPA07-48, isolated from a combat injury wound",2016-05-04T00:00:00Z,,,2016-05-23T14:15:53.538Z,2016-05-23T14:15:53.538Z,,,66.03,CP015377,7021552,Pseudomonas aeruginosa strain BAMCPA07-48,Complete,Pseudomonas,,,,,,,"Human, Homo sapiens",,,,combat injury wound,,,,,287,,,,,,,6840,,,,NZ_CP015377.1,6483,,1,The Forsyth Institute,200x,PacBio; Illumina HiSeq,,,,BAMCPA07-48,,,"Included in the study, passed QC/QA"
77,287.2816,collected_by:First Affiliated Hospital of Guangzhou Medical University,,,,GCF_001679685.1,HGAP v. 2013,,PRJNA321921,SAMN05006707,,,,,1,04-Jun-2012,Whole genome sequencing of multidrug resistant strain Pseudomonas aeruginosa PA121617,2016-07-05T00:00:00Z,,,2016-08-26T18:20:11.350Z,2016-08-26T18:20:11.350Z,,,65.81,"CP016214,CP016215",6853510,Pseudomonas aeruginosa strain PA121617,Complete,Pseudomonas,China: Guangzhou,,,,,Respiratory disease,"Human, Homo sapiens",,China,,sputum,,,,,287,,,,,,,6574,,1,,"NZ_CP016214.1,NZ_CP016215.1",6272,,2,South China University of Technology,120x,Illumina; PacBio,,,,PA121617,,,"Included in the study, passed QC/QA"
78,287.2899,collected_by:Wang Ke,,,,GCF_001721745.1,HGAP v. 3; CLC genomic workbench v. 8.0.3,,PRJNA294254,SAMN04910034,,,,,1,2013-12-14,"In this project, 25 Pseudomonas aeruginosa isolates were collected from 4 patients with ventilator associated infections. 8 of the 25 genomes were fully assembled using Pacbio and Illumina Hi-seq sequencing data, while the other 17 were assembled into draft genomes. We aim to compare these 25 strains to understand if there is any evolution/clonal variation/acquisition of genes along disease progression.",2016-09-08T00:00:00Z,,,2016-11-16T01:04:39.887Z,2016-11-16T01:04:39.887Z,,,66.21,CP012585,6643823,Pseudomonas aeruginosa strain PA_D1,Complete,Pseudomonas,China: Nanning,,,50,male,Ventilator associated pneumonia,"Human, Homo sapiens",,China,,Sputum; Early isolate from VAP patient 1,,,,,287,C,,host_subject_id:VAP1,,,,6277,,,,NZ_CP012585.1,6025,,1,Nanyang Technological University,106.46,PacBio; Illumina Hi-seq,,,,PA_D1,,,"Included in the study, passed QC/QA"
79,287.29,collected_by:Wang Ke,,,,GCF_001721765.1,HGAP v. 3; CLC genomic workbench v. 8.0.3,,PRJNA294254,SAMN04910045,,,,,1,2013-12-24,"In this project, 25 Pseudomonas aeruginosa isolates were collected from 4 patients with ventilator associated infections. 8 of the 25 genomes were fully assembled using Pacbio and Illumina Hi-seq sequencing data, while the other 17 were assembled into draft genomes. We aim to compare these 25 strains to understand if there is any evolution/clonal variation/acquisition of genes along disease progression.",2016-09-08T00:00:00Z,,,2016-11-16T01:06:11.974Z,2016-11-16T01:06:11.974Z,,,66.22,CP012578,6642996,Pseudomonas aeruginosa strain PA_D2,Complete,Pseudomonas,China: Nanning,,,76,male,Ventilator associated pneumonia,"Human, Homo sapiens",,China,,Sputum; Early isolate from VAP patient 2,,,,,287,C,,host_subject_id:VAP2,,,,6280,,,,NZ_CP012578.1,6023,,1,Nanyang Technological University,91.24,PacBio; Illumina Hi-seq,,,,PA_D2,,,"Included in the study, passed QC/QA"
80,287.2901,collected_by:Wang Ke,,,,GCF_001721785.1,HGAP v. 3; CLC genomic workbench v. 8.0.3,,PRJNA294254,SAMN04910066,,,,,1,2014-01-21,"In this project, 25 Pseudomonas aeruginosa isolates were collected from 4 patients with ventilator associated infections. 8 of the 25 genomes were fully assembled using Pacbio and Illumina Hi-seq sequencing data, while the other 17 were assembled into draft genomes. We aim to compare these 25 strains to understand if there is any evolution/clonal variation/acquisition of genes along disease progression.",2016-09-08T00:00:00Z,,,2016-11-16T01:08:35.442Z,2016-11-16T01:08:35.442Z,,,66.21,CP012580,6645477,Pseudomonas aeruginosa strain PA_D9,Complete,Pseudomonas,China: Nanning,,,50,male,Ventilator associated pneumonia,"Human, Homo sapiens",,China,,Sputum; Late isolate from VAP patient 1,,,,,287,C,,host_subject_id:VAP1,,,,6284,,,,NZ_CP012580.1,6028,,1,Nanyang Technological University,68.59,PacBio; Illumina Hi-seq,,,,PA_D9,,,"Included in the study, passed QC/QA"
81,287.2902,collected_by:Wang Ke,,,,GCF_001721805.1,HGAP v. 3; CLC genomic workbench v. 8.0.3,,PRJNA294254,SAMN04914381,,,,,1,2014-03-06,"In this project, 25 Pseudomonas aeruginosa isolates were collected from 4 patients with ventilator associated infections. 8 of the 25 genomes were fully assembled using Pacbio and Illumina Hi-seq sequencing data, while the other 17 were assembled into draft genomes. We aim to compare these 25 strains to understand if there is any evolution/clonal variation/acquisition of genes along disease progression.",2016-09-08T00:00:00Z,,,2016-11-16T01:08:21.556Z,2016-11-16T01:08:21.556Z,,,66.16,CP012581,6681975,Pseudomonas aeruginosa strain PA_D16,Complete,Pseudomonas,China: Nanning,,,46,male,Ventilator associated pneumonia,"Human, Homo sapiens",,China,,Sputum; Early isolate from VAP patient 4,,,,,287,C,,host_subject_id:VAP4,,,,6320,,,,NZ_CP012581.1,6051,,1,Nanyang Technological University,46.48,PacBio; Illumina Hi-seq,,,,PA_D16,,,"Included in the study, passed QC/QA"
82,287.2903,collected_by:Wang Ke,,,,GCF_001721825.1,HGAP v. 3; CLC genomic workbench v. 8.0.3,,PRJNA294254,SAMN04914475,,,,,1,2014-03-21,"In this project, 25 Pseudomonas aeruginosa isolates were collected from 4 patients with ventilator associated infections. 8 of the 25 genomes were fully assembled using Pacbio and Illumina Hi-seq sequencing data, while the other 17 were assembled into draft genomes. We aim to compare these 25 strains to understand if there is any evolution/clonal variation/acquisition of genes along disease progression.",2016-09-08T00:00:00Z,,,2016-11-16T01:08:29.487Z,2016-11-16T01:08:29.487Z,,,66.16,CP012583,6681981,Pseudomonas aeruginosa strain PA_D22,Complete,Pseudomonas,China: Nanning,,,82,male,Ventilator associated pneumonia,"Human, Homo sapiens",,China,,Sputum; Late isolate from VAP patient 3,,,,,287,C,,host_subject_id:VAP3,,,,6319,,,,NZ_CP012583.1,6057,,1,Nanyang Technological University,56.71,PacBio; Illumina Hi-seq,,,,PA_D22,,,"Included in the study, passed QC/QA"
83,287.2904,collected_by:Wang Ke,,,,GCF_001721845.1,HGAP v. 3; CLC genomic workbench v. 8.0.3,,PRJNA294254,SAMN04914479,,,,,1,2014-03-29,"In this project, 25 Pseudomonas aeruginosa isolates were collected from 4 patients with ventilator associated infections. 8 of the 25 genomes were fully assembled using Pacbio and Illumina Hi-seq sequencing data, while the other 17 were assembled into draft genomes. We aim to compare these 25 strains to understand if there is any evolution/clonal variation/acquisition of genes along disease progression.",2016-09-08T00:00:00Z,,,2016-11-16T01:13:14.187Z,2016-11-16T01:13:14.187Z,,,66.16,CP012584,6683204,Pseudomonas aeruginosa strain PA_D25,Complete,Pseudomonas,China: Nanning,,,46,male,46,"Human, Homo sapiens",,China,,Sputum; Late isolate from VAP patient 4,,,,,287,C,,host_subject_id:VAP4,,,,6331,,,,NZ_CP012584.1,6052,,1,Nanyang Technological University,40.86,PacBio; Illumina Hi-seq,,,,PA_D25,,,"Included in the study, passed QC/QA"
84,287.2905,sample_type:whole organism,,,,GCF_001722005.1,Celera Assembler v. Newbler2.8,,PRJNA341318,SAMN05717682,,,,,1,2013,Whole genome sequence of Pseudomonas aeruginosa DN1 provide more information for the biodegradation of PAHs .,2016-09-08T00:00:00Z,,,2016-11-16T01:21:02.969Z,2016-11-16T01:21:02.969Z,,,66.29,CP017099,6641902,Pseudomonas aeruginosa strain DN1,Complete,Pseudomonas,China,,,,,,,,China,,soil,,,,,287,,,,,,,6323,,,,,6071,,1,Northwest University,197.13x,Illumina MiSeq,,,,DN1,,,"Included in the study, passed QC/QA"
85,287.2906,collected_by:Wang Ke,,,,GCF_001722025.1,HGAP v. 3; CLC genomic workbench v. 8.0.3,,PRJNA294254,SAMN04910061,,,,,1,2014-01-13,"In this project, 25 Pseudomonas aeruginosa isolates were collected from 4 patients with ventilator associated infections. 8 of the 25 genomes were fully assembled using Pacbio and Illumina Hi-seq sequencing data, while the other 17 were assembled into draft genomes. We aim to compare these 25 strains to understand if there is any evolution/clonal variation/acquisition of genes along disease progression.",2016-09-08T00:00:00Z,,,2016-11-16T01:17:20.783Z,2016-11-16T01:17:20.783Z,,,66.16,CP012579,6681992,Pseudomonas aeruginosa strain PA_D5,Complete,Pseudomonas,China: Guangxi,,,82,male,Ventilator associated pneumonia,"Human, Homo sapiens",,China,,Sputum; Early isolate from VAP patient 3,,,,,287,C,,host_subject_id:VAP3,,,,6319,,,,NZ_CP012579.1,6050,,1,Nanyang Technological University,86.57,PacBio; Illumina Hi-seq,,,,PA_D5,,,"Included in the study, passed QC/QA"
86,287.2907,collected_by:Wang Ke,,,,GCF_001722045.1,HGAP v. 3; CLC genomic workbench v. 8.0.3,,PRJNA294254,SAMN04914386,,,,,1,2014-03-10,"In this project, 25 Pseudomonas aeruginosa isolates were collected from 4 patients with ventilator associated infections. 8 of the 25 genomes were fully assembled using Pacbio and Illumina Hi-seq sequencing data, while the other 17 were assembled into draft genomes. We aim to compare these 25 strains to understand if there is any evolution/clonal variation/acquisition of genes along disease progression.",2016-09-08T00:00:00Z,,,2016-11-16T01:18:49.844Z,2016-11-16T01:18:49.844Z,,,66.21,CP012582,6639108,Pseudomonas aeruginosa strain PA_D21,Complete,Pseudomonas,China: Guangxi,,,76,male,Ventilator associated pneumonia,"Human, Homo sapiens",,China,,Sputum; Late isolate from VAP patient 2,,,,,287,C,,host_subject_id:VAP2,,,,6279,,,,NZ_CP012582.1,6022,,1,Nanyang Technological University,48.8,PacBio; Illumina Hi-seq,,,,PA_D21,,,"Included in the study, passed QC/QA"
87,287.2908,sample_type:cell culture,,,,GCF_001729505.1,SMRT portal v. 2.3,,PRJNA340360,SAMN05715193,,,,,1,,Pseudomonas aeruginosa ATCC 15692 was sequenced with PacBio platform,2016-09-16T00:00:00Z,,ATCC 15692,2016-11-16T10:49:14.456Z,2016-11-16T10:49:14.456Z,,,66.54,CP017149,6276434,Pseudomonas aeruginosa strain ATCC 15692,Complete,Pseudomonas,,,,,,,,,,,Infected wound,,,,,287,,,,,,,5909,,,,NZ_CP017149.1,5687,,1,"Dalian Hissen Bio-pharm., Ltd.",200x,PacBio,,,,ATCC 15692,,,"Included in the study, passed QC/QA"
88,287.2914,sample_type:cell culture,,,,GCF_001750705.1,Hierarchical genome-assembly process(HGAP),,PRJNA341834,SAMN05729608,,,,,1,2015-01-01,Strain FA-HZ1 is a DBF degrader which is isolated from wastewater in China.It could efficiently degrade DBF and transform it into harmless or less toxic intermediates.,2016-10-03T00:00:00Z,,,2016-11-16T20:11:20.638Z,2016-11-16T20:11:20.638Z,,,66.16,CP017353,6866790,Pseudomonas aeruginosa strain FA-HZ1,Complete,Pseudomonas,China,,,,,,,isolated from wastewater in China,China,,wastewater,,,,,287,,,,,,,6728,,,,NZ_CP017353.1,6307,,1,Shanghai Jiao Tong University,300,454; Illumina,,,,FA-HZ1,,,"Included in the study, passed QC/QA"
89,287.2965,sample_type:whole organism,,,,GCF_001792835.1,Newbler v. 3,,PRJNA310735,SAMN04455104,,,,,1,1997,"This study was undertaken to determine the possible presence of genetic factors associated with the emergence, successful spread, and persistence of this clone in the Brazilian institutions. In addition, we also aimed to compare the genome of the SPM-1-producing Pseudomonas aeruginosa strains collected from a single intensive care unit in a twelve-year period in order to evaluate if this clone had suffered any temporal changes.",2016-10-20T00:00:00Z,,,2016-11-17T22:57:45.955Z,2016-11-17T22:57:45.955Z,,,66.15,CP015001,6721480,Pseudomonas aeruginosa strain PA1088,Complete,Pseudomonas,"Brazil: Sao Paulo, SP",,,,,,"Human, Homo sapiens",,Brazil,,urine,,,,,287,C,,,,,,6433,,,,NZ_CP015001.1,6199,,1,LNCC,161x,454,,,,PA1088,,,"Included in the study, passed QC/QA"
90,287.2966,sample_type:whole organism,,,,GCF_001792855.1,Newbler v. 3,,PRJNA310741,SAMN04455156,,,,,1,2007,"This study was undertaken to determine the possible presence of genetic factors associated with the emergence, successful spread, and persistence of this clone in the Brazilian institutions. In addition, we also aimed to compare the genome of the SPM-1-producing Pseudomonas aeruginosa strains collected from a single intensive care unit in a twelve-year period in order to evaluate if this clone had suffered any temporal changes.",2016-10-20T00:00:00Z,,,2016-11-17T22:53:11.214Z,2016-11-17T22:53:11.214Z,,,66.01,CP015002,6928736,Pseudomonas aeruginosa strain PA8281,Complete,Pseudomonas,"Brazil: Sao Paulo, SP",,,,,,"Human, Homo sapiens",,Brazil,,tracheal aspirate,,,,,287,C,,,,,,6678,,,,NZ_CP015002.1,6426,,1,LNCC,171x,454,,,,PA8281,,,"Included in the study, passed QC/QA"
91,287.2967,sample_type:whole organism,,,,GCF_001792875.1,Newbler v. 3,,PRJNA310742,SAMN04455162,,,,,1,2011,"This study was undertaken to determine the possible presence of genetic factors associated with the emergence, successful spread, and persistence of this clone in the Brazilian institutions. In addition, we also aimed to compare the genome of the SPM-1-producing Pseudomonas aeruginosa strains collected from a single intensive care unit in a twelve-year period in order to evaluate if this clone had suffered any temporal changes.",2016-10-20T00:00:00Z,,,2016-11-17T22:57:51.545Z,2016-11-17T22:57:51.545Z,,,65.97,CP015003,7006578,Pseudomonas aeruginosa strain PA11803,Complete,Pseudomonas,"Brazil: Sao Paulo, SP",,,,,,"Human, Homo sapiens",,Brazil,,bloodstream,,,,,287,C,,,,,,6845,,,,NZ_CP015003.1,6582,,1,LNCC,176x,454,,,,PA11803,,,"Included in the study, passed QC/QA"
92,287.297,sample_type:whole organism,,,,GCF_001870265.1,Newbler v. 3,,PRJNA310740,SAMN04455155,,,,,1,2006,"This study was undertaken to determine the possible presence of genetic factors associated with the emergence, successful spread, and persistence of this clone in the Brazilian institutions. In addition, we also aimed to compare the genome of the SPM-1-producing Pseudomonas aeruginosa strains collected from a single intensive care unit in a twelve-year period in order to evaluate if this clone had suffered any temporal changes.",2016-11-07T00:00:00Z,,,2016-11-19T10:59:04.914Z,2016-11-19T10:59:04.914Z,,,65.92,"CP014999,CP015000",7067711,Pseudomonas aeruginosa strain PA7790,Complete,Pseudomonas,"Brazil: Sao Paulo, SP",,,,,,"Human, Homo sapiens",,Brazil,,tracheal aspirate,,,,,287,C,,,,,,6887,,1,,"NZ_CP014999.1,NZ_CP015000.1",6600,,2,LNCC,170x,454,,,,PA7790,,,"Included in the study, passed QC/QA"
93,287.2971,collected_by:Tao Yan,,,,GCF_001874465.1,HGAP assembly v. 3,,PRJNA352277,SAMN05969160,,,,,1,2008-06,To understand the relationship between triclosan resistance and multi-drug resistance in the community through wastewater sampling,2016-11-10T00:00:00Z,,,2016-11-19T13:49:06.154Z,2016-11-19T13:49:06.154Z,,,66.18,CP017969,6723378,Pseudomonas aeruginosa strain B10W,Complete,Pseudomonas,USA: Honolulu,,,,,,,,United States,,wastewater,,,,,287,,,,,,,6438,,,,NZ_CP017969.1,6150,,1,University of Hawaii,118.75x,PacBio,,,,B10W,,,"Included in the study, passed QC/QA"
94,287.2973,,,Resistant;Susceptible,AMR Panel,GCF_001874805.1,HGAP v. 3,,PRJNA292904,SAMN04014933,,,,,,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2016-11-10T00:00:00Z,1,,2016-11-19T14:04:11.821Z,2016-11-19T14:04:11.821Z,,,66.02,MPBS00000000,6963676,Pseudomonas aeruginosa strain AR_0092,Complete,Pseudomonas,,,,,,,,,,,,,,,,287,,,,,,,6620,,,,,,,1,Centers for Disease Control and Prevention,116x,PacBio,,,,AR_0092,,,"Included in the study, passed QC/QA"
95,287.2981,,,,,GCF_900095805.1,,,PRJEB14496,SAMEA4393802,,,,,1,,The representative of the P. aeruginosa PA14 reference strain was sequenced by comparison with the PA14 genome. DNA was prepared from a culture derived from a single colony.,2016-09-07T00:00:00Z,,,2016-11-19T16:21:32.110Z,2016-11-19T16:21:32.110Z,,,66.29,LT608330,6541482,Pseudomonas aeruginosa strain PA14Or_reads,Complete,Pseudomonas,,,,,,,,derived from a single colony,,,single colony,,,,,287,,,,,,,6171,,,,NZ_LT608330.1,5894,,1,INSTITUT DE GENETIQUE ET MICROBIOLOGIE,,,,,,PA14Or_reads,,,"Included in the study, passed QC/QA"
96,287.3101,sample_type:cell culture,,,,GCF_001879525.1,Nwebler v. 2.9; primer walking,,PRJNA299511,SAMN04209275,,,,,1,,The goal of this study was to determine the complete nucleotide sequence of the Pseudomonas aeriginosa strain for the propagation of certain phiKZ-like therapeutic phages.,2016-11-16T00:00:00Z,,,2017-01-16T02:27:45.323Z,2017-01-16T02:27:45.323Z,,,66.37,CP013113,6504659,Pseudomonas aeruginosa strain PAER4_119,Complete,Pseudomonas,,,,,,,,,,,Lindberg collection,,,,,287,C,,,,,,6084,,,,NZ_CP013113.1,5881,,1,Institute of Biochemistry and Biophysics of the Polish Academy of Sciences,57x,GS FLX+ Titanium (454); Illumina MiSeq;,,,,Paer4_119,,,"Included in the study, passed QC/QA"
97,287.3102,sample_type:cell culture,,,,GCF_001900195.1,HGAP3 SMRTPortal v. 2.2.0,,PRJNA291145,SAMN03940423,,,,,1,01-Jan-2013,Large scale genome inversion in P. aeruginosa drives adaptation to chronic infection in cystic fibrosis,2016-12-12T00:00:00Z,,DSM:100778,2017-01-16T16:58:35.909Z,2017-01-16T16:58:35.909Z,,,66.57,CP013477,6213026,Pseudomonas aeruginosa strain SCVFeb,Complete,Pseudomonas,"United Kingdom: Scotland, Glasgow",,,,,,,,,,murine model,,,,,287,C,,,,,,5813,,,,NZ_CP013477.1,5619,,1,Leibniz Institute DSMZ,41x,PacBio; Illumina GAIIx,,,,SCVFeb,,,"Included in the study, passed QC/QA"
98,287.3103,sample_type:cell culture,,,,GCF_001900225.1,HGAP SMRTPortal v. 2.1.1,,PRJNA291144,SAMN03940421,,,,,1,01-Jan-2013,Large scale genome inversion in P. aeruginosa drives adaptation to chronic infection in cystic fibrosis,2016-12-12T00:00:00Z,,DSM:100777,2017-01-16T16:58:39.869Z,2017-01-16T16:58:39.869Z,,,66.57,CP013478,6213029,Pseudomonas aeruginosa strain SCVJan,Complete,Pseudomonas,"United Kingdom: Scotland, Glasgow",,,,,,,,,,murine model,,,,,287,C,,,,,,5813,,,,NZ_CP013478.1,5619,,1,Leibniz Institute DSMZ,208x,PacBio; Illumina HiSeq2500,,,,SCVJan,,,"Included in the study, passed QC/QA"
99,287.3104,sample_type:cell culture,,,,GCF_001900265.1,HGAP2 SMRTPortal v. 2.1.1,,PRJNA291143,SAMN03940420,,,,,1,01-Jan-2013,Large scale genome inversion in P. aeruginosa drives adaptation to chronic infection in cystic fibrosis,2016-12-12T00:00:00Z,,DSM:100776,2017-01-16T16:59:34.725Z,2017-01-16T16:59:34.725Z,,,66.57,CP013479,6213276,Pseudomonas aeruginosa strain NHmuc,Complete,Pseudomonas,Netherlands,,,,,,"Human, Homo sapiens",,,,,,,,,287,C,,,,,,5814,,,,NZ_CP013479.1,5619,,1,Leibniz Institute DSMZ,100x,PacBio; Illumina GAIIx,,,,NHmuc,,,"Included in the study, passed QC/QA"
100,287.3741,,,Susceptible,Computational Prediction,GCF_900149285.1,,,PRJEB18612,SAMEA26686918,,,,,1,,"PcyII-10 is a clinical strain recovered from a burn patient in Percy hospital, Clamart, France",2017-01-26T00:00:00Z,,,2017-03-20T09:14:34.569Z,2017-03-20T09:14:34.569Z,,,66.51,LT673656,6288645,Pseudomonas aeruginosa strain PcyII-10,Complete,Pseudomonas,,,,,,,,,,,,,,MLST.Pseudomonas_aeruginosa.1233,,287,,,,,,,5905,,,,NZ_LT673656.1,5706,,1,INSTITUT DE GENETIQUE ET MICROBIOLOGIE,,,,,,PcyII-10,,,"Included in the study, passed QC/QA"
101,287.3867,,,,,,SPAdes v. 3.6.2,,PRJNA310413,SAMN04452263,,,,,1,,in preparation,2017-03-29T00:00:00Z,,,2017-05-28T05:58:13.448Z,2017-05-28T05:58:13.448Z,,,66.38,CP014866,6445239,Pseudomonas aeruginosa strain PA_154197,Complete,Pseudomonas,Hong Kong,,,,,,"Human, Homo sapiens",,,,,,,,,287,C,,,,,,6102,,,,,5842,,1,HKU,21.29x,Illumna; Sanger,,,,PA_154197,,,"Included in the study, passed QC/QA"
102,287.3868,collected_by:EMC,,,,,CLC Genomic Workbench v. 9.0.1,,PRJNA339235,SAMN05583819,,,,,1,,reference genome,2017-04-11T00:00:00Z,,,2017-05-28T13:02:40.899Z,2017-05-28T13:02:40.899Z,,,65.66,CP016955,7380063,Pseudomonas aeruginosa strain RIVM-EMC2982,Complete,Pseudomonas,Netherlands: Bilthoven,,,,,unavailable,"Human, Homo sapiens",,,,unavailable,,,,,287,,,,,,,7188,,,,,6844,,1,RIVM,40,Illumina; PacBio,,,,RIVM-EMC2982,,,"Included in the study, passed QC/QA"
103,287.3869,collected_by:St. Joseph's Hospital,,,,,Celera Assembler v. AUG-2014,,PRJNA376024,SAMN06349407,,,,,1,2014,strain resistant to all current antibiotics,2017-04-11T00:00:00Z,,,2017-05-28T13:09:37.909Z,2017-05-28T13:09:37.909Z,,,65.83,"CP020603,CP020602",7077406,Pseudomonas aeruginosa strain E6130952,Complete,Pseudomonas,Canada: Toronto,,,,,respiratory failure,"Human, Homo sapiens",,,,sputum,,,,,287,,,host_disease_outcome:death,,,,6888,,1,,,6586,,2,Universite Laval,73.0x,PacBio,,O11,,E6130952,,,"Included in the study, passed QC/QA"
104,287.3877,collected_by:Jeanette WP Teo,,,,,Celera Assembler,,PRJNA381838,SAMN06689794,,,,,1,2015-05-02,The aim of this study is to elucidate the complete genome map of NDM-1 producing P. aeruginosa clinical isolate. We also aim to understand the transmission of blaNDM-1 into P. aeruginosa.,2017-04-18T00:00:00Z,,,2017-05-29T01:45:54.451Z,2017-05-29T01:45:54.451Z,,,66.07,CP020703,6893164,Pseudomonas aeruginosa strain PASGNDM345,Complete,Pseudomonas,Singapore,,,,,N.A.,"Human, Homo sapiens",,,,sputum,,,,,287,,,,,,,6681,,,,,6552,,1,Nanyang Technological University,163x,PacBio,,,,PASGNDM345,,,"Included in the study, passed QC/QA"
105,287.3878,collected_by:Jeanette WP Teo,,,,,Celera Assembler,,PRJNA381838,SAMN06689795,,,,,1,2015-04-11,The aim of this study is to elucidate the complete genome map of NDM-1 producing P. aeruginosa clinical isolate. We also aim to understand the transmission of blaNDM-1 into P. aeruginosa.,2017-04-18T00:00:00Z,,,2017-05-29T01:45:33.317Z,2017-05-29T01:45:33.317Z,,,66,CP020704,6985102,Pseudomonas aeruginosa strain PASGNDM699,Complete,Pseudomonas,Singapore,,,,,N.A.,"Human, Homo sapiens",,,,sputum,,,,,287,,,,,,,6791,,,,,6661,,1,Nanyang Technological University,161x,PacBio,,,,PASGNDM699,,,"Included in the study, passed QC/QA"
106,287.405,collected_by:not applicable,,Resistant,Computational Prediction,,other v. HGAP 3,,PRJNA389181,SAMN05020323,,,,,1,01-Nov-2006,"To understand the importance of the genomic islands, and the relevance of the instrinsec and acquired resistome in the pathogenesis of Pseudomonas aeruginosa",2017-06-13T00:00:00Z,,,2017-07-22T17:39:32.138Z,2017-07-22T17:39:32.138Z,,,65.84,CP021774,7008516,Pseudomonas aeruginosa strain 124,Complete,Pseudomonas,Mexico: Mexico city,,,,,ventilator-associated pneumonia,"Human, Homo sapiens",,Mexico,,bronchial washing,,,MLST.Pseudomonas_aeruginosa.309,,287,,,,,,,6785,,,,,6617,,1,"Facultad de Medicina, Universidad Nacional Autonoma de Mexico",91.0x,PacBio,,,,not applicable,,,"Included in the study, passed QC/QA"
107,287.4051,collected_by:not applicable,,Resistant,Computational Prediction,,HGAP v. 3,,PRJNA389181,SAMN05020321,,,,,1,25-Oct-2005,"To understand the importance of the genomic islands, and the relevance of the instrinsec and acquired resistome in the pathogenesis of Pseudomonas aeruginosa",2017-06-13T00:00:00Z,,,2017-07-22T17:45:03.092Z,2017-07-22T17:45:03.092Z,,,65.8,CP021775,7241575,Pseudomonas aeruginosa strain 58,Complete,Pseudomonas,Mexico: Mexico city,,,,,ventilator-associated pneumonia,"Human, Homo sapiens",,Mexico,,bronchial washing,,,MLST.Pseudomonas_aeruginosa.308,,287,,,,,,,7146,,,,,6927,,1,"Facultad de Medicina, Universidad Nacional Autonoma de Mexico",83.0x,PacBio,,,,not applicable,,,"Included in the study, passed QC/QA"
108,287.409,collected_by:not applicable,,Susceptible,Computational Prediction,,HGAP v. 3,,PRJNA389181,SAMN05020322,,,,,1,20-Jul-2005,"To understand the importance of the genomic islands, and the relevance of the instrinsec and acquired resistome in the pathogenesis of Pseudomonas aeruginosa",2017-06-22T00:00:00Z,,,2017-07-22T23:46:34.279Z,2017-07-22T23:46:34.279Z,,,66.23,CP021999,6566724,Pseudomonas aeruginosa strain 84,Complete,Pseudomonas,Mexico: Mexico city,,,,,ventilator-associated pneumonia,"Human, Homo sapiens",,Mexico,,bronchial washing,,,,,287,,,,,,,6348,,,,,6202,,1,"Facultad de Medicina, Universidad Nacional Autonoma de Mexico",89.0x,PacBio,,,,not applicable,,,"Included in the study, passed QC/QA"
109,287.4091,collected_by:not applicable,,Resistant,Computational Prediction,,HGAP v. 3,,PRJNA389181,SAMN05020324,,,,,1,10-Nov-2006,"To understand the importance of the genomic islands, and the relevance of the instrinsec and acquired resistome in the pathogenesis of Pseudomonas aeruginosa",2017-06-22T00:00:00Z,,,2017-07-22T23:36:05.839Z,2017-07-22T23:36:05.839Z,,,65.74,CP022000,7148302,Pseudomonas aeruginosa strain 127,Complete,Pseudomonas,Mexico: Mexico city,,,,,ventilator-associated pneumonia,"Human, Homo sapiens",,Mexico,,bronchial washing,,,MLST.Pseudomonas_aeruginosa.309,,287,,,,,,,7025,,,,,6777,,1,"Facultad de Medicina, Universidad Nacional Autonoma de Mexico",91.0x,PacBio,,,,not applicable,,,"Included in the study, passed QC/QA"
110,287.4092,collected_by:not applicable,,Resistant,Computational Prediction,,HGAP v. 3,,PRJNA389181,SAMN05020326,,,,,1,02-May-2014,"To understand the importance of the genomic islands, and the relevance of the instrinsec and acquired resistome in the pathogenesis of Pseudomonas aeruginosa",2017-06-22T00:00:00Z,,,2017-07-22T23:44:44.237Z,2017-07-22T23:44:44.237Z,,,65.83,CP022002,7050510,Pseudomonas aeruginosa strain 1242,Complete,Pseudomonas,Mexico: Mexico city,,,12 years,female,Chiari malformation,"Human, Homo sapiens",,Mexico,,Blood,,,,,287,,,,,,,6967,,,,,6654,,1,"Facultad de Medicina, Universidad Nacional Autonoma de Mexico",181.0x,PacBio,,,,not applicable,,,"Included in the study, passed QC/QA"
111,287.4094,collected_by:not applicable,,Susceptible,Computational Prediction,,HGAP v. 3,,PRJNA389181,SAMN05020325,,,,,1,27-Jun-2012,"To understand the importance of the genomic islands, and the relevance of the instrinsec and acquired resistome in the pathogenesis of Pseudomonas aeruginosa",2017-06-22T00:00:00Z,,,2017-07-23T01:15:26.990Z,2017-07-23T01:15:26.990Z,,,65.73,CP022001,7411863,Pseudomonas aeruginosa strain 1207,Complete,Pseudomonas,Mexico: Mexico city,,,3 years and 3 months,male,Comunity-adquired pneumonia,"Human, Homo sapiens",,Mexico,,Blood,,,,,287,,,,,,,7297,,,,,7072,,1,"Facultad de Medicina, Universidad Nacional Autonoma de Mexico",146.0x,PacBio,,,,not applicable,,,"Included in the study, passed QC/QA"
112,287.4461,sample_type:culture,,Resistant,Computational Prediction,GCA_002237425.1,HGAP v. 3,,PRJNA394047,SAMN07347485,,,,,1,01-Jun-2003,This study was conducted to reveal adaptation mechanisms of oceanic Pseudomonas aeruginosa,2017-07-31T00:00:00Z,,,2017-09-29T15:17:37.421Z,2017-09-29T15:17:37.421Z,,,66.03,CP022525,6943220,Pseudomonas aeruginosa strain Ocean-1175,Complete,Pseudomonas,Pacific Ocean,,,,,,,,,,Open Ocean,,,,,287,,,,,,,6724,,,,,6592,,1,"Atmosphere and Ocean Research Institute, The University of Tokyo",149x,PacBio RS II,,,,Ocean-1175,,,"Included in the study, passed QC/QA"
113,287.4462,sample_type:culture,,Resistant,Computational Prediction,GCA_002237405.1,HGAP v. 3,,PRJNA394047,SAMN07347483,,,,,1,01-Jun-2003,This study was conducted to reveal adaptation mechanisms of oceanic Pseudomonas aeruginosa,2017-07-31T00:00:00Z,,,2017-09-29T15:17:25.493Z,2017-09-29T15:17:25.493Z,,,66.01,CP022526,6952237,Pseudomonas aeruginosa strain Ocean-1155,Complete,Pseudomonas,Pacific Ocean,,,,,,,,,,Open Ocean,,,,,287,,,,,,,6733,,,,,6601,,1,"Atmosphere and Ocean Research Institute, The University of Tokyo",230x,PacBio RS II,,,,Ocean-1155,,,"Included in the study, passed QC/QA"
114,287.4463,sample_type:tissue sample,,Susceptible,Computational Prediction,GCA_002223805.1,Celera Assembler v. 8.3rc2,,PRJNA361478,SAMN06234157,,,,,1,Mar-2014,We aim to get the important genes related to the produciton of biosurfactant and biodegradation of hydrocarbon by whole genome sequencing.,2017-07-21T00:00:00Z,,,2017-09-29T15:26:22.519Z,2017-09-29T15:26:22.519Z,,,66.13,CP019338,6661962,Pseudomonas aeruginosa strain L10,Complete,Pseudomonas,China: Binzhou,,,,,,,,China,,Halobiotic reed,,,,,287,,,,,,,6353,,,,,6228,,1,Binzhou Univesity,100.0x,Illumina HiSeq; PacBio,,,,L10,,,"Included in the study, passed QC/QA"
115,287.4464,sample_type:blood,,Resistant,Computational Prediction,GCA_002215345.1,HGAP SMRTPortal v. 2.3.0,,PRJNA343072,SAMN05773092,,,,,1,Dec-2013,Analyses of rapid and consistent evolution of colistin resistance in XDR Pseudomonas aeruginosa during morbidostat culture,2017-07-06T00:00:00Z,,,2017-09-29T15:36:13.254Z,2017-09-29T15:36:13.254Z,,,65.7,"CP017293,CP017294",7214314,Pseudomonas aeruginosa strain PA83,Complete,Pseudomonas,Germany,,,,,,"Human, Homo sapiens",,,,,,,,,287,,,,,genotype:ST233,,6889,,1,28630206,,6610,,2,Leibniz Institute DSMZ-German Collection of Microrganisms and Cell Cultures,134x,PacBio; Illumina HISEQ,,,,PA83,,,"Included in the study, passed QC/QA"
116,287.4468,sample_type:culture,,Resistant,Computational Prediction,GCA_002237425.1,HGAP v. 3,,PRJNA394047,SAMN07347485,,,,,1,01-Jun-2003,This study was conducted to reveal adaptation mechanisms of oceanic Pseudomonas aeruginosa,2017-07-31T00:00:00Z,,,2017-09-29T21:34:13.730Z,2017-09-29T21:34:13.730Z,,,66.03,CP022525,6943220,Pseudomonas aeruginosa strain Ocean-1175,Complete,Pseudomonas,Pacific Ocean,,,,,,,,,,Open Ocean,,,,,287,,,,,,,6724,,,,,6592,,1,"Atmosphere and Ocean Research Institute, The University of Tokyo",149x,PacBio RS II,,,,Ocean-1175,,,"Included in the study, passed QC/QA"
117,287.4469,sample_type:culture,,Resistant,Computational Prediction,GCA_002237405.1,HGAP v. 3,,PRJNA394047,SAMN07347483,,,,,1,01-Jun-2003,This study was conducted to reveal adaptation mechanisms of oceanic Pseudomonas aeruginosa,2017-07-31T00:00:00Z,,,2017-09-29T21:34:03.624Z,2017-09-29T21:34:03.624Z,,,66.01,CP022526,6952237,Pseudomonas aeruginosa strain Ocean-1155,Complete,Pseudomonas,Pacific Ocean,,,,,,,,,,Open Ocean,,,,,287,,,,,,,6733,,,,,6601,,1,"Atmosphere and Ocean Research Institute, The University of Tokyo",230x,PacBio RS II,,,,Ocean-1155,,,"Included in the study, passed QC/QA"
118,287.4554,,,Resistant,Computational Prediction,GCA_002442855.1,SPAdes v. 3.6.2,,PRJNA310413,SAMN04452273,,,,,1,,in preparation,2017-10-04T00:00:00Z,,,2017-11-23T02:53:17.972Z,2017-11-23T02:53:17.972Z,,,66.5,CP017306,6334472,Pseudomonas aeruginosa strain PA_150577,Complete,Pseudomonas,Hong Kong,,,,,,"Human, Homo sapiens",,,,,,,MLST.Pseudomonas_aeruginosa.1239,,287,C,,,,,,5981,,,,,5749,,1,HKU,20.0x,Illumina HiSeq,,,,PA_150577,,,"Included in the study, passed QC/QA"
119,287.4566,,,Resistant,Computational Prediction,GCA_002753655.1,Newbler v. 3.0,,PRJNA415682,SAMN07831757,,,,,1,2013,Complete genome sequence of Pseudomonas aeruginosa 12939,2017-11-06T00:00:00Z,,,2017-11-24T17:16:20.264Z,2017-11-24T17:16:20.264Z,,,66.2,CP024477,6621378,Pseudomonas aeruginosa strain 12939,Complete,Pseudomonas,China,,,,,,"Human, Homo sapiens",,,,,,,,,287,,,,,,,6285,,,,,,,1,Beijing Institute of Microbiology and Epidemiology,52.0x,PacBio,,,,12939,,,"Included in the study, passed QC/QA"
120,287.4621,"sample_type:culture;biomaterial_provider:Guiqing Wang, Ph.D.;collected_by:Westchester Medical Center",,Resistant,Computational Prediction,GCA_002812825.1,HGAP & SPAdes v. v2.3.0 & v3.10.0,,PRJNA419916,SAMN08101547,,,,,1,2014-12-09,complete genomes of three isogenic pairs of Pseudomonas aeruginosa clinical isolates,2017-12-06T00:00:00Z,,,2018-01-01T04:13:57.124Z,2018-01-01T04:13:57.124Z,,,66.02,CP025049,6526814,Pseudomonas aeruginosa strain PB369,Complete,Pseudomonas,USA: New York,,,,,,Homo sapiens,,USA,,Abscess,,,MLST.Pseudomonas_aeruginosa.319,,287,,,,,,,6351,,,,,6216,,1,New York Medical College,100x,PacBio & Illumina,,,,PB369,,,"Included in the study, passed QC/QA"
121,287.4622,"sample_type:culture;biomaterial_provider:Guiqing Wang, Ph.D.;collected_by:Westchester Medical Center",,Resistant,Computational Prediction,GCA_002812845.1,HGAP & SPAdes v. v2.3.0 & v3.10.0,,PRJNA419916,SAMN08101546,,,,,1,2014-11-12,complete genomes of three isogenic pairs of Pseudomonas aeruginosa clinical isolates,2017-12-06T00:00:00Z,,,2018-01-01T04:12:53.283Z,2018-01-01T04:12:53.283Z,,,65.96,CP025050,6638559,Pseudomonas aeruginosa strain PB368,Complete,Pseudomonas,USA: New York,,,,,,Homo sapiens,,USA,,Abscess,,,,,287,,,,,,,6461,,,,,6320,,1,New York Medical College,100x,PacBio & Illumina,,,,PB368,,,"Included in the study, passed QC/QA"
122,287.4623,"sample_type:culture;biomaterial_provider:Guiqing Wang, Ph.D.;collected_by:Westchester Medical Center",,Resistant,Computational Prediction,GCA_002812905.1,HGAP & SPAdes v. v2.3.0 & v3.10.0,,PRJNA419916,SAMN08101543,,,,,1,2016-04-17,complete genomes of three isogenic pairs of Pseudomonas aeruginosa clinical isolates,2017-12-06T00:00:00Z,,,2018-01-01T04:13:11.744Z,2018-01-01T04:13:11.744Z,,,66.2,CP025055,6752870,Pseudomonas aeruginosa strain PB350,Complete,Pseudomonas,USA: New York,,,,,,Homo sapiens,,USA,,sputum,,,,,287,,,,,,,6462,,,,,6340,,1,New York Medical College,100x,PacBio & Illumina,,,,PB350,,,"Included in the study, passed QC/QA"
123,287.4624,"sample_type:culture;biomaterial_provider:Guiqing Wang, Ph.D.;collected_by:Westchester Medical Center",,Resistant,Computational Prediction,GCA_002812925.1,HGAP & SPAdes v. v2.3.0 & v3.10.0,,PRJNA419916,SAMN08101542,,,,,1,2016-04-03,complete genomes of three isogenic pairs of Pseudomonas aeruginosa clinical isolates,2017-12-06T00:00:00Z,,,2018-01-01T04:15:17.328Z,2018-01-01T04:15:17.328Z,,,66.2,CP025056,6752906,Pseudomonas aeruginosa strain PB367,Complete,Pseudomonas,USA: New York,,,,,,Homo sapiens,,USA,,tracheal aspirate,,,MLST.Pseudomonas_aeruginosa.235,,287,,,,,,,6457,,,,,6340,,1,New York Medical College,100x,PacBio & Illumina,,,,PB367,,,"Included in the study, passed QC/QA"
124,303.167,,,,,GCF_000691565.1,Velvet v.1.0.14; Newbler v. 2.8,,PRJNA244741,SAMN02730082,,,,,1,31-Mar-2000,"p-Nitrophenol (PNP) is widely used in the manufacture of pesticides, dyes, explosives, and drug intermediates. PNP can alsoaccumulate in soil as a result of the hydrolysis of several organophosphorous insecticides, such as parathion or methyl parathion. Due to its potential toxicity and persistencein the environment, the US ATSDR and US EPA listed PNP on its “Priority Pollutants List”. Pseudomonas putida DLL-E4 is an efficient degrader of PNP. The genes of enzymes in the core genome and a genomic island encode the proteins responsible for PNP catabolism. It is significative to get complete genome of DLL-E4 to analyse the degradation process of PNP.",2014-06-24T00:00:00Z,,,2016-01-17T15:35:21.375Z,2016-01-17T15:35:21.375Z,,,62.46,CP007620,6484062,Pseudomonas putida strain DLL-E4,Complete,Pseudomonas,China,,,,,,,,China,,soil,,,,,303,,,,,,,6252,,,24948765,NZ_CP007620.1,5861,,1,Nanjing Agricultural University,100x,illumina hiseq2500; 454 GS FLX Titanium,,,,DLL-E4,,,"Included in the study, passed QC/QA"
125,303.2,sample_type:single microbe;collected_by:Dong-Hong Chen,,,,GCF_001636055.1,HGAP v. V2.0,,PRJNA286152,SAMN03765648,,,,,1,1-Nov-14,To isolate the specific lipase gene from Pseudomonas putida PC2 for biodiesel production,2016-05-02T00:00:00Z,,CCTCC:M 2015318,2016-05-23T19:18:31.874Z,2016-05-23T19:18:31.874Z,,,63.19,CP011789,5808624,Pseudomonas putida strain PC2,Complete,Pseudomonas,China: Fujian,,,,,,"Chinese pistachio, Pistacia chinensis Bunge",,China,,seeds,,,,,303,C,,,,,,5262,,,,NZ_CP011789.1,5029,,1,Hunan Agricultural University,206X,Illumina; Pacific Biosciences,,,,PC2,,,"Included in the study, passed QC/QA"
126,303.397,collected_by:First Affiliated Hospital of Guangzhou Medical University,,,,GCF_001886975.1,HGAP v. 2013,,PRJNA340924,SAMN05715224,,,,,1,2011-10-11,Whole genome sequencing of multidrug resistant strain Pseudomonas putida PP112420,2016-11-28T00:00:00Z,,,2017-01-16T05:54:18.813Z,2017-01-16T05:54:18.813Z,,,62.01,CP017073,6031212,Pseudomonas putida strain PP112420,Complete,Pseudomonas,China: Guangzhou,,,,,Urinary tract infection,"Human, Homo sapiens",,,,Urine,,,,,303,,,,,,,5496,,,,NZ_CP017073.1,5314,,1,South China University of Technology,138,Illumina; PacBio,,,,PP112420,,,"Included in the study, passed QC/QA"
127,303.41,sample_type:cell culture,,,,GCF_002025705.1,HGAP v. OCT-2015,,PRJNA357031,SAMN06130965,,,,,1,December-2012,The whole genomes of seven maize root-associated bacterial strains have been sequenced to facilitate the understanding of bacterium-bacterium and plant-bacterium interactions.,2017-03-13T00:00:00Z,,,2017-03-20T09:12:38.347Z,2017-03-20T09:12:38.347Z,,,62.53,CP018846,6137024,Pseudomonas putida strain AA7,Complete,Pseudomonas,USA:Boston,,,,,,"Corn, Zea mays",,,,root,,,,,303,,,,,,,5582,,,28275097,NZ_CP018846.1,,,1,Harvard University,103.45x,PacBio,,,,not applicable,,,"Included in the study, passed QC/QA"
128,303.411,,,,,GCF_900156185.1,,,PRJEB18870,SAMN05216501,,,,,1,not collected,Pseudomonas putida N1R,2017-01-14T00:00:00Z,,,2017-03-20T09:17:04.847Z,2017-03-20T09:17:04.847Z,,,61.96,LT707061,5729155,Pseudomonas putida strain N1R,Complete,Pseudomonas,,,,,,,,,,,,,,,,303,,,,,,,5257,,,,,5091,,1,DOE - JOINT GENOME INSTITUTE,,,,,,N1R,,,"Included in the study, passed QC/QA"
129,303.427,,,,,,,,PRJEB19718,SAMN05216307,,,,,1,not collected,Pseudomonas putida KT2440,2017-03-08T00:00:00Z,,,2017-05-30T13:31:11.827Z,2017-05-30T13:31:11.827Z,,,61.52,LT799039,6203063,Pseudomonas putida strain KT2440,Complete,Pseudomonas,,,,,,,,,,,,,,,,303,,,,,,,5781,,,,,5567,,1,DOE - JOINT GENOME INSTITUTE,,,,,,KT2440,,,"Included in the study, passed QC/QA"
130,303.447,,,,,GCA_002356095.1,Newbler v. 2.6,,PRJDB3359,SAMD00023463,,,,,5,1983,"This project focus is the complete genome sequencing of biphenyl/PCB-degrading bacterium,KF715 isolated from soil sample in Japan.",2016-12-06T00:00:00Z,,,2017-11-23T02:27:47.034Z,2017-11-23T02:27:47.034Z,4m,,61.36,"AP015029,AP015030,AP015031,AP015032,AP015033",7467685,Pseudomonas putida strain KF715,Complete,Pseudomonas,Japan:Kitakyushu,,,,,,,isolated from soil sample in Japan,,,soil sample,,,,,303,,,,,,,7257,,,,,7022,,5,National Institute of Advanced Industrial Science and Technology (AIST),124x,454 GS FLX; Hiseq1000; Miseq,,,,KF715,,,"Included in the study, passed QC/QA"
131,303.451,,,,,GCA_002736045.1,HGAP4 denovo v. OCT-2017,,PRJNA414589,SAMN07795048,,,,,1,2014-08,Comparative Genomics of Pseudomonas isolates recovered from Miscanthus x giganteus and Sida hermaphrodita: perspective for enhanced biomass production and phytoremediation of trace elements,2017-10-30T00:00:00Z,,,2017-11-24T17:04:01.780Z,2017-11-24T17:04:01.780Z,,,62.27,CP024086,6180967,Pseudomonas putida strain E46,Complete,Pseudomonas,"Poland: Silesia, next to Bytom city",,,,,,Sida hermaphrodita,,Poland,,Surface sterilized roots of Sida hermaphrodita,,,,,303,,,,,,,5520,,,,,5352,,1,Helmholtz Zentrum Muenchen GmbH,480.0x,PacBio; Illumina MiSeq,,,,E46,,,"Included in the study, passed QC/QA"
132,303.452,,,,,GCA_002736125.1,HGAP4 denovo v. OCT-2017,,PRJNA414589,SAMN07795037,,,,,1,2014-08,Comparative Genomics of Pseudomonas isolates recovered from Miscanthus x giganteus and Sida hermaphrodita: perspective for enhanced biomass production and phytoremediation of trace elements,2017-10-30T00:00:00Z,,,2017-11-24T17:04:06.261Z,2017-11-24T17:04:06.261Z,,,62.23,CP024085,6093023,Pseudomonas putida strain E41,Complete,Pseudomonas,"Poland: Silesia, next to Bytom city",,,,,,Sida hermaphrodita,,Poland,,Surface sterilized roots of Sida hermaphrodita,,,,,303,,,,,,,5510,,,,,5404,,1,Helmholtz Zentrum Muenchen GmbH,230.0x,PacBio; Illumina MiSeq,,,,E41,,,"Included in the study, passed QC/QA"
133,303.453,collected_by:Cintya Oliveira;passage_history:2,,,,GCA_002741075.1,SPAdes v. 3.6.2,,PRJNA316875,SAMN04591545,,,,,1,22-Apr-2015,Multiresistant bacteria in the watershed of the Aura: An environmental and health issue public,2016-08-05T00:00:00Z,,,2017-11-24T17:07:58.757Z,2017-11-24T17:07:58.757Z,,,62.25,"CP016634,CP016446",5847120,Pseudomonas putida strain IEC33019,Complete,Pseudomonas,"Brazil: Belem, Aura river, Amazon region",,,,,,,,Brazil,,,,,,,303,,,,,,,5423,,1,,,5240,,2,Universidade de Sao Paulo,120x,Illumina MiSeq,,,,IEC33019,,,"Included in the study, passed QC/QA"
134,351746.6,,,,,GCA_000016865.1,,,PRJNA13909,SAMN00623058,,,,Rod,1,,"Pseudomonas putida F1.This strain was isolated from a polluted creek in Urbana, Illinois by enrichment culture with ethylbenzyne as a sole source of carbon and energy. Its ability to degrade several different compounds including benzene, toluene, and ethylbenzene makes this species useful in the bioremediation of sites contaminated with multiple aromatic hydrocarbons. Underground gasoline tanks which have developed leaks can contaminate soil and water with a variety of these compounds. A more detailed knowledge of the metabolic pathways which allow Pseudomonas putida F1 to degrade aromatic hydrocarbons will be invaluable for the bioremediation industry.  ",2007-05-31T00:00:00Z,,,2014-12-08T22:12:38.992Z,2015-03-16T03:17:09.594Z,,,61.9,CP000712,5959964,Pseudomonas putida F1,Complete,Pseudomonas,Urbana Illinois,-,Multiple,,,,,"isolated from a polluted creek in Urbana, Illinois by enrichment culture with ethylbenzyne as a sole source of carbon and energy",United States,,polluted creek,,,,Yes,351746,-,Pseudomonas putida F1,,,,Aerobic,5377,,,,NC_009512,5252,Non-halophilic,1,DOE Joint Genome Institute,,,complete,,,F1,Mesophilic,,"Included in the study, passed QC/QA"
135,381754.6,,,,,GCA_000017205.1,,,PRJNA16720,SAMN02603435,,,,Rod,1,, Pseudomonas aeruginosa PA7. This strain is a clinical isolate and will be used for comparative genomics.,2007-07-05T00:00:00Z,,,2014-12-08T22:12:37.731Z,2015-03-16T03:17:09.594Z,,,66.4,CP000744,6588339,Pseudomonas aeruginosa PA7,Complete,Pseudomonas,,-,Multiple,,,,"Human, Homo sapiens",This strain is a clinical isolate,,,clinical isolate,,,MLST.Pseudomonas_aeruginosa.1195,Yes,381754,25-30,Pseudomonas aeruginosa PA7,,,,Aerobic,6064,,,20107499,NC_009656,6286,,1,J. Craig Venter Institute,,,complete,,,PA7,Mesophilic,,"Included in the study, passed QC/QA"
136,390235.5,,,,,GCA_000019445.1,,,PRJNA17053,SAMN02598376,,,,Rod,1,,Pseudomonas putida W619. Pseudomonas putida is a common endophytic and rhizosphere bacterium. Pseudomonas putida W619 was isolated from the Black Cottonwood tree and is closely related to other endophytic and rhizosphere strains of Pseudomonas putida. This strain is being sequenced for comparative genome analysis.,2008-03-11T00:00:00Z,,,2014-12-08T22:12:39.190Z,2015-03-16T03:17:09.594Z,,,61.4,CP000949,5774330,Pseudomonas putida W619,Complete,Pseudomonas,,-,Multiple,,,,"Black Cottonwood, Populus balsamifera subsp. Trichocarpa",isolated from the Black Cottonwood tree and is closely related to other endophytic and rhizosphere strains of Pseudomonas putida,,,Black Cottonwood tree,,,,Yes,390235,-,Pseudomonas putida W619,,,,Aerobic,5246,,,,NC_010501,5182,Non-halophilic,1,DOE Joint Genome Institute,,,complete,,,W619,Mesophilic,,"Included in the study, passed QC/QA"
137,557722.4,,,,,GCA_000026645.1,,,PRJNA31101,SAMEA1705916,,,,Rod,1,,Pseudomonas aeruginosa LESB58. Pseudomonas aeruginosa LESB58 is a member of the Liverpool epidemic strains (LES) first isolated at the Liverpool Cystic Fibrosis (CF) clinic center. These isolates are highly virulent and readily transfered between CF patients and to non-CF individuals. This organism will be used for comparative genomics with other Pseudomonas aeruginosa strains.,2008-12-24T00:00:00Z,,,2014-12-08T22:12:37.482Z,2015-03-16T03:17:09.594Z,,Respiratory tract infections,66.3,FM209186,6601757,Pseudomonas aeruginosa LESB58,Complete,Pseudomonas,Liverpool Cystic Fibrosis clinic center,-,Multiple,,,,,isolated at the Liverpool Cystic Fibrosis (CF) clinic center,United Kingdom,,,,,MLST.Pseudomonas_aeruginosa.146,Yes,557722,-,Pseudomonas aeruginosa LESB58,,,,Aerobic,6137,,,19047519,NC_011770,5925,,1,Wellcome Trust Sanger Institute,,,complete,,,LESB58,Mesophilic,,"Included in the study, passed QC/QA"
138,76869.5,,,,,GCA_000019125.1,,,PRJNA17629,SAMN00623059,,,,Rod,1,,Pseudomonas putida GB-1. This strain is able to oxidize soluble manganese(II) to the insoluble manganese(IV) which is deposited outside the cell. Pseudomonas putida GB-1 is being sequenced for comparative genome analysis.,2008-02-05T00:00:00Z,,,2014-12-08T22:12:39.002Z,2015-03-16T03:17:09.594Z,,,61.9,CP000926,6078430,Pseudomonas putida GB-1,Complete,Pseudomonas,,-,Multiple,,,,,,,,,,,,Yes,76869,-,Pseudomonas putida GB-1,,,,Aerobic,5438,,,,NC_010322,5409,Non-halophilic,1,DOE Joint Genome Institute,,,complete,,,GB-1,Mesophilic,,"Included in the study, passed QC/QA"
139,910265.3,,,Susceptible,Computational Prediction,,,,PRJEB5222,SAMEA104083446,,,,,1,1985-12-05,In this study we closed the contig of the most common Pseudomonas aerugiosa clone C followed by an annotation step. In addition RNA-seq was performed to identify transcriptional start sites (TSS) und small RNA.,2017-06-09T00:00:00Z,,,2017-07-28T00:03:46.296Z,2017-07-28T00:03:46.296Z,,,66.12,LT883143,6902967,Pseudomonas aeruginosa C-NN2 strain early isolate NN2 (clone C),Complete,Pseudomonas,,,,,,,Homo sapiens sapiens,,,,Cystic fibrosis lung,,,,,910265,,,host_health_state:diseased,,,,6586,,,,,6601,,1,MHH,,,,,,early isolate NN2 (clone C),,,"Included in the study, passed QC/QA"
140,931281.3,,,,,GCA_000183645.1,,,PRJNA54033,SAMN02603225,,,,,1,,"Estacion Experimental del Zaidin (CSIC) Granada, Spain.Pseudomonas putida BIRD-1 is a metabollically versatile plant-growth promoting rhizobacteria, which is commercially available as a biofertilizer.",2010-12-03T00:00:00Z,,,2014-12-08T22:12:38.965Z,2015-03-16T03:17:09.594Z,,,61.74,CP002290,5731541,Pseudomonas putida BIRD-1,Complete,Pseudomonas,,,,,,,,,,,,,,,,931281,-,Pseudomonas putida BIRD-1,,,,,5176,,,21183676,NC_017530.1,4960,,1,"Estacion Experimental del Zaidin, CSIC",,,complete,,,BIRD1,,,"Included in the study, passed QC/QA"
141,941193.4,,,,,GCA_000226155.1,,,PRJNA61423,SAMN02603849,,,,,1,,No description available.,2011-09-19T00:00:00Z,,,2014-12-08T22:12:37.535Z,2015-03-16T03:17:09.594Z,,,66.5,CP002496,6327754,Pseudomonas aeruginosa M18,Complete,Pseudomonas,,,,,,,,,,,,,,MLST.Pseudomonas_aeruginosa.1239,,941193,-,Pseudomonas aeruginosa M18,,,,,5892,,,21884571,NC_017548.1,5684,,1,"Division of Environmental Science and Ecological Engineering, Korea University",,,unfinished,,,M18,,,"Included in the study, passed QC/QA"
142,1008297.7,,,,,GCA_000252875.1,,,PRJNA66023,SAMN02604223,,,,,1,,Salmonella enterica var. Typhimurium strain 798 causes persistent infections in pigs and can spread to other animals and cause food-borne disease in humans.,2012-03-15T00:00:00Z,, ,2014-12-08T22:12:52.568Z,2015-03-16T03:17:09.594Z,,,52.217,"CP003386.1,CP003387.1",4970096,Salmonella enterica subsp. enterica serovar Typhimurium str. 798,Complete,Salmonella,,,,,,,,,,,,,,,,1008297,,Salmonella enterica subsp. enterica serovar Typhimurium str. 798,,,,,5068,,1,,"NC_017046.1,NC_017054.1",4430,,2,University of Minnesota,,,complete,serovar Typhimurium,,798,,,"Included in the study, passed QC/QA"
143,1016998.12,,,,,GCF_000018705.1,,,PRJNA27803,SAMN02603951,,,,Bacilli,1,,"Salmonella enterica subsp. enterica serovar Paratyphi B strain SPB7. This strain (SGSC 4150; ATCC BAA-1250) was isolated from a stool sample of an infected woman in Penang, Malaysia, May 16, 2002. This strain is susceptible to antibiotics, and was classified as serovar Paratyphi B because it was unable to metabolize D-tartrate.",2014-01-31T00:00:00Z,,ATCC:BAA-1250,2016-01-17T15:28:08.928Z,2016-01-17T15:28:08.928Z,,Typhoid-like disease,52.11,CP000886,4858887,Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7,Complete,Salmonella,Penang Malaysia May,Negative,HostAssociated,,,,"Human, Homo sapiens","isolated from a stool sample of an infected woman in Penang, Malaysia, May 16, 2002",,,stool sample of an infected woman,,,,No,1016998,37,,,,,Facultative,5418,,,,NC_010102.1,5601,,1,Washington University Genome Sequencing Center,,,,Paratyphi B,,SGSC4150; SPB7,Mesophilic,,"Included in the study, passed QC/QA"
144,1064551.5,,,,,GCA_000473275.1,Roche Newbler v. 2.3; Geneious 6.1,,PRJNA70669,SAMN02604282,,,,,1,,"Non-typhoid Salmonella enterica are food-borne bacterial pathogens of worldwide importance and are classified into serovars differing in virulence and host range. S. enterica serovar Thompson causes both human and zoonotic diseases, and has caused human outbreaks associated with fresh vegetables. The genomic sequence of this serovar should provide a measures of interserovar diversity.",2013-09-30T00:00:00Z,, ,2014-12-08T22:12:52.297Z,2015-03-16T03:17:09.594Z,,,52.2,CP006717.1,4707648,Salmonella enterica subsp. enterica serovar Thompson str. RM6836,Complete,Salmonella,,,,,,,,,,,,,,MLST.Salmonella_enterica.26,,1064551,,Salmonella enterica subsp. enterica serovar Thompson str. RM6836,,,,,4640,,,24233585,NC_022525.1,4357,,1,USDA-ARS-WRRC-PSM,>100X,Sanger dideoxy sequencing; 454; Illumina,complete,serovar Thompson,,RM6836,,,"Included in the study, passed QC/QA"
145,1081093.3,,,,,GCA_000235545.1,,,PRJNA72821,SAMN02603246,,,,,1,,,,,,2014-12-08T22:13:55.870Z,2015-03-16T03:17:09.594Z,,,52.21,CP003047.1,4637962,Salmonella enterica subsp. enterica serovar Gallinarum/pullorum str. RKS5078,Complete,Salmonella,,,,,,,,,,,,,,MLST.Salmonella_enterica.92,,1081093,,,,,,,4694,,,,NC_016831.1,4325,,1,,,,,,,,,,"Included in the study, passed QC/QA"
146,108619.119,collected_by:U Penn Salmonella Reference Center,,,,,SMRTanalysis v. 2.3.0,,PRJNA285350,SAMN03744301,,,,,1,Dec-2001,The goal is to use genomic data to track the origin of outbreak as well as the antibiotic resistance profile,2016-09-03T00:00:00Z,,,2017-07-21T16:33:31.390Z,2017-07-21T16:33:31.390Z,,,52.23,CP012597,4538916,Salmonella enterica subsp. enterica serovar Newport strain 0112-791,Complete,Salmonella,USA,,HostAssociated,,,gastroenteritis,Bos taurus,,United States,,stool,,,,,108619,37 C,,,,,,4904,,,,,3722,,1,university of pennyslvania,100X,PacBio RS II P6-C4,,Newport,,0112-791,,,"Included in the study, passed QC/QA"
147,108619.12,collected_by:U Penn Salmonella Reference Center,,,,,SMRTanalysis v. 2.3.0,,PRJNA285350,SAMN03744302,,,,,1,Nov-2002,The goal is to use genomic data to track the origin of outbreak as well as the antibiotic resistance profile,2016-09-03T00:00:00Z,,,2017-07-21T16:28:44.521Z,2017-07-21T16:28:44.521Z,,,52.2,CP012598,4962150,Salmonella enterica subsp. enterica serovar Newport strain 0211-109,Complete,Salmonella,USA,,HostAssociated,,,gastroenteritis,Bos taurus,,United States,,stool,,,MLST.Salmonella_enterica.45,,108619,37 C,,,,,,5169,,,,,4465,,1,university of pennyslvania,100X,PacBio RS II P6-C4,,Newport,,0211-109,,,"Included in the study, passed QC/QA"
148,108619.121,collected_by:U Penn Salmonella Reference Center,,,,,SMRTanalysis v. 2.3.0,,PRJNA285350,SAMN03744303,,,,,1,Jul-2003,The goal is to use genomic data to track the origin of outbreak as well as the antibiotic resistance profile,2016-09-03T00:00:00Z,,,2017-07-21T16:25:22.940Z,2017-07-21T16:25:22.940Z,,,51.86,CP012599,4512838,Salmonella enterica subsp. enterica serovar Newport strain 0307-213,Complete,Salmonella,USA,,HostAssociated,,,gastroenteritis,Equine,,United States,,stool,,,,,108619,37 C,,,,,,4702,,,,,4310,,1,university of pennyslvania,100X,PacBio RS II P6-C4,,Newport,,0307-213,,,"Included in the study, passed QC/QA"
149,108619.34,,,,,GCF_001890165.1,HGAP v. 3.0,,PRJNA186035,SAMN05172400,,,,,1,,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,2016-12-07T00:00:00Z,,,2017-01-16T08:01:15.094Z,2017-01-16T08:01:15.094Z,,,52.15,"CP016010,CP016011",4901721,Salmonella enterica subsp. enterica serovar Newport strain CFSAN001660,Complete,Salmonella,USA: VA,,,,,,,,United States,,,,,,,108619,,,,,,,5001,,1,,"NZ_CP016010.1,NZ_CP016011.1",4660,,2,Center for Food Safety and Applied Nutrition,100,PacBio,,Newport,,CFSAN001660,,,"Included in the study, passed QC/QA"
150,108619.35,collected_by:WCFS,,,,GCF_001890185.1,HGAP v. 3.0,,PRJNA186035,SAMN05172402,,,,,1,04-Oct-2007,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,2016-12-07T00:00:00Z,,,2017-01-16T07:57:23.266Z,2017-01-16T07:57:23.266Z,,,52.17,"CP016012,CP016013",5028098,Salmonella enterica subsp. enterica serovar Newport strain CFSAN003890,Complete,Salmonella,USA: CA,,,,,,,,United States,,"almond kernel (raw, variety carmel)",,,,,108619,,,,,,,5183,,1,,"NZ_CP016012.1,NZ_CP016013.1",4798,,2,Center for Food Safety and Applied Nutrition,600,PacBio,,Newport,,CFSAN003890,,,"Included in the study, passed QC/QA"
151,108619.36,collected_by:WCFS,,,,GCF_001890445.1,HGAP v. 3.0,,PRJNA186035,SAMN05172401,,,,,1,27-Sep-2006,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,2016-12-07T00:00:00Z,,,2017-01-16T08:08:23.462Z,2017-01-16T08:08:23.462Z,,,52.18,CP016014,4746969,Salmonella enterica subsp. enterica serovar Newport strain CFSAN003887,Complete,Salmonella,USA: CA,,,,,,,,United States,,"almond kernel (raw, variety nonpariel)",,,,,108619,,,,,,,4723,,,,NZ_CP016014.1,4419,,1,Center for Food Safety and Applied Nutrition,500,PacBio,,Newport,,CFSAN003887,,,"Included in the study, passed QC/QA"
152,108619.37,collected_by:U Penn Salmonella Reference Center,,,,GCF_001922165.1,,,PRJNA285350,SAMN03744300,,,,,1,Jul-2000,The goal is to use genomic data to track the origin of outbreak as well as the antibiotic resistance profile,2016-12-27T00:00:00Z,,,2017-01-17T18:49:48.972Z,2017-01-17T18:49:48.972Z,,,52.21,CP013685,4846742,Salmonella enterica subsp. enterica serovar Newport strain 0007-33,Complete,Salmonella,USA,,HostAssociated,,,gastroenteritis,Bos taurus,,United States,,stool,,,,,108619,37 C,,,,,,4855,,,,NZ_CP013685.1,4515,,1,university of pennyslvania,,,,Newport,,0007-33,,,"Included in the study, passed QC/QA"
153,1124936.4,,,,,GCA_000430105.1,SMRT Analysis v. 1.3.4,,PRJNA78477,SAMN01088008,,,,,1,2011,Genome sequencing project,2013-07-16T00:00:00Z,,,2014-12-08T22:12:50.115Z,2015-03-16T03:17:09.594Z,,,52.1153,"CP004086.1,CP004857.1,CP004088.1,CP004087.1",4951478,Salmonella enterica subsp. enterica serovar Heidelberg str. 41578,Complete,Salmonella,USA: OH,,,,,,"Human, Homo sapiens",,United States,,Stool,,,MLST.Salmonella_enterica.15,,1124936,,Salmonella enterica subsp. enterica serovar Heidelberg str. 41578,,,,,4980,,3,,"NC_021810.1,NC_021869.1,NC_021841.1,NC_021811.1",4712,,4,FDA,80x,PacBio,complete,Heidelberg,,41578,,,"Included in the study, passed QC/QA"
154,1129117.3,"collected_by:National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB",,,,GCF_001975605.1,SMRT Analysis v. 1.3.3,,PRJNA294451,SAMN04160827,,,,,1,,"Genome sequence of Salmonella Nitra (serogroup A; 2,12:g,m:-)",2017-01-30T00:00:00Z,,,2017-03-20T06:33:26Z,2017-03-20T06:33:26Z,,,52.19,CP019416,4691807,Salmonella enterica subsp. enterica serovar Nitra strain S-1687,Complete,Salmonella,,,Unknown,,,,,,,,,,,,,1129117,37 C,,,,,Facultative,4809,,,,NZ_CP019416.1,4613,,1,Laboratory for Foodborne Zoonoses,99.0x,Illumina MiSeq; PacBio,,Nitra,,S-1687,Mesophilic,,"Included in the study, passed QC/QA"
155,1132507.4,,,,,GCA_000245535.1,,,PRJNA80939,SAMN02603101,,,,,1,,Genome sequencing of S. Typhi P-stx-12 will provide a better understanding on the causative agent of Typhoid Fever.  Salmonella enterica subspecies enterica serovar Typhi P-stx-12 is a clinical isolate obtained from a Typhoid Carrier in India.,2012-02-01T00:00:00Z,,,2014-12-08T22:12:52.439Z,2015-03-16T03:17:09.594Z,,,51.86,"CP003279,CP003278",4949783,Salmonella enterica subsp. enterica serovar Typhi str. P-stx-12,Complete,Salmonella,India,,,,,,,isolate obtained from a Typhoid Carrier in India,India,,Typhoid Carrier,,,MLST.Salmonella_enterica.1,,1132507,,Salmonella enterica subsp. enterica serovar Typhi str. P-stx-12,,,,,5147,,1,,"NC_016832.1,NC_016825.1",4924,,2,Centre for Chemical Biology (CCB@USM),,,,serovar Typhi,,serovar Typhi P-stx-12,,,"Included in the study, passed QC/QA"
156,1160717.4,,,,,GCA_000258365.1,,,PRJNA88529,SAMN02603149,,,,,1,,This strain is a natural mutator isolate of Salmonella enterica subsp. enterica serotype Heidelberg.,2012-04-10T00:00:00Z,,,2014-12-08T22:12:50.147Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,52.1137,"CP003416.1,CP003417.1",4788046,Salmonella enterica subsp. enterica serovar Heidelberg str. B182,Complete,Salmonella,,Negative,,,,,,,,,,,,MLST.Salmonella_enterica.15,,1160717,,Salmonella enterica subsp. enterica serovar Heidelberg str. B182,,,,,4728,,1,22689230,"NC_017623.1,NC_017624.1",4334,,2,CNRS-UMR6290,,,complete,serovar Heidelberg,,Strain B182,,,"Included in the study, passed QC/QA"
157,1171376.3,,,,,GCA_000380325.1,CLC Genomics workbench,,PRJNA157919,SAMN02604233,,,,Bacilli,1,,"Over the last decade Salmonella Typhimurium U288 (STU288) has established itself in UK pig production premises.  The microorganism displays enhanced pathogenicity towards pigs compared with other serovars, and as such has proven to be of both economic and veterinary importance.  Also, an outbreak of STU288 in Denmark during 2008 resulted in the death of a number of elderly pepople.  Due to the position of STU288 in the food-chain, knowledge of the genetic make-up of this multi drug resistant strain is essential if efforts are to be made to reduce its prevalence in the UK.",2013-04-23T00:00:00Z,,,2014-12-08T22:12:52.928Z,2015-03-16T03:17:09.594Z,,,52.2438,"CP003836.1,CP004059.1,CP004058.1,CP004060.1",5017059,Salmonella enterica subsp. enterica serovar Typhimurium str. U288,Complete,Salmonella,,Negative,,,,,,,,,,,,,Yes,1171376,,Salmonella enterica subsp. enterica serovar Typhimurium str. U288,,,,,5099,,3,,"NC_021151.1,NC_021156.1,NC_021155.1,NC_021157.1",4798,,4,University of Nottingham,,454,complete,serovar Typhimurium,No,U288,,,"Included in the study, passed QC/QA"
158,1173427.3,,,,,GCA_000439415.1,SMRT Analysis v. 1.3.3,,PRJNA159279,SAMN01823701,,,,,1,2003,Genome sequencing project,2013-07-16T00:00:00Z,,,2014-12-08T22:12:48.333Z,2015-03-16T03:17:09.594Z,,,52.174,"CP006053.1,CP006054.1",4808805,Salmonella enterica subsp. enterica serovar Bareilly str. CFSAN000189,Complete,Salmonella,,,,,,,,,,,"Shrimp, Frozen Raw",,,MLST.Salmonella_enterica.909,,1173427,,Salmonella enterica subsp. enterica serovar Bareilly str. CFSAN000189,,,,,4755,,1,,"NC_021844.1,NC_021817.1",4441,,2,FDA,80x,PacBio RS,complete,Bareilly,,CFSAN000189,,,"Included in the study, passed QC/QA"
159,1173939.4,collected_by:FDA,,,,GCF_001612515.1,SMRT Portal HGAP v. 2.3,,PRJNA161807,SAMN02568587,,,,,,2005-02-10,Genome sequencing project,2016-04-06T00:00:00Z,1,,2016-04-28T03:50:05.411Z,2016-04-28T03:50:05.411Z,,,52.13,"CP014996,CP014997",5129059,Salmonella enterica subsp. enterica serovar Weltevreden str. 1655,Complete,Salmonella,USA:VA,,,,,,,,United States,,tuna,,,,,1173939,,,,,,,5284,,1,,"NZ_CP014996.1,NZ_CP014997.1",4879,,2,FDA,326X,PacBio RS,,Weltevreden,,1655,,,"Included in the study, passed QC/QA"
160,1197719.3,,,,,GCA_000439255.1,SMRTanalysis v. 2.01,,PRJNA168043,SAMN02603391,,,,Bacilli,1,2008,Genome sequencing of a S. bongori isolate for taxonomic studies and investigation of the evolution of this species,2013-07-23T00:00:00Z,,,2014-12-08T22:12:46.970Z,2015-03-16T03:17:09.594Z,,,51.2793,"CP006608.1,CP006609.1",4773537,Salmonella bongori N268-08,Complete,Salmonella,Switzerland,Negative,HostAssociated,,,,,,Switzerland,,,,,,Yes,1197719,37C,Salmonella bongori N268-08,,,,Facultative,4745,,1,,"NC_021870.1,NC_021871.1",4770,Unknown,2,"Institute of Food, Nutrition and Health, ETH Zurich",25x; 300x,PacBio; IonTorrent; Sanger,complete,,No,N268-08,Mesophilic,,"Included in the study, passed QC/QA"
161,119912.1,,,,,GCF_000742815.1,Soapdenovo v. 2012,,PRJNA245852,SAMN02741042,,,,,1,2010-01-01,Salmonella enterica subsp. enterica serovar Choleraesuis str. C500 genome,2014-10-16T00:00:00Z,,,2016-01-17T15:38:52.238Z,2016-01-17T15:38:52.238Z,,,52.18,CP007639,4751585,Salmonella enterica subsp. enterica serovar Choleraesuis strain C500,Complete,Salmonella,china: yangzhou,,,,,,,,China,,chicken intestinal,,,,,119912,,,,,,,4873,,,25301657,NZ_CP007639.1,4232,,1,Yangzhou University,250x,Illumina,,serovar Choleraesuis,,C500,,,"Included in the study, passed QC/QA"
162,1225522.3,,,,,GCA_000462995.1,,,PRJNA173203,SAMN01884234,,,,,1,,,,,,2014-12-08T22:12:49.911Z,2015-03-16T03:17:09.594Z,,,52.23,CP003786.1,4623089,Salmonella enterica subsp. enterica serovar Gallinarum/pullorum str. CDC1983-67,Complete,Salmonella,,,,,,,,,,,,,,MLST.Salmonella_enterica.92,,1225522,,,,,,,4698,,,,NC_022221.1,4331,,1,,,,,,,,,,"Included in the study, passed QC/QA"
163,1240694.4,"collected_by:National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB",,,,GCA_001975265.1,SMRT Analysis v. 1.3.3,,PRJNA177073,SAMN04160822,,,,Bacilli,1,,Sequence of the genome of Salmonella Blegdam.,2017-01-30T00:00:00Z,,,2017-03-20T06:31:12.064Z,2017-03-20T06:31:12.064Z,,,52.25,CP019406,4693979,Salmonella enterica subsp. enterica serovar Blegdam str. S-1824 strain S-1824,Complete,Salmonella,,Negative,Unknown,,,,,,,,,,,MLST.Salmonella_enterica.2912,Yes,1240694,37C,,,,,Facultative,4842,,,,NZ_CP019406.1,4618,,1,Laboratory for Foodnorne Zoonoses,107.0x,Illumina MiSeq; PacBio,,Blegdam,,S-1824,Mesophilic,,"Included in the study, passed QC/QA"
164,1240708.3,"collected_by:Animal and Plant Health Agency, UK",,,,GCF_001975325.1,SMRT Analysis v. 1.3.3,,PRJNA177119,SAMN04160814,,,,Bacilli,1,15-Jul-1991,Sequence of the genome of Salmonella Bergen.,2017-01-30T00:00:00Z,,,2017-03-20T06:31:58.611Z,2017-03-20T06:31:58.611Z,,,52.27,CP019405,4801835,Salmonella enterica subsp. enterica serovar Bergen str. ST350 strain ST350,Complete,Salmonella,United Kingdom,Negative,Unknown,,,,,,United Kingdom,,Animal feed,,,MLST.Salmonella_enterica.1356,Yes,1240708,37C,,,,,Facultative,4970,,,,NZ_CP019405.1,4735,,1,Laboratory for Foodborne Zoonoses,61.0x,Illumina MiSeq; PacBio,,Bergen,,ST350,Mesophilic,,"Included in the study, passed QC/QA"
165,1242087.3,"collected_by:National Salmonella, Shigella and Listeria Reference Laboratory, Galway University Hospital, Galway, Ireland",,,,GCF_001956735.1,SMRT Analysis v. 1.3.3,,PRJNA177204,SAMN04160831,,,,Bacilli,1,01-Jun-2001,"Genome sequence of Salmonella Antsalova O51 (51:z:1,5).",2017-01-18T00:00:00Z,,,2017-03-20T05:57:17.380Z,2017-03-20T05:57:17.380Z,,,52.27,CP019116,4648086,Salmonella enterica subsp. enterica serovar Antsalova str. S01-0511 strain S01-0511,Complete,Salmonella,,Negative,Unknown,,,,,,,,Egusi seeds,,,,Yes,1242087,37C,,,,,Facultative,4779,,,,NZ_CP019116.1,4577,,1,Laboratory for Foodnorne Zoonoses,97.0x,Illumina MiSeq; PacBio,,Antsalova,,S01-0511,Mesophilic,,"Included in the study, passed QC/QA"
166,1242088.3,"collected_by:Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON",,,,GCF_001975285.1,SMRT Analysis v. 1.3.3,,PRJNA177205,SAMN04160810,,,,Bacilli,1,22-Jan-2006,"Genome sequence of Salmonella Apapa (serogroup W; serotype 45:m,t:-)",2017-01-30T00:00:00Z,,,2017-03-20T06:33:59.930Z,2017-03-20T06:33:59.930Z,,,52.17,CP019403,4801658,Salmonella enterica subsp. enterica serovar Apapa str. SA20060561 strain SA20060561,Complete,Salmonella,Canada: Ontario: Hamilton,Negative,Unknown,,,,,,Canada,,Pogona vitticeps: Feces,,,MLST.Salmonella_enterica.647,Yes,1242088,37C,,,,,Facultative,4958,,,,NZ_CP019403.1,4698,,1,Laboratory for Foodnorne Zoonoses,57.0x,Illumina MiSeq; PacBio,,Apapa,,SA20060561,Mesophilic,,"Included in the study, passed QC/QA"
167,1242089.3,"collected_by:Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON",,,,GCF_001975345.1,SMRT Analysis v. 1.3.3,,PRJNA177206,SAMN04160805,,,,Bacilli,1,05-Nov-1990,"Genome sequence of Salmonella Borreze (serogroup 054; serotype 54:f,g,s:-)",2017-01-30T00:00:00Z,,,2017-03-20T06:31:17.907Z,2017-03-20T06:31:17.907Z,,,52.1,CP019407,4777558,Salmonella enterica subsp. enterica serovar Borreze str. SA20041063 strain SA20041063,Complete,Salmonella,Canada: Ontario: Guelph,Negative,Unknown,,,,,,Canada,,,,,MLST.Salmonella_enterica.13,Yes,1242089,37C,,,,,Facultative,4925,,,,NZ_CP019407.1,4677,,1,Laboratory for Foodnorne Zoonoses,64.0x,Illumina MiSeq; PacBio,,Borreze,,SA20041063,Mesophilic,,"Included in the study, passed QC/QA"
168,1242090.3,"collected_by:Institut Pasteur, Paris, France",,,,GCF_001975245.1,SMRT Analysis v. 1.3.3,,PRJNA177207,SAMN04160812,,,,Bacilli,1,15-Jul-1973,"Genome sequence of Salmonella Crossness (serogroup 067; serotype 67:r:1,2)",2017-01-30T00:00:00Z,,,2017-03-20T06:31:02.046Z,2017-03-20T06:31:02.046Z,,,52.21,CP019408,4847468,Salmonella enterica subsp. enterica serovar Crossness str. 1422-74 strain 1422-74,Complete,Salmonella,United Kingdom: Great Britain,Negative,Unknown,,,,,,United Kingdom,,Sewage,,,MLST.Salmonella_enterica.15,Yes,1242090,37C,,,,,Facultative,5008,,,,NZ_CP019408.1,4775,,1,Laboratory for Foodnorne Zoonoses,115.0x,Illumina MiSeq; PacBio,,Crossness,,1422-74,Mesophilic,,"Included in the study, passed QC/QA"
169,1242091.3,"collected_by:National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB",,,,GCF_001975365.1,SMRT Analysis v. 1.3.3,,PRJNA177208,SAMN04160823,,,,Bacilli,1,,"Genome sequence of Salmonella Djakarta (serogroup Y; serotype 48:z4,z24:-)",2017-01-30T00:00:00Z,,,2017-03-20T06:35:05.180Z,2017-03-20T06:35:05.180Z,,,52.34,CP019409,4668861,Salmonella enterica subsp. enterica serovar Djakarta str. S-1087 strain S-1087,Complete,Salmonella,,Negative,Unknown,,,,,,,,,,,MLST.Salmonella_enterica.2719,Yes,1242091,37C,,,,,Facultative,4806,,,,NZ_CP019409.1,4583,,1,Laboratory for Foodborne Zoonoses,82.0x,Illumina MiSeq; PacBio,,Djakarta,,S-1087,Mesophilic,,"Included in the study, passed QC/QA"
170,1242096.3,"collected_by:Institute for Veterinary Bacteriology, University of Berne, Postfach, Langgass-Strasse 122, CH-3001 Berne, Switzerland",,,,GCF_001975385.1,SMRT Analysis v. 1.3.3,,PRJNA177215,SAMN04160821,,,,Bacilli,1,,"Genome sequence of Salmonella Hillingdon (serogroup D; serotype 9,46:g,m:-)",2017-01-30T00:00:00Z,,,2017-03-20T06:34:13.848Z,2017-03-20T06:34:13.848Z,,,52.19,CP019410,4618056,Salmonella enterica subsp. enterica serovar Hillingdon str. N1529-D3 strain N1529-D3,Complete,Salmonella,,Negative,Unknown,,,,,,,,,,,,Yes,1242096,37C,,,,,Facultative,4702,,,,NZ_CP019410.1,4478,,1,Laboratory for Foodborne Zoonoses,81.0x,Illumina MiSeq; PacBio,,Hillingdon,,N1529-D3,Mesophilic,,"Included in the study, passed QC/QA"
171,1242098.3,"collected_by:Laboratoire d'epidemiosurveillance animale du Quebec, Saint-Hyacinthe, QC",,,,,HGAP v. v. 1.3,,PRJNA177230,SAMN04160811,,,,Bacilli,1,01-Sep-2008,"Genome sequence of Salmonella India (serogroup D; ; serotype 9,46:l,v:1,5)",2017-06-26T00:00:00Z,,,2017-07-23T01:08:03.169Z,2017-07-23T01:08:03.169Z,,,51.55,"CP022015,CP022016",5868736,Salmonella enterica subsp. enterica serovar India str. SA20085604 strain SA20085604,Complete,Salmonella,Canada: Quebec: Saint-Hyacinthe,Negative,Unknown,,,,,,Canada,,,,,,Yes,1242098,37C,,,,,Facultative,6451,,1,,,5993,,2,Laboratory for Foodborne Zoonoses,70.0x,Illumina; PacBio,,India,,SA20085604,Mesophilic,,"Included in the study, passed QC/QA"
172,1242101.3,"collected_by:Animal and Plant Health Agency, UK",,,,GCF_001975405.1,SMRT Analysis v. 1.3.3,,PRJNA177234,SAMN04160815,,,,Bacilli,1,15-Jul-1991,"Genome sequence of Salmonella Johannesburg (serogroup R; serotype 40:b:e,n,x)",2017-01-30T00:00:00Z,,,2017-03-20T06:31:50.217Z,2017-03-20T06:31:50.217Z,,,52.29,CP019411,4651794,Salmonella enterica subsp. enterica serovar Johannesburg str. ST203 strain ST203,Complete,Salmonella,United Kingdom,Negative,Unknown,,,,,,United Kingdom,,Animal feed,,,,Yes,1242101,37C,,,,,Facultative,4803,,,,NZ_CP019411.1,4602,,1,Laboratory for Foodborne Zoonoses,95.0x,Illumina MiSeq; PacBio,,Johannesburg,,ST203,Mesophilic,,"Included in the study, passed QC/QA"
173,1242105.3,"collected_by:National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB",,,,GCF_001975425.1,SMRT Analysis v. 1.3.3,,PRJNA177317,SAMN04160824,,,,Bacilli,1,,"Genome sequence of Salmonella Koessen (serogroup A; serotype 2,12:l,v:1,5)",2017-01-30T00:00:00Z,,,2017-03-20T06:32:05.736Z,2017-03-20T06:32:05.736Z,,,52.28,CP019412,4566169,Salmonella enterica subsp. enterica serovar Koessen str. S-1501 strain S-1501,Complete,Salmonella,,Negative,Unknown,,,,,,,,,,,,Yes,1242105,37C,,,,,Facultative,4669,,,,NZ_CP019412.1,4481,,1,Laboratory for Foodborne Zoonoses,135.0x,Illumina MiSeq; PacBio,,Koessen,,S-1501,Mesophilic,,"Included in the study, passed QC/QA"
174,1242106.3,"collected_by:Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Saint-Hyacinthe, QC",,,,GCF_001975445.1,SMRT Analysis v. 1.3.3,,PRJNA177321,SAMN04160800,,,,Bacilli,1,19-Dec-2002,"Genome sequence of Salmonella Krefeld (serogroup E4; serotype 1,3,19:y:l,w)",2017-01-30T00:00:00Z,,,2017-03-20T06:33:34.161Z,2017-03-20T06:33:34.161Z,,,52.01,CP019413,4942273,Salmonella enterica subsp. enterica serovar Krefeld str. SA20030536 strain SA20030536,Complete,Salmonella,Canada: Ontario,Negative,Unknown,,,,,,Canada,,Sus scrofa: Cecal content,,,,Yes,1242106,37C,,,,,Facultative,5119,,,,NZ_CP019413.1,4859,,1,Laboratory for Foodborne Zoonoses,104.0x,Illumina MiSeq; PacBio,,Krefeld,,SA20030536,Mesophilic,,"Included in the study, passed QC/QA"
175,1242107.3,"collected_by:National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB",,,,,HGAP v. v 1.3,,PRJNA177326,SAMN04160825,,,,Bacilli,1,,"Genome sequence of Salmonella Macclesfield (serogroup D2; serotype 9,46:g,m,s:1,2,7)",2017-06-30T00:00:00Z,,,2017-07-23T03:35:41.090Z,2017-07-23T03:35:41.090Z,,,51.96,"CP022117,CP022118,CP022119",5268613,Salmonella enterica subsp. enterica serovar Macclesfield str. S-1643 strain S-1643,Complete,Salmonella,,Negative,Unknown,,,,,,,,,,,,Yes,1242107,37C,,,,,Facultative,5586,,2,,,5248,,3,Laboratory for Foodborne Zoonoses,122.0x,Illumina; PacBio,,Macclesfield,,S-1643,Mesophilic,,"Included in the study, passed QC/QA"
176,1242108.3,"collected_by:Animal and Plant Health Agency, UK",,,,GCF_001975515.1,SMRT Analysis v. 1.3.3,,PRJNA177327,SAMN04160817,,,,Bacilli,1,15-Jul-1970,"Genome sequence of Salmonella Manchester(serogroup C2; serotype 6,8:l,v:1,7)",2017-01-30T00:00:00Z,,,2017-03-20T06:34:39.339Z,2017-03-20T06:34:39.339Z,,,52.28,CP019414,4532753,Salmonella enterica subsp. enterica serovar Manchester str. ST278 strain ST278,Complete,Salmonella,,Negative,Unknown,,,,,,,,,,,MLST.Salmonella_enterica.491,Yes,1242108,37C,,,,,Facultative,4606,,,,NZ_CP019414.1,4438,,1,Laboratory for Foodborne Zoonoses,105.0x,Illumina MiSeq; PacBio,,Manchester,,ST278,Mesophilic,,"Included in the study, passed QC/QA"
177,1243579.4,"collected_by:National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB",,,,GCF_001975555.1,SMRT Analysis v. 1.3.3,,PRJNA177578,SAMN04160826,,,,Bacilli,1,,"Genome sequence of Salmonella Moscow (serogroup D; serotype 9,12:g,q:-)",2017-01-30T00:00:00Z,,,2017-03-20T06:32:51.155Z,2017-03-20T06:32:51.155Z,,,52.25,CP019415,4690402,Salmonella enterica subsp. enterica serovar Moscow str. S-1843 strain S-1843,Complete,Salmonella,,Negative,Unknown,,,,,,,,,,,,Yes,1243579,37C,,,,,Facultative,4880,,,,NZ_CP019415.1,4626,,1,Laboratory for Foodborne Zoonoses,107.0x,Illumina MiSeq; PacBio,,Moscow,,S-1843,Mesophilic,,"Included in the study, passed QC/QA"
178,1243584.3,"collected_by:Animal Health Laboratory, University of Guelph, Guelph, ON",,,,,HGAP v. v 1.3,,PRJNA177585,SAMN04160808,,,,Bacilli,1,19-Aug-1998,"Genome sequence of Salmonella Onderstepoort (serogroup H; serotype 6,14,25:e,h:1,5)",2017-06-26T00:00:00Z,,,2017-07-23T01:04:11.593Z,2017-07-23T01:04:11.593Z,,,51.85,"CP022034,CP022036,CP022035",5005424,Salmonella enterica subsp. enterica serovar Onderstepoort str. SA20060086 strain SA20060086,Complete,Salmonella,Canada: Ontario: Guelph,Negative,Unknown,,,,,,Canada,,,,,,Yes,1243584,37C,,,,,Facultative,5301,,2,,,5039,,3,Laboratory for Foodborne Zoonoses,100.0x,Illumina; PacBio,,Onderstepoort,,SA20060086,Mesophilic,,"Included in the study, passed QC/QA"
179,1243585.3,isolate:GTN-01;collected_by:Dr. Mohamed Fakhr,,,,GCF_001077835.1,CLC genomic workbench v. 7.5.2014,,PRJNA288309,SAMN03798087,,,,,,22-Jun-2009,Isolated from the food sample which has the direct impact on human health.,2015-07-14T00:00:00Z,1,,2016-01-17T16:20:45.629Z,2016-01-17T16:20:45.629Z,,,52.53,"CP012038,CP012039",5198166,Salmonella enterica subsp. enterica serovar Ouakam,Complete,Salmonella,USA: Tulsa Oklahoma,,,,,,"Human, Homo sapiens",Isolated from the food sample which has the direct impact on human health,United States,,Turkey Breakfast sausage,,,,,1243585,C,,,,,,5276,,1,,,4713,,2,University of Tulsa,100x,Illumia MiSeq,,Ouakam,,Ouakam,,,"Included in the study, passed QC/QA"
180,1243586.3,"collected_by:Animal Health Laboratory, University of Guelph, Guelph, ON",,,,,HGAP v. v 1.3,,PRJNA177587,SAMN04160801,,,,Bacilli,1,12-Nov-2003,"Genome sequence of Salmonella Ouakam (serogroup D2; serotype 9,46:z29:-)",2017-06-30T00:00:00Z,,,2017-07-23T02:54:17.185Z,2017-07-23T02:54:17.185Z,,,52.25,CP022116,4874915,Salmonella enterica subsp. enterica serovar Ouakam str. SA20034636 strain SA20034636,Complete,Salmonella,Canada: Ontario,Negative,Unknown,,,,,,Canada,,Gallus gallus,,,MLST.Salmonella_enterica.1610,Yes,1243586,37C,,,,,Facultative,5026,,,,,4827,,1,Laboratory for Foodborne Zoonoses,70.0x,Illumina; PacBio,,Ouakam,,SA20034636,Mesophilic,,"Included in the study, passed QC/QA"
181,1243591.3,"collected_by:National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB",,,,,HGAP v. v 1.3,,PRJNA177594,SAMN04160828,,,,Bacilli,1,,Genome sequence of Salmonella Quebec (serogroup V; serotype 44:c:enz15),2017-06-26T00:00:00Z,,,2017-07-23T00:58:28.030Z,2017-07-23T00:58:28.030Z,,,52.22,"CP022017,CP022018,CP022019",4645312,Salmonella enterica subsp. enterica serovar Quebec str. S-1267 strain S-1267,Complete,Salmonella,,Negative,Unknown,,,,,,,,,,,,Yes,1243591,37C,,,,,Facultative,4740,,2,,,4552,,3,Laboratory for Foodborne Zoonoses,200.524x,Illumina,,Quebec,,S-1267,Mesophilic,,"Included in the study, passed QC/QA"
182,1243595.3,"collected_by:Animal Health Laboratory, University of Guelph, Guelph, ON",,,,GCF_001975625.1,SMRT Analysis v. 1.3.3,,PRJNA177599,SAMN04160802,,,,Bacilli,1,31-Mar-2009,"Genome sequence of Salmonella Wandsworth (serogroup Q; serotype 39:b:1,2)",2017-01-30T00:00:00Z,,,2017-03-20T06:34:32.540Z,2017-03-20T06:34:32.540Z,,,52.17,CP019417,4916040,Salmonella enterica subsp. enterica serovar Wandsworth str. SA20092095 strain SA20092095,Complete,Salmonella,Canada: Ontario,Negative,Unknown,,,,,,Canada,,Shellfish: Shrimp,,,MLST.Salmonella_enterica.1498,Yes,1243595,37C,,,,,Facultative,5091,,,,NZ_CP019417.1,4863,,1,Laboratory for Foodborne Zoonoses,115.0x,Illumina MiSeq; PacBio,,Wandsworth,,SA20092095,Mesophilic,,"Included in the study, passed QC/QA"
183,1243600.3,"collected_by:National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB",,,,GCF_001975645.1,SMRT Analysis v. 1.3.3,,PRJNA177608,SAMN04160829,,,,Bacilli,1,,"Genome sequence of Salmonella Yovokome (serogroup C2; serotype 8,20:d:1,5)",2017-01-30T00:00:00Z,,,2017-03-20T06:32:45.449Z,2017-03-20T06:32:45.449Z,,,52.23,CP019418,4640929,Salmonella enterica subsp. enterica serovar Yovokome str. S-1850 strain S-1850,Complete,Salmonella,,Negative,Unknown,,,,,,,,,,,,Yes,1243600,37C,,,,,Facultative,4696,,,,NZ_CP019418.1,4508,,1,Laboratory for Foodborne Zoonoses,135.0x,Illumina MiSeq; PacBio,,Yovokome,,S-1850,Mesophilic,,"Included in the study, passed QC/QA"
184,1243602.3,"collected_by:Institut Pasteur, Paris, France",,,,,HGAP v. v 1.3,,PRJNA177609,SAMN04160813,,,,Bacilli,1,1961-07-15,Genome sequence of Salmonella salamae (serogroup O55; serotype 55:k:z39),2017-06-30T00:00:00Z,,,2017-07-23T03:21:04.017Z,2017-07-23T03:21:04.017Z,,,51.6,"CP022139,CP022140,CP022141",5051440,Salmonella enterica subsp. salamae serovar 55:k:z39 str. 1315K strain 1315K,Complete,Salmonella,Madagascar,Negative,Unknown,,,,,,Madagascar,,Chamaeleonidae,,,MLST.Salmonella_enterica.1121,Yes,1243602,37C,,,,,Facultative,5234,,2,,,4926,,3,Laboratory for Foodborne Zoonoses,200.0x,Illumina,,55:k:z39,,1315K,Mesophilic,,"Included in the study, passed QC/QA"
185,1243612.3,"collected_by:Vaccine Research Institute of San Diego, San Diego, CA",,,,,HGAP v. v 1.3,,PRJNA177617,SAMN04160830,,,,Bacilli,1,,Genome sequence of Salmonella Diarizonae (serogroup Z; serotype (50:k:z),2017-06-30T00:00:00Z,,,2017-07-23T03:39:41.195Z,2017-07-23T03:39:41.195Z,,,51.54,CP022142,5076950,Salmonella enterica subsp. diarizonae serovar 50:k:z str. MZ0080 strain MZ0080,Complete,Salmonella,,Negative,Unknown,,,,,,,,,,,MLST.Salmonella_enterica.430,Yes,1243612,37C,,,,,Facultative,5258,,,,,4910,,1,Laboratory for Foodborne Zoonoses,40.0x,Illumina; PacBio,,50:k:z,,MZ0080,Mesophilic,,"Included in the study, passed QC/QA"
186,1243616.3,"collected_by:Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON",,,,,HGAP v. v 1.3,,PRJNA177620,SAMN04160806,,,,Bacilli,1,1993-03-11,Genome sequence of Salmonella Diarizonae (serogroup 065; serotype 65:c:z),2017-06-30T00:00:00Z,,,2017-07-23T03:33:37.537Z,2017-07-23T03:33:37.537Z,,,51.5,"CP022135,CP022136,CP022137",5066092,Salmonella enterica subsp. diarizonae serovar 65:c:z str. SA20044251 strain SA20044251,Complete,Salmonella,Canada: Ontario: Guelph,Negative,Unknown,,,,,,Canada,,,,,,Yes,1243616,37C,,,,,Facultative,5216,,2,,,4887,,3,Laboratory for Foodborne Zoonoses,200.0x,Illumina; PacBio,,65:c:z,,SA20044251,Mesophilic,,"Included in the study, passed QC/QA"
187,1243617.3,"collected_by:Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON",,,,,HGAP v. v 1.3,,PRJNA177621,SAMN04160809,,,,Bacilli,1,1998-12-01,Genome sequence of Salmonella bongori (serogroup 066; serotype 66:z41:-),2017-06-30T00:00:00Z,,,2017-07-23T03:16:26.386Z,2017-07-23T03:16:26.386Z,,,51.33,CP022120,4468959,Salmonella bongori serovar 66:z41:- str. SA19983605 strain SA19983605,Complete,Salmonella,Canada: Ontario: Guelph,Negative,Unknown,,,,,,Canada,,,,,,Yes,1243617,37C,,,,,Facultative,4470,,,,,4277,,1,Laboratory for Foodborne Zoonoses,90.0x,Illumina; PacBio,,66:z41:-,,SA19983605,Mesophilic,,"Included in the study, passed QC/QA"
188,1243618.3,,,,,GCA_000626315.1,MIRA v. 4.0,,PRJNA219482,SAMN02384170,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:33:11.961Z,2015-03-16T03:17:09.594Z,,,52.1,CP007251.1,4710450,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110353,Complete,Salmonella,Canada: Alberta,Negative,,,,,,,Canada,,Food - Pork dumpling-Outbreak,,,,,1243618,,,,,,,4968,,,24786953,-,3934,,1,LFZ,>100x,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
189,1243619.3,,,,,GCA_000626175.1,MIRA v. 4,,PRJNA219482,SAMN02384160,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:33:12.598Z,2015-03-16T03:17:09.594Z,,,52.2,CP007175.1,4711160,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110354,Complete,Salmonella,Canada: Alberta,Negative,,,,,"Human, Homo sapiens",,Canada,,,,,,,1243619,,,,,,,4609,,,24786953,NZ_CP007175.1,4366,,1,LFZ,>100X,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
190,1243620.3,,,,,GCA_000626295.1,MIRA v. 4.0,,PRJNA219482,SAMN02384171,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:33:13.096Z,2015-03-16T03:17:09.594Z,,,52.2,CP007250.1,4681840,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110355,Complete,Salmonella,Canada: Alberta,Negative,,,,,,,Canada,,Food Breast-Outbreak,,,,,1243620,,,,,,,4579,,,24786953,NZ_CP007250.1,4334,,1,LFZ,>100x,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
191,1243621.3,,,,,GCA_000623375.1,MIRA v. 4.0,,PRJNA219482,SAMN02384161,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:33:14.024Z,2015-03-16T03:17:09.594Z,,,52.2,CP007262.1,4682810,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110356,Complete,Salmonella,Canada: Alberta,Negative,,,,,"Human, Homo sapiens",,Canada,,Human-Outbreak,,,,,1243621,,,,,,,4586,,,24786953,NZ_CP007262.1,4336,,1,LFZ,>100x,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
192,1244111.3,,,,,GCA_000623355.1,MIRA v. 4.0,,PRJNA219482,SAMN02384162,,,,Bacilli,1,2003,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:33:14.569Z,2015-03-16T03:17:09.594Z,,,52.2,CP007261.1,4678420,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110357,Complete,Salmonella,Canada: Alberta,Negative,,,,,"Human, Homo sapiens",,Canada,,Human-Sporadic,,,,,1244111,,,,,,,4578,,,24786953,NZ_CP007261.1,4333,,1,LFZ,>100x,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
193,1244112.3,,,,,GCA_000623335.1,MIRA v. 4.0,,PRJNA219482,SAMN02384163,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:33:15.138Z,2015-03-16T03:17:09.594Z,,,52.2,CP007260.1,4678690,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110358,Complete,Salmonella,Canada: Alberta,Negative,,,,,"Human, Homo sapiens",,Canada,,Human-Sporadic,,,,,1244112,,,,,,,4583,,,24786953,NZ_CP007260.1,4333,,1,LFZ,>100x,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
194,1244113.3,,,,,GCA_000623315.1,MIRA v. 4.0,,PRJNA219482,SAMN02384164,,,,Bacilli,1,2004,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:33:15.704Z,2015-03-16T03:17:09.594Z,,,52.2,CP007259.1,4711470,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110359,Complete,Salmonella,Canada: Alberta,Negative,,,,,"Human, Homo sapiens",,Canada,,Human-Sporadic,,,,,1244113,,,,,,,4615,,,24786953,NZ_CP007259.1,4371,,1,LFZ,>100x,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
195,1244118.3,,,,,GCA_000623295.1,MIRA v. 4.0,,PRJNA219482,SAMN02384166,,,,Bacilli,1,2004,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:33:16.728Z,2015-03-16T03:17:09.594Z,,,52.2,CP007258.1,4678620,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110360,Complete,Salmonella,Canada: Alberta,Negative,,,,,"Human, Homo sapiens",,Canada,,Human-Sporadic,,,,,1244118,,,,,,,4579,,,24786953,NZ_CP007258.1,4326,,1,LFZ,>100x,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
196,1244119.3,,,,,GCA_000623275.1,MIRA v. 4.0,,PRJNA219482,SAMN02384167,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:33:17.418Z,2015-03-16T03:17:09.594Z,,,52.2,CP007263.1,4682910,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110361,Complete,Salmonella,Canada: Alberta,Negative,,,,,"Human, Homo sapiens",,Canada,,Human-Sporadic,,,,,1244119,,,,,,,4590,,,24786953,NZ_CP007263.1,4327,,1,LFZ,>100x,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
197,1244120.3,,,,,GCA_000626375.1,MIRA v. 4.0,,PRJNA219482,SAMN02384168,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:33:17.907Z,2015-03-16T03:17:09.594Z,,,52.2,CP007254.1,4679950,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20111095,Complete,Salmonella,Canada: Quebec,Negative,,,,,"Human, Homo sapiens",,Canada,,Human-Outbreak,,,,,1244120,,,,,,,4574,,,24786953,NZ_CP007254.1,4330,,1,LFZ,>100x,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
198,1244121.3,,,,,GCA_000626335.1,MIRA v. 4.0,,PRJNA219482,SAMN02384176,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:33:18.390Z,2015-03-16T03:17:09.594Z,,,52.2,CP007252.1,4679810,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20111175,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,Environmental (Chicken Fluff)-Outbreak,,,,,1244121,,,,,,,4583,,,24786953,NZ_CP007252.1,4328,,1,LFZ,>100x,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
199,1244122.3,,,,,GCA_000626355.1,MIRA v. 4.0,,PRJNA219482,SAMN02384177,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:33:19.384Z,2015-03-16T03:17:09.594Z,,,52.2,CP007253.1,4683800,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20111174,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,Environmental (Chicken Fluff)-Outbreak,,,,,1244122,,,,,,,4589,,,24786953,NZ_CP007253.1,4330,,1,LFZ,>100x,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
200,1267753.3,,,,,GCA_000341425.1,SMRT Analysis v. 1.3.3,,PRJNA183458,SAMN01832085,,,,,1,2012,De novo assembly of Salmonella Javiana genome.,2013-02-20T00:00:00Z,, ,2014-12-08T22:12:50.319Z,2015-03-16T03:17:09.594Z,,,52.1662,"CP004027.1,CP004026.1,CP004028.1",4675267,Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992,Complete,Salmonella,USA: Arizona,,,,,,"Human, Homo sapiens",,United States,,Stool,,,MLST.Salmonella_enterica.24,,1267753,,Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992,,,,,4708,,2,23516208,"NC_020307.1,NC_020306.1,NC_020308.1",4407,,3,FDA,80x,PacBio,complete,serovar Javiana,,CFSAN001992,,,"Included in the study, passed QC/QA"
201,1271862.5,,,,,GCA_000430145.3,SMRT Analysis v. 1.3.3,,PRJNA184140,SAMN01832087,,,,,1,1905,Genome sequencing project,2013-07-16T00:00:00Z,,,2014-12-08T22:12:52.950Z,2015-03-16T03:17:09.594Z,,,52.1726,"CP006048.1,CP006050.1,CP006052.1,CP006051.1",5089224,Salmonella enterica subsp. enterica serovar Typhimurium var. 5- str. CFSAN001921,Complete,Salmonella,,,,,,,,,,,chicken breast,,,MLST.Salmonella_enterica.19,,1271862,,Salmonella enterica subsp. enterica serovar Typhimurium var. 5- str. CFSAN001921,,,,,5084,,3,,"NC_021814.1,NC_021815.1,NC_021816.1,NC_021843.1",4801,,4,FDA,80x,PacBio RS,complete,Typhimurium,,CFSAN001921,,,"Included in the study, passed QC/QA"
202,1271863.3,,,,,GCA_000430125.1,Celera Assembler v. 7,,PRJNA184141,SAMN01832088,,,,,1,2012,Genome sequencing project,2013-07-16T00:00:00Z,,,2014-12-08T22:12:48.669Z,2015-03-16T03:17:09.594Z,,,51.8899,"CP006055.1,CP006056.1,CP006057.1",5267011,Salmonella enterica subsp. enterica serovar Cubana str. CFSAN002050,Complete,Salmonella,,,,,,,,,,,Fresh alfalfa sprouts,,,MLST.Salmonella_enterica.286,,1271863,,Salmonella enterica subsp. enterica serovar Cubana str. CFSAN002050,,,,,5269,,2,,"NC_021818.1,NC_021845.1,NC_021819.1",4979,,3,FDA,90X,PacBio RS,complete,Cubana,,CFSAN002050,,,"Included in the study, passed QC/QA"
203,1271864.3,,,,,GCA_000430085.2,Celera Assembler v. 7,,PRJNA184142,SAMN01832089,,,,,1,,Genome sequencing project,2013-07-16T00:00:00Z,,,2014-12-08T22:12:50.157Z,2015-03-16T03:17:09.594Z,,,52.1202,"CP005390.1,CP005391.1,CP005389.1",4932086,Salmonella enterica subsp. enterica serovar Heidelberg str. CFSAN002069,Complete,Salmonella,USA: WA,,,,,,,,United States,,Chicken,,,MLST.Salmonella_enterica.15,,1271864,,Salmonella enterica subsp. enterica serovar Heidelberg str. CFSAN002069,,,,,4941,,2,,"NC_021812.1,NC_021842.1,NC_021813.1",4603,,3,FDA,80x,PacBio RS,complete,Heidelberg,,CFSAN002069,,,"Included in the study, passed QC/QA"
204,1298917.3,,,,,GCA_000444445.1,Soapdenovo v. 2012,,PRJNA191133,SAMN02603462,,,,,1,,Salmonella enterica Serovar Pullorum China strain S06004.,2013-08-06T00:00:00Z,,,2014-12-08T22:12:51.955Z,2015-03-16T03:17:09.594Z,,,52.1,CP006575.1,4682599,Salmonella enterica subsp. enterica serovar Pullorum str. S06004,Complete,Salmonella,,,,,,,,,,,,,,,,1298917,,Salmonella enterica subsp. enterica serovar Pullorum str. S06004,,,,,4971,,,,NC_021984.1,4052,,1,"Jiangsu Key Laboratory of Zoonosis, Yangzhou University",,Illumina,complete,Pullorum,,S06004,,,"Included in the study, passed QC/QA"
205,1299044.4,,,,,GCA_000505705.1,SMRT Analysis v. 2.0.1,,PRJNA191769,SAMN01933202,,,,,1,2012,Genome Sequencing Project,2013-12-11T00:00:00Z,2,,2014-12-08T22:36:07.452Z,2015-03-16T03:17:09.594Z,,,52.114,"CP005995.1,CP005994.1",4821560,Salmonella enterica subsp. enterica serovar Heidelberg str. CFSAN002064,Complete,Salmonella,,,,,,,"Human, Homo sapiens",,,,stool,,,,,1299044,,,,,,,4759,,1,24903882,"NZ_CP005995.1,NZ_CP005994.1",4402,,2,FDA,200X,PacBio RS,,serovar Heidelberg,,CFSAN002064,,,"Included in the study, passed QC/QA"
206,1320309.3,,,,,GCA_000499465.2,,,PRJEB1776,SAMEA3138815,,,,,1,,"Background Non-typhoidal Salmonella (NTS) are an important cause of invasive disease in children and HIV-infected adults in sub-Saharan Africa, causing bacteraemia, neonatal meningitis and septic arthritis. Our NTS collection from Malawi, spanning a six year period (1998 to 2004), showed that amongst isolates of NTS associated with invasive bacteraemia, Salmonella Bovismorbificans (antigen profile 6,8:r:1,5) was the third most common serovar after Typhimurium and Enteritidis.  S. Bovismorbificans is an important veterinary pathogen causing salmonellosis in cattle, sheep and horses. It also poses a problem as a zoonotic agent sporadically infecting humans. Methodology Using Next Generation Sequencing technology, the genome of S. Bovismorbificans strain 3114, a paediatric bacteraemia isolate from Malawi, was sequenced. We further investigated the genomes of 13 additional Malawian bacteraemia isolates and four veterinary isolates from the UK, to identify genomic variations. Principal Findings The core genome of S. Bovismorbificans is highly stable, sharing high similarity and co-linearity with that of S. Typhimurium.  Three prophage-related regions of difference (RODs), define the major regions of genetic variation between S. Bovismorbificans human bacteraemia isolates from Malawi and veterinary isolates from the UK. Isolates differed further in the carriage of a S. Bovismorbificans virulence plasmid (pVIRBov), which was present in all bacteraemia isolates but absent from three of the four veterinary isolates investigated. Although genome degradation through pseudogene formation was observed in S. Bovismorbificans isolates, the identity of the pseudogenes was different from those identified previously in genome sequenced S. Typhimurium isolates, and there was no clear distinction between Malawi and UK isolates. In contrast to S. Typhimurium, where a distinct MLST type is associated with invasive disease in sub-Saharan Africa, we found that S. Bovismorbificans isolates from Malawi belong to the most common international S. Bovismorbificans Sequence Type, ST-142.  Conclusions Differences in the accessory genome of S. Bovismorbificans isolates from Malawi may have contributed to the development of a more specialized pathotype of S. Bovismorbificans ST142 in sub-Saharan Africa.",,,,2014-12-08T22:12:48.373Z,2015-03-16T03:17:09.594Z,,,52.2,"HF969015.2,HF969016.1",4770529,Salmonella enterica subsp. enterica serovar Bovismorbificans str. 3114,Complete,Salmonella,,,,,,,,"isolate from Malawi, was sequenced",Malawi,,,,,MLST.Salmonella_enterica.142,,1320309,,Salmonella enterica subsp. enterica serovar Bovismorbificans str. 3114,,,,,4803,,1,,-,4739,,2,IGH,,,complete,Bovismorbificans,,3114,,,"Included in the study, passed QC/QA"
207,1382510.3,,,,,GCA_000709535.1,SOAPdenovo v. 1.05; velvet v. 1.2.09,,PRJNA214181,SAMN03081475,,,,Bacilli,1,,Comparative genomic analysis for a stare of salmonella bongori,2014-06-17T00:00:00Z,1,,2014-12-09T00:33:41.861Z,2015-03-16T03:17:09.594Z,,,51.4,CP006692.1,4394500,Salmonella bongori serovar 48:z41:-- str. RKS3044,Complete,Salmonella,,Negative,Multiple,,,,,,,,,,,,Yes,1382510,,,,,,,4238,,,24928416,NZ_CP006692.1,3940,,1,Harbin Medical University,100X,Illumina (Platform HiSeq2000); SOLiD3,,serovar 48,,RKS3044,,,"Included in the study, passed QC/QA"
208,1386967.3,,,,,GCA_000756465.1,SOAPdenovo v. 1.05; velvet v. 1.2.09,,PRJNA215272,SAMN03072812,,,,Bacilli,1,1985,Comparative genomic analysis for a stain of salmonella arizonae,2014-09-22T00:00:00Z,1,,2015-03-12T13:42:57.321Z,2015-03-16T03:17:09.594Z,,,51.47,CP006693.1,4574846,Salmonella enterica subsp. arizonae serovar 62:z36:- str. RKS2983,Complete,Salmonella,USA:California,Negative,Multiple,,,,,,United States,,,,,,Yes,1386967,,,,,,,4561,,,-,NZ_CP006693.1,4188,,1,Harbin Medical University,100X,Illumina (PlatformHiSeq2000); SOLiD3,,serovar 62,,RKS2983,,,"Included in the study, passed QC/QA"
209,1406860.5,,,,,GCF_000503845.1,Newbler v. 2.6,,PRJNA222376,SAMN02641385,,,,,1,,Salmonella enterica subsp. enterica Serovar Agona str. 24249 genome sequence,2014-03-04T00:00:00Z,,,2016-01-17T15:33:54.074Z,2016-01-17T15:33:54.074Z,,,52.11,CP006876,4762840,Salmonella enterica subsp. enterica serovar Agona str. 24249,Complete,Salmonella,,,Terrestrial,,,,,,,,,,,,,1406860,,,,,,Aerobic,4774,,,24459278,NC_022991.1,4342,,1,University College Dublin,30x,Sanger dideoxy sequencing; 454,,Agona,,24249,Unknown,,"Included in the study, passed QC/QA"
210,1412451.3,,,,,GCA_000623175.1,MIRA v. 4.0,,PRJNA219482,SAMN02384165,,,,Bacilli,1,2005,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:00.418Z,2015-03-16T03:17:09.594Z,,,52.2,CP007266.1,4771580,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110223,Complete,Salmonella,Canada: Ontario,Negative,,,,,"Human, Homo sapiens",,Canada,,Human- mung bean-Outbreak,,,,,1412451,,,,,,,4713,,,24786953,-,4429,,1,LFZ,,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
211,1412452.3,,,,,GCA_000623455.1,MIRA v. 4.0,,PRJNA219482,SAMN02384169,,,,Bacilli,1,1998,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:00.910Z,2015-03-16T03:17:09.594Z,,,52.1,CP007291.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19992322,Complete,Salmonella,Canada: Quebec,Negative,,,,,"Human, Homo sapiens",,Canada,,Human-Stool,,,,,1412452,,,,,,,4599,,,24786953,-,4327,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
212,1412453.3,,,,,GCA_000626275.1,,,PRJNA219482,SAMN02384172,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:01.811Z,2015-03-16T03:17:09.594Z,,,52.2,CP007249.1,4714280,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20090641,Complete,Salmonella,Canada: Alberta,Negative,,,,,,,Canada,,chicken-abbatoir-Sporadic,,,,,1412453,,,,,,,4617,,,24786953,-,4375,,1,LFZ,,,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
213,1412454.3,,,,,GCA_000626255.1,,,PRJNA219482,SAMN02384173,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:02.261Z,2015-03-16T03:17:09.594Z,,,52.2,CP007248.1,4681000,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20090698,Complete,Salmonella,Canada: Alberta,Negative,,,,,,,Canada,,chicken-abbatoir-Sporadic,,,,,1412454,,,,,,,4581,,,24786953,NZ_CP007248.1,4332,,1,LFZ,,,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
214,1412455.3,,,,,GCA_000626235.1,,,PRJNA219482,SAMN02384174,,,,Bacilli,1,2005,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:02.809Z,2015-03-16T03:17:09.594Z,,,52.2,CP007247.1,4709030,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110221,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food- mung bean-Outbreak,,,,,1412455,,,,,,,4609,,,24786953,NZ_CP007247.1,4372,,1,LFZ,,,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
215,1412456.3,,,,,GCA_000624275.1,MIRA v. 4.0,,PRJNA219482,SAMN02384175,,,,Bacilli,1,2005,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:03.909Z,2015-03-16T03:17:09.594Z,,,52.2,CP007323.1,4686120,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20110222,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food- mung bean-Outbreak,,,,,1412456,,,,,,,4536,,,24786953,-,4288,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
216,1412457.3,,,,,GCA_000626215.1,,,PRJNA219482,SAMN02384178,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:04.694Z,2015-03-16T03:17:09.594Z,,,52.2,CP007246.1,4654160,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20100101,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,chicken,,,,,1412457,,,,,,,4557,,,24786953,NZ_CP007246.1,4303,,1,LFZ,,,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
217,1412458.3,,,,,GCA_000626115.1,MIRA v. 4.0,,PRJNA219482,SAMN02384179,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:05.325Z,2015-03-16T03:17:09.594Z,,,52.2,CP007420.1,4735380,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20100103,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,chicken,,,,,1412458,,,,,,,4677,,,24786953,-,4402,,1,LFZ,,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
218,1412459.3,,,,,GCA_000623775.1,MIRA v. 4.0,,PRJNA219482,SAMN02384180,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:05.929Z,2015-03-16T03:17:09.594Z,,,52.1,CP007321.1,4774400,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20090193,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,chicken,,,,,1412459,,,,,,,4716,,,24786953,-,4371,,1,LFZ,,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
219,1412460.3,,,,,GCA_000623755.1,MIRA v. 4.0,,PRJNA219482,SAMN02384181,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:06.456Z,2015-03-16T03:17:09.594Z,,,52.2,CP007320.1,4771190,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20090135,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,chicken,,,,,1412460,,,,,,,4713,,,24786953,-,4368,,1,LFZ,,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
220,1412461.3,,,,,GCA_000623795.1,MIRA v. 4.0,,PRJNA219482,SAMN02384182,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:07.575Z,2015-03-16T03:17:09.594Z,,,52.2,CP007322.1,4785190,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20090332,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,chicken,,,,,1412461,,,,,,,4734,,,24786953,-,4381,,1,LFZ,,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
221,1412462.3,,,,,GCA_000626155.1,MIRA v. 4.0,,PRJNA219482,SAMN02384183,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:08.285Z,2015-03-16T03:17:09.594Z,,,52.2,CP007422.1,4734890,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20090531,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,chicken,,,,,1412462,,,,,,,4679,,,24786953,-,4402,,1,LFZ,,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
222,1412463.3,,,,,GCA_000626135.1,MIRA v. 4.0,,PRJNA219482,SAMN02384184,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:08.757Z,2015-03-16T03:17:09.594Z,,,52.1,CP007421.1,4760450,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20090884,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,chicken,,,,,1412463,,,,,,,4714,,,24786953,-,4441,,1,LFZ,,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
223,1412464.3,collected_by:undisclosed,,,,GCF_000831045.1,MIRA v. 4.0,,PRJNA219482,SAMN02384185,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-05-14T00:00:00Z,,,2016-01-17T15:43:13.640Z,2016-01-17T15:43:13.640Z,,,52.15,CP007358,4773474,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20100130,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,chicken,,,,,1412464,,,,,,,4824,,,24786953,,4372,,1,LFZ,,454; Illumina,,,,EC20100130,,,"Included in the study, passed QC/QA"
224,1412465.3,collected_by:undisclosed,,,,GCF_000831025.1,MIRA v. 4.0,,PRJNA219482,SAMN02384186,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-05-14T00:00:00Z,,,2016-01-17T15:43:13.259Z,2016-01-17T15:43:13.259Z,,,52.15,CP007359,4766248,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20100134,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,chicken,,,,,1412465,,,,,,,4819,,,24786953,,4365,,1,LFZ,,454; Illumina,,,,EC20100134,,,"Included in the study, passed QC/QA"
225,1412466.3,,,,,GCA_000624395.1,MIRA v. 4.0,,PRJNA219482,SAMN02384187,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:09.257Z,2015-03-16T03:17:09.594Z,,,52.1,CP007329.1,4733560,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120002,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Broiler,,,,,1412466,,,,,,,4701,,,24786953,-,4421,,1,LFZ,,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
226,1412467.3,,,,,GCA_000624415.1,MIRA v. 4.0,,PRJNA219482,SAMN02384188,,,,Bacilli,1,2005,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:10.191Z,2015-03-16T03:17:09.594Z,,,52.2,CP007330.1,4730650,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120003,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Cattle,,,,,1412467,,,,,,,4684,,,24786953,-,4405,,1,LFZ,,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
227,1412468.3,,,,,GCA_000623195.1,MIRA v. 4.0,,PRJNA219482,SAMN02384189,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:10.712Z,2015-03-16T03:17:09.594Z,,,52.1,CP007267.1,4767670,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120005,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Broiler,,,,,1412468,,,,,,,4725,,,24786953,-,4446,,1,LFZ,,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
228,1412469.3,,,,,GCA_000624435.1,MIRA v. 4.0,,PRJNA219482,SAMN02384190,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:11.236Z,2015-03-16T03:17:09.594Z,,,52.1,CP007331.1,4744530,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120007,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Broiler,,,,,1412469,,,,,,,4707,,,24786953,-,4436,,1,LFZ,,454; Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
229,1412470.3,,,,,GCA_000626195.1,,,PRJNA219482,SAMN02384191,,,,Bacilli,1,2006,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:11.788Z,2015-03-16T03:17:09.594Z,,,52.2,CP007245.1,4711920,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120008,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Reptile,,,,,1412470,,,,,,,4622,,,24786953,NZ_CP007245.1,4346,,1,LFZ,,,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
230,1412471.3,,,,,GCA_000626395.1,MIRA v. 4.0,,PRJNA219482,SAMN02384192,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:12.381Z,2015-03-16T03:17:09.594Z,,,52.1,CP007438.1,4754530,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120009,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Rodent,,,,,1412471,,,,,,,7851,,,24786953,-,1814,,1,LFZ,,454; Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
231,1412472.3,,,,,GCA_000623715.1,MIRA v. 4.0,,PRJNA219482,SAMN02384193,,,,Bacilli,1,1998,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:13.781Z,2015-03-16T03:17:09.594Z,,,52.1,CP007285.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19980677,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,Animal - Chicken-Environment swab,,,,,1412472,,,,,,,4603,,,24786953,-,4278,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
232,1412473.3,,,,,GCA_000623655.1,MIRA v. 4.0,,PRJNA219482,SAMN02384194,,,,Bacilli,1,1997,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:14.449Z,2015-03-16T03:17:09.594Z,,,52.1,CP007282.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19970510,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,Animal - Chicken-Environment swab,,,,,1412473,,,,,,,4581,,,24786953,-,4334,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
233,1412474.3,,,,,GCA_000623675.1,MIRA v. 4.0,,PRJNA219482,SAMN02384195,,,,Bacilli,1,1997,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:14.949Z,2015-03-16T03:17:09.594Z,,,52.1,CP007283.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19970769,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,Animal - Chicken-Egg,,,,,1412474,,,,,,,4588,,,24786953,-,4301,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
234,1412475.3,,,,,GCA_000623155.1,MIRA v. 4.0,,PRJNA219482,SAMN02384196,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:15.834Z,2015-03-16T03:17:09.594Z,,,52.2,CP007274.1,4746770,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20093266,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken-Feces,,,,,1412475,,,,,,,4854,,,24786953,-,4182,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
235,1412476.3,,,,,GCA_000625695.1,MIRA v. 4.0,,PRJNA219482,SAMN02384197,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:16.292Z,2015-03-16T03:17:09.594Z,,,52.1,CP007431.1,4686040,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094682,Complete,Salmonella,Canada: Manitoba,Negative,,,,,,,Canada,,Animal - Chicken-Cecum,,,,,1412476,,,,,,,4537,,,24786953,-,4174,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
236,1412477.3,,,,,GCA_000623535.1,MIRA v. 4.0,,PRJNA219482,SAMN02384198,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:16.756Z,2015-03-16T03:17:09.594Z,,,52,CP007295.1,4685720,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20084384,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412477,,,,,,,4514,,,24786953,-,4121,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
237,1412478.3,,,,,GCA_000626495.1,MIRA v. 4.0,,PRJNA219482,SAMN02384199,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:17.331Z,2015-03-16T03:17:09.594Z,,,52.2,CP007467.1,4581500,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20084824,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken-Fluff (hatchery),,,,,1412478,,,,,,,4546,,,24786953,-,4224,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
238,1412479.3,,,,,GCA_000626515.1,MIRA v. 4.0,,PRJNA219482,SAMN02384200,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:17.832Z,2015-03-16T03:17:09.594Z,,,52.1,CP007468.1,4654470,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094177,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412479,,,,,,,4634,,,24786953,-,4287,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
239,1412480.3,,,,,GCA_000626475.1,MIRA v. 4.0,,PRJNA219482,SAMN02384201,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:18.507Z,2015-03-16T03:17:09.594Z,,,52.2,CP007466.1,4572800,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20084644,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Avian,,,,,1412480,,,,,,,4535,,,24786953,-,4218,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
240,1412481.3,,,,,GCA_000625735.1,MIRA v. 4.0,,PRJNA219482,SAMN02384202,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:19.503Z,2015-03-16T03:17:09.594Z,,,49.6,CP007427.1,4685690,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20100239,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Bovine-Liver,,,,,1412481,,,,,,,2333,,,24786953,-,2200,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
241,1412482.3,collected_by:undisclosed,,,,GCA_000968795.1,MIRA v. 4.0,,PRJNA219482,SAMN02384203,,,,Bacilli,,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-05-14T00:00:00Z,1,,2016-01-17T15:52:49.513Z,2016-01-17T15:52:49.513Z,,,44.28,CP007361,4685250,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20100349,Complete,Salmonella,Canada: Manitoba,Negative,,,,,,,Canada,,Animal - Avian-Yolk sac,,,,,1412482,,,,,,,5893,,,24786953,,3057,,1,LFZ,,Illumina,,,,SA20100349,,,"Excluded from the study, failed QC/QA."
242,1412483.3,,,,,GCA_000624815.1,MIRA v. 4.0,,PRJNA219482,SAMN02384204,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:20.180Z,2015-03-16T03:17:09.594Z,,,52.1,CP007372.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20121703,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412483,,,,,,,4531,,,24786953,-,4276,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
243,1412484.3,,,,,GCA_000624115.1,MIRA v. 4.0,,PRJNA219482,SAMN02384205,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:20.685Z,2015-03-16T03:17:09.594Z,,,52.1,CP007315.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094521,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412484,,,,,,,4528,,,24786953,-,4257,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
244,1412485.3,,,,,GCA_000623735.1,MIRA v. 4.0,,PRJNA219482,SAMN02384206,,,,Bacilli,1,1998,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:21.244Z,2015-03-16T03:17:09.594Z,,,52.1,CP007286.1,4685820,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19981522,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,Animal - Avian-Environment swab,,,,,1412485,,,,,,,4588,,,24786953,-,4323,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
245,1412486.3,,,,,GCA_000623395.1,MIRA v. 4.0,,PRJNA219482,SAMN02384207,,,,Bacilli,1,1998,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:22.290Z,2015-03-16T03:17:09.594Z,,,52.1,CP007288.1,4685840,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19981857,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,Animal - Avian,,,,,1412486,,,,,,,4582,,,24786953,-,4328,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
246,1412487.3,,,,,GCA_000623615.1,MIRA v. 4.0,,PRJNA219482,SAMN02384208,,,,Bacilli,1,1996,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:22.892Z,2015-03-16T03:17:09.594Z,,,52.1,CP007280.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19960848,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken-Litter,,,,,1412487,,,,,,,4579,,,24786953,-,4336,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
247,1412488.3,,,,,GCA_000625855.1,MIRA v. 4.0,,PRJNA219482,SAMN02384209,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:23.455Z,2015-03-16T03:17:09.594Z,,,49.2,CP007425.1,4683790,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20082034,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Environment - Litter/Manure,,,,,1412488,,,,,,,3288,,,24786953,-,2486,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
248,1412489.3,,,,,GCA_000625655.1,MIRA v. 4.0,,PRJNA219482,SAMN02384210,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:24.015Z,2015-03-16T03:17:09.594Z,,,48.5,CP007426.1,4685150,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20085285,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Environment - Litter/Manure,,,,,1412489,,,,,,,2496,,,24786953,-,1852,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
249,1412490.3,,,,,GCA_000623515.1,MIRA v. 4.0,,PRJNA219482,SAMN02384211,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:24.982Z,2015-03-16T03:17:09.594Z,,,52.1,CP007294.1,4685840,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20083636,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Environment - Litter/Manure,,,,,1412490,,,,,,,4583,,,24786953,-,4312,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
250,1412491.3,,,,,GCA_000624055.1,MIRA v. 4.0,,PRJNA219482,SAMN02384212,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:26.012Z,2015-03-16T03:17:09.594Z,,,52.1,CP007312.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094352,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken broiler growers,,,,,1412491,,,,,,,4582,,,24786953,-,4337,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
251,1412492.3,,,,,GCA_000624255.1,MIRA v. 4.0,,PRJNA219482,SAMN02384213,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:27.139Z,2015-03-16T03:17:09.594Z,,,50.5,CP007319.1,4685540,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20095440,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken growers,,,,,1412492,,,,,,,3582,,,24786953,-,2868,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
252,1412493.3,,,,,GCA_000623575.1,MIRA v. 4.0,,PRJNA219482,SAMN02384214,,,,Bacilli,1,1994,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:27.645Z,2015-03-16T03:17:09.594Z,,,52.1,CP007278.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19942384,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food - Turkey,,,,,1412493,,,,,,,4530,,,24786953,-,4269,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
253,1412494.3,,,,,GCA_000623595.1,MIRA v. 4.0,,PRJNA219482,SAMN02384215,,,,Bacilli,1,1994,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:28.129Z,2015-03-16T03:17:09.594Z,,,52.1,CP007279.1,4685790,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19943269,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food - Turkey,,,,,1412494,,,,,,,4537,,,24786953,-,4273,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
254,1412495.3,,,,,GCA_000625995.1,MIRA v. 4.0,,PRJNA219482,SAMN02384216,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:28.648Z,2015-03-16T03:17:09.594Z,,,52.1,CP007417.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20123395,Complete,Salmonella,Canada: Alberta,Negative,,,,,,,Canada,,Animal - Rodent,,,,,1412495,,,,,,,4533,,,24786953,-,4271,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
255,1412496.3,,,,,GCA_000623695.1,MIRA v. 4.0,,PRJNA219482,SAMN02384217,,,,Bacilli,1,1997,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:29.187Z,2015-03-16T03:17:09.594Z,,,52.1,CP007284.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19971331,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Animal - Avian,,,,,1412496,,,,,,,4531,,,24786953,-,4257,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
256,1412497.3,,,,,GCA_000623635.1,MIRA v. 4.0,,PRJNA219482,SAMN02384218,,,,Bacilli,1,1996,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:29.712Z,2015-03-16T03:17:09.594Z,,,52.1,CP007281.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19961622,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Animal - Avian,,,,,1412497,,,,,,,4518,,,24786953,-,4280,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
257,1412498.3,,,,,GCA_000623435.1,MIRA v. 4.0,,PRJNA219482,SAMN02384219,,,,Bacilli,1,1998,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:30.378Z,2015-03-16T03:17:09.594Z,,,52.1,CP007290.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19983126,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken,,,,,1412498,,,,,,,4534,,,24786953,-,4271,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
258,1412499.3,,,,,GCA_000623475.1,MIRA v. 4.0,,PRJNA219482,SAMN02384220,,,,Bacilli,1,1999,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:31.366Z,2015-03-16T03:17:09.594Z,,,49.9,CP007292.1,4685820,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19994216,Complete,Salmonella,Canada: Alberta,Negative,,,,,,,Canada,,Animal - Porcine-Feces,,,,,1412499,,,,,,,3794,,,24786953,-,2872,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
259,1412500.3,,,,,GCA_000623555.1,MIRA v. 4.0,,PRJNA219482,SAMN02384221,,,,Bacilli,1,1993,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:32.465Z,2015-03-16T03:17:09.594Z,,,52.1,CP007277.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19930684,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken,,,,,1412500,,,,,,,4540,,,24786953,-,4263,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
260,1412501.3,,,,,GCA_000626455.1,MIRA v. 4.0,,PRJNA219482,SAMN02384222,,,,Bacilli,1,1994,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:33.352Z,2015-03-16T03:17:09.594Z,,,52.1,CP007465.1,4707070,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19940857,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken-Environment swab,,,,,1412501,,,,,,,4575,,,24786953,-,4214,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
261,1412502.3,,,,,GCA_000623415.1,MIRA v. 4.0,,PRJNA219482,SAMN02384223,,,,Bacilli,1,1998,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:33.814Z,2015-03-16T03:17:09.594Z,,,52.1,CP007289.1,4685790,Salmonella enterica subsp. enterica serovar Enteritidis str. SA19982831,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,Animal - Chicken-Environment swab,,,,,1412502,,,,,,,4526,,,24786953,-,4265,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
262,1412503.3,,,,,GCA_000624215.1,MIRA v. 4.0,,PRJNA219482,SAMN02384224,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:34.336Z,2015-03-16T03:17:09.594Z,,,52.1,CP007317.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094803,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken-Fluff,,,,,1412503,,,,,,,4532,,,24786953,-,4257,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
263,1412504.3,,,,,GCA_000624035.1,MIRA v. 4.0,,PRJNA219482,SAMN02384225,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:35.010Z,2015-03-16T03:17:09.594Z,,,52.1,CP007311.1,4685780,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094350,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken brooder,,,,,1412504,,,,,,,4531,,,24786953,-,4279,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
264,1412505.3,,,,,GCA_000626535.1,MIRA v. 4.0,,PRJNA219482,SAMN02384226,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:36.048Z,2015-03-16T03:17:09.594Z,,,52.1,CP007469.1,4664600,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094301,Complete,Salmonella,Canada: Newfoundland,Negative,,,,,,,Canada,,Animal - Chicken-Fluff,,,,,1412505,,,,,,,4628,,,24786953,-,4297,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
265,1412506.3,,,,,GCA_000623495.1,MIRA v. 4.0,,PRJNA219482,SAMN02384227,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:36.590Z,2015-03-16T03:17:09.594Z,,,52.1,CP007293.1,4685810,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20083456,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken Broiler,,,,,1412506,,,,,,,4517,,,24786953,-,4278,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
266,1412507.3,,,,,GCA_000624235.1,MIRA v. 4.0,,PRJNA219482,SAMN02384228,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:37.162Z,2015-03-16T03:17:09.594Z,,,52.1,CP007318.1,4685840,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20095309,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Environment - Water-River,,,,,1412507,,,,,,,4530,,,24786953,-,4264,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
267,1412508.3,,,,,GCA_000624195.1,MIRA v. 4.0,,PRJNA219482,SAMN02384229,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:38.109Z,2015-03-16T03:17:09.594Z,,,52.1,CP007334.1,4752630,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20092320,Complete,Salmonella,,Negative,,,,,,,,,Animal - Chicken,,,,,1412508,,,,,,,4941,,,24786953,-,4061,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
268,1412509.3,,,,,GCA_000623935.1,MIRA v. 4.0,,PRJNA219482,SAMN02384230,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:39.162Z,2015-03-16T03:17:09.594Z,,,52.1,CP007306.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20093784,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412509,,,,,,,4524,,,24786953,-,4278,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
269,1412510.3,,,,,GCA_000623995.1,MIRA v. 4.0,,PRJNA219482,SAMN02384231,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:39.733Z,2015-03-16T03:17:09.594Z,,,52.1,CP007309.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20093977,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Animal - Chicken,,,,,1412510,,,,,,,4518,,,24786953,-,4279,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
270,1412511.3,,,,,GCA_000623955.1,MIRA v. 4.0,,PRJNA219482,SAMN02384232,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:40.216Z,2015-03-16T03:17:09.594Z,,,52.1,CP007307.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20093788,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412511,,,,,,,4521,,,24786953,-,4276,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
271,1412512.3,,,,,GCA_000623875.1,MIRA v. 4.0,,PRJNA219482,SAMN02384233,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:40.709Z,2015-03-16T03:17:09.594Z,,,52.1,CP007303.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20093430,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Animal - Chicken,,,,,1412512,,,,,,,4531,,,24786953,-,4279,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
272,1412513.3,,,,,GCA_000625375.1,MIRA v. 4.0,,PRJNA219482,SAMN02384234,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:41.225Z,2015-03-16T03:17:09.594Z,,,52.1,CP007297.1,4685770,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20090435,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Animal - Chicken,,,,,1412513,,,,,,,4538,,,24786953,-,4265,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
273,1412514.3,,,,,GCA_000623855.1,MIRA v. 4.0,,PRJNA219482,SAMN02384235,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:41.777Z,2015-03-16T03:17:09.594Z,,,52.1,CP007302.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20093421,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken,,,,,1412514,,,,,,,4520,,,24786953,-,4262,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
274,1412515.3,,,,,GCA_000624095.1,MIRA v. 4.0,,PRJNA219482,SAMN02384236,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:42.654Z,2015-03-16T03:17:09.594Z,,,52.1,CP007314.1,4685810,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094389,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412515,,,,,,,4530,,,24786953,-,4272,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
275,1412516.3,,,,,GCA_000624075.1,MIRA v. 4.0,,PRJNA219482,SAMN02384237,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:43.244Z,2015-03-16T03:17:09.594Z,,,52.1,CP007313.1,4685830,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094383,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412516,,,,,,,4518,,,24786953,-,4277,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
276,1412517.3,,,,,GCA_000625355.1,MIRA v. 4.0,,PRJNA219482,SAMN02384238,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:43.753Z,2015-03-16T03:17:09.594Z,,,48.5,CP007296.1,4685810,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20090419,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Animal - Chicken,,,,,1412517,,,,,,,2454,,,24786953,-,1866,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
277,1412518.3,,,,,GCA_000624135.1,MIRA v. 4.0,,PRJNA219482,SAMN02384239,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:45.209Z,2015-03-16T03:17:09.594Z,,,52.1,CP007316.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094642,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,Animal - Chicken,,,,,1412518,,,,,,,4537,,,24786953,-,4250,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
278,1412519.3,,,,,GCA_000623975.1,MIRA v. 4.0,,PRJNA219482,SAMN02384240,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:45.687Z,2015-03-16T03:17:09.594Z,,,52.1,CP007308.1,4685840,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20093950,Complete,Salmonella,Canada: Saskatchewan,Negative,,,,,,,Canada,,Food,,,,,1412519,,,,,,,4523,,,24786953,-,4284,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
279,1412520.3,,,,,GCA_000623915.1,MIRA v. 4.0,,PRJNA219482,SAMN02384241,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:46.143Z,2015-03-16T03:17:09.594Z,,,52.1,CP007305.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20093543,Complete,Salmonella,Canada: Saskatchewan,Negative,,,,,,,Canada,,Food,,,,,1412520,,,,,,,4521,,,24786953,-,4278,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
280,1412521.3,,,,,GCA_000623815.1,MIRA v. 4.0,,PRJNA219482,SAMN02384242,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:46.598Z,2015-03-16T03:17:09.594Z,,,52.1,CP007300.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20090877,Complete,Salmonella,Canada: Saskatchewan,Negative,,,,,,,Canada,,Food,,,,,1412521,,,,,,,4522,,,24786953,-,4273,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
281,1412522.3,,,,,GCA_000623895.1,MIRA v. 4.0,,PRJNA219482,SAMN02384243,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:47.475Z,2015-03-16T03:17:09.594Z,,,52.1,CP007304.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20093538,Complete,Salmonella,Canada: Saskatchewan,Negative,,,,,,,Canada,,Food,,,,,1412522,,,,,,,4534,,,24786953,-,4278,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
282,1412523.3,,,,,GCA_000623835.1,MIRA v. 4.0,,PRJNA219482,SAMN02384244,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:48.038Z,2015-03-16T03:17:09.594Z,,,52.1,CP007301.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20091739,Complete,Salmonella,Canada: Saskatchewan,Negative,,,,,,,Canada,,Food,,,,,1412523,,,,,,,4528,,,24786953,-,4273,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
283,1412524.3,,,,,GCA_000624015.1,MIRA v. 4.0,,PRJNA219482,SAMN02384245,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:48.549Z,2015-03-16T03:17:09.594Z,,,52.1,CP007310.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. SA20094079,Complete,Salmonella,Canada: Saskatchewan,Negative,,,,,,,Canada,,Food,,,,,1412524,,,,,,,4519,,,24786953,-,4283,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
284,1412525.3,,,,,GCA_000624715.1,MIRA v. 4.0,,PRJNA219482,SAMN02384246,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:49.416Z,2015-03-16T03:17:09.594Z,,,50,CP007367.1,4685130,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121541,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412525,,,,,,,3118,,,24786953,-,2535,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
285,1412526.3,,,,,GCA_000625275.1,MIRA v. 4.0,,PRJNA219482,SAMN02384247,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:49.978Z,2015-03-16T03:17:09.594Z,,,52.1,CP007382.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121825,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412526,,,,,,,4520,,,24786953,-,4275,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
286,1412527.3,,,,,GCA_000625295.1,MIRA v. 4.0,,PRJNA219482,SAMN02384248,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:50.928Z,2015-03-16T03:17:09.594Z,,,52.1,CP007383.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121826,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412527,,,,,,,4536,,,24786953,-,4262,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
287,1412528.3,,,,,GCA_000624455.1,MIRA v. 4.0,,PRJNA219482,SAMN02384249,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:51.388Z,2015-03-16T03:17:09.594Z,,,51.7,CP007344.1,4684980,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120213,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412528,,,,,,,4404,,,24786953,-,3604,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
288,1412529.3,,,,,GCA_000626095.1,MIRA v. 4.0,,PRJNA219482,SAMN02384250,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:51.861Z,2015-03-16T03:17:09.594Z,,,51.9,CP007434.1,4685830,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120200,Complete,Salmonella,Canada: Nova Scotia,Negative,,,,,,,Canada,,Food,,,,,1412529,,,,,,,4562,,,24786953,-,4012,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
289,1412530.3,,,,,GCA_000624695.1,MIRA v. 4.0,,PRJNA219482,SAMN02384251,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:52.353Z,2015-03-16T03:17:09.594Z,,,49.2,CP007366.1,4683320,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121004,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412530,,,,,,,1716,,,24786953,-,1705,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
290,1412531.3,,,,,GCA_000625175.1,MIRA v. 4.0,,PRJNA219482,SAMN02384252,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:52.876Z,2015-03-16T03:17:09.594Z,,,52.1,CP007377.1,4685840,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120963,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412531,,,,,,,4535,,,24786953,-,4264,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
291,1412532.3,,,,,GCA_000625075.1,MIRA v. 4.0,,PRJNA219482,SAMN02384253,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:53.803Z,2015-03-16T03:17:09.594Z,,,52.1,CP007406.1,4685820,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120776,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412532,,,,,,,4529,,,24786953,-,4283,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
292,1412533.3,,,,,GCA_000625055.1,MIRA v. 4.0,,PRJNA219482,SAMN02384254,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:54.361Z,2015-03-16T03:17:09.594Z,,,52.1,CP007405.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120775,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412533,,,,,,,4523,,,24786953,-,4280,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
293,1412534.3,,,,,GCA_000625535.1,MIRA v. 4.0,,PRJNA219482,SAMN02384255,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:54.959Z,2015-03-16T03:17:09.594Z,,,50.6,CP007339.1,4685750,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120685,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412534,,,,,,,3681,,,24786953,-,2868,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
294,1412535.3,,,,,GCA_000624375.1,MIRA v. 4.0,,PRJNA219482,SAMN02384256,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:56.003Z,2015-03-16T03:17:09.594Z,,,52.1,CP007328.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20111576,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412535,,,,,,,4525,,,24786953,-,4281,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
295,1412536.3,,,,,GCA_000623215.1,MIRA v. 4.0,,PRJNA219482,SAMN02384257,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:57.064Z,2015-03-16T03:17:09.594Z,,,52.1,CP007362.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120544,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412536,,,,,,,4519,,,24786953,-,4279,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
296,1412537.3,,,,,GCA_000624655.1,MIRA v. 4.0,,PRJNA219482,SAMN02384258,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:57.543Z,2015-03-16T03:17:09.594Z,,,51.7,CP007354.1,4685780,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120528,Complete,Salmonella,Canada: Nova Scotia,Negative,,,,,,,Canada,,Food,,,,,1412537,,,,,,,4447,,,24786953,-,3753,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
297,1412538.3,,,,,GCA_000624315.1,MIRA v. 4.0,,PRJNA219482,SAMN02384259,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:58.007Z,2015-03-16T03:17:09.594Z,,,52.1,CP007325.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20111515,Complete,Salmonella,Canada: Alberta,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412538,,,,,,,4522,,,24786953,-,4281,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
298,1412539.3,,,,,GCA_000624295.1,MIRA v. 4.0,,PRJNA219482,SAMN02384260,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:34:58.782Z,2015-03-16T03:17:09.594Z,,,52.1,CP007324.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20111514,Complete,Salmonella,Canada: Alberta,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412539,,,,,,,4533,,,24786953,-,4280,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
299,1412540.3,,,,,GCA_000624915.1,MIRA v. 4.0,,PRJNA219482,SAMN02384261,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:59.284Z,2015-03-16T03:17:09.594Z,,,52.1,CP007397.1,4685830,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121751,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412540,,,,,,,4532,,,24786953,-,4259,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
300,1412541.3,,,,,GCA_000624895.1,MIRA v. 4.0,,PRJNA219482,SAMN02384262,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:34:59.810Z,2015-03-16T03:17:09.594Z,,,52.1,CP007396.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121750,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412541,,,,,,,4532,,,24786953,-,4245,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
301,1412542.3,,,,,GCA_000625235.1,MIRA v. 4.0,,PRJNA219482,SAMN02384263,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:00.727Z,2015-03-16T03:17:09.594Z,,,52.1,CP007380.1,4685840,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120970,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412542,,,,,,,4530,,,24786953,-,4277,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
302,1412543.3,,,,,GCA_000623235.1,MIRA v. 4.0,,PRJNA219482,SAMN02384264,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:01.272Z,2015-03-16T03:17:09.594Z,,,52.1,CP007363.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120548,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412543,,,,,,,4515,,,24786953,-,4280,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
303,1412544.3,,,,,GCA_000624635.1,MIRA v. 4.0,,PRJNA219482,SAMN02384265,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:01.806Z,2015-03-16T03:17:09.594Z,,,51.6,CP007353.1,4685200,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120505,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412544,,,,,,,4348,,,24786953,-,3616,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
304,1412545.3,,,,,GCA_000624615.1,MIRA v. 4.0,,PRJNA219482,SAMN02384266,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:02.869Z,2015-03-16T03:17:09.594Z,,,52,CP007352.1,4685810,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120498,Complete,Salmonella,Canada: Saskatchewan,Negative,,,,,,,Canada,,Food,,,,,1412545,,,,,,,4527,,,24786953,-,3996,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
305,1412546.3,,,,,GCA_000624515.1,MIRA v. 4.0,,PRJNA219482,SAMN02384267,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:03.371Z,2015-03-16T03:17:09.594Z,,,52.1,CP007347.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120240,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412546,,,,,,,4515,,,24786953,-,4277,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
306,1412547.3,,,,,GCA_000624495.1,MIRA v. 4.0,,PRJNA219482,SAMN02384268,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:03.887Z,2015-03-16T03:17:09.594Z,,,52.1,CP007346.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120229,Complete,Salmonella,Canada: Saskatchewan,Negative,,,,,,,Canada,,Food,,,,,1412547,,,,,,,4539,,,24786953,-,4267,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
307,1412548.3,,,,,GCA_000624475.1,MIRA v. 4.0,,PRJNA219482,SAMN02384269,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:04.445Z,2015-03-16T03:17:09.594Z,,,52.1,CP007345.1,4685840,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120219,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,Food,,,,,1412548,,,,,,,4537,,,24786953,-,4264,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
308,1412549.3,,,,,GCA_000626555.1,MIRA v. 4.0,,PRJNA219482,SAMN02384270,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:05.386Z,2015-03-16T03:17:09.594Z,,,52.1,CP007498.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20111510,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412549,,,,,,,4520,,,24786953,-,4197,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
309,1412550.3,,,,,GCA_000625615.1,MIRA v. 4.0,,PRJNA219482,SAMN02384271,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:05.917Z,2015-03-16T03:17:09.594Z,,,52.1,CP007343.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120722,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412550,,,,,,,4522,,,24786953,-,4279,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
310,1412551.3,,,,,GCA_000624935.1,MIRA v. 4.0,,PRJNA219482,SAMN02384272,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:06.464Z,2015-03-16T03:17:09.594Z,,,52.1,CP007398.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121753,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412551,,,,,,,4540,,,24786953,-,4256,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
311,1412552.3,,,,,GCA_000624555.1,MIRA v. 4.0,,PRJNA219482,SAMN02384273,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:07.231Z,2015-03-16T03:17:09.594Z,,,52.1,CP007349.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120469,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412552,,,,,,,4529,,,24786953,-,4280,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
312,1412553.3,,,,,GCA_000625595.1,MIRA v. 4.0,,PRJNA219482,SAMN02384274,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:07.754Z,2015-03-16T03:17:09.594Z,,,50,CP007342.1,4685810,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120697,Complete,Salmonella,,Negative,,,,,,,,,ANIMAL-chicken,,,,,1412553,,,,,,,3038,,,24786953,-,2479,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
313,1412554.3,,,,,GCA_000624835.1,MIRA v. 4.0,,PRJNA219482,SAMN02384275,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:08.869Z,2015-03-16T03:17:09.594Z,,,52.1,CP007373.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121744,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412554,,,,,,,4512,,,24786953,-,4280,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
314,1412555.3,,,,,GCA_000625775.1,MIRA v. 4.0,,PRJNA219482,SAMN02384276,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:09.296Z,2015-03-16T03:17:09.594Z,,,52.1,CP007429.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121765,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,FOOD-Pig,,,,,1412555,,,,,,,4526,,,24786953,-,4279,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
315,1412556.3,,,,,GCA_000624575.1,MIRA v. 4.0,,PRJNA219482,SAMN02384277,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:09.740Z,2015-03-16T03:17:09.594Z,,,52.1,CP007350.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120496,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412556,,,,,,,4518,,,24786953,-,4281,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
316,1412557.3,,,,,GCA_000624735.1,MIRA v. 4.0,,PRJNA219482,SAMN02384278,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:10.227Z,2015-03-16T03:17:09.594Z,,,52.1,CP007368.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121542,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412557,,,,,,,4526,,,24786953,-,4279,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
317,1412558.3,,,,,GCA_000625195.1,MIRA v. 4.0,,PRJNA219482,SAMN02384279,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:11.020Z,2015-03-16T03:17:09.594Z,,,52.1,CP007378.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120968,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412558,,,,,,,4526,,,24786953,-,4276,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
318,1412559.3,,,,,GCA_000625755.1,MIRA v. 4.0,,PRJNA219482,SAMN02384280,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:11.542Z,2015-03-16T03:17:09.594Z,,,49.9,CP007428.1,4685710,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120677,Complete,Salmonella,Canada: Alberta,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412559,,,,,,,2912,,,24786953,-,2349,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
319,1412560.3,,,,,GCA_000624875.1,MIRA v. 4.0,,PRJNA219482,SAMN02384281,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:12.133Z,2015-03-16T03:17:09.594Z,,,52.1,CP007395.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121748,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412560,,,,,,,4533,,,24786953,-,4246,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
320,1412561.3,,,,,GCA_000624775.1,MIRA v. 4.0,,PRJNA219482,SAMN02384282,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:12.927Z,2015-03-16T03:17:09.594Z,,,52.1,CP007370.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121672,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,FOOD,,,,,1412561,,,,,,,4536,,,24786953,-,4260,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
321,1412562.3,,,,,GCA_000626435.1,MIRA v. 4.0,,PRJNA219482,SAMN02384283,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:13.451Z,2015-03-16T03:17:09.594Z,,,52.1,CP007464.1,4690770,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121747,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,FOOD-Turkey,,,,,1412562,,,,,,,4537,,,24786953,-,4194,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
322,1412563.3,,,,,GCA_000624855.1,MIRA v. 4.0,,PRJNA219482,SAMN02384284,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:14.438Z,2015-03-16T03:17:09.594Z,,,52.1,CP007374.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121746,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412563,,,,,,,4521,,,24786953,-,4278,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
323,1412564.3,,,,,GCA_000624995.1,MIRA v. 4.0,,PRJNA219482,SAMN02384285,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:14.901Z,2015-03-16T03:17:09.594Z,,,52.1,CP007402.1,4685880,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120765,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412564,,,,,,,4532,,,24786953,-,4278,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
324,1412565.3,,,,,GCA_000624755.1,MIRA v. 4.0,,PRJNA219482,SAMN02384286,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:15.390Z,2015-03-16T03:17:09.594Z,,,52.1,CP007369.1,4685810,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121671,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412565,,,,,,,4547,,,24786953,-,4253,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
325,1412566.3,,,,,GCA_000623255.1,MIRA v. 4.0,,PRJNA219482,SAMN02384287,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:15.863Z,2015-03-16T03:17:09.594Z,,,52.1,CP007364.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120555,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,FOOD-porcine,,,,,1412566,,,,,,,4522,,,24786953,-,4281,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
326,1412567.3,,,,,GCA_000624335.1,MIRA v. 4.0,,PRJNA219482,SAMN02384288,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:16.396Z,2015-03-16T03:17:09.594Z,,,52.1,CP007326.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20111554,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412567,,,,,,,4522,,,24786953,-,4286,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
327,1412568.3,,,,,GCA_000624595.1,MIRA v. 4.0,,PRJNA219482,SAMN02384289,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:17.222Z,2015-03-16T03:17:09.594Z,,,52.1,CP007351.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120497,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412568,,,,,,,4526,,,24786953,-,4284,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
328,1412569.3,,,,,GCA_000624675.1,MIRA v. 4.0,,PRJNA219482,SAMN02384290,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:17.738Z,2015-03-16T03:17:09.594Z,,,50.8,CP007365.1,4685770,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120994,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412569,,,,,,,3992,,,24786953,-,3164,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
329,1412570.3,,,,,GCA_000624155.1,MIRA v. 4.0,,PRJNA219482,SAMN02384291,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:18.271Z,2015-03-16T03:17:09.594Z,,,52.1,CP007332.1,4807990,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120916,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412570,,,,,,,4828,,,24786953,NZ_CP007332.1,4492,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
330,1412571.3,,,,,GCA_000625255.1,MIRA v. 4.0,,PRJNA219482,SAMN02384292,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:19.118Z,2015-03-16T03:17:09.594Z,,,52.1,CP007381.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121812,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,Food,,,,,1412571,,,,,,,4545,,,24786953,-,4273,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
331,1412572.3,,,,,GCA_000624355.1,MIRA v. 4.0,,PRJNA219482,SAMN02384293,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:20.188Z,2015-03-16T03:17:09.594Z,,,52.1,CP007327.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20111561,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412572,,,,,,,4527,,,24786953,-,4280,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
332,1412573.3,,,,,GCA_000625975.1,MIRA v. 4.0,,PRJNA219482,SAMN02384294,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:20.706Z,2015-03-16T03:17:09.594Z,,,52.2,CP007416.1,4686090,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20122045,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412573,,,,,,,4542,,,24786953,-,4290,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
333,1412574.3,,,,,GCA_000625955.1,MIRA v. 4.0,,PRJNA219482,SAMN02384295,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:21.208Z,2015-03-16T03:17:09.594Z,,,52.2,CP007415.1,4686090,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20122033,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412574,,,,,,,4540,,,24786953,-,4290,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
334,1412575.3,,,,,GCA_000625935.1,MIRA v. 4.0,,PRJNA219482,SAMN02384296,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:22.016Z,2015-03-16T03:17:09.594Z,,,52.1,CP007414.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20122031,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412575,,,,,,,4528,,,24786953,-,4277,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
335,1412576.3,,,,,GCA_000625915.1,MIRA v. 4.0,,PRJNA219482,SAMN02384297,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:22.501Z,2015-03-16T03:17:09.594Z,,,52.1,CP007413.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20122026,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412576,,,,,,,4537,,,24786953,-,4275,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
336,1412577.3,,,,,GCA_000625895.1,MIRA v. 4.0,,PRJNA219482,SAMN02384298,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:23.058Z,2015-03-16T03:17:09.594Z,,,52.1,CP007412.1,4685830,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20122022,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412577,,,,,,,4541,,,24786953,-,4253,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
337,1412578.3,,,,,GCA_000625875.1,MIRA v. 4.0,,PRJNA219482,SAMN02384299,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:24.031Z,2015-03-16T03:17:09.594Z,,,52.1,CP007411.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121990,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412578,,,,,,,4516,,,24786953,-,4283,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
338,1412579.3,,,,,GCA_000625815.1,MIRA v. 4.0,,PRJNA219482,SAMN02384300,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:24.619Z,2015-03-16T03:17:09.594Z,,,52.1,CP007388.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121989,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412579,,,,,,,4520,,,24786953,-,4286,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
339,1412580.3,,,,,GCA_000625795.1,MIRA v. 4.0,,PRJNA219482,SAMN02384301,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:25.172Z,2015-03-16T03:17:09.594Z,,,52.1,CP007387.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121986,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412580,,,,,,,4520,,,24786953,-,4279,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
340,1412581.3,,,,,GCA_000625635.1,MIRA v. 4.0,,PRJNA219482,SAMN02384302,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:26.225Z,2015-03-16T03:17:09.594Z,,,52.1,CP007386.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121976,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412581,,,,,,,4528,,,24786953,-,4286,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
341,1412582.3,,,,,GCA_000625335.1,MIRA v. 4.0,,PRJNA219482,SAMN02384303,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:26.696Z,2015-03-16T03:17:09.594Z,,,52.1,CP007385.1,4685880,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121970,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412582,,,,,,,4530,,,24786953,-,4279,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
342,1412583.3,,,,,GCA_000625315.1,MIRA v. 4.0,,PRJNA219482,SAMN02384304,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:27.212Z,2015-03-16T03:17:09.594Z,,,52.1,CP007384.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121969,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412583,,,,,,,4530,,,24786953,-,4284,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
343,1412584.3,,,,,GCA_000625715.1,MIRA v. 4.0,,PRJNA219482,SAMN02384305,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:27.865Z,2015-03-16T03:17:09.594Z,,,52.1,CP007432.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20100131,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412584,,,,,,,4532,,,24786953,-,4199,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
344,1412585.3,,,,,GCA_000625395.1,MIRA v. 4.0,,PRJNA219482,SAMN02384306,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:28.628Z,2015-03-16T03:17:09.594Z,,,52.1,CP007298.1,4685830,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20090530,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412585,,,,,,,4549,,,24786953,-,4217,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
345,1412586.3,collected_by:undisclosed,,,,GCF_000968775.1,MIRA v. 4.0,,PRJNA219482,SAMN02384307,,,,Bacilli,,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-05-14T00:00:00Z,1,,2016-01-17T15:52:49.131Z,2016-01-17T15:52:49.131Z,,,51.42,CP007357,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20100100,Complete,Salmonella,Canada: Saskatchewan,Negative,,,,,,,Canada,,Food,,,,,1412586,,,,,,,4671,,,24786953,,4272,,1,LFZ,,Illumina,,,,EC20100100,,,"Excluded from the study, failed QC/QA."
346,1412587.3,,,,,GCA_000625675.1,MIRA v. 4.0,,PRJNA219482,SAMN02384308,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:29.222Z,2015-03-16T03:17:09.594Z,,,52.1,CP007430.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20090195,Complete,Salmonella,Canada: Saskatchewan,Negative,,,,,,,Canada,,Food,,,,,1412587,,,,,,,4520,,,24786953,-,4194,,1,LFZ,,454,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
347,1412588.3,,,,,GCA_000626015.1,MIRA v. 4.0,,PRJNA219482,SAMN02384309,,,,Bacilli,1,2008,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:30.215Z,2015-03-16T03:17:09.594Z,,,52.2,CP007418.1,4686160,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20130345,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412588,,,,,,,4544,,,24786953,-,4293,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
348,1412589.3,,,,,GCA_000626035.1,MIRA v. 4.0,,PRJNA219482,SAMN02384310,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:30.783Z,2015-03-16T03:17:09.594Z,,,52.2,CP007419.1,4686060,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20130346,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412589,,,,,,,4544,,,24786953,-,4292,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
349,1412590.3,,,,,GCA_000626055.1,MIRA v. 4.0,,PRJNA219482,SAMN02384311,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:31.376Z,2015-03-16T03:17:09.594Z,,,50.5,CP007423.1,4685810,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20130347,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412590,,,,,,,3617,,,24786953,-,2803,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
350,1412591.3,,,,,GCA_000626075.1,MIRA v. 4.0,,PRJNA219482,SAMN02384312,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:32.516Z,2015-03-16T03:17:09.594Z,,,52.1,CP007424.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20130348,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412591,,,,,,,4534,,,24786953,-,4266,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
351,1412592.3,,,,,GCA_000623055.2,MIRA v. 4.0,,PRJNA219482,SAMN02384313,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:33.230Z,2015-03-16T03:17:09.594Z,,,52.2,CP007269.2,4679950,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121175,Complete,Salmonella,Canada: Ontario,Negative,,,,,"Human, Homo sapiens",,Canada,,chick paper,,,,,1412592,,,,,,,4574,,,24786953,NZ_CP007269.1,4367,,1,LFZ,>70X,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
352,1412593.3,,,,,GCA_000623075.1,MIRA v. 4.0,,PRJNA219482,SAMN02384314,,,,Bacilli,1,,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:33.699Z,2015-03-16T03:17:09.594Z,,,51.5,CP007270.1,4942220,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121176,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,Food,,,,,1412593,,,,,,,4509,,,24786953,-,4980,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
353,1412594.3,,,,,GCA_000624175.1,MIRA v. 4.0,,PRJNA219482,SAMN02384315,,,,Bacilli,1,,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:34.154Z,2015-03-16T03:17:09.594Z,,,51.6,CP007333.1,4942740,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121177,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412594,,,,,,,4576,,,24786953,-,4959,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
354,1412595.3,,,,,GCA_000623095.1,MIRA v. 4.0,,PRJNA219482,SAMN02384316,,,,Bacilli,1,,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:35.108Z,2015-03-16T03:17:09.594Z,,,51.6,CP007271.1,4949110,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121178,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,environmental-chicken,,,,,1412595,,,,,,,4546,,,24786953,-,4997,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
355,1412596.3,,,,,GCA_000623115.1,MIRA v. 4.0,,PRJNA219482,SAMN02384317,,,,Bacilli,1,,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:35.646Z,2015-03-16T03:17:09.594Z,,,51.6,CP007272.1,4898080,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121179,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,environmental-quail,,,,,1412596,,,,,,,4488,,,24786953,-,4908,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
356,1412597.3,,,,,GCA_000623135.1,MIRA v. 4.0,,PRJNA219482,SAMN02384318,,,,Bacilli,1,,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:36.254Z,2015-03-16T03:17:09.594Z,,,51.6,CP007273.1,5052170,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121180,Complete,Salmonella,Canada: Quebec,Negative,,,,,,,Canada,,environmental-chicken,,,,,1412597,,,,,,,4711,,,24786953,-,5180,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
357,1412598.3,,,,,GCA_000625415.1,MIRA v. 4.0,,PRJNA219482,SAMN02384319,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:36.800Z,2015-03-16T03:17:09.594Z,,,52,CP007355.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20100088,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL,,,,,1412598,,,,,,,4536,,,24786953,-,4169,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
358,1412599.3,,,,,GCA_000625435.1,MIRA v. 4.0,,PRJNA219482,SAMN02384320,,,,Bacilli,1,2009,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:37.444Z,2015-03-16T03:17:09.594Z,,,52.1,CP007356.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20100089,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL,,,,,1412599,,,,,,,4529,,,24786953,-,4212,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
359,1412600.3,,,,,GCA_000626695.1,MIRA v. 4.0,,PRJNA219482,SAMN02384321,,,,Bacilli,1,2010,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-11T00:00:00Z,1,,2014-12-09T00:35:38.549Z,2015-03-16T03:17:09.594Z,,,52.1,CP007360.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20100325,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,food,,,,,1412600,,,,,,,4587,,,24786953,-,4308,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
360,1412601.3,,,,,GCA_000625835.1,MIRA v. 4.0,,PRJNA219482,SAMN02384322,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:39.032Z,2015-03-16T03:17:09.594Z,,,51.9,CP007433.1,4685790,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120051,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-Domestic Cattle,,,,,1412601,,,,,,,4490,,,24786953,-,4009,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
361,1412602.3,,,,,GCA_000624535.1,MIRA v. 4.0,,PRJNA219482,SAMN02384323,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:39.840Z,2015-03-16T03:17:09.594Z,,,52.1,CP007348.1,4685840,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120356,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-Domestic Cattle,,,,,1412602,,,,,,,4522,,,24786953,-,4243,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
362,1412603.3,,,,,GCA_000625455.1,MIRA v. 4.0,,PRJNA219482,SAMN02384324,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:40.312Z,2015-03-16T03:17:09.594Z,,,52,CP007335.1,4685840,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120580,Complete,Salmonella,,Negative,,,,,,,,,ANIMAL-chicken,,,,,1412603,,,,,,,4506,,,24786953,-,4096,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
363,1412604.3,,,,,GCA_000625475.1,MIRA v. 4.0,,PRJNA219482,SAMN02384325,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:40.773Z,2015-03-16T03:17:09.594Z,,,52.1,CP007336.1,4685770,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120581,Complete,Salmonella,,Negative,,,,,,,,,ANIMAL-chicken,,,,,1412604,,,,,,,4516,,,24786953,-,4277,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
364,1412605.3,,,,,GCA_000625495.1,MIRA v. 4.0,,PRJNA219482,SAMN02384326,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:41.713Z,2015-03-16T03:17:09.594Z,,,52.1,CP007337.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120590,Complete,Salmonella,Canada: Nova Scotia,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412605,,,,,,,4534,,,24786953,-,4273,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
365,1412606.3,,,,,GCA_000625515.1,MIRA v. 4.0,,PRJNA219482,SAMN02384327,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:42.257Z,2015-03-16T03:17:09.594Z,,,52.1,CP007338.1,4685830,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120597,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412606,,,,,,,4522,,,24786953,-,4280,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
366,1412607.3,,,,,GCA_000625555.1,MIRA v. 4.0,,PRJNA219482,SAMN02384328,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:42.823Z,2015-03-16T03:17:09.594Z,,,52.1,CP007340.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120686,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412607,,,,,,,4531,,,24786953,-,4271,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
367,1412608.3,,,,,GCA_000625575.1,MIRA v. 4.0,,PRJNA219482,SAMN02384329,,,,Bacilli,1,2011,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:43.447Z,2015-03-16T03:17:09.594Z,,,52.1,CP007341.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120687,Complete,Salmonella,Canada: British Columbia,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412608,,,,,,,4530,,,24786953,-,4258,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
368,1412609.3,,,,,GCA_000624955.1,MIRA v. 4.0,,PRJNA219482,SAMN02384330,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:44.823Z,2015-03-16T03:17:09.594Z,,,52.1,CP007400.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120734,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412609,,,,,,,4537,,,24786953,-,4255,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
369,1412610.3,,,,,GCA_000624975.1,MIRA v. 4.0,,PRJNA219482,SAMN02384331,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:45.276Z,2015-03-16T03:17:09.594Z,,,52.1,CP007401.1,4685850,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120738,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412610,,,,,,,4541,,,24786953,-,4263,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
370,1412611.3,,,,,GCA_000625015.1,MIRA v. 4.0,,PRJNA219482,SAMN02384332,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:45.758Z,2015-03-16T03:17:09.594Z,,,52.1,CP007403.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120773,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412611,,,,,,,4516,,,24786953,-,4281,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
371,1412612.3,,,,,GCA_000625035.1,MIRA v. 4.0,,PRJNA219482,SAMN02384333,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:46.563Z,2015-03-16T03:17:09.594Z,,,52.1,CP007404.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120774,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412612,,,,,,,4527,,,24786953,-,4282,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
372,1412613.3,,,,,GCA_000625095.1,MIRA v. 4.0,,PRJNA219482,SAMN02384334,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:47.084Z,2015-03-16T03:17:09.594Z,,,52.1,CP007407.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120917,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412613,,,,,,,4527,,,24786953,-,4273,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
373,1412614.3,,,,,GCA_000625115.1,MIRA v. 4.0,,PRJNA219482,SAMN02384335,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:47.583Z,2015-03-16T03:17:09.594Z,,,52.1,CP007408.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120918,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412614,,,,,,,4533,,,24786953,-,4265,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
374,1412615.3,,,,,GCA_000625135.1,MIRA v. 4.0,,PRJNA219482,SAMN02384336,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:48.081Z,2015-03-16T03:17:09.594Z,,,52.1,CP007375.1,4685870,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120925,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-domestic cattle,,,,,1412615,,,,,,,4526,,,24786953,-,4276,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Excluded from the study, failed QC/QA."
375,1412616.3,,,,,GCA_000624795.1,MIRA v. 4.0,,PRJNA219482,SAMN02384337,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-01T00:00:00Z,1,,2014-12-09T00:35:48.622Z,2015-03-16T03:17:09.594Z,,,52,CP007371.1,4685750,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20121689,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412616,,,,,,,4509,,,24786953,-,4089,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
376,1412617.3,,,,,GCA_000625155.1,MIRA v. 4.0,,PRJNA219482,SAMN02384338,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:49.152Z,2015-03-16T03:17:09.594Z,,,52.1,CP007376.1,4685790,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120927,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412617,,,,,,,4539,,,24786953,-,4215,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
377,1412618.3,,,,,GCA_000626415.1,MIRA v. 4.0,,PRJNA219482,SAMN02384339,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:50.155Z,2015-03-16T03:17:09.594Z,,,52.2,CP007463.1,4623510,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120929,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,ANIMAL-chicken,,,,,1412618,,,,,,,4538,,,24786953,-,4184,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
378,1412619.3,,,,,GCA_000625215.1,MIRA v. 4.0,,PRJNA219482,SAMN02384340,,,,Bacilli,1,2012,develop molecular sub typing scheme based on whole genome sequencing data,2014-04-02T00:00:00Z,1,,2014-12-09T00:35:50.998Z,2015-03-16T03:17:09.594Z,,,52,CP007379.1,4685860,Salmonella enterica subsp. enterica serovar Enteritidis str. EC20120969,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Food,,,,,1412619,,,,,,,4525,,,24786953,-,4138,,1,LFZ,,Illumina,,serovar enteritidis,,enteritidis,,,"Included in the study, passed QC/QA"
379,1454583.3,collected_by:CDC,,,,GCF_001620155.1,Celera v. 7.0,,PRJNA236652,SAMN02716860,,,,,,Oct-10,Salmonella comparative genomics,2016-04-15T00:00:00Z,1,,2016-04-28T11:29:37.588Z,2016-04-28T11:29:37.588Z,,,52.21,"CP014661,CP014662",4804699,Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1783,Complete,Salmonella,USA: BIFSCo Region 1,,,,,,"Human, Homo sapiens",,United States,,stool,,,MLST.Salmonella_enterica.64,,1454583,,,,,,,4844,,1,,"NZ_CP014661.1,NZ_CP014662.1",4513,,2,USDA-ARS-USMARC,146.33,PacBio RS II C3 P5,,Anatum,,CDC 2010K-2577,,,"Included in the study, passed QC/QA"
380,1454584.3,collected_by:USMARC,,,,GCF_001620205.1,Celera v. 7.0,,PRJNA236655,SAMN02716850,,,,,1,Jul-05,Salmonella comparative genomics,2016-04-15T00:00:00Z,,,2016-04-28T11:32:20.630Z,2016-04-28T11:32:20.630Z,,,52.1,"CP014621,CP014622",4991101,Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1727,Complete,Salmonella,USA: BIFSCo Region 3,,,,,,Bos taurus,,United States,,bovine pre-evisceration carcass,,,,,1454584,,,,,,,5138,,1,,,4775,,2,USDA-ARS-USMARC,125.32,PacBio RS II C3 P5,,Anatum,,SAN1261-1,,,"Included in the study, passed QC/QA"
381,1454585.3,isolate:SAN2113-2;collected_by:USMARC,,,,GCF_000988525.1,Celera Assembler v. 7.0,,PRJNA236656,SAMN02716852,,,,,1,30-Oct-2005,Salmonella comparative genomics,2015-05-06T00:00:00Z,,,2016-01-17T15:57:02.172Z,2016-01-17T15:57:02.172Z,,,52.13,CP007584,4844415,Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1735,Complete,Salmonella,USA: BIFSCo Region 3,,,,,,Bos taurus,,United States,,bovine pre-evisceration carcass,,,,,1454585,,,,,,,4893,,,,,4761,,1,USDA-ARS-USMARC,complete: 22 X coverage : reads >= 9500,PacBio RS II C3 P5,,Anatum,,USDA-ARS-USMARC-1735,,,"Included in the study, passed QC/QA"
382,1454586.3,collected_by:USMARC,,,,GCF_001620115.1,Celera v. 7.0,,PRJNA236657,SAMN02716853,,,,,,Apr-06,Salmonella comparative genomics,2016-04-15T00:00:00Z,1,,2016-04-28T11:28:34.155Z,2016-04-28T11:28:34.155Z,,,52.23,"CP014657,CP014658",4864598,Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1736,Complete,Salmonella,USA: BIFSCo Region 2,,,,,,Bos taurus,,United States,,bovine hide,,,,,1454586,,,,,,,4932,,1,,"NZ_CP014657.1,NZ_CP014658.1",4611,,2,USDA-ARS-USMARC,192.43,PacBio RS II C3 P5,,Anatum,,SAN4231-1,,,"Included in the study, passed QC/QA"
383,1454587.3,collected_by:USMARC,,,,GCF_001620225.1,Celera v. 7.0,,PRJNA236658,SAMN02716848,,,,,1,Mar-07,Salmonella comparative genomics,2016-04-15T00:00:00Z,,,2016-04-28T11:32:49.280Z,2016-04-28T11:32:49.280Z,,,52.24,CP014620,4676958,Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1676,Complete,Salmonella,USA: BIFSCo Region 5,,,,,,Bos taurus,,United States,,ground beef,,,,,1454587,,,,,,,4700,,,,NZ_CP014620.1,4382,,1,USDA-ARS-USMARC,125.69,PacBio RS II C3 P5,,Anatum,,SAN082,,,"Included in the study, passed QC/QA"
384,1454588.3,collected_by:USMARC,,,,GCF_001623545.1,Celera v. 7.0,,PRJNA236659,SAMN02716849,,,,,1,Jul-05,Salmonella comparative genomics,2016-04-19T00:00:00Z,,,2016-04-28T13:04:27.692Z,2016-04-28T13:04:27.692Z,,,52.17,CP014663,4836394,Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1677,Complete,Salmonella,USA: BIFSCo Region 6,,,,,,Bos taurus,,United States,,ground beef,,,,,1454588,,,,,,,4929,,,,,4603,,1,USDA-ARS-USMARC,112.97,PacBio RS II C3 P5,,Anatum,,SAN222,,,"Included in the study, passed QC/QA"
385,1454589.3,collected_by:USMARC,,,,GCF_001623585.1,Celera v. 7.0,,PRJNA236660,SAMN02716851,,,,,1,Aug-06,Salmonella comparative genomics,2016-04-19T00:00:00Z,,,2016-04-28T13:06:52.870Z,2016-04-28T13:06:52.870Z,,,52.16,CP014664,4783492,Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1728,Complete,Salmonella,USA: BIFSCo Region 2,,,,,,Bos taurus,,United States,,ground beef,,,MLST.Salmonella_enterica.64,,1454589,,,,,,,4847,,,,NZ_CP014664.1,4514,,1,USDA-ARS-USMARC,136.2,PacBio RS II C3 P5,,Anatum,,SAN051,,,"Included in the study, passed QC/QA"
386,1454590.3,,,,,GCF_000963535.1,Celera Assembler v. 7.0,,PRJNA236661,SAMN02712199,,,,,1,Sep-06,Salmonella comparative genomics,2015-03-26T00:00:00Z,,,2016-01-17T15:51:24.062Z,2016-01-17T15:51:24.062Z,,,52.17,CP007483,4731586,Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1175,Complete,Salmonella,USA: United States BIFSCo Region 3,,,,,,Bos taurus,,United States,,ground beef,,,,,1454590,,,,,,,4712,,,,,4602,,1,USDA-ARS-USMARC,complete: 22 X coverage : reads >= 8500,PacBio RS II C2 P4,,,,USDA-ARS-USMARC-1175,,,"Included in the study, passed QC/QA"
387,1454592.3,,,,,GCF_000940895.1,Celera Assembler v. 7.0,,PRJNA236663,SAMN02712195,,,,,1,2006,Salmonella comparative genomics,2015-04-02T00:00:00Z,,,2016-01-17T15:45:55.142Z,2016-01-17T15:45:55.142Z,,,52.18,CP007211,4667736,Salmonella enterica subsp. enterica serovar Anatum str. CDC 06-0532 strain USDA-ARS-USMARC-1764,Complete,Salmonella,USA: United States BIFSCo Region 5,,,,,,"Human, Homo sapiens",,United States,,stool,,,,,1454592,,,,,,,4655,,,,,4516,,1,USDA-ARS-USMARC,"complete: 21 X coverage : reads >= 11,500",PacBio RS II C3 P5,,,,USDA-ARS-USMARC-1764,,,"Included in the study, passed QC/QA"
388,1454593.3,collected_by:CDC,,,,GCF_001620135.1,Celera v. 7.0,,PRJNA236664,SAMN02716855,,,,,,Jul-06,Salmonella comparative genomics,2016-04-15T00:00:00Z,1,,2016-04-28T11:30:15.950Z,2016-04-28T11:30:15.950Z,,,52.17,"CP014659,CP014660",4955431,Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1765,Complete,Salmonella,USA: BIFSCo Region 5,,,,,,"Human, Homo sapiens",,United States,,stool,,,,,1454593,,,,,,,5089,,1,,,4749,,2,USDA-ARS-USMARC,261.99,PacBio RS II C3 P5,,Anatum,,CDC 06-0624,,,"Included in the study, passed QC/QA"
389,1454594.3,collected_by:CDC,,,,GCF_001623625.1,Celera v. 7.0,,PRJNA236665,SAMN02716856,,,,,1,Jul-06,Salmonella comparative genomics,2016-04-19T00:00:00Z,,,2016-04-28T13:12:07.306Z,2016-04-28T13:12:07.306Z,,,52.2,CP014665,4751034,Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1766,Complete,Salmonella,USA: BIFSCo Region 8,,,,,,"Human, Homo sapiens",,United States,,stool,,,MLST.Salmonella_enterica.64,,1454594,,,,,,,4796,,,,NZ_CP014665.1,4475,,1,USDA-ARS-USMARC,134.27,PacBio RS II C3 P5,,Anatum,,CDC 06-0855,,,"Included in the study, passed QC/QA"
390,1454596.3,collected_by:CDC,,,,GCF_001623665.1,Celera v. 7.0,,PRJNA236667,SAMN02716858,,,,,1,May-07,Salmonella comparative genomics,2016-04-19T00:00:00Z,,,2016-04-28T13:12:27.270Z,2016-04-28T13:12:27.270Z,,,52.21,CP014666,4636307,Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1781,Complete,Salmonella,USA: BIFSCo Region 8,,,,,,"Human, Homo sapiens",,United States,,stool,,,,,1454596,,,,,,,4649,,,,,4333,,1,USDA-ARS-USMARC,184.92,PacBio RS II C3 P5,,Anatum,,CDC 08-1092,,,"Included in the study, passed QC/QA"
391,1454598.3,collected_by:USMARC,,,,,HGAP v. 3,,PRJNA236653,SAMN02716873,,,,,1,Aug-2011,Salmonella comparative genomics,2017-11-07T00:00:00Z,,,2017-11-24T17:21:23.794Z,2017-11-24T17:21:23.794Z,,,52.34,CP017971,4587202,Salmonella enterica subsp. enterica serovar Montevideo str. USDA-ARS-USMARC-1901,Complete,Salmonella,USA: BIFSCo Region 5,,,,,,Bos taurus,,United States,,bovine peripheral lymph node,,,,,1454598,,,,,,,4668,,,,,4512,,1,USDA-ARS-USMARC,242.4,PacBio,,Montevideo,,USDA-ARS-USMARC-1901,,,"Included in the study, passed QC/QA"
392,1454599.3,collected_by:USMARC,,,,,HGAP v. 3,,PRJNA236669,SAMN02716872,,,,,1,Jul-2005,Salmonella comparative genomics,2017-11-07T00:00:00Z,,,2017-11-24T17:20:35.149Z,2017-11-24T17:20:35.149Z,,,52.35,CP017970,4593026,Salmonella enterica subsp. enterica serovar Montevideo str. USDA-ARS-USMARC-1900,Complete,Salmonella,USA: BIFSCo Region 3,,,,,,Bos taurus,,United States,,bovine hide,,,MLST.Salmonella_enterica.138,,1454599,,,,,,,4680,,,,,4522,,1,USDA-ARS-USMARC,303.2,PacBio,,Montevideo,,USDA-ARS-USMARC-1900,,,"Included in the study, passed QC/QA"
393,1454600.3,collected_by:USMARC,,,,,HGAP v. 3,,PRJNA236670,SAMN02716882,,,,,1,Jul-2005,Salmonella comparative genomics,2017-11-07T00:00:00Z,,,2017-11-24T17:21:40.195Z,2017-11-24T17:21:40.195Z,,,52.33,CP017973,4547966,Salmonella enterica subsp. enterica serovar Montevideo str. USDA-ARS-USMARC-1912,Complete,Salmonella,USA: BIFSCo Region 3,,,,,,Bos taurus,,United States,,bovine hide,,,,,1454600,,,,,,,4632,,,,,4476,,1,USDA-ARS-USMARC,150.78,PacBio,,Montevideo,,USDA-ARS-USMARC-1912,,,"Included in the study, passed QC/QA"
394,1454603.3,,,,,GCF_000940975.1,Celera Assembler v. 7.0,,PRJNA236673,SAMN02712197,,,,,1,Oct-06,Salmonella comparative genomics,2015-03-04T00:00:00Z,,,2016-01-17T15:45:56.080Z,2016-01-17T15:45:56.080Z,,,52.34,CP007222,4565462,Salmonella enterica subsp. enterica serovar Montevideo str. USDA-ARS-USMARC-1903,Complete,Salmonella,USA: United States BIFSCo Region 6,,,,,,Bos taurus,,United States,,ground beef,,,,,1454603,,,,,,,4485,,,,NZ_CP007222.1,4370,,1,USDA-ARS-USMARC,"complete: 20 X coverage : reads >= 6,500",PacBio RS II C2 P4 and C3 P5,,,,USDA-ARS-USMARC-1903,,,"Included in the study, passed QC/QA"
395,1454604.3,collected_by:USMARC,,,,,HGAP v. 3,,PRJNA236674,SAMN02716875,,,,,1,Jun-2006,Salmonella comparative genomics,2017-11-07T00:00:00Z,,,2017-11-24T17:21:19.518Z,2017-11-24T17:21:19.518Z,,,52.3,CP017972,4598213,Salmonella enterica subsp. enterica serovar Montevideo str. USDA-ARS-USMARC-1904,Complete,Salmonella,USA: BIFSCo Region 3,,,,,,Bos taurus,,United States,,ground beef,,,,,1454604,,,,,,,4689,,,,,4530,,1,USDA-ARS-USMARC,186.47,PacBio,,Montevideo,,USDA-ARS-USMARC-1904,,,"Included in the study, passed QC/QA"
396,1454606.3,isolate:B94-007410;collected_by:CDC,,,,GCF_000973665.1,Celera Assembler v. 7.0,,PRJNA236676,SAMN02716891,,,,,1,Feb-1994,Salmonella comparative genomics,2015-04-20T00:00:00Z,,,2016-01-17T15:53:59.907Z,2016-01-17T15:53:59.907Z,,,52.36,CP007540,4488371,Salmonella enterica subsp. enterica serovar Montevideo str. USDA-ARS-USMARC-1921,Complete,Salmonella,USA,,,,,,"Human, Homo sapiens",,United States,,stool,,,,,1454606,,,,,,,4379,,,,,4277,,1,USDA-ARS-USMARC,complete: 21 X coverage : reads >= 7000,PacBio RS II C3 P5,,Montevideo,,USDA-ARS-USMARC-1921,,,"Included in the study, passed QC/QA"
397,1454607.3,collected_by:CDC,,,,,HGAP v. 3,,PRJNA236677,SAMN02716884,,,,,1,Oct-2007,Salmonella comparative genomics,2017-11-07T00:00:00Z,,,2017-11-24T17:21:54.653Z,2017-11-24T17:21:54.653Z,,,52.36,CP017974,4773383,Salmonella enterica subsp. enterica serovar Montevideo str. USDA-ARS-USMARC-1914,Complete,Salmonella,USA: BIFSCo Region 7,,,,,,"Human, Homo sapiens",,United States,,stool,,,,,1454607,,,,,,,4785,,,,,4492,,1,USDA-ARS-USMARC,188.09,PacBio,,Montevideo,,USDA-ARS-USMARC-1914,,,"Included in the study, passed QC/QA"
398,1454608.3,collected_by:CDC,,,,,HGAP v. 3,,PRJNA236678,SAMN02716885,,,,,1,Sep-2008,Salmonella comparative genomics,2017-11-07T00:00:00Z,,,2017-11-24T17:21:27.726Z,2017-11-24T17:21:27.726Z,,,52.33,CP017975,4700953,Salmonella enterica subsp. enterica serovar Montevideo str. USDA-ARS-USMARC-1915,Complete,Salmonella,USA: BIFSCo Region 3,,,,,,"Human, Homo sapiens",,United States,,stool,,,,,1454608,,,,,,,4683,,,,,4405,,1,USDA-ARS-USMARC,108.2,PacBio,,Montevideo,,USDA-ARS-USMARC-1915,,,"Included in the study, passed QC/QA"
399,1454610.3,collected_by:CDC,,,,,HGAP v. 3,,PRJNA236680,SAMN02716887,,,,,1,Sep-2011,Salmonella comparative genomics,2017-11-07T00:00:00Z,,,2017-11-24T17:21:35.868Z,2017-11-24T17:21:35.868Z,,,52.35,CP017976,4693862,Salmonella enterica subsp. enterica serovar Montevideo str. USDA-ARS-USMARC-1917,Complete,Salmonella,USA: BIFSCo Region 7,,,,,,"Human, Homo sapiens",,United States,,stool,,,,,1454610,,,,,,,4793,,,,,4618,,1,USDA-ARS-USMARC,154.51,PacBio,,Montevideo,,USDA-ARS-USMARC-1917,,,"Included in the study, passed QC/QA"
400,1454611.3,collected_by:CDC,,,,,HGAP v. 3,,PRJNA236681,SAMN02716888,,,,,1,Oct-2012,Salmonella comparative genomics,2017-11-07T00:00:00Z,,,2017-11-24T17:20:42.131Z,2017-11-24T17:20:42.131Z,,,52.11,CP017977,4726140,Salmonella enterica subsp. enterica serovar Montevideo str. USDA-ARS-USMARC-1918,Complete,Salmonella,USA: BIFSCo Region 7,,,,,,"Human, Homo sapiens",,United States,,stool,,,MLST.Salmonella_enterica.316,,1454611,,,,,,,4711,,,,,4427,,1,USDA-ARS-USMARC,96.16,PacBio,,Montevideo,,USDA-ARS-USMARC-1918,,,"Included in the study, passed QC/QA"
401,1454612.3,collected_by:CDC,,,,,HGAP v. 3,,PRJNA236682,SAMN02716889,,,,,1,2013,Salmonella comparative genomics,2017-11-07T00:00:00Z,,,2017-11-24T17:35:46.800Z,2017-11-24T17:35:46.800Z,,,52.28,CP017978,4655223,Salmonella enterica subsp. enterica serovar Montevideo str. USDA-ARS-USMARC-1919,Complete,Salmonella,USA: BIFSCo Region 8,,,,,,"Human, Homo sapiens",,United States,,,,,,,1454612,,,,,,,4741,,,,,4603,,1,USDA-ARS-USMARC,148.9,PacBio,,Montevideo,,USDA-ARS-USMARC-1919,,,"Included in the study, passed QC/QA"
402,1454620.4,,,,,GCF_000940935.1,Celera Assembler v. 7.0,,PRJNA236689,SAMN02712196,,,,,1,Jan-11,Salmonella comparative genomics,2015-03-04T00:00:00Z,,,2016-01-17T15:45:55.771Z,2016-01-17T15:45:55.771Z,,,52.18,CP007216,4695590,Salmonella enterica subsp. enterica serovar Newport str. USDA-ARS-USMARC-1927,Complete,Salmonella,USA: United States BIFSCo Region 6,,,,,,Bos taurus,,United States,,fecal swab,,,,,1454620,,,,,,,4692,,,,NZ_CP007216.1,4581,,1,USDA-ARS-USMARC,"complete: 20 X coverage : reads >= 6,500",PacBio RS II C2 P4 and C3 P5,,,,USDA-ARS-USMARC-1927,,,"Included in the study, passed QC/QA"
403,1454627.3,isolate:USDA-ARS-USMARC-1934;collected_by:CDC,,,,GCF_000973685.1,Celera Assembler v. 7.0,,PRJNA236696,SAMN02716903,,,,,1,Aug-10,Salmonella comparative genomics,2015-04-20T00:00:00Z,,,2016-01-17T15:54:00.274Z,2016-01-17T15:54:00.274Z,,,52.26,CP007559,4790387,Salmonella enterica subsp. enterica serovar Newport str. CDC 2010K-2159,Complete,Salmonella,USA: BIFSCo Region 7,,,,,,"Human, Homo sapiens",,United States,,stool,,,,,1454627,,,,,,,4795,,,,NZ_CP007559.1,4662,,1,USDA-ARS-USMARC,complete: 20 X coverage : reads >= 8500,PacBio RS II C3 P5,,Newport,,CDC 2010K-2159,,,"Included in the study, passed QC/QA"
404,1454630.3,collected_by:USMARC,,,,GCF_001623725.1,Celera v. 7.0,,PRJNA236699,SAMN02716861,,,,,,Jul-05,Salmonella comparative genomics,2016-04-19T00:00:00Z,1,,2016-04-28T13:13:05.403Z,2016-04-28T13:13:05.403Z,,,52.14,"CP014969,CP014970",5030908,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1808,Complete,Salmonella,USA: BIFSCo Region 8,,,,,,Bos taurus,,United States,,bovine post-intervention carcass,,,,,1454630,,,,,,,5186,,1,,"NZ_CP014969.1,NZ_CP014970.1",4792,,2,USDA-ARS-USMARC,123.59,PacBio RS II C3 P5,,Typhimurium,,ST1126-1,,,"Included in the study, passed QC/QA"
405,1454634.3,collected_by:USMARC,,,,GCF_001623705.1,Celera v. 7.0,,PRJNA236703,SAMN02716867,,,,,,Jun-03,Salmonella comparative genomics,2016-04-19T00:00:00Z,1,,2016-04-28T13:12:23.352Z,2016-04-28T13:12:23.352Z,,,52.21,CP014981,4815208,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1880,Complete,Salmonella,USA: BIFSCo Region 5,,,,,,Bos taurus,,United States,,bovine pre-evisceration carcass,,,,,1454634,,,,,,,4862,,,,NZ_CP014981.1,4528,,1,USDA-ARS-USMARC,159.31,PacBio RS II C3 P5,,Typhimurium,,ST13123,,,"Included in the study, passed QC/QA"
406,1454636.3,collected_by:USMARC,,,,GCF_001623845.1,Celera v. 7.0,,PRJNA236705,SAMN02716869,,,,,,Mar-11,Salmonella comparative genomics,2016-04-19T00:00:00Z,1,,2016-04-28T13:20:20.054Z,2016-04-28T13:20:20.054Z,,,52.12,"CP014977,CP014978",5003736,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1896,Complete,Salmonella,USA: BIFSCo Region 2,,,,,,Bos taurus,,United States,,bovine adipose trim,,,MLST.Salmonella_enterica.19,,1454636,,,,,,,5138,,1,,"NZ_CP014977.1,NZ_CP014978.1",4758,,2,USDA-ARS-USMARC,99.73,PacBio RS II C3 P5,,Typhimurium,,ST03-F34,,,"Included in the study, passed QC/QA"
407,1454638.3,collected_by:USMARC,,,,GCF_001623765.1,Celera v. 7.0,,PRJNA236707,SAMN02716871,,,,,,Feb-07,Salmonella comparative genomics,2016-04-19T00:00:00Z,1,,2016-04-28T13:15:55.078Z,2016-04-28T13:15:55.078Z,,,52.1,"CP014971,CP014972,CP014973,CP014974",5010089,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898,Complete,Salmonella,USA: BIFSCo Region 3,,,,,,Bos taurus,,United States,,ground beef,,,MLST.Salmonella_enterica.19,,1454638,,,,,,,5127,,3,,,4728,,4,USDA-ARS-USMARC,181.54,PacBio RS II C3 P5,,Typhimurium,,ST073,,,"Included in the study, passed QC/QA"
408,1454639.3,,,,,GCF_000941015.1,Celera Assembler v. 7.0,,PRJNA236708,SAMN02712198,,,,,1,May-07,Salmonella comparative genomics,2015-03-04T00:00:00Z,,,2016-01-17T15:45:56.972Z,2016-01-17T15:45:56.972Z,,,52.2,CP007235,4856450,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1899,Complete,Salmonella,USA: United States BIFSCo Region 1,,,,,,Bos taurus,,United States,,ground beef,,,,,1454639,,,,,,,4870,,,,,4745,,1,USDA-ARS-USMARC,"complete: 20 X coverage : reads >= 10,500",PacBio RS II C3 P5,,,,USDA-ARS-USMARC-1899,,,"Included in the study, passed QC/QA"
409,1454640.3,collected_by:CDC,,,,GCF_001623825.1,Celera v. 7.0,,PRJNA236709,SAMN02716865,,,,,,Aug-97,Salmonella comparative genomics,2016-04-19T00:00:00Z,1,,2016-04-28T13:19:37.159Z,2016-04-28T13:19:37.159Z,,,52.14,"CP014979,CP014980",4985715,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1878,Complete,Salmonella,USA,,,,,,"Human, Homo sapiens",,United States,,,,,,,1454640,,,,,,,5133,,1,,,4740,,2,USDA-ARS-USMARC,152.44,PacBio RS II C3 P5,,Typhimurium,,H2662-08-1997,,,"Included in the study, passed QC/QA"
410,1454641.3,collected_by:CDC,,,,GCF_001623645.1,Celera v. 7.0,,PRJNA236710,SAMN02716879,,,,,,Jun-06,Salmonella comparative genomics,2016-04-19T00:00:00Z,1,,2016-04-28T13:11:58.563Z,2016-04-28T13:11:58.563Z,,,52.12,"CP014965,CP014966",5008298,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1908,Complete,Salmonella,USA: BIFSCo Region 8,,,,,,"Human, Homo sapiens",,United States,,stool,,,,,1454641,,,,,,,5132,,1,,"NZ_CP014965.1,NZ_CP014966.1",4755,,2,USDA-ARS-USMARC,122.88,PacBio RS II C3 P5,,Typhimurium,,CDC 2010K-1587,,,"Included in the study, passed QC/QA"
411,1454642.3,,,,,GCF_000973645.1,Celera Assembler v. 8.1,,PRJNA236711,SAMN02712200,,,,,1,27-Feb-2011,Salmonella comparative genomics,2015-04-20T00:00:00Z,,,2016-01-17T15:53:59.532Z,2016-01-17T15:53:59.532Z,,,52.23,CP007523,4769471,Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2011K-0870,Complete,Salmonella,USA: BIFSCo Region 7,,,,,,"Human, Homo sapiens",,United States,,stool,,,,,1454642,,,,,,,4735,,,,NZ_CP007523.1,4623,,1,USDA-ARS-USMARC,complete: 22 X coverage : reads >= 8000,PacBio RS II C3 P5,,,,CDC 2011K-0870,,,"Included in the study, passed QC/QA"
412,1454643.3,collected_by:CDC,,,,GCF_001623685.1,Celera v. 7.0,,PRJNA236712,SAMN02716880,,,,,,Jul-11,Salmonella comparative genomics,2016-04-19T00:00:00Z,1,,2016-04-28T13:12:44.979Z,2016-04-28T13:12:44.979Z,,,52.13,"CP014967,CP014968",5000337,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1910,Complete,Salmonella,USA: BIFSCo Region 7,,,,,,"Human, Homo sapiens",,United States,,urine,,,MLST.Salmonella_enterica.19,,1454643,,,,,,,5141,,1,,"NZ_CP014967.1,NZ_CP014968.1",4745,,2,USDA-ARS-USMARC,134.63,PacBio RS II C3 P5,,Typhimurium,,CDC 2011K-1702,,,"Included in the study, passed QC/QA"
413,1454644.3,collected_by:CDC,,,,GCF_001623805.1,Celera v. 7.0,,PRJNA236713,SAMN02716877,,,,,,2009,Salmonella comparative genomics,2016-04-19T00:00:00Z,1,,2016-04-28T13:19:33.105Z,2016-04-28T13:19:33.105Z,,,52.13,"CP014975,CP014976",5027726,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1906,Complete,Salmonella,USA: BIFSCo Region 2,,,,,,"Human, Homo sapiens",,United States,,,,,,,1454644,,,,,,,5172,,1,,"NZ_CP014975.1,NZ_CP014976.1",4786,,2,USDA-ARS-USMARC,88.13,PacBio RS II C3 P5,,Typhimurium,,CDC 2009K-1640,,,"Included in the study, passed QC/QA"
414,1454645.3,collected_by:CDC,,,,GCF_001623775.1,Celera v. 7.0,,PRJNA236714,SAMN02716878,,,,,,Oct-09,Salmonella comparative genomics,2016-04-19T00:00:00Z,1,,2016-04-28T13:16:04.300Z,2016-04-28T13:16:04.300Z,,,52.18,CP014983,4823793,Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2009K-2059,Complete,Salmonella,USA: BIFSCo Region 2,,,,,,"Human, Homo sapiens",,United States,,stool,,,MLST.Salmonella_enterica.19,,1454645,,,,,,,4884,,,,NZ_CP014983.1,4536,,1,USDA-ARS-USMARC,147.03,PacBio RS II C3 P5,,Typhimurium,,CDC 2009K-2059,,,"Included in the study, passed QC/QA"
415,1454647.3,collected_by:USMARC,,,,GCF_001623745.1,Celera v. 7.0,,PRJNA236651,SAMN02716863,,,,,,Oct-05,Salmonella comparative genomics,2016-04-19T00:00:00Z,1,,2016-04-28T13:16:00.587Z,2016-04-28T13:16:00.587Z,,,52.16,CP014982,4927870,Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1810,Complete,Salmonella,USA: BIFSCo Region 5,,,,,,Bos taurus,,United States,,bovine pre-evisceration carcass,,,MLST.Salmonella_enterica.19,,1454647,,,,,,,5037,,,,,4667,,1,USDA-ARS-USMARC,132.98,PacBio RS II C3 P5,,Typhimurium,,ST2254-1,,,"Included in the study, passed QC/QA"
416,149539.1142,collected_by:Shanghai Municipal Center for Disease Control and Prevention,,,,GCA_002813975.1,CLC v. 5.5,,PRJNA320034,SAMN04924824,,,,,1,2010-06-22,Comparative genomics study,2017-12-07T00:00:00Z,,,2018-01-01T04:20:32.586Z,2018-01-01T04:20:32.586Z,,,52.17,"CP015524,CP015525",4739362,Salmonella enterica subsp. enterica serovar Enteritidis strain SJTUF10978,Complete,Salmonella,China: Shanghai,,,,,,,,China,,chicken,,,,,149539,,,,,,,4916,,1,,,4733,,2,"School of Agriculture and Biology, Shanghai Jiao Tong University",327x,Illumina,,Enteritidis,,SJTUF10978,,,"Included in the study, passed QC/QA"
417,149539.316,collected_by:Graham Hatfull and William Pascule,,,,GCF_000612325.1,Newbler v. 2.6; CLC Genomics Workbench,,PRJNA241513,SAMN02712059,,,,Bacilli,1,15-Jul-2013,"The genome sequence of a pathogenic strain of Salmonella enterica, isolated from a patient who was infected in Durban, South Africa.",2014-04-04T00:00:00Z,,,2016-01-17T15:34:44.690Z,2016-01-17T15:34:44.690Z,,,52.17,"CP007507,CP007508",4738298,Salmonella enterica subsp. enterica serovar Enteritidis strain Durban,Complete,Salmonella,South Africa: Durban,Negative,,,,,"Human, Homo sapiens","isolated from a patient who was infected in Durban, South Africa",South Africa,,blood,,,,,149539,,,,,,,4774,,1,,"NZ_CP007507.1,NZ_CP007508.1",4312,,2,University of Pittsburgh,65,IonTorrent,,Enteritidis,,Durban,,,"Included in the study, passed QC/QA"
418,149539.317,isolate:OLF-SE7,,,,GCF_000750215.1,CLC Genomics Workbench v. version 6,,PRJNA256209,SAMN02941163,,,,,1,2010,Whole genome sequencing to characterize an important and prevalent foodborne pathogen,2014-09-09T00:00:00Z,,,2016-01-17T15:39:18.740Z,2016-01-17T15:39:18.740Z,,,52.16,CP009089,4710936,Salmonella enterica subsp. enterica serovar Enteritidis,Complete,Salmonella,Canada,,,,,,,,Canada,,environment,,,,,149539,,,,,,,4727,,,25156331,NZ_CP009089.1,4273,,1,Canadian Food Inspection Agency,,454,,Enteritidis,,,,,"Included in the study, passed QC/QA"
419,149539.318,isolate:OLF-SE8,,,,GCF_000750255.1,GS Denovo  Assembler v. version 2,,PRJNA256209,SAMN02941164,,,,,1,2010,Whole genome sequencing to characterize an important and prevalent foodborne pathogen,2014-09-09T00:00:00Z,,,2016-01-17T15:39:19.051Z,2016-01-17T15:39:19.051Z,,,52.17,CP009090,4667283,Salmonella enterica subsp. enterica serovar Enteritidis,Complete,Salmonella,Canada,,,,,,,,Canada,,chicken,,,,,149539,,,,,,,4676,,,,NZ_CP009090.1,4235,,1,Canadian Food Inspection Agency,,454,,Enteritidis,,,,,"Included in the study, passed QC/QA"
420,149539.319,isolate:OLF-SE9,,,,GCF_000750295.1,GS Denovo assembler v. version 2,,PRJNA256209,SAMN02941165,,,,,1,2009,Whole genome sequencing to characterize an important and prevalent foodborne pathogen,2014-09-09T00:00:00Z,,,2016-01-17T15:39:19.851Z,2016-01-17T15:39:19.851Z,,,52.1,CP009091,4671261,Salmonella enterica subsp. enterica serovar Enteritidis,Complete,Salmonella,Canada,,,,,,,,Canada,,shellfish monitoring program,,,,,149539,,,,,,,4714,,,25156331,NZ_CP009091.1,4212,,1,Canadian Food Inspection Agency,,454,,Enteritidis,,,,,"Included in the study, passed QC/QA"
421,149539.32,isolate:OLF-SE10,,,,GCF_000750335.1,GS Denovo assembler v. version 2,,PRJNA256209,SAMN02941166,,,,,1,2010,Whole genome sequencing to characterize an important and prevalent foodborne pathogen,2014-09-09T00:00:00Z,,,2016-01-17T15:39:20.581Z,2016-01-17T15:39:20.581Z,,,52.16,CP009092,4709890,Salmonella enterica subsp. enterica serovar Enteritidis,Complete,Salmonella,Canada,,,,,,,,Canada,,environment,,,,,149539,,,,,,,4716,,,25156331,NZ_CP009092.1,4277,,1,Canadian Food Inspection Agency,,454,,Enteritidis,,,,,"Included in the study, passed QC/QA"
422,149539.321,isolate:OLF-SE11,,,,GCF_000750375.1,GS Denovo assembler v. version 2,,PRJNA256209,SAMN02941167,,,,,1,2010,Whole genome sequencing to characterize an important and prevalent foodborne pathogen,2014-09-09T00:00:00Z,,,2016-01-17T15:39:20.893Z,2016-01-17T15:39:20.893Z,,,52.17,CP009093,4702741,Salmonella enterica subsp. enterica serovar Enteritidis,Complete,Salmonella,Canada,,,,,,,,Canada,,environment,,,,,149539,,,,,,,4753,,,,NZ_CP009093.1,4373,,1,Canadian Food Inspection Agency,,454,,Enteritidis,,,,,"Included in the study, passed QC/QA"
423,149539.322,collected_by:staff;isolate:OLF-SE3,,,,GCF_000750395.2,CLC Genomics Workbench v. version 6,,PRJNA256209,SAMN02937349,,,,,1,2000,Whole genome sequencing to characterize an important and prevalent foodborne pathogen,2015-02-06T00:00:00Z,,,2016-01-17T15:39:21.411Z,2016-01-17T15:39:21.411Z,,,52.17,CP009085,4679127,Salmonella enterica subsp. enterica serovar Enteritidis strain OLF-SE3-98983-4,Complete,Salmonella,Canada,,,,,,,,Canada,,environment,,,,,149539,,,,,,,4704,,,,NZ_CP009085.2,4363,,1,Canadian Food Inspection Agency,,Illumina,,Enteritidis,,OLF-SE3-98983-4,,,"Included in the study, passed QC/QA"
424,149539.323,collected_by:staff;isolate:OLF-SE2,,,,GCF_000750415.2,CLC Genomics Workbench v. version 6,,PRJNA256209,SAMN02937348,,,,,1,2000,Whole genome sequencing to characterize an important and prevalent foodborne pathogen,2015-02-06T00:00:00Z,,,2016-01-17T15:39:21.761Z,2016-01-17T15:39:21.761Z,,,52.17,CP009084,4679126,Salmonella enterica subsp. enterica serovar Enteritidis strain OLF-SE2-98984-6,Complete,Salmonella,Canada,,,,,,,,Canada,,environment,,,,,149539,,,,,,,4703,,,,NZ_CP009084.2,4365,,1,Canadian Food Inspection Agency,,Illumina,,Enteritidis,,OLF-SE2-98984-6,,,"Included in the study, passed QC/QA"
425,149539.324,collected_by:staff;isolate:OLF-SE4,,,,GCF_000750435.1,CLC Genomics Workbench v. version 6,,PRJNA256209,SAMN02937350,,,,,1,2009,Whole genome sequencing to characterize an important and prevalent foodborne pathogen,2014-09-09T00:00:00Z,,,2016-01-17T15:39:22.432Z,2016-01-17T15:39:22.432Z,,,52.17,CP009086,4678377,Salmonella enterica subsp. enterica serovar Enteritidis,Complete,Salmonella,Canada,,,,,,,,Canada,,environment,,,,,149539,,,,,,,4707,,,25156331,NZ_CP009086.1,4362,,1,Canadian Food Inspection Agency,,Illumina,,Enteritidis,,,,,"Included in the study, passed QC/QA"
426,149539.325,collected_by:staff;isolate:OLF-SE5,,,,GCF_000750455.1,CLC Genomics Workbench v. version 6,,PRJNA256209,SAMN02937351,,,,,1,2008,Whole genome sequencing to characterize an important and prevalent foodborne pathogen,2014-09-09T00:00:00Z,,,2016-01-17T15:39:22.752Z,2016-01-17T15:39:22.752Z,,,52.17,CP009087,4678571,Salmonella enterica subsp. enterica serovar Enteritidis,Complete,Salmonella,Canada,,,,,,,,Canada,,environment,,,,,149539,,,,,,,4700,,,25156331,NZ_CP009087.1,4365,,1,Canadian Food Inspection Agency,,Illumina,,Enteritidis,,,,,"Included in the study, passed QC/QA"
427,149539.326,collected_by:staff;isolate:OLF-SE1,,,,GCF_000750475.1,CLC Genomics Workbench v. version 6,,PRJNA256209,SAMN02937347,,,,,1,2010,Whole genome sequencing to characterize an important and prevalent foodborne pathogen,2014-09-09T00:00:00Z,,,2016-01-17T15:39:23.070Z,2016-01-17T15:39:23.070Z,,,52.17,CP009083,4678914,Salmonella enterica subsp. enterica serovar Enteritidis,Complete,Salmonella,Canada,,,,,,,,Canada,,environment,,,,,149539,,,,,,,4701,,,25156331,NZ_CP009083.1,4367,,1,Canadian Food Inspection Agency,,Illumina,,Enteritidis,,,,,"Included in the study, passed QC/QA"
428,149539.327,collected_by:staff;isolate:OLF-SE6,,,,GCF_000750495.1,CLC Genomics Workbench v. version 6,,PRJNA256209,SAMN02937352,,,,,1,2010,Whole genome sequencing to characterize an important and prevalent foodborne pathogen,2014-09-09T00:00:00Z,,,2016-01-17T15:39:23.451Z,2016-01-17T15:39:23.451Z,,,52.17,CP009088,4677619,Salmonella enterica subsp. enterica serovar Enteritidis,Complete,Salmonella,Canada,,,,,,,,Canada,,environment,,,,,149539,,,,,,,4731,,,25156331,NZ_CP009088.1,4318,,1,Canadian Food Inspection Agency,,454,,Enteritidis,,,,,"Included in the study, passed QC/QA"
429,149539.328,biomaterial_provider:USAMRIID,,,,GCF_000754375.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA244356,SAMN02904629,,,,Bacilli,1,,Salmonella enteridis SEJ Genome Assembly,2014-10-31T00:00:00Z,,,2016-01-17T15:39:55.329Z,2016-01-17T15:39:55.329Z,,,52.17,"CP008928,CP008927",4738299,Salmonella enterica subsp. enterica serovar Enteritidis strain SEJ,Complete,Salmonella,,Negative,,,,,,,,,,,,,,149539,,,,,,,4739,,1,25342692,"NZ_CP008928.1,NZ_CP008927.1",4399,,2,Los Alamos National Laboratory,314x,Illumina,,Enteritidis,,SEJ,,,"Included in the study, passed QC/QA"
430,149539.339,,,,,GCF_001185215.1,SeqMan Pro v. 11.0.0 (172),,PRJNA280705,SAMN03465493,,,,,1,2010-01,Salmonella Enteritidis isolated from a shell egg.,2015-09-23T00:00:00Z,,,2016-01-17T16:41:01.471Z,2016-01-17T16:41:01.471Z,,,52.17,CP011790,4678365,Salmonella enterica subsp. enterica serovar Enteritidis strain SEE1,Complete,Salmonella,USA: Pennsylvania,,HostAssociated,,,,,isolated from a shell egg,United States,,shell egg,,,,,149539,37 C,,,,,Facultative,4699,,,26358589,NZ_CP011790.1,4299,,1,Pennsylvania State University,100,IonTorrent,,Enteritidis,,SEE1,Mesophilic,,"Included in the study, passed QC/QA"
431,149539.34,,,,,GCF_001185245.1,Seqman Pro v. 11.0.0 (172),,PRJNA280707,SAMN03468068,,,,,1,2007,Salmonella enterica Serovar Enteritidis isolated from Egg. This is the second isolate sequenced.,2015-09-23T00:00:00Z,,,2016-01-17T16:41:01.851Z,2016-01-17T16:41:01.851Z,,,52.17,CP011791,4677830,Salmonella enterica subsp. enterica serovar Enteritidis strain SEE2,Complete,Salmonella,USA: Pennsylvania,,HostAssociated,,,,,isolated from Egg,United States,,Egg,,,,,149539,37 C,,,,,Facultative,4700,,,26358589,NZ_CP011791.1,4269,,1,Pennsylvania State University,100,IonTorrent,,Enteritidis,,SEE2,Mesophilic,,"Included in the study, passed QC/QA"
432,149539.369,collected_by:Gyeongbuk Health and Environment Institute,,,,GCA_001305235.1,CLC Genomics Workbench v. 7.0.4; PacBio,,PRJNA262006,SAMN03140319,,,,,1,2014-04-10,Salmonella Enteritidis is one of the well-known food-borne pathogen. It was isolated from the contaminated food in South Korea.,2015-10-01T00:00:00Z,,,2016-01-17T17:13:07.579Z,2016-01-17T17:13:07.579Z,,,52.1,"CP009768,CP009767",4781905,Salmonella enterica subsp. enterica serovar Enteritidis strain FORC_007,Complete,Salmonella,South Korea: Gyeongbuk,,,,,,,isolated from the contaminated food in South Korea,South Korea,,steamed conch,,,,,149539,,,,,,,4847,,1,,"NZ_CP009768.1,NZ_CP009767.1",4522,,2,"Food-borne Pathogen Omics Research Center, FORC",,Illumina; PacBio,,,,FORC_007,,,"Included in the study, passed QC/QA"
433,149539.392,,,,,GCF_001484025.1,,,PRJNA288744,SAMN03837761,,,,,1,,Genome sequencing and assembly,2016-01-04T00:00:00Z,,CMCC:50041,2016-01-31T23:23:16.083Z,2016-01-31T23:23:16.083Z,,,52.17,"CP013097,CP013098",4735702,Salmonella enterica subsp. enterica serovar Enteritidis strain CMCC50041,Complete,Salmonella,Denmark,,,,,,,,Denmark,,,,,MLST.Salmonella_enterica.11,,149539,C,,,,,,4801,,1,,"NZ_CP013097.1,NZ_CP013098.1",4438,,2,Yangzhou University,,,,Enteritidis,,CMCC50041,,,"Included in the study, passed QC/QA"
434,149539.441,collected_by:Canadian Food Inspection Agency,,,,GCF_001647045.1,CLC Genomics Workbench v. version 6; MIRA,,PRJNA274686,SAMN03328998,,,,,1,2000,Whole genome sequencing to characterize an important and prevalent foodborne pathogen,2016-05-18T00:00:00Z,,,2016-07-05T05:10:00.009Z,2016-07-05T05:10:00.009Z,,,52.17,"CP011942,CP011944,CP011945,CP011943",4744327,Salmonella enterica subsp. enterica serovar Enteritidis strain OLF-00D989 87-1,Complete,Salmonella,Canada,,,,,,,,Canada,,Poultry environment,,,MLST.Salmonella_enterica.11,,149539,,,,,,,4807,,3,,"NZ_CP011942.1,NZ_CP011944.1,NZ_CP011945.1,NZ_CP011943.1",4444,,4,Canadian Food Inspection Agency,,Illumina; IonTorrent; Pacific Biosciences,,,,OLF-00D989 87-1,,,"Included in the study, passed QC/QA"
435,149539.858,"collected_by:Ministry of Food and Drug Safety, Republic of Korea",,,,GCA_002220345.1,PacBio SMRT Analysis v. 2.3.0,,PRJNA328055,SAMN05363482,,,,,1,2014-03-02,Complete genome sequene of Salmonella enterica FORC_052,2017-07-17T00:00:00Z,,,2017-09-29T15:34:04.232Z,2017-09-29T15:34:04.232Z,,,52.17,CP016754,4686254,Salmonella enterica subsp. enterica serovar Enteritidis strain FORC_052,Complete,Salmonella,South Korea: Seoul,,,,,,,,South Korea,,Lettuce,,,,,149539,,,,,,,4683,,,,,4548,,1,"Food-borne Pathogen Omics Research Center, FORC",x265.57,PacBio,,enteritidis,,FORC_052,,,"Included in the study, passed QC/QA"
436,149539.883,,,,,GCA_002760915.1,HGAP v. 3.0,,PRJNA354706,SAMN06050726,,,,,1,1956,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:19:08.704Z,2017-11-24T17:19:08.704Z,,,52.17,"CP018635,CP018636",4737486,Salmonella enterica subsp. enterica serovar Enteritidis strain 56-3991,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,,,149539,,,,,,,4912,,1,,,4715,,2,FDA,missing,PacBio,,enteritidis,,56-3991,,,"Included in the study, passed QC/QA"
437,149539.885,,,,,GCA_002760955.1,HGAP v. 3.0,,PRJNA354706,SAMN06050729,,,,,1,1974,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:19:20.490Z,2017-11-24T17:19:20.490Z,,,52.11,"CP018642,CP018643",4816868,Salmonella enterica subsp. enterica serovar Enteritidis strain 74-1357,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,,,149539,,,,,,,4993,,1,,,4805,,2,FDA,missing,PacBio,,enteritidis,,74-1357,,,"Included in the study, passed QC/QA"
438,149539.886,,,,,GCA_002760975.1,HGAP v. 3.0,,PRJNA354706,SAMN06050730,,,,,1,1977,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:19:37.179Z,2017-11-24T17:19:37.179Z,,,52.19,CP018644,4686089,Salmonella enterica subsp. enterica serovar Enteritidis strain 77-2980,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,,,149539,,,,,,,4897,,,,,4635,,1,FDA,missing,PacBio,,enteritidis,,77-2980,,,"Included in the study, passed QC/QA"
439,149539.887,,,,,GCA_002760995.1,HGAP v. 3.0,,PRJNA354706,SAMN06050731,,,,,1,1979,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:19:33.024Z,2017-11-24T17:19:33.024Z,,,52.18,"CP018645,CP018646",4739705,Salmonella enterica subsp. enterica serovar Enteritidis strain 79-2359,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,,,149539,,,,,,,4926,,1,,,4703,,2,FDA,missing,PacBio,,enteritidis,,79-2359,,,"Included in the study, passed QC/QA"
440,149539.888,,,,,GCA_002761015.1,HGAP v. 3.0,,PRJNA354706,SAMN06050732,,,,,1,1981,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:19:28.702Z,2017-11-24T17:19:28.702Z,,,52.25,CP018647,4699764,Salmonella enterica subsp. enterica serovar Enteritidis strain 81-1435,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,,,149539,,,,,,,4859,,,,,4667,,1,FDA,missing,PacBio,,enteritidis,,81-1435,,,"Included in the study, passed QC/QA"
441,149539.889,,,,,GCA_002761035.1,HGAP v. 3.0,,PRJNA354706,SAMN06050735,,,,,1,1981,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:19:50.830Z,2017-11-24T17:19:50.830Z,,,52.04,"CP018655,CP018656",4944010,Salmonella enterica subsp. enterica serovar Enteritidis strain 81-1706,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,MLST.Salmonella_enterica.11,,149539,,,,,,,5235,,1,,,4969,,2,FDA,missing,PacBio,,enteritidis,,81-1706,,,"Included in the study, passed QC/QA"
442,149539.89,,,,,GCA_002761055.1,HGAP v. 3.0,,PRJNA354706,SAMN06050736,,,,,1,1992,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:19:56.375Z,2017-11-24T17:19:56.375Z,,,52.13,"CP018657,CP018658",5028552,Salmonella enterica subsp. enterica serovar Enteritidis strain 92-0392,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,MLST.Salmonella_enterica.19,,149539,,,,,,,5320,,1,,,5082,,2,FDA,missing,PacBio,,enteritidis,,92-0392,,,"Included in the study, passed QC/QA"
443,149539.891,,,,,GCA_002761075.1,HGAP v. 3.0,,PRJNA354706,SAMN06050737,,,,,1,1993,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:20:03.459Z,2017-11-24T17:20:03.459Z,,,52.17,"CP018659,CP018660",4738679,Salmonella enterica subsp. enterica serovar Enteritidis strain 93-0639,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,,,149539,,,,,,,4940,,1,,,4714,,2,FDA,missing,PacBio,,enteritidis,,93-0639,,,"Included in the study, passed QC/QA"
444,149539.892,,,,,GCA_002761095.1,HGAP v. 3.0,,PRJNA354706,SAMN06050738,,,,,1,1995,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:20:08.929Z,2017-11-24T17:20:08.929Z,,,52.1,"CP018661,CP018662,CP018663",4790958,Salmonella enterica subsp. enterica serovar Enteritidis strain 95-0621,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,,,149539,,,,,,,5016,,2,,,4771,,3,FDA,missing,PacBio,,enteritidis,,95-0621,,,"Included in the study, passed QC/QA"
445,149539.893,,,,,GCA_002761115.1,HGAP v. 3.0,,PRJNA354706,SAMN06050725,,,,,1,1949,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:20:12.850Z,2017-11-24T17:20:12.850Z,,,52.2,"CP018633,CP018634",4754716,Salmonella enterica subsp. enterica serovar Enteritidis strain 49-2444,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,,,149539,,,,,,,4967,,1,,,4726,,2,FDA,missing,PacBio,,enteritidis,,49-2444,,,"Included in the study, passed QC/QA"
446,149539.894,,,,,GCA_002761135.1,HGAP v. 3.0,,PRJNA354706,SAMN06050727,,,,,1,1969,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:20:51.756Z,2017-11-24T17:20:51.756Z,,,52.11,"CP018637,CP018638,CP018639",4845989,Salmonella enterica subsp. enterica serovar Enteritidis strain 69-3861,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,,,149539,,,,,,,5096,,2,,,4874,,3,FDA,missing,PacBio,,enteritidis,,69-3861,,,"Included in the study, passed QC/QA"
447,149539.895,,,,,GCA_002761155.1,HGAP v. 3.0,,PRJNA354706,SAMN06050733,,,,,1,1981,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:35:59.375Z,2017-11-24T17:35:59.375Z,,,52.19,"CP018648,CP018649,CP018650",4802885,Salmonella enterica subsp. enterica serovar Enteritidis strain 81-1607,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,,,149539,,,,,,,4995,,2,,,4776,,3,FDA,missing,PacBio,,enteritidis,,81-1607,,,"Included in the study, passed QC/QA"
448,149539.896,,,,,GCA_002763415.1,HGAP v. 3.0,,PRJNA354706,SAMN06050734,,,,,1,1981,Contain whole genome sequencing data of foodborne pathogens recovered between 1940s to 1990s,2017-11-07T00:00:00Z,,,2017-11-24T17:24:24.538Z,2017-11-24T17:24:24.538Z,,,52.03,"CP018651,CP018652,CP018653,CP018654",4991608,Salmonella enterica subsp. enterica serovar Enteritidis strain 81-1705,Complete,Salmonella,USA,,,,,,,,United States,,Human,,,,,149539,,,,,,,5273,,3,,,5022,,4,FDA,missing,PacBio,,enteritidis,,81-1705,,,"Included in the study, passed QC/QA"
449,1710356.3,"collected_by:Animal and Plant Health Agency, UK",,,,GCA_002234475.1,HGAP v. v 1.3,,PRJNA294448,SAMN04160816,,,,,1,1970-07-15,Genome sequence of Salmonella Locarno (serogroup O57; 57:z29;z42),2017-07-27T00:00:00Z,,,2017-09-28T19:33:39.471Z,2017-09-28T19:33:39.471Z,,,52.05,CP022467,4719375,Salmonella enterica subsp. salamae serovar 57:z29:z42,Complete,Salmonella,,,Unknown,,,,,,,,,,,,,1710356,37 C,,,,,Facultative,4773,,,,,4579,,1,Laboratory for Foodborne Zoonoses,80.0x,Illumina; PacBio,,57:z29:z42,,ST114,Mesophilic,,"Included in the study, passed QC/QA"
450,1911681.3,collected_by:FDA,,,,GCA_002777175.1,HGAP v. 3.0,,PRJNA186035,SAMN04992706,,,,,1,2016-04-26,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,2017-11-16T00:00:00Z,,,2017-11-24T17:30:11.140Z,2017-11-24T17:30:11.140Z,,,52.15,CP017719,4765719,Salmonella enterica subsp. enterica serovar Hayindogo strain CFSAN050752,Complete,Salmonella,Mexico,,,,,,,,Mexico,,anaheim pepper,,,MLST.Salmonella_enterica.64,,1911681,,,,,,,4813,,,,,4499,,1,Center for Food Safety and Applied Nutrition,396,PacBio,,Hayindogo,,CFSAN050752,,,"Included in the study, passed QC/QA"
451,209261.6,,,,,GCA_000007545.1,,,PRJNA371,SAMN02604095,,,,Rod,1,," Salmonella enterica subsp. enterica serovar Typhi. This serovar is a human-specific organism that causes the life-threatening illness Typhoid fever which is acquired by coming into contact with contaminated food or water. Annually, 17 million people are infected, with 600,000 fatalities, mostly in developing countries. It contains multiple fimbrial operons that may be used to create extracellular appendages for attachment and entry into host intestinal epithelial cells.  Salmonella enterica subsp. enterica serovar Typhi strain Ty2. This pathogenic strain of Salmonella typhi was isolated in the early 1970s. It contains no multidrug resistance plasmids and has been used for vaccine development.",2003-03-20T00:00:00Z,,,2014-12-08T22:12:52.490Z,2015-03-16T03:17:09.594Z,,Typhoid fever,52.1,AE014613,4791961,Salmonella enterica subsp. enterica serovar Typhi str. Ty2,Complete,Salmonella,,-,Host-associated,,,,,isolated in the early 1970s,,,,,,MLST.Salmonella_enterica.1,Yes,209261,37,Salmonella enterica subsp. enterica serovar Typhi str. Ty2,,,,Facultative,5017,,,12644504,NC_004631,4318,,1,"University of Wisconsin-Madison, USA",,,complete,serovar Typhi,,Ty2,Mesophilic,,"Included in the study, passed QC/QA"
452,216597.6,,,,,GCA_000210855.2,,,PRJNA50407,SAMEA3138382,,,,,1,,-,2010-07-23T00:00:00Z,,,2014-12-08T22:12:52.737Z,2015-03-16T03:17:09.594Z,,,52.18,FQ312003,4878012,Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344,Complete,Salmonella,,,,,,,,,,,,,,,,216597,-,Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344,,,,,5014,,,,"NC_016810.1,NC_017718.1,NC_017719.1,NC_017720.1",4515,,1,The Wellcome Trust Sanger Institute,,,complete,serovar Typhimurium,,,,,"Included in the study, passed QC/QA"
453,218493.5,,,,,GCA_000252995.1,,,PRJNA351,SAMEA3138409,,,,Rod,1,,NCTC 12419 (ATCC 43975; culture collection SGSC:SARC11) is the type strain.,2011-07-06T00:00:00Z,,NCTC 12419,2014-12-08T22:12:46.979Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,52,FR877557,4460105,Salmonella bongori NCTC 12419,Complete,Salmonella,,-,Host-associated,,,,,,,,,,,,Yes,218493,37,Salmonella bongori NCTC 12419,,,,Facultative,4276,,,,NC_015761,3863,,1,Wellcome Trust Sanger Institute,,,complete,,,NCTC 12419; culture collection SGSC:SARC11,Mesophilic,Yes,"Included in the study, passed QC/QA"
454,220341.7,,,,,GCA_000195995.1,,,PRJNA236,SAMEA1705914,,,,Rod,1,1993," Salmonella enterica subsp. enterica serovar Typhi. This serovar is a human-specific organism that causes the life-threatening illness Typhoid fever which is acquired by coming into contact with contaminated food or water. Annually, 17 million people are infected, with 600,000 fatalities, mostly in developing countries. It contains multiple fimbrial operons that may be used to create extracellular appendages for attachment and entry into host intestinal epithelial cells.  Salmonella enterica subsp. enterica serovar Typhi strain CT18. This strain is a multidrug resistant strain of Salmonella typhi. It contains a large number of pseudogenes as compared to related organisms. CT18 also has two plasmids, pHCM1 and pHCM2, which mediate drug resistance and may also encode virulence functions.",2001-10-26T00:00:00Z,,,2014-12-08T22:12:52.348Z,2015-03-16T03:17:09.594Z,,Typhoid fever,51.9,"AL513382,AL513383,AL513384",5027197,Salmonella enterica subsp. enterica serovar Typhi str. CT18,Complete,Salmonella,Vietnam: Mekong Delta region,-,Host-associated,,,,"Human, Homo sapiens",isolated from blood,Vietnam,,isolated from blood,,,MLST.Salmonella_enterica.2,Yes,220341,37,Salmonella enterica subsp. enterica serovar Typhi str. CT18,,,,Facultative,5297,,1,11677608,"NC_003198,NC_003384,NC_003385",4758,,3,Wellcome Trust Sanger Institute,,,complete,serovar Typhi,,CT18,Mesophilic,,"Included in the study, passed QC/QA"
455,224729.9,,,,,GCF_900086565.1,,,PRJEB6403,SAMEA3468845,,,,,1,,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,2016-05-19T00:00:00Z,,,2016-07-06T23:34:19.490Z,2016-07-06T23:34:19.490Z,,,52.21,LT571437,4756780,Salmonella enterica subsp. enterica serovar Java strain NCTC5706,Complete,Salmonella,,,,,,,,,,,,,,MLST.Salmonella_enterica.42,,224729,,,,,,,4748,,,,NZ_LT571437.1,4376,,1,SC,,,,,,NCTC5706,,,"Included in the study, passed QC/QA"
456,28150.13,,,,,GCF_001457675.1,,,PRJEB6403,SAMEA2517359,,,,,1,1964,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,2015-07-08T00:00:00Z,,,2016-01-30T13:23:30.666Z,2016-01-30T13:23:30.666Z,,,52.08,"LN868943,LN868944,LN868945,LN868946",4763085,Salmonella enterica subsp. enterica serovar Senftenberg strain NCTC10384,Complete,Salmonella,,,,,,,"Human, Homo sapiens",,,,faeces,,,MLST.Salmonella_enterica.14,,28150,,,host_health_state:disease,,,,4721,,3,,"NZ_LN868943.1,NZ_LN868944.1,NZ_LN868945.1,NZ_LN868946.1",4342,,4,SC,,,,Senftenberg,,NCTC10384,,,"Included in the study, passed QC/QA"
457,28150.29,,,,,GCF_001969425.1,Celera v. 7.0,,PRJNA337942,SAMN05514141,,,,,1,1941,Comparative analysis of thermotolerance loci found within various Proteobacteria with an emphasis on microbial pathogens associated with food safety.,2017-01-23T00:00:00Z,,ATCC:43845,2017-03-20T06:04:10.005Z,2017-03-20T06:04:10.005Z,,,51.91,"CP016837,CP016838",5262033,Salmonella enterica subsp. enterica serovar Senftenberg strain 775W,Complete,Salmonella,USA: Massachusetts Department of Public Health,,,,,,,,United States,,Chinese egg powder,,,MLST.Salmonella_enterica.185,,28150,,,,,,,5440,,1,,"NZ_CP016837.1,NZ_CP016838.1",4980,,2,USDA-ARS-USMARC,173.43,PacBio RS II C4 P6,,Senftenberg,,775W (ATCC 43845),,,"Included in the study, passed QC/QA"
458,286783.14,collected_by:henan CDC,,,,GCA_002224405.1,GS De Novo Assembler v. DEc-2016,,PRJNA393900,SAMN07344413,,,,,1,2013,"Complete genetic analysis of a Salmonella enterica serovar Indiana isolate accompanying four plasmids with mcr-1, ESBL and other resistance-encoding genes in China",2017-07-24T00:00:00Z,,ATCC:25922,2017-09-29T15:24:24.117Z,2017-09-29T15:24:24.117Z,,,51.68,"CP022450,CP022451,CP022452,CP022453,CP022454",5119391,Salmonella enterica subsp. enterica serovar Indiana strain D90,Complete,Salmonella,China:Henan,,,,,,"Chicken, Gallus gallus",,China,,chicken,,,,,286783,,,,,,,5397,,4,,,5163,,5,China National Center For Food Safety and Risk Assessment,12.0x,PacBio,,serovar Indiana,,D90,,,"Included in the study, passed QC/QA"
459,28901.1015,collected_by:Wang Wei,,,,GCF_001647755.1,RS HGAP Assembly v. 3,,PRJNA320977,SAMN04961653,,,,,1,5-Dec-14,A carbapenem-resistant Salmonella Indiana strain isolated from chicken carcass,2016-05-19T00:00:00Z,,,2016-07-05T07:04:26.742Z,2016-07-05T07:04:26.742Z,,,51.94,"CP015724,CP015725",5001829,Salmonella enterica strain C629,Complete,Salmonella,China,,,,,,,,China,,chicken carcass,,,MLST.Salmonella_enterica.17,,28901,,,,,,,5168,,1,,"NZ_CP015724.1,NZ_CP015725.1",4739,,2,China National Center for Food Safety Risk Assessment,200.0x,PacBio,,,,C629,,,"Included in the study, passed QC/QA"
460,28901.1106,collected_by:National Culture Collection for Pathogens,,,,GCF_001705055.1,CLCbio CLC Genomics Workbench v. 7.5.1;,,PRJNA290698,SAMN03896006,,,,,1,2014,Salmonella enterica is one of the well-known food-borne pathogen. It was isolated from the blood of food-poisoning patient in South Korea.,2016-08-16T00:00:00Z,,,2016-09-11T20:09:02.541Z,2016-09-11T20:09:02.541Z,,,52.17,"CP012396,CP012397",4797690,Salmonella enterica strain FORC_019,Complete,Salmonella,South Korea,,,,,not reported,"Human, Homo sapiens",isolated from the blood of food-poisoning patient in South Korea,South Korea,,blood,,,,,28901,C,,,,,,4870,,1,,"NZ_CP012396.1,NZ_CP012397.1",4568,,2,Food-borne Pathogen Omics Research Center,483.38x,Illumina; PacBio,,,,FORC_019,,,"Included in the study, passed QC/QA"
461,28901.2334,collected_by:Korea Center for Disease Control and Prevention,,,,,SMRT v. 2.3.0,,PRJNA315190,SAMN04550937,,,,,1,2009-12-09,Salmonella is one of the well-known food-borne pathogen. It was isolated from stool of foodborne poisoning patient in South Korea.,2017-04-05T00:00:00Z,,,2017-05-28T07:36:49.282Z,2017-05-28T07:36:49.282Z,,,52.14,"CP015598,CP015599",5037523,Salmonella enterica strain FORC_030,Complete,Salmonella,South Korea: Gangwon,,,,,Not reported,"Human, Homo sapiens",isolated from stool of foodborne poisoning patient in South Korea,South Korea,,stool,,,,,28901,,,,,,,5330,,1,,,4976,,2,Ajou University,119x,PacBio,,,,FORC_030,,,"Included in the study, passed QC/QA"
462,28901.2626,collected_by:FDA CVM,,,,,CA v. 8.2,,PRJNA231221,SAMN06173325,,,,,1,2011,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-06-27T00:00:00Z,,FDA:FDAARGOS_312,2017-07-23T01:15:31.220Z,2017-07-23T01:15:31.220Z,,,52,"CP022062,CP022060,CP022061,CP022063,CP022064,CP022065",5213250,Salmonella enterica strain FDAARGOS_312,Complete,Salmonella,USA:MD,,,Not applicable,Not applicable,Not applicable,,,United States,,Ground turkey,,,,,28901,,,host_description:Not applicable;host_disease_outcome:Not applicable;host_disease_stage:Not applicable;host_health_state:Not applicable,,,,5709,,5,,,5309,,6,US Food and Drug Administration,22.57x,PacBio,,Typhimurium var. 5-,,Not applicable,,,"Included in the study, passed QC/QA"
463,28901.2627,collected_by:FDA CVM,,,,,"SMRT v. 2.3.0, HGAP v. 3.0",,PRJNA231221,SAMN06173326,,,,,1,2011,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-06-27T00:00:00Z,,FDA:FDAARGOS_313,2017-07-23T01:21:03.874Z,2017-07-23T01:21:03.874Z,,,52.11,"CP022069,CP022066,CP022067,CP022068",4944051,Salmonella enterica strain FDAARGOS_313,Complete,Salmonella,USA:MN,,,Not applicable,Not applicable,Not applicable,,,United States,,Ground turkey,,,MLST.Salmonella_enterica.33,,28901,,,host_description:Not applicable;host_disease_outcome:Not applicable;host_disease_stage:Not applicable;host_health_state:Not applicable,,,,5224,,3,,,4963,,4,US Food and Drug Administration,13.0066261912905x,PacBio,,Hadar,,Not applicable,,,"Included in the study, passed QC/QA"
464,28901.2696,,,,,GCA_002234515.1,HGAP v. v. 1.3,,PRJNA354244,SAMN06044996,,,,,1,,This project contains the raw sequencing data for isolates sequenced at the National Microbiology laboratory at Guelph.,2017-07-27T00:00:00Z,,,2017-09-28T19:33:47.632Z,2017-09-28T19:33:47.632Z,,,52.24,CP022489,4796292,Salmonella enterica strain SA20026234,Complete,Salmonella,,,,,,,,,,,,,,,,28901,,,,,,,4987,,,,,4783,,1,Laboratory for Foodborne Zoonoses,80.0x,Illumina MiSeq; PacBio,,,,SA20026234,,,"Included in the study, passed QC/QA"
465,28901.2697,,,,,GCA_002234735.1,HGAP v. v 1.3,,PRJNA354244,SAMN06045033,,,,,1,,This project contains the raw sequencing data for isolates sequenced at the National Microbiology laboratory at Guelph.,2017-07-27T00:00:00Z,,,2017-09-28T19:34:11.419Z,2017-09-28T19:34:11.419Z,,,52.24,"CP022491,CP022492,CP022493",4908724,Salmonella enterica strain SA20031783,Complete,Salmonella,,,,,,,,,,,,,,,,28901,,,,,,,5087,,2,,,4879,,3,Laboratory for Foodborne Zoonoses,70.0x,Illumina MiSeq; PacBio,,,,SA20031783,,,"Included in the study, passed QC/QA"
466,28901.2698,,,,,GCA_002234755.1,HGAP v. v 1.3,,PRJNA354244,SAMN06045055,,,,,1,,This project contains the raw sequencing data for isolates sequenced at the National Microbiology laboratory at Guelph.,2017-07-27T00:00:00Z,,,2017-09-28T19:34:24.074Z,2017-09-28T19:34:24.074Z,,,51.72,"CP022494,CP022495,CP022496",5088787,Salmonella enterica strain SA20035215,Complete,Salmonella,,,,,,,,,,,,,,,,28901,,,,,,,5353,,2,,,5077,,3,Laboratory for Foodborne Zoonoses,90.0x,Illumina MiSeq; PacBio,,,,SA20035215,,,"Included in the study, passed QC/QA"
467,28901.2699,,,,,GCA_002234775.1,HGAP v. v 1.3,,PRJNA354244,SAMN06044997,,,,,1,,This project contains the raw sequencing data for isolates sequenced at the National Microbiology laboratory at Guelph.,2017-07-27T00:00:00Z,,,2017-09-28T19:34:03.475Z,2017-09-28T19:34:03.475Z,,,52.3,CP022490,4734880,Salmonella enterica strain SA20026289,Complete,Salmonella,,,,,,,,,,,,,,,,28901,,,,,,,4862,,,,,4680,,1,Laboratory for Foodborne Zoonoses,90.0x,Illumina MiSeq; PacBio,,,,SA20026289,,,"Included in the study, passed QC/QA"
468,28901.27,,,,,GCA_002234795.1,HGAP v. v 1.3,,PRJNA354244,SAMN06045126,,,,,1,,This project contains the raw sequencing data for isolates sequenced at the National Microbiology laboratory at Guelph.,2017-07-27T00:00:00Z,,,2017-09-28T19:34:07.527Z,2017-09-28T19:34:07.527Z,,,52.29,"CP022497,CP022498,CP022499",4802602,Salmonella enterica strain SA20084699,Complete,Salmonella,,,,,,,,,,,,,,,,28901,,,,,,,4948,,2,,,4778,,3,Laboratory for Foodborne Zoonoses,85.0x,Illumina MiSeq; PacBio,,,,SA20084699,,,"Included in the study, passed QC/QA"
469,28901.2706,collected_by:Samsung Seoul Hospital,,,,GCA_002313085.1,SMRT Analysis v. 2.3.0,,PRJNA342395,SAMN05756207,,,,,1,2016,"As a food-borne pathogen, Salmonella exhibits profound food-poisoning activities with high prevalence, every year. This sample was isolated from the blood of a food-poisoned patient in Seoul, Korea.",2017-09-19T00:00:00Z,,,2017-09-29T01:44:44.172Z,2017-09-29T01:44:44.172Z,,,52.12,"CP017232,CP017233",4776636,Salmonella enterica strain FORC_051,Complete,Salmonella,Korea: Seoul,,,,,Not reported,"Human, Homo sapiens","isolated from the blood of a food-poisoned patient in Seoul, Korea",South Korea,,blood,,,,,28901,,,,,,,4896,,1,,,4902,,2,Seoul National University,134.36x,PacBio,,,,FORC_051,,,"Included in the study, passed QC/QA"
470,28901.2707,collected_by:MFDS,,,,GCA_002313105.1,PacBio SMRT Analysis v. 2.3.0,,PRJNA340047,SAMN05631013,,,,,1,2015-01-27,Salmonella enterica is one of the well-known food-borne pathogen. It was isolated from the a fish sample in South Korea.,2017-09-19T00:00:00Z,,,2017-09-29T01:44:51.724Z,2017-09-29T01:44:51.724Z,,,52.16,"CP017177,CP017178",4745601,Salmonella enterica strain FORC_056,Complete,Salmonella,South Korea: Seoul,,,,,,,isolated from the a fish sample in South Korea,South Korea,,fish,,,,,28901,,,,,,,4785,,1,,,4503,,2,Food-borne Pathogen Omics Research Center,224.62x,PacBio,,,,FORC_056,,,"Included in the study, passed QC/QA"
471,28901.2721,collected_by:ministry of food and drug safety,,,,GCA_002119485.1,CLCbio CLC Genomics Workbench v. 7.5.1;,,PRJNA320341,SAMN04932651,,,,,1,,Salmonella enterica genome sequencing,2017-05-09T00:00:00Z,,,2017-10-24T14:06:38.808Z,2017-10-24T14:06:38.808Z,,,51.92,CP015574,4938076,Salmonella enterica strain FORC_038,Complete,Salmonella,South Korea,,,,,,,,South Korea,,Braised Spicy Chicken,,,,,28901,,,,,,,5017,,,,,4735,,1,Food-borne Pathogen Omics Research,498.01X,Illumina; PacBio,,,,FORC_038,,,"Included in the study, passed QC/QA"
472,28901.2759,collected_by:USDA/ARS,,,,GCA_002741925.1,HGAP v. v.3.0,,PRJNA186035,SAMN04323527,,,,,1,,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,2017-11-02T00:00:00Z,,,2017-11-24T17:10:01.027Z,2017-11-24T17:10:01.027Z,,,52.3,CP024169,4860307,Salmonella enterica strain CFSAN024439,Complete,Salmonella,,,,,,,,,,,,,,,,28901,,,,,,,5011,,,,,4789,,1,Center for Food Safety and Applied Nutrition,100.0x,PacBio,,Tennessee,,CFSAN024439,,,"Included in the study, passed QC/QA"
473,28901.866,collected_by:FDA CFSAN <-- NIST <-- ATCC,,,,GCF_001558355.1,HGAP3 v. Nov 2014,,PRJNA231221,SAMN03996249,,,,,1,1948,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",2016-02-11T00:00:00Z,,FDA:FDAARGOS_94,2016-03-01T19:36:19.515Z,2016-03-01T19:36:19.515Z,,,52.24,"CP014051,CP014050",4951385,Salmonella enterica strain LT2,Complete,Salmonella,USA,,,,,,,,United States,,Wild type strain isolated from a natural source,,,,,28901,,,,,,,5068,,1,,"NZ_CP014051.1,NZ_CP014050.1",4682,,2,US Food and Drug Administration,23.217x,Pacbio,,Typhimurium (S. typhimurium),,CFSAN008157,,,"Included in the study, passed QC/QA"
474,295319.15,,,,,GCA_000011885.1,,,PRJNA13086,SAMN02604316,,,,Rod,1,,"Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. This serovar has a narrow host range and causes a typhoid-like (paratyphoid fever) illness in humans. It is especially prevalent in southern and eastern Asia, and has been associated with some particularly virulent outbreaks. A number of isolates are increasingly antibiotic resistant. This strain is considered wild-type.",2004-11-09T00:00:00Z,,ATCC 9150,2014-12-08T22:12:51.744Z,2015-03-16T03:17:09.594Z,,Paratyphoid fever,52.2,CP000026,4585229,Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150,Complete,Salmonella,,-,Host-associated,,,,,,,,,,,MLST.Salmonella_enterica.85,Yes,295319,37,Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150,,,,Facultative,4679,,,15531882,NC_006511,4093,,1,Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine,,,complete,serovar Paratyphi,,ATCC 9150,Mesophilic,,"Included in the study, passed QC/QA"
475,321314.9,,,,,GCA_000008105.1,,,PRJNA9618,SAMN02603109,,,,Rod,1,," Salmonella enterica subsp. enterica serovar Choleraesuis strain SC-B67. This organism is an extremely invasive serovar that is increasingly becoming resistant to multiple antibiotics such as fluoroquinolones, which severly inhibits the treatment of systemic infections caused by this organism. This strain was isolated from a 58-year old man with sepsis and has been shown to be resistant to ciprofloxacin and ceftriaxone. Mutations in the gyrase and topoisomerase genes appear to be the cause of the ciprofloxacin resistance while the presence of an ampC gene on a transmissable plasmid was responsible for ceftriaxone resistance. This organism also causes severe disease (swine paratyphoid) in pigs.",2005-04-01T00:00:00Z,,,2014-12-08T22:12:48.619Z,2015-03-16T03:17:09.594Z,,Salmonellosis;Swine paratyphoid,52.1,"AY509003,AE017220,AY509004",4944000,Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67,Complete,Salmonella,,-,Host-associated,58,,,"Human, Homo sapiens",isolated from a 58-year old man with sepsis and has been shown to be resistant to ciprofloxacin and ceftriaxone,,,58-year old man with sepsis and has been shown to be resistant to ciprofloxacin and ceftriaxone,,,MLST.Salmonella_enterica.66,Yes,321314,37,Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67,,,,Facultative,5089,,2,"15781495,16257053","NC_006855,NC_006905,NC_006856",4634,,3,Chang Gung Memorial Hospital,,,complete,serovar Choleraesuis,,SC-B67,Mesophilic,,"Included in the study, passed QC/QA"
476,340188.13,"biomaterial_provider:Toshiyuki Murase, Laboratory of Veterinary Microbiology, Tottori University, 4-101 Koyama, Tottori 680-8553, Japan;collected_by:Toshiyuki Murase",,,,GCF_001941405.1,Hierarchical genome assembly process(HGAP),,PRJNA252640,SAMN02910521,,,,,1,2004,Salmonella enterica serovar Cerro 87 SMRT Genome sequencing,2017-01-10T00:00:00Z,,,2017-01-22T10:50:37.058Z,2017-01-22T10:50:37.058Z,,,52.31,CP008925,4602439,Salmonella enterica subsp. enterica serovar Cerro strain serovar Cerro 87,Complete,Salmonella,Japan:west,,,,,,,,Japan,,chicken farm,,,,,340188,,,,,,,4598,,,,NZ_CP008925.1,4526,,1,Wuhan University,195,PacBio,,serovar Cerro,,serovar Cerro 87,,,"Included in the study, passed QC/QA"
477,41514.7,,,,,GCA_000018625.1,,,PRJNA13030,SAMN02604141,,,,Rod,1,1986,"Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- strain RSK2980. This subspecies (IIIa) is usually found associated with reptiles, although contact with infected animals can result in the spread of the organism to humans or animals such as turkeys. This strain was originally isolated from a cornsnake in 1986 in Oregon.",2007-11-21T00:00:00Z,,,2014-12-08T22:12:47.011Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,51.4,CP000880,4600800,"Salmonella enterica subsp. arizonae serovar 62:z4,z23:- strain RSK2980",Complete,Salmonella,Oregon,-,Host-associated,,,,"Cornsnake, Pantherophis guttatus guttatus",isolated from a cornsnake in 1986 in Oregon,United States,,cornsnake,,,,Yes,41514,-,"Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- str. RSK2980",,,,Facultative,4452,,,,NC_010067,4498,,1,Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine,,,complete,serovar 62,,RSK2980,Mesophilic,,"Included in the study, passed QC/QA"
478,423368.8,,,,,GCA_000016045.1,,,PRJNA18747,,,,,Rod,1,,"Salmonella enterica subsp. enterica serovar Newport. Salmonella enterica subsp. enterica serovar Newport is common worldwide. Outbreak investigations and targeted studies have identified dairy cattle as the main reservoir this serotype. Antimicrobial resistance (Newport MDR-AmpC) is particularly problematic in this serotype, and the prevalence of Newport MDR-AmpC isolates from humans in the United States has increased from 0% during 1996-1997 to 26% in 2001. MDR strains have been recorded as resistant to ampicillin, chloramphenicol, streptomycin, sulphonamides and tetracycline (ACSSuT) and many of these strains show intermediate or full resistance to third-generation cephalosporins, kanamycin, potentiated sulphonamides, and gentamicin. Salmonella enterica subsp. enterica serovar Newport str SL254. The SL254 strain is an MDR strain from one of two distinct lineages of the Newport serovar.",2008-07-24T00:00:00Z,,,2014-12-08T22:12:51.562Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,52.2,"CP001113,CP001112,CP000604",5007719,Salmonella enterica subsp. enterica serovar Newport str. SL254,Complete,Salmonella,,-,Multiple,,,,,,,,,,,MLST.Salmonella_enterica.45,Yes,423368,-,Salmonella enterica subsp. enterica serovar Newport str. SL254,,,,Facultative,4921,,2,17375195,"NC_011080,NC_011079,NC_009140",4805,,3,"J. Craig Venter Institute, USA, Rockville|TIGR",,,complete,serovar Newport,,SL254,Mesophilic,,"Included in the study, passed QC/QA"
479,439843.8,,,,,GCA_000020745.1,,,PRJNA19459,SAMN02604064,,,,Rod,1,,"Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633. This serovar is the predominant cause of Salmonellosis in Southeast Asia, a major source of imported food products to the United States. It was also the cause of the first recognized outbreak of fluoroquinolone-resistant salmonellosis in the U.S.. Recent reports suggest that high-level fluoroquinolone resistance is emerging in S. Schwarzengrund in different parts of the world. This serovar is remarkably disposed to nosocomial spread, and presents a unique opportunity to identify factors that facilitate this important type of transmission. MDR strain CVM19633 and susceptible strain DBS_GA_F25499 belong to the S. Schwarzengrund serovar.Sequence was obtained from two libraries - a fosmid library (33-39 kb; 6,718 reads) and a small insert library (4-6 kb; 44,521 reads).",2008-07-30T00:00:00Z,,,2014-12-08T22:12:52.078Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,52.2,"CP001127,CP001126,CP001125",4823887,Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633,Complete,Salmonella,,-,Multiple,,,,,,,,,,,MLST.Salmonella_enterica.322,Yes,439843,-,Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633,,,,Facultative,4798,,2,,"NC_011094,NC_011093,NC_011092",4627,,3,TIGR,,,complete,serovar Schwarzengrund,,CVM19633,Mesophilic,,"Included in the study, passed QC/QA"
480,439851.8,,,,,GCA_000020925.1,,,PRJNA19467,SAMN02604065,,,,Rod,1,,"Salmonella enterica subsp. enterica serovar Dublin str CT_02021853. This is a bovine-adapted serovar that is genetically related to S. Enteritidis that lives in the bovine intestinal tract and can causes disease in humans. While rare in incidence, S. dublin infection classically produces a syndrome of sustained bacteremia with fever, resulting in high morbidity and mortality.Sequence was obtained from two libraries - a fosmid library (33-39 kb; 21,645 reads) and a small insert library (4-6 kb; 29,869 reads).",2008-09-04T00:00:00Z,,,2014-12-08T22:12:48.699Z,2015-03-16T03:17:09.594Z,,Bacteremia;Gastroenteritis,52.1,"CP001144,CP001143",4917459,Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853,Complete,Salmonella,,-,Multiple,,,,,,,,,,,MLST.Salmonella_enterica.10,Yes,439851,-,Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853,,,,Facultative,4898,,1,,"NC_011205,NC_011204",4617,,2,TIGR,,,complete,serovar Dublin,,CT_02021853,Mesophilic,,"Included in the study, passed QC/QA"
481,454166.8,,,,,GCA_000020885.1,,,PRJNA20063,SAMN02604068,,,,Rod,1,,Salmonella enterica subsp. enterica serovar Agona str. SL483. Salmonella enterica subsp. enterica serovar Agona causes gastroenteritis in humans and is also pathogenic to swine and other food animals. This serovar is able to contain the Salmonella genomic island 1 multidrug resistance gene cluster. This strain will be used for comparative analysis with other Salmonella serovars. ,2008-08-22T00:00:00Z,,,2014-12-08T22:12:48.207Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,52,"CP001138,CP001137",4836638,Salmonella enterica subsp. enterica serovar Agona str. SL483,Complete,Salmonella,,-,Multiple,,,,,,,,,,,MLST.Salmonella_enterica.13,Yes,454166,-,Salmonella enterica subsp. enterica serovar Agona str. SL483,,,,Facultative,4756,,1,,"NC_011149,NC_011148",4614,,2,J. Craig Venter Institute,,,complete,serovar Agona,,SL483,Mesophilic,,"Included in the study, passed QC/QA"
482,454169.8,,,,,GCA_000020705.1,,,PRJNA20045,SAMN02604067,,,,Rod,1,,Salmonella enterica subsp. enterica serovar Heidelberg. Salmonella enterica subsp. enterica serovar Heidelberg is one of the more common serovars causing disease in the United States. Salmonella enterica subsp. enterica serovar Heidelberg str. SL476 (CVM30485). This is a multidrug resistant strain and will be used for comparative analysis. ,2008-07-24T00:00:00Z,,,2014-12-08T22:12:50.225Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,52.1,"CP001120,CP001119,CP001118",4983515,Salmonella enterica subsp. enterica serovar Heidelberg str. SL476,Complete,Salmonella,,-,Multiple,,,,,,,,,,,MLST.Salmonella_enterica.15,Yes,454169,-,Salmonella enterica subsp. enterica serovar Heidelberg str. SL476,,,,Facultative,4711,,2,,"NC_011083,NC_011082,NC_011081",4779,,3,J. Craig Venter Institute,,,complete,serovar Heidelberg,,SL476,Mesophilic,,"Included in the study, passed QC/QA"
483,476213.4,,,,,GCA_000018385.1,,,PRJNA20993,,,,,Rod,1,,"Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594. The genome of this strain harbors a large pathogenicity island, SPI7, with genes coding for the Vi (virulence) antigen and other genes potentially associated with virulence. The genome of strain RKS4594, when compared to other S. enterica subsp. enterica serovar Paratyphi C strains, features several insertions, deletions and rearrangements.",2009-03-03T00:00:00Z,,,2014-12-08T22:12:51.893Z,2015-03-16T03:17:09.594Z,,Paratyphoid fever,52.2,"CP000857,CP000858",4888494,Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594,Complete,Salmonella,,-,Host-associated,,,,,,,,,,,MLST.Salmonella_enterica.114,Yes,476213,37,Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594,,,,Facultative,4754,,1,19229335,"NC_012125,NC_012124",4639,,2,Genomics Research Center of Harbin Medical,,,complete,serovar Paratyphi,,RKS4594,Mesophilic,,"Included in the study, passed QC/QA"
484,527001.3,,,,,GCA_000385905.1,,,PRJNA34855,SAMN02603210,,,,,1,,"Salmonella enterica serovar typhi Ty21a.Ty21a is the only licensed attenuated Salmonella typhi vaccine strain in the world. It was derived from the virulent S. typhi strain Ty2 by chemical (NTG) mutagenesis. However, the attenuating mechanisms for its remarkable track record of stability, safety and efficacy remaining undefined. The purpose of our sequence analysis is to define the key attenuating properties of Ty21a.",2013-05-01T00:00:00Z,,,2014-12-08T22:12:52.500Z,2015-03-16T03:17:09.594Z,,,52,CP002099.1,4791958,Salmonella enterica subsp. enterica serovar Typhi str. Ty21a,Complete,Salmonella,,,,,,,,derived from the virulent S. typhi strain Ty2 by chemical (NTG) mutagenesis,,,the virulent S,,,MLST.Salmonella_enterica.1,,527001,,Salmonella enterica subsp. enterica serovar Typhi str. Ty21a,,,,,4967,,,,NC_021176.1,4509,,1,"Division of Bacterial, Parasitic and Allergenic Products, LESTD, FDA-CBER, USA",,,complete,serovar Typhi,,Ty21A,,,"Included in the study, passed QC/QA"
485,54388.102,,,,,GCF_000985155.1,,,PRJEB5654,SAMEA2637240,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:22.153Z,2016-01-17T15:56:22.153Z,,,52.14,CCLE01000000,4568400,Salmonella enterica subsp. enterica serovar Paratyphi A strain 83,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4736,,,,,4208,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,83,,,"Included in the study, passed QC/QA"
486,54388.103,,,,,GCF_000985175.1,,,PRJEB5628,SAMEA2639480,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:22.882Z,2016-01-17T15:56:22.882Z,,,52.16,CCTR01000000,4604167,Salmonella enterica subsp. enterica serovar Paratyphi A strain Banker Type4,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4796,,,,,4245,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,Banker Type4,,,"Included in the study, passed QC/QA"
487,54388.105,,,,,GCF_000985215.1,,,PRJEB5586,SAMEA2639686,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:23.612Z,2016-01-17T15:56:23.612Z,,,51.98,CCLP01000000,4579012,Salmonella enterica subsp. enterica serovar Paratyphi A strain 1K,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4757,,,,,4219,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,1K,,,"Included in the study, passed QC/QA"
488,54388.108,,,,,GCF_000985275.1,,,PRJEB5690,SAMEA2633604,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:24.723Z,2016-01-17T15:56:24.723Z,,,52.1,CCSO01000000,4518368,Salmonella enterica subsp. enterica serovar Paratyphi A strain Reil90,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4679,,,,,4168,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,Reil90,,,"Included in the study, passed QC/QA"
489,54388.111,,,,,GCF_000985335.1,,,PRJEB5562,SAMEA2646069,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:25.791Z,2016-01-17T15:56:25.791Z,,,52.12,CCVC01000000,4582103,Salmonella enterica subsp. enterica serovar Paratyphi A strain 03 7001,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4757,,,,,4215,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,03 7001,,,"Included in the study, passed QC/QA"
490,54388.116,,,,,GCF_000985435.1,,,PRJEB5614,SAMEA2639579,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:28.081Z,2016-01-17T15:56:28.081Z,,,52.15,CCUA01000000,4578638,Salmonella enterica subsp. enterica serovar Paratyphi A strain A63-72,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4739,,,,,4202,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,A63-72,,,"Included in the study, passed QC/QA"
491,54388.123,,,,,GCF_000985575.1,,,PRJEB5551,SAMEA2646092,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:30.428Z,2016-01-17T15:56:30.428Z,,,52.11,CCTF01000000,4569411,Salmonella enterica subsp. enterica serovar Paratyphi A strain 01 1852,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4749,,,,,4209,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,01 1852,,,"Included in the study, passed QC/QA"
492,54388.125,,,,,GCF_000985615.1,,,PRJEB5641,SAMEA2638658,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:31.097Z,2016-01-17T15:56:31.097Z,,,52.13,CCMF01000000,4559770,Salmonella enterica subsp. enterica serovar Paratyphi A strain 138-69,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4747,,,,,4189,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,138-69,,,"Included in the study, passed QC/QA"
493,54388.126,,,,,GCF_000985655.1,,,PRJEB5615,SAMEA2639578,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:31.809Z,2016-01-17T15:56:31.809Z,,,52.14,CCTY01000000,4564863,Salmonella enterica subsp. enterica serovar Paratyphi A strain A63-73,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4745,,,,,4204,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,A63-73,,,"Included in the study, passed QC/QA"
494,54388.128,,,,,GCF_000985695.1,,,PRJEB5624,SAMEA2639572,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:32.542Z,2016-01-17T15:56:32.542Z,,,52.12,CCTV01000000,4573964,Salmonella enterica subsp. enterica serovar Paratyphi A strain Balt8,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4736,,,,,4208,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,Balt8,,,"Included in the study, passed QC/QA"
495,54388.13,,,,,GCF_000983235.1,,,PRJEB5579,SAMEA2639712,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:55:49.269Z,2016-01-17T15:55:49.269Z,,,52.14,CCUS01000000,4578214,Salmonella enterica subsp. enterica serovar Paratyphi A strain 06 2633,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4736,,,,,4215,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,06 2633,,,"Included in the study, passed QC/QA"
496,54388.134,,,,,GCF_000985815.1,,,PRJEB5693,SAMEA2633136,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:34.825Z,2016-01-17T15:56:34.825Z,,,52.12,CCSK01000000,4571481,Salmonella enterica subsp. enterica serovar Paratyphi A strain 99 7863,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4737,,,,,4210,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,99 7863,,,"Included in the study, passed QC/QA"
497,54388.137,"collected_by:The National Center for Medical Culture Collections (Beijing, China).",,,,GCF_001045395.1,Bowtie 2 v. version 2.0.0-beta5,,PRJNA287753,SAMN03786808,,,,,,1955,"S. Paratyphi A CMCC50093 was used as parent strain for constructing an attenuated vaccine candidate in our recent study. To obtain its genetic background, we isolated bacterial genomic DNA and sent for genome re-sequencing by Illumina Solexa system.",2015-07-02T00:00:00Z,1,CMCC:50093,2016-01-17T16:11:24.564Z,2016-01-17T16:11:24.564Z,,,52.14,CP011967,4585229,Salmonella enterica subsp. enterica serovar Paratyphi A strain CMCC50093,Complete,Salmonella,China:Beijing,,,,,Enteric fever,"Human, Homo sapiens",isolated bacterial genomic DNA and sent for genome re-sequencing by Illumina Solexa system,China,,feces,,,,,54388,C,,,,,,4732,,,,,4187,,1,Third Military Medical University,221,Illumina,,Paratyphi A,,CMCC50093,,,"Included in the study, passed QC/QA"
498,54388.139,collected_by:Geroge Washington University,,,,GCA_002386165.1,"SMRT v. 2.3.0, HGAP v. 3",,PRJNA231221,SAMN07312412,,,,,1,01-Aug-2014,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-09-28T00:00:00Z,,FDA:FDAARGOS_368,2017-11-23T02:34:48.079Z,2017-11-23T02:34:48.079Z,,,52.15,CP023508,4588003,Salmonella enterica subsp. enterica serovar Paratyphi A strain FDAARGOS_368 strain Not applicable,Complete,Salmonella,USA:DC,,,31Y,male,,"Human, Homo sapiens",,United States,,blood,,,MLST.Salmonella_enterica.129,,54388,,,,,,,4842,,,,,4586,,1,US Food and Drug Administration,12.68x,PacBio; Illumina,,Paratyphi A,,Not applicable,,,"Included in the study, passed QC/QA"
499,54388.14,,,,,GCF_000983255.1,,,PRJEB5568,SAMEA2646063,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:55:49.639Z,2016-01-17T15:55:49.639Z,,,52.11,CCNZ01000000,4580053,Salmonella enterica subsp. enterica serovar Paratyphi A strain 04 6500,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4737,,,25092320,,4219,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,04 6500,,,"Included in the study, passed QC/QA"
500,54388.24,,,,,GCF_000983485.1,,,PRJEB5567,SAMEA2646064,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:55:53.442Z,2016-01-17T15:55:53.442Z,,,52.14,CCLS01000000,4579999,Salmonella enterica subsp. enterica serovar Paratyphi A strain 04 6031,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4741,,,,,4213,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,04 6031,,,"Included in the study, passed QC/QA"
501,54388.26,,,,,GCF_000983535.1,,,PRJEB5601,SAMEA2639632,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:55:54.139Z,2016-01-17T15:55:54.139Z,,,52.09,CCVL01000000,4574321,Salmonella enterica subsp. enterica serovar Paratyphi A strain 99 10258,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4740,,,,,4205,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,99 10258,,,"Included in the study, passed QC/QA"
502,54388.29,,,,,GCF_000983625.1,,,PRJEB5583,SAMEA2639689,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:55:55.273Z,2016-01-17T15:55:55.273Z,,,52.04,CCUP01000000,4539713,Salmonella enterica subsp. enterica serovar Paratyphi A strain 06 7153,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4709,,,,,4192,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,06 7153,,,"Included in the study, passed QC/QA"
503,54388.34,,,,,GCF_000983755.1,,,PRJEB5581,SAMEA2639691,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:55:57.405Z,2016-01-17T15:55:57.405Z,,,52.13,CCLQ01000000,4575406,Salmonella enterica subsp. enterica serovar Paratyphi A strain 06 5568,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4743,,,,,4199,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,06 5568,,,"Included in the study, passed QC/QA"
504,54388.38,,,,,GCF_000983855.1,,,PRJEB5595,SAMEA2639638,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:55:58.710Z,2016-01-17T15:55:58.710Z,,,52.04,CCUI01000000,4567049,Salmonella enterica subsp. enterica serovar Paratyphi A strain 97 1822,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4737,,,,,4210,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,97 1822,,,"Included in the study, passed QC/QA"
505,54388.39,,,,,GCF_000983875.1,,,PRJEB5648,SAMEA2637246,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:55:59.140Z,2016-01-17T15:55:59.140Z,,,52.14,CCTL01000000,4568888,Salmonella enterica subsp. enterica serovar Paratyphi A strain 40,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4736,,,,,4213,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,40,,,"Included in the study, passed QC/QA"
506,54388.4,,,,,GCF_000983915.1,,,PRJEB5592,SAMEA2639641,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:55:59.872Z,2016-01-17T15:55:59.872Z,,,52.15,CCUJ01000000,4521252,Salmonella enterica subsp. enterica serovar Paratyphi A strain 9-65,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4674,,,,,4145,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,9-65,,,"Included in the study, passed QC/QA"
507,54388.41,,,,,GCF_000983895.1,,,PRJEB5604,SAMEA2639629,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:55:59.490Z,2016-01-17T15:55:59.490Z,,,52.11,CCUH01000000,4531413,Salmonella enterica subsp. enterica serovar Paratyphi A strain A103(ParaA),Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4685,,,,,4151,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,A103(ParaA),,,"Included in the study, passed QC/QA"
508,54388.42,,,,,GCF_000983955.1,,,PRJEB5589,SAMEA2639663,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:00.575Z,2016-01-17T15:56:00.575Z,,,52.16,CCUM01000000,4533276,Salmonella enterica subsp. enterica serovar Paratyphi A strain 6-60,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4691,,,,,4155,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,6-60,,,"Included in the study, passed QC/QA"
509,54388.43,,,,,GCF_000983935.1,,,PRJEB5575,SAMEA2646049,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:00.183Z,2016-01-17T15:56:00.183Z,,,51.89,CCUV01000000,4576138,Salmonella enterica subsp. enterica serovar Paratyphi A strain 05 6792,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4753,,,,,4213,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,05 6792,,,"Excluded from the study, failed QC/QA."
510,54388.46,,,,,GCF_000984025.1,,,PRJEB5656,SAMEA2637239,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:01.629Z,2016-01-17T15:56:01.629Z,,,52.13,CCTI01000000,4609601,Salmonella enterica subsp. enterica serovar Paratyphi A strain A1338,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4797,,,,,4249,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,A1338,,,"Included in the study, passed QC/QA"
511,54388.49,,,,,GCF_000984095.1,,,PRJEB5553,SAMEA2646078,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:03.020Z,2016-01-17T15:56:03.020Z,,,52.13,CCLX01000000,4566060,Salmonella enterica subsp. enterica serovar Paratyphi A strain 01 5766,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4741,,,,,4206,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,01 5766,,,"Included in the study, passed QC/QA"
512,54388.5,,,,,GCA_000818075.1,SOAPdenovo v. 2011.04,,PRJNA255737,SAMN02909989,,,,,1,2003-06-01,"We want to compare the genome of two Salmonella paratyphi A strains. One of these bacteria (named 50973), is more virulent than the other strain (named 50503), which was used in killed-vaccine production in China.",2015-01-14T00:00:00Z,1,,2015-03-12T13:56:41.093Z,2015-03-16T03:17:09.594Z,,,52.15,CP009049.1,4599018,Salmonella enterica subsp. enterica serovar Paratyphi A CMCC 50973,Complete,Salmonella,China:Jiangsu,,,,,,"Human, Homo sapiens",,China,,,,,,,54388,,,,,,,4657,,,-,NZ_CP009049.1,4016,,1,Beijing Institute of Biotechnology,133x,Illumina,,serovar Paratyphi,,50973,,,"Included in the study, passed QC/QA"
513,54388.5,,,,,GCF_000984115.1,,,PRJEB5609,SAMEA2639584,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:03.431Z,2016-01-17T15:56:03.431Z,,,52.11,CCUD01000000,4615665,Salmonella enterica subsp. enterica serovar Paratyphi A strain A61-139,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4801,,,,,4260,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,A61-139,,,"Included in the study, passed QC/QA"
514,54388.56,,,,,GCF_000984235.1,,,PRJEB5610,SAMEA2639583,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:05.401Z,2016-01-17T15:56:05.401Z,,,52.15,CCUB01000000,4493890,Salmonella enterica subsp. enterica serovar Paratyphi A strain A61-149,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4623,,,,,4101,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,A61-149,,,"Included in the study, passed QC/QA"
515,54388.6,,,,,GCA_000818115.1,SOAPdenovo v. 2011.04,,PRJNA261865,SAMN03076563,,,,,1,,"We want to compare the genome of two Salmonella paratyphi A strains. One of these bacteria (named 50973), is more virulent than the other strain (named 50503), which was used in killed-vaccine production in China.",2015-01-14T00:00:00Z,1,,2015-03-12T13:56:41.538Z,2015-03-16T03:17:09.594Z,,,52.12,CP009559.1,4612373,Salmonella enterica subsp. enterica serovar Paratyphi A CMCC 50503,Complete,Salmonella,China:Jiangsu,,,,,,"Human, Homo sapiens",,China,,,,,,,54388,,,,,,,4649,,,-,NZ_CP009559.1,4192,,1,Beijing Institute of Biotechnology,149 fold coverage of the genome,Illumina,,serovar Paratyphi,,CMCC 50503,,,"Included in the study, passed QC/QA"
516,54388.69,,,,,GCF_000984495.1,,,PRJEB5680,SAMEA2633626,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:09.853Z,2016-01-17T15:56:09.853Z,,,52.14,CCST01000000,4565803,Salmonella enterica subsp. enterica serovar Paratyphi A strain C4672,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4742,,,,,4206,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,C4672,,,"Included in the study, passed QC/QA"
517,54388.74,,,,,GCF_000984595.1,,,PRJEB5657,SAMEA2637238,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:11.789Z,2016-01-17T15:56:11.789Z,,,52.13,CCLG01000000,4566803,Salmonella enterica subsp. enterica serovar Paratyphi A strain A1345,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4742,,,,,4209,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,A1345,,,"Included in the study, passed QC/QA"
518,54388.78,,,,,GCF_000984675.1,,,PRJEB5653,SAMEA2637241,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:13.362Z,2016-01-17T15:56:13.362Z,,,52.15,CCTJ01000000,4578697,Salmonella enterica subsp. enterica serovar Paratyphi A strain 68-178,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4743,,,,,4218,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,68-178,,,"Included in the study, passed QC/QA"
519,54388.86,,,,,GCF_000984835.1,,,PRJEB5618,SAMEA2639575,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:16.261Z,2016-01-17T15:56:16.261Z,,,52.14,CCTW01000000,4540006,Salmonella enterica subsp. enterica serovar Paratyphi A strain A73-2,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4696,,,,,4181,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,A73-2,,,"Included in the study, passed QC/QA"
520,54388.87,,,,,GCF_000984855.1,,,PRJEB5564,SAMEA2646067,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:16.682Z,2016-01-17T15:56:16.682Z,,,52.14,CCLU01000000,4578989,Salmonella enterica subsp. enterica serovar Paratyphi A strain 04 0406,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4753,,,,,4220,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,04 0406,,,"Included in the study, passed QC/QA"
521,54388.89,,,,,GCF_000984895.1,,,PRJEB5612,SAMEA2639581,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:17.302Z,2016-01-17T15:56:17.302Z,,,52.18,CCNU01000000,4525118,Salmonella enterica subsp. enterica serovar Paratyphi A strain A61-81,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4662,,,25092320,,4147,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,A61-81,,,"Included in the study, passed QC/QA"
522,54388.9,,,,,GCF_000984915.1,,,PRJEB5598,SAMEA2639635,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:17.954Z,2016-01-17T15:56:17.954Z,,,52.1,CCNV01000000,4559873,Salmonella enterica subsp. enterica serovar Paratyphi A strain 98 9652,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4720,,,,,4202,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,98 9652,,,"Included in the study, passed QC/QA"
523,54388.94,,,,,GCF_000984995.1,,,PRJEB5691,SAMEA2633141,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:19.292Z,2016-01-17T15:56:19.292Z,,,52.12,CCSM01000000,4538993,Salmonella enterica subsp. enterica serovar Paratyphi A strain A5291,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4699,,,,,4161,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,A5291,,,"Included in the study, passed QC/QA"
524,54388.96,,,,,GCF_000985035.1,,,PRJEB5560,SAMEA2646060,,,,,,,Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.,2015-04-25T00:00:00Z,1,,2016-01-17T15:56:20Z,2016-01-17T15:56:20Z,,,52.13,CCLT01000000,4579603,Salmonella enterica subsp. enterica serovar Paratyphi A strain 02 4282,Complete,Salmonella,,,,,,,,,,,,,,,,54388,,,,,,,4750,,,,,4213,,1,UNIVERSITY OF WARWICK,,,,serovar Paratyphi,,02 4282,,,"Included in the study, passed QC/QA"
525,550537.5,,,,,GCA_000009505.1,,,PRJNA30687,SAMEA1705941,,,,Rod,1,,Salmonella enterica subsp. enterica serovar Enteriditis str. P125109. Salmonella enterica subsp. enterica serovar Enteriditis str. P125109 is a virulent phage type 4 strain and will be used for comparative analysis. Ongoing USDA analysis has uncovered a number of SNPs from two phenotypically different strains: Salmonella SNP Resource.,2008-09-25T00:00:00Z,,,2014-12-08T22:12:49.793Z,2015-03-16T03:17:09.594Z,,Salmonellosis,52.2,AM933172,4685848,Salmonella enterica subsp. enterica serovar Enteritidis str. P125109,Complete,Salmonella,,-,Specialized,,,,,,,,,,,MLST.Salmonella_enterica.11,Yes,550537,-,Salmonella enterica subsp. enterica serovar Enteritidis str. P125109,,,,Facultative,4429,,,18583645,NC_011294,4206,,1,Wellcome Trust Sanger Institute,,,complete,serovar Enteritidis,No,P125109,Mesophilic,,"Included in the study, passed QC/QA"
526,550538.5,,,,,GCA_000009525.1,,,PRJNA30689,SAMEA1705927,,,,Rod,1,,"Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91. Salmonella gallinarum is the causative agent of Fowl typhoid, a severe systemic disease of poultry. Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91 will be used for comparative analysis.",2008-09-18T00:00:00Z,,,2014-12-08T22:12:49.881Z,2015-03-16T03:17:09.594Z,,Fowl typhoid,52.2,AM933173,4658697,Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91,Complete,Salmonella,,-,Multiple,,,,,,,,,,,MLST.Salmonella_enterica.331,Yes,550538,-,Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91,,,,Facultative,4711,,,18583645,NC_011274,3965,,1,Wellcome Trust Sanger Institute,,,complete,serovar Gallinarum,No,287/91,Mesophilic,,"Included in the study, passed QC/QA"
527,554290.9,,,,,GCA_000026565.1,,,PRJNA30943,SAMEA1705953,,,,Rod,1,2004,"Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601This strain is a clinical isolate collected from a child with paratyphoid fever in Karachi, Pakistan, 2004 and has been sequenced for comparative genome analysis. ",2008-08-19T00:00:00Z,,,2014-12-08T22:12:51.724Z,2015-03-16T03:17:09.594Z,,Paratyphoid fever,52.2,FM200053,4581797,Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601,Complete,Salmonella,"Karachi, Pakistan",-,Multiple,,,,,"This strain is a clinical isolate collected from a child with paratyphoid fever in Karachi, Pakistan, 2004",Pakistan,,child with paratyphoid fever,,,MLST.Salmonella_enterica.85,Yes,554290,-,Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601,,,,Facultative,4684,,,19159446,NC_011147,4078,,1,Wellcome Trust Sanger Institute,,,complete,serovar Paratyphi,No,AKU_12601,Mesophilic,,"Included in the study, passed QC/QA"
528,568708.3,,,,,GCA_000027025.1,,,PRJNA40625,SAMEA2272777,,,,Rod,1,,"Salmonella enterica subsp. enterica serovar Typhimurium str. D23580.Whereas most non-typhoidal Salmonella (NTS) are associated with gastroenteritis there has been a dramatic increase in reports of NTS-associated invasive disease in Sub-Saharan Africa. Salmonella enterica serovar Typhimurium isolates are responsible for a significant proportion of the reported invasive NTS in this region. Multi locus sequence analysis of invasive S. Typhimurium from Malawi and Kenya identified a dominant type, designated ST313, currently rarely reported outside Africa. Whole genome sequencing of a multiple drug resistant (MDR) ST313 NTS isolate, D23580, identified a distinct prophage repertoire and a composite genetic element encoding MDR genes located on a virulence-associated plasmid. Further, there was evidence of genome degradation, including pseudogene formation and chromosomal  deletions, when compared to other S. Typhimurium genome sequences. Some of this genome degradation involved genes previously implicated in virulence of S. Typhimurium or genes for which the orthologues in S. Typhi are either pseudogenes or are absent. Genome analysis of other epidemic ST313 isolates from Malawi and Kenya provided evidence for micro-evolution and clonal replacement in the field.",2009-10-10T00:00:00Z,,,2014-12-08T22:12:52.628Z,2015-03-16T03:17:09.594Z,,,52.2,FN424405,4879400,Salmonella enterica subsp. enterica serovar Typhimurium str. D23580,Complete,Salmonella,,-,,,,,,,,,,,,MLST.Salmonella_enterica.313,,568708,-,Salmonella enterica subsp. enterica serovar Typhimurium,,,,Facultative,4856,,,19901036,NC_016854.1,4521,,1,Wellcome Trust Sanger Institute,,,complete,serovar Typhimurium,,D23580,Mesophilic,,"Included in the study, passed QC/QA"
529,568709.5,,,,,GCA_000493535.1,,,PRJEB4149,SAMEA2272227,,,,,1,,The genome of Salmonella enterica subsp. enterica serovar Typhimurium str. DT2 has been fully sequenced and annotated.,2013-09-30T00:00:00Z,, ,2014-12-08T22:12:52.651Z,2015-03-16T03:17:09.594Z,,,52.2,HG326213.1,4814801,Salmonella enterica subsp. enterica serovar Typhimurium str. DT2,Complete,Salmonella,,,,,,,,,,,,,,MLST.Salmonella_enterica.128,,568709,,Salmonella enterica subsp. enterica serovar Typhimurium str. DT2,,,,,4810,,,,NC_022544.1,4441,,1,WTSI,,,complete,serovar Typhimurium,,DT2,,,"Included in the study, passed QC/QA"
530,57743.4,,,,,GCF_001409135.1,,,PRJEB1397,SAMEA1904377,,,,,1,,"http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2015-10-20T00:00:00Z,,,2016-01-17T17:38:33.452Z,2016-01-17T17:38:33.452Z,,,52.1,"LN890518,LN890519",5161692,Salmonella enterica subsp. enterica serovar Weltevreden,Complete,Salmonella,,,,,,,,,,,Human Stool,,,,,57743,,,,,,,5265,,1,,"NZ_LN890518.1,NZ_LN890519.1",4818,,2,SC,,,,,,,,,"Included in the study, passed QC/QA"
531,57743.5,,,,,GCA_001409155.1,,,PRJEB1397,SAMEA2336231,,,,,1,,"http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2015-10-20T00:00:00Z,,,2016-01-17T17:38:33.769Z,2016-01-17T17:38:33.769Z,,,52.16,"LN890522,LN890523",4957530,Salmonella enterica subsp. enterica serovar Weltevreden strain 9811262,Complete,Salmonella,,,,,,,,,,,Human Stool,,,,,57743,,,,,,,4939,,1,,"NZ_LN890522.1,NZ_LN890523.1",4548,,2,SC,,,,,,9811262,,,"Included in the study, passed QC/QA"
532,57743.6,,,,,GCA_001409175.1,,,PRJEB1397,SAMEA2336232,,,,,1,,"http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2015-10-20T00:00:00Z,,,2016-01-17T17:38:34.119Z,2016-01-17T17:38:34.119Z,,,52.11,"LN890524,LN890525,LN890526",5099111,Salmonella enterica subsp. enterica serovar Weltevreden strain 99 3134,Complete,Salmonella,,,,,,,,,,,Human Blood,,,,,57743,,,,,,,5188,,2,,"NZ_LN890524.1,NZ_LN890525.1,NZ_LN890526.1",4766,,3,SC,,,,,,99 3134,,,"Included in the study, passed QC/QA"
533,57743.7,,,,,GCF_001409195.1,,,PRJEB1397,SAMEA1904401,,,,,1,,"http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2015-10-20T00:00:00Z,,,2016-01-17T17:38:34.541Z,2016-01-17T17:38:34.541Z,,,52.12,"LN890520,LN890521",5228621,Salmonella enterica subsp. enterica serovar Weltevreden,Complete,Salmonella,,,,,,,,,,,Human Stool,,,,,57743,,,,,,,5312,,1,,"NZ_LN890520.1,NZ_LN890521.1",4860,,2,SC,,,,,,,,,"Included in the study, passed QC/QA"
534,58101.3,"collected_by:Enteric Section, Public Health Ontario Laboratory, Toronto, ON",,,,,HGAP v. v 1.3,,PRJNA316728,SAMN04160804,,,,,1,01-Apr-2004,National Microbiology Laboratory at Guelph (formerly LFZ),2017-06-30T00:00:00Z,,,2017-07-23T03:35:16.916Z,2017-07-23T03:35:16.916Z,,,52.04,CP022138,4812886,Salmonella enterica subsp. enterica serovar Waycross strain SA20041608,Complete,Salmonella,Canada: Ontario: Etobicoke,,,,,,,,Canada,,Stool,,,,,58101,,,,,,,4974,,,,,4775,,1,Laboratory for Foodborne Zoonoses,70.0x,Illumina; PacBio,,Waycross,,SA20041608,,,"Included in the study, passed QC/QA"
535,58712.6,collected_by:Mohamed Fakhr,,,,GCA_001447095.1,CLC genomic workbench v. 7.5,,PRJNA302481,SAMN04274532,,,,,1,2009,Salmonella spp are one of the major food borne pathogen causing a lot of death yearly.,2015-11-20T00:00:00Z,1,,2016-01-17T17:48:59.139Z,2016-01-17T17:48:59.139Z,,,52.23,"CP013226,CP013224,CP013225",4946154,Salmonella enterica subsp. enterica serovar Anatum strain GT-38,Complete,Salmonella,USA: Tulsa,,,,,,,,United States,,ground turkey,,,,,58712,C,,,,,,5055,,1,,"NZ_CP013226.1,NZ_CP013224.1,NZ_CP013225.1",4647,,3,University of Tulsa,121X,"Illumina, Miseq",,,,GT-38,,,"Included in the study, passed QC/QA"
536,58712.7,collected_by:Mohamed Fakhr,,,,GCA_001447115.1,"CLC genomic workbench v. 7.5, 2014",,PRJNA302481,SAMN04274533,,,,,1,2009,Salmonella spp are one of the major food borne pathogen causing a lot of death yearly.,2015-11-20T00:00:00Z,1,,2016-01-17T17:48:59.452Z,2016-01-17T17:48:59.452Z,,,52.32,"CP013222,CP013221,CP013223",4995362,Salmonella enterica subsp. enterica serovar Anatum strain GT-01,Complete,Salmonella,USA: Tulsa,,,,,,,,United States,,ground turkey,,,,,58712,C,,,,,,5101,,1,,"NZ_CP013222.1,NZ_CP013221.1,NZ_CP013223.1",4695,,3,University of Tulsa,121X,"Illumina, Miseq",,,,GT-01,,,"Included in the study, passed QC/QA"
537,588858.6,,,,,GCA_000022165.1,,,PRJNA33067,SAMN02604137,,,,Rod,1,,Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S.This is the substrain of strain LT2 that is most commonly used in laboratory research on this species.This strain will be used for comparative genome analysis.,2009-11-13T00:00:00Z,,,2014-12-08T22:12:52.529Z,2015-03-16T03:17:09.594Z,,,52.2,"CP001363,CP001362",4964097,Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S,Complete,Salmonella,,,Multiple,,,,,,,,,,,MLST.Salmonella_enterica.19,Yes,588858,-,Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S,,,,Facultative,4993,,1,19897643,"NC_016856.1,NC_016855.1",5474,,2,University of Arizona,,,complete,serovar Typhimurium,No,LT2 14028S,Mesophilic,,"Included in the study, passed QC/QA"
538,59201.121,collected_by:FDA,,,,GCF_000772635.1,ARGO-CD v. 2.1,,PRJNA186035,SAMN02678551,,,,,,2010-02-14,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,2014-11-05T00:00:00Z,1,,2016-01-17T15:40:44.119Z,2016-01-17T15:40:44.119Z,,,52.21,JSWT01000000,4694374,Salmonella enterica subsp. enterica strain FCC0146,Complete,Salmonella,USA,,,,,,,,United States,,red pepper,,,,,59201,,,,,,,4678,,,,,4369,,1,Center for Food Safety and Applied Nutrition,89x,ILLUMINA,,Montevideo,,FCC0146,,,"Included in the study, passed QC/QA"
539,59201.158,isolate:YUHS 05-78;collected_by:Mussaret Zaidi,,,,GCF_001006525.1,HGAP2 v. 2.2.0,,PRJNA271539,SAMN03653812,,,,Bacilli,1,2005,Complete genome sequencing of a multidrug-resistant and human-invasive Mexican strain of the emerging ST213 genotype.,2015-05-14T00:00:00Z,,,2016-01-17T16:02:10.089Z,2016-01-17T16:02:10.089Z,,Salmonellosis,51.95,"CP011428,CP011435,CP011434,CP011433,CP011432,CP011430,CP011429,CP011431",5190370,Salmonella enterica subsp. enterica strain YU39,Complete,Salmonella,Mexico: Yucatan,Negative,HostAssociated,eight years,male,Salmonellosis,"Human, Homo sapiens",,Mexico,,blood,,,,Yes,59201,37C,,host_disease_outcome:recovered;host_disease_stage:hepatomegaly and severe thrombocytopenia with hemorrhagic syndrome,,genotype:ST213,Facultative,5313,,7,,"NZ_CP011428.1,NZ_CP011435.1,NZ_CP011434.1,NZ_CP011433.1,NZ_CP011432.1,NZ_CP011430.1,NZ_CP011429.1,NZ_CP011431.1",4916,,8,Centro de Ciencias Genomicas - UNAM,150x,PacBio; 454; Illumina GAIIx,,Typhimurium,,YU39,Mesophilic,,"Included in the study, passed QC/QA"
540,59201.251,,,,,GCF_001700595.1,SOAPdenovo v. 2.04,,PRJNA241066,SAMN02688040,,,,,1,Aug-2002,Complete genome sequence of Salmonella enterica serovar Typhimurium SA972816,2016-08-02T00:00:00Z,,,2016-09-11T18:31:15.261Z,2016-09-11T18:31:15.261Z,,,52.15,"CP007484,CP007488,CP007485,CP007486,CP007487,CP007489",5085029,Salmonella enterica subsp. enterica strain SA972816,Complete,Salmonella,China: Heilongjiang,,,,,,,,China,,"Bovine; diarrhoea, faecal isolate",,,,,59201,,,,,,,5278,,5,,,4820,,6,Genome Center,50,Illumina,,serovar Typhimurium,,SA972816,,,"Included in the study, passed QC/QA"
541,59201.445,collected_by:USDA-FSIS,,,,,HGAP v. v.3.0,,PRJNA242847,SAMN03702839,,,,,1,2012,CDC isolated strains of Salmonella enterica,2017-05-11T00:00:00Z,,,2017-05-29T14:56:01.669Z,2017-05-29T14:56:01.669Z,,,52.17,"CP020825,CP020826",4738764,Salmonella enterica subsp. enterica strain CFSAN033543,Complete,Salmonella,USA:OH,,,,,,,,United States,,product-eggs-raw-whole,,,,,59201,,,,,,,4931,,1,,,4709,,2,FDA,330.0x,PacBio,,Enteritidis,,CFSAN033543,,,"Included in the study, passed QC/QA"
542,59201.446,collected_by:USDA-FSIS,,,,,HGAP v. v.3.0,,PRJNA242847,SAMN03702837,,,,,1,2013,CDC isolated strains of Salmonella enterica,2017-05-11T00:00:00Z,,,2017-05-29T14:56:50.494Z,2017-05-29T14:56:50.494Z,,,52.17,"CP020823,CP020824",4738436,Salmonella enterica subsp. enterica strain CFSAN033541,Complete,Salmonella,USA:PA,,,,,,,,United States,,product-eggs-raw-whites,,,,,59201,,,,,,,4922,,1,,,4710,,2,FDA,380.0x,PacBio,,Enteritidis,,CFSAN033541,,,"Included in the study, passed QC/QA"
543,59201.502,collected_by:YongKwan Kim,,,,,HGAP v. 3,,PRJNA380521,SAMN06646159,,,,,1,02-Aug-2016,Provide an information about genome sequece isolated from wild bird(Ardea cinerea),2017-06-02T00:00:00Z,,,2017-07-22T03:53:41.587Z,2017-07-22T03:53:41.587Z,,,52.03,"CP020922,CP020923,CP020924",5064695,Salmonella enterica subsp. enterica strain 16A242,Complete,Salmonella,South Korea,,,,,,Ardea cinerea,,South Korea,,Jeonju-si,,,MLST.Salmonella_enterica.99,,59201,,,,,,,5238,,2,,,4844,,3,National Institute of Environmental Research,211x,PacBio,,,,Ardea cinerea,,,"Included in the study, passed QC/QA"
544,59201.506,collected_by:Kangwon National University,,,,,HGAP v. 3.0,,PRJNA387390,SAMN06622672,,,,,1,Oct-2000,"The goal of this study was to provide insights into the pathogenesis of Salmonella enterica Typhimurium ST1120, isolated from a swine",2017-06-20T00:00:00Z,,,2017-07-22T22:11:22.470Z,2017-07-22T22:11:22.470Z,,,52.18,"CP021909,CP021910",4861864,Salmonella enterica subsp. enterica strain ST1120,Complete,Salmonella,South Korea: Kangwon-do wonju,,,,,,,,South Korea,,pig feces,,,,,59201,,,,,,,4874,,1,,,4577,,2,Ajou University,205,PacBio,,,,ST1120,,,"Included in the study, passed QC/QA"
545,59201.545,collected_by:Laboratory for Foodborne Zoonoses - Guelph Salmonella Typing Laboratory,,,,GCA_002234855.1,HGAP v. v 1.3,,PRJNA177613,SAMN04160807,,,,Bacilli,1,1995-05-17,Genome sequence of Salmonella Arizonae (serogroup O53; serotype (53:-:-),2017-07-27T00:00:00Z,,,2017-09-28T19:34:19.639Z,2017-09-28T19:34:19.639Z,,,51.45,CP022504,4586333,Salmonella enterica subsp. enterica strain SA20100345,Complete,Salmonella,Canada: Ontario: Guelph,Negative,Unknown,,,,,,Canada,,Unkown,,,,No,59201,37C,,,,,Facultative,4868,,,,,4543,,1,Laboratory for Foodborne Zoonoses,73.0x,Illumina MiSeq; PacBio,,ssp-IIIa O53,,SA20100345,Mesophilic,,"Included in the study, passed QC/QA"
546,59201.547,collected_by:Federal Institute for Risk Assessment,,,,GCA_002238275.1,HGAP v. 3,,PRJNA380613,SAMN06645218,,,,,1,2008,Genome of Salmonella enterica subspecies enterica serovar Paratyphi B dT+ isolate 08-00436 harbouring mcr-1,2017-08-01T00:00:00Z,,,2017-09-29T15:15:37.267Z,2017-09-29T15:15:37.267Z,,,51.96,"CP020492,CP020493,CP020494",5070907,Salmonella enterica subsp. enterica strain 08-00436,Complete,Salmonella,Germany,,,,,,,,Germany,,chicken skin,,,,,59201,,,,,,,5311,,2,,,5071,,3,Federal Institute for Risk Assessment,140,PacBio,,serovar Paratyphi,,08-00436,,,"Included in the study, passed QC/QA"
547,59201.548,collected_by:Federal Institute for Risk Assessment,,,,GCA_002238275.1,HGAP v. 3,,PRJNA380613,SAMN06645218,,,,,1,2008,Genome of Salmonella enterica subspecies enterica serovar Paratyphi B dT+ isolate 08-00436 harbouring mcr-1,2017-08-01T00:00:00Z,,,2017-09-29T21:29:00.399Z,2017-09-29T21:29:00.399Z,,,51.96,"CP020492,CP020493,CP020494",5070907,Salmonella enterica subsp. enterica strain 08-00436,Complete,Salmonella,Germany,,,,,,,,Germany,,chicken skin,,,,,59201,,,,,,,5311,,2,,,5071,,3,Federal Institute for Risk Assessment,140,PacBio,,serovar Paratyphi,,08-00436,,,"Included in the study, passed QC/QA"
548,59201.619,"collected_by:Lisa Gorski, Produce Safety and Microbiology Research Unit, USDA ARS",,,,GCA_002504105.1,HGAP v.3 as available in the SMRT,,PRJNA393473,SAMN07334225,,,,,1,2009-04-29,"To better understand the genomic relationship of Salmonella enterica subsp. enterica strains, we sequenced and assembled the genomes of two serogroup C2 (O:6,8) strains that were isolated from water sources in California.",2017-10-10T00:00:00Z,,,2017-11-23T05:18:34.220Z,2017-11-23T05:18:34.220Z,,,51.96,"CP022663,CP022661,CP022662",5267516,Salmonella enterica subsp. enterica strain RM11065,Complete,Salmonella,"USA:San Benito, California",,,,female,none,Canis latrans,isolated from water sources in California,United States,,feces,,,MLST.Salmonella_enterica.2712,,59201,,,host_description:Coyote,,,,5625,,2,,,5375,,3,USDA ARS,222.0x,PacBio; Illumina MiSeq,,,,RM11065,,,"Included in the study, passed QC/QA"
549,59201.62,"collected_by:Lisa Gorski, Produce Safety and Microbiology Research Unit, USDA ARS",,,,GCA_002504125.1,HGAP v.3 as available in the SMRT,,PRJNA393473,SAMN07334224,,,,,1,2009-03-09,"To better understand the genomic relationship of Salmonella enterica subsp. enterica strains, we sequenced and assembled the genomes of two serogroup C2 (O:6,8) strains that were isolated from water sources in California.",2017-10-10T00:00:00Z,,,2017-11-23T05:18:56.453Z,2017-11-23T05:18:56.453Z,,,52.04,"CP022658,CP022659,CP022660",5253258,Salmonella enterica subsp. enterica strain RM11060,Complete,Salmonella,"USA:King City, California",,,,,,,isolated from water sources in California,United States,,river water,,,MLST.Salmonella_enterica.112,,59201,,,,,,,5589,,2,,,5291,,3,USDA ARS,216.0x,PacBio; Illumina MiSeq,,"C2, O:6,8",,RM11060,,,"Included in the study, passed QC/QA"
550,59204.12,collected_by:University Hospital Erlangen,,,,GCF_001628755.1,BWA-SW 0.7.10-r789; Samtools,,PRJNA276399,SAMN03371466,,,,Bacilli,1,2011-01-31,"With this project the genomic variation of three Salmonella enterica subsp. diarizonae 60:r:z strains isolated from a single patient will be investigated. The genome of the first isolate will be sequenced and assembled using a combination of PacBio and Illumina (MiSeq) sequencing technology, the two subsequent isolates will be sequenced using the Illumina MiSeq only.",2016-04-22T00:00:00Z,,,2016-04-28T18:07:07.304Z,2016-04-28T18:07:07.304Z,,,51.51,CP011288,4779347,Salmonella enterica subsp. diarizonae strain 11-01855,Complete,Salmonella,Germany: Erlangen,Negative,,77 years,male,Salmonella gastroenteritis,"Human, Homo sapiens",isolated from a single patient will be investigated,Germany,,stool,,,,Yes,59204,,,host_disease_outcome:death;host_health_state:advanced rectal cancer,,,,4741,,,,NZ_CP011288.1,4224,,1,Robert Koch-Institut,60x,Illumina MiSeq,,60:r:z,,11-01855,,,"Included in the study, passed QC/QA"
551,59204.13,collected_by:University Hospital Erlangen,,,,GCF_001629755.1,HGAP3; BWA-SW 0.7.10-r789; Samtools,,PRJNA276399,SAMN03371464,,,,Bacilli,,2010-07-06,"With this project the genomic variation of three Salmonella enterica subsp. diarizonae 60:r:z strains isolated from a single patient will be investigated. The genome of the first isolate will be sequenced and assembled using a combination of PacBio and Illumina (MiSeq) sequencing technology, the two subsequent isolates will be sequenced using the Illumina MiSeq only.",2016-04-22T00:00:00Z,1,,2016-04-28T18:22:26.425Z,2016-04-28T18:22:26.425Z,,,51.33,"CP011289,CP011290,CP011291",4869451,Salmonella enterica subsp. diarizonae strain 11-01853,Complete,Salmonella,Germany: Erlangen,Negative,,77 years,male,Salmonella gastroenteritis,"Human, Homo sapiens",isolated from a single patient will be investigated,Germany,,stool,,,,Yes,59204,,,host_disease_outcome:death;host_health_state:advanced rectal cancer,,,,4887,,2,,"NZ_CP011289.1,NZ_CP011290.1,NZ_CP011291.1",4339,,3,Robert Koch-Institut,147x; 37x,PacBio RSII; Illumina MiSeq,,60:r:z,,11-01853,,,"Included in the study, passed QC/QA"
552,59204.14,collected_by:University Hospital Erlangen,,,,GCF_001629775.1,BWA-SW 0.7.10-r789; Samtools,,PRJNA276399,SAMN03371465,,,,Bacilli,,2011-01-27,"With this project the genomic variation of three Salmonella enterica subsp. diarizonae 60:r:z strains isolated from a single patient will be investigated. The genome of the first isolate will be sequenced and assembled using a combination of PacBio and Illumina (MiSeq) sequencing technology, the two subsequent isolates will be sequenced using the Illumina MiSeq only.",2016-04-22T00:00:00Z,1,,2016-04-28T18:22:40.707Z,2016-04-28T18:22:40.707Z,,,51.33,"CP011292,CP011293,CP011294",4869400,Salmonella enterica subsp. diarizonae strain 11-01854,Complete,Salmonella,Germany: Erlangen,Negative,,77 years,male,systemic Salmonella infection,"Human, Homo sapiens",isolated from a single patient will be investigated,Germany,,alloplastic vascular graft,,,,Yes,59204,,,host_disease_outcome:death;host_health_state:advanced rectal cancer,,,,4885,,2,,"NZ_CP011292.1,NZ_CP011293.1,NZ_CP011294.1",4342,,3,Robert Koch-Institut,60x,Illumina MiSeq,,60:r:z,,11-01854,,,"Included in the study, passed QC/QA"
553,59204.19,collected_by:Chen Qiong,,,,GCA_002794415.1,SMRTanalysis v. R2.3.0,,PRJNA406863,SAMN07633032,,,,,1,2016-09,Genomic analysis of Salmonella enterica subsp. diarizonae isolated from pus of a patient with bacterial enteropathy,2017-11-21T00:00:00Z,,,2018-01-01T00:06:53.416Z,2018-01-01T00:06:53.416Z,,,51.36,CP023345,5087369,Salmonella enterica subsp. diarizonae strain HZS154,Complete,Salmonella,China: Hangzhou,,,83,male,bacterial enteropathy,"Human, Homo sapiens",,China,,stool,,,,,59204,,,,,,,5270,,,,,4933,,1,The First Affiliated Hospital College of Medicine Zhejiang University,151.67x,PacBio,,,,HZS154,,,"Included in the study, passed QC/QA"
554,595.18,,,,,GCF_000953495.1,,,PRJEB7580,SAMEA3106395,,,,,1,1973,We have sequenced. assembled and annotated the genome of the bacterial pathogen Salmonella enterica subsp. enterica serovar Infantis strain 1326/28,2015-03-14T00:00:00Z,,,2016-01-17T15:49:04.150Z,2016-01-17T15:49:04.150Z,,,52.29,LN649235,4710675,Salmonella enterica subsp. enterica serovar Infantis strain 1326/28,Complete,Salmonella,United Kingdom,,,,,,"Chicken, Gallus gallus",,United Kingdom,,"Central Veterinary Lab, Weybridge",,,,,595,,,host_health_state:healthy,,,,4708,,,25676749,NZ_LN649235.1,4671,,1,SC,,,,Infantis,,1326/28,,,"Included in the study, passed QC/QA"
555,595.67,collected_by:CDC,,,,GCF_001931615.1,HGAP v. 3.0,,PRJNA242614,SAMN05255999,,,,,1,09-May-2014,The study goal is to look at the phenotype and genotype correlation in Salmonella enterica with different antibiotic resistance patterns.,2017-01-04T00:00:00Z,,,2017-01-24T04:08:21.826Z,2017-01-24T04:08:21.826Z,,,52.15,"CP016412,CP016413",5043245,Salmonella enterica subsp. enterica serovar Infantis strain 2014am-3028,Complete,Salmonella,USA: MA,,,,,,,,United States,,clinical,,,,,595,,,,,,,5172,,1,,"NZ_CP016412.1,NZ_CP016413.1",4755,,2,FDA,275,PacBio,,Infantis,,2014am-3028,,,"Included in the study, passed QC/QA"
556,595.68,collected_by:FDA,,Susceptible;Resistant;Intermediate,AMR Panel,GCF_001931595.1,HGAP v. 3.0,,PRJNA292661,SAMN03988471,,,,,1,2014,Whole genome sequencing of foodborne pathogens as part of the US Food and Drug Administration surveillance project for NARMS.,2017-01-04T00:00:00Z,,,2017-01-24T04:10:06.843Z,2017-01-24T04:10:06.843Z,,,52.15,"CP016410,CP016411",5043928,Salmonella enterica subsp. enterica serovar Infantis strain N55391,Complete,Salmonella,USA: TN,,,,,,,,United States,,chicken breast,,,,,595,C,,,,,,5174,,1,,"NZ_CP016410.1,NZ_CP016411.1",4759,,2,FDA,449,PacBio,,Infantis,,N55391,,,"Included in the study, passed QC/QA"
557,595.69,collected_by:USDA-FSIS,,,,GCF_001931575.1,HGAP v. 3.0,,PRJNA292666,SAMN04364590,,,,,1,2015,Whole genome sequencing of foodborne pathogens as part of the US Department of Agriculture surveillance project for NARMS.,2017-01-04T00:00:00Z,,,2017-01-24T04:16:50.592Z,2017-01-24T04:16:50.592Z,,,52.15,"CP016408,CP016409",5050625,Salmonella enterica subsp. enterica serovar Infantis strain FSIS1502916,Complete,Salmonella,USA: NJ,,,,,,,,United States,,comminuted chicken,,,,,595,C,,,,,,5179,,1,,"NZ_CP016408.1,NZ_CP016409.1",4768,,2,FDA,405,PacBio,,Infantis,,FSIS1502916,,,"Included in the study, passed QC/QA"
558,595.7,collected_by:USDA-FSIS,,,,GCF_001931555.1,HGAP v. 3.0,,PRJNA292666,SAMN04285042,,,,,1,2015,Whole genome sequencing of foodborne pathogens as part of the US Department of Agriculture surveillance project for NARMS.,2017-01-04T00:00:00Z,,,2017-01-24T04:17:59.178Z,2017-01-24T04:17:59.178Z,,,52.15,"CP016406,CP016407",5050248,Salmonella enterica subsp. enterica serovar Infantis strain FSIS1502169,Complete,Salmonella,USA: NC,,,,,,young chicken,,United States,,,,,,,595,C,,,,,,5190,,1,,"NZ_CP016406.1,NZ_CP016407.1",4766,,2,FDA,216,PacBio,,Infantis,,FSIS1502169,,,"Included in the study, passed QC/QA"
559,600.18,,,,,,HGAP v. v. 3.0,,PRJNA186035,SAMN06192066,,,,,1,,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,2017-01-17T00:00:00Z,,ATCC:BAA-1738,2017-05-27T07:10:44.270Z,2017-05-27T07:10:44.270Z,,,52.25,CP019196,4710704,Salmonella enterica subsp. enterica serovar Thompson strain CFSAN000738,Complete,Salmonella,,,,,,,,,,,,,,,,600,,,,,,,4800,,,,,4595,,1,Center for Food Safety and Applied Nutrition,363,PacBio,,Thompson,,CFSAN000738,,,"Included in the study, passed QC/QA"
560,600.8,collected_by:California Department of Public Health,,,,GCF_001305815.1,Roche Newbler v. 2.3; Geneious,,PRJNA292003,SAMN03959817,,,,,1,Mar-1999,"Salmonella enterica subsp. enterica serovar Thompson strains RM1984 (CADPH-99A2334) and RM1986 (CADPH -99A2345) are clinical isolates from 1999, putatively related to an outbreak in California from contaminated cilantro.",2015-10-02T00:00:00Z,,,2016-01-17T17:13:10.858Z,2016-01-17T17:13:10.858Z,,,52.25,CP012513,4708710,Salmonella enterica subsp. enterica serovar Thompson strain RM1984,Complete,Salmonella,USA: California,,,,,Salmonella gastroenteritis,"Human, Homo sapiens",,United States,,stool sample,,,,,600,C,,,,,,4698,,,,NZ_CP012513.1,4372,,1,USDA ARS,252X,Illumina,,Thompson,,RM1984,,,"Included in the study, passed QC/QA"
561,600.9,collected_by:California Department of Public Health,,,,GCF_001305835.1,Roche Newbler v. 2.3; Geneious,,PRJNA292007,SAMN03959818,,,,,1,Mar-1999,"Salmonella enterica subsp. enterica serovar Thompson strains RM1984 (CADPH-99A2334) and RM1986 (CADPH -99A2345) are clinical isolates from 1999, putatively related to an outbreak in California from contaminated cilantro.",2015-10-02T00:00:00Z,,,2016-01-17T17:13:11.162Z,2016-01-17T17:13:11.162Z,,,52.25,CP012514,4701355,Salmonella enterica subsp. enterica serovar Thompson strain RM1986,Complete,Salmonella,USA: California,,,,,Salmonella gastroenteritis,"Human, Homo sapiens",,United States,,stool sample,,,,,600,C,,,,,,4691,,,,NZ_CP012514.1,4368,,1,USDA ARS,418X,Illumina,,Thompson,,RM1986,,,"Included in the study, passed QC/QA"
562,605.11,,,,,GCF_000953595.1,,,PRJEB5986,SAMEA2438684,,,,,1,,"Many bacterial pathogens are specialised, infecting only one, or a few, hosts, and this is often associated with more acute disease presentation. By looking at specific genomes we can see markers of this specialisation, which often reflect a balance between gene acquisition and functional gene loss. Within Salmonella enterica subspecies enterica, a single lineage exists that includes human and animal pathogens adapted to cause infection in different hosts, including S. enterica serovar Enteritidis (multiple hosts), S. Gallinarum and S. Pullorum (birds) and S. Dublin (cattle). This provides an excellent evolutionary context in which differences between these pathogen genomes can be related to host range. Genome sequences were obtained from ~60 isolates selected to represent the known diversity of this lineage. Examination and comparison of the clades within the phylogeny of this lineage revealed signs of host restriction as well as evolutionary events that mark a path to host generalism. We have identified the nature and order of events for both evolutionary trajectories. The impact of functional gene loss was predicted based upon position within metabolic pathways and confirmed with phenotyping assays. In the host adapted clades, loss of particular traits such as tetrathionate reduction and adenosylcobalamin biosynthesis could be related to their role in host infection. The structure of S. Enteritidis is more complex than previously known, as a second clade of S. Enteritidis was revealed that is distinct from those commonly seen to cause disease in humans or animals, and which are more closely related to S. Gallinarum. Isolates from this novel clade were tested in a chick model of infection, and exhibited a reduced colonisation phenotype, which we postulate represents an intermediate stage in pathogen-host adaptation.",2014-11-01T00:00:00Z,,,2016-02-29T18:14:21.541Z,2016-02-29T18:14:21.541Z,,,52.13,LK931482,4620579,Salmonella enterica subsp. enterica serovar Pullorum strain S44987,Complete,Salmonella,,,,,,,,,,,,,,MLST.Salmonella_enterica.2151,,605,,,,,,,4765,,,,,4282,,1,SC,,,,serovar Enteritidis,,S44987,,,"Included in the study, passed QC/QA"
563,611.105,collected_by:University of Guelph - Animal Health Laboratory,,,,GCF_001690055.1,MIRA v. 4.9.3,,PRJNA298211,SAMN05263553,,,,,1,2011,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2016-07-21T00:00:00Z,,,2016-08-26T23:35:25.397Z,2016-08-26T23:35:25.397Z,,,52.06,"CP016514,CP016515,CP016516",4888142,Salmonella enterica subsp. enterica serovar Heidelberg strain 11-004736-1-7,Complete,Salmonella,Canada: Ontario,,Unknown,,,,Bos taurus,,Canada,,Bovine Organ,,,,,611,37 C,,,,,Facultative,4967,,2,,"NZ_CP016514.1,NZ_CP016515.1,NZ_CP016516.1",4616,,3,Laboratory for Foodborne Zoonoses,70x,Illumina MiSeq; PacBio,,Heidelberg,,11-004736-1-7,Mesophilic,,"Included in the study, passed QC/QA"
564,611.108,collected_by:CIPARS,,,,GCF_001690115.1,MIRA v. 4.9.3,,PRJNA298211,SAMN05263513,,,,,1,2009,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2016-07-21T00:00:00Z,,,2016-08-26T23:37:13.972Z,2016-08-26T23:37:13.972Z,,,52.06,"CP016521,CP016522,CP016523,CP016524",4891990,Salmonella enterica subsp. enterica serovar Heidelberg strain SA02DT09004001,Complete,Salmonella,Canada: British Columbia,,Unknown,,,,,,Canada,,Chicken Meat,,,,,611,37 C,,,,,Facultative,4978,,3,,"NZ_CP016521.1,NZ_CP016522.1,NZ_CP016523.1,NZ_CP016524.1",4618,,4,Laboratory for Foodborne Zoonoses,65x,PacBio; Illumina MiSeq,,Heidelberg,,SA02DT09004001,Mesophilic,,"Included in the study, passed QC/QA"
565,611.111,collected_by:CIPARS,,,,GCF_001692515.1,MIRA v. 4.9.3,,PRJNA298211,SAMN05263516,,,,,1,2013-10-18,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2016-07-22T00:00:00Z,,,2016-08-27T01:50:43.313Z,2016-08-27T01:50:43.313Z,,,52.11,"CP016573,CP016574,CP016575",4791396,Salmonella enterica subsp. enterica serovar Heidelberg strain AMR588-04-00435,Complete,Salmonella,Canada: Ontario,,Unknown,,,,,,Canada,,Chicken feces,,,,,611,37 C,,,,,Facultative,4848,,2,,"NZ_CP016573.1,NZ_CP016574.1,NZ_CP016575.1",4504,,3,Laboratory for Foodborne Zoonoses,127x,Illumina HiSeq; PacBio,,Heidelberg,,AMR588-04-00435,Mesophilic,,"Included in the study, passed QC/QA"
566,611.112,collected_by:hospital,,,,GCF_001692535.1,MIRA v. 4.9.5_2,,PRJNA305824,SAMN04334642,,,,,1,2013-11,"This study was conducted to evaluate whole-genome sequencing and phylogenetic analysis as an alternative to conventional pulsed-field gel electrophoresis subtyping for Salmonella enterica serovar Heidelberg isolates. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013 and 2014) supported by strong epidemiological evidence, as well as 13 sporadic isolates (2008-2012) were sequenced.",2016-07-22T00:00:00Z,,,2016-08-27T01:52:02.021Z,2016-08-27T01:52:02.021Z,,,52.1,"CP016579,CP016580",4788026,Salmonella enterica subsp. enterica serovar Heidelberg strain SH13-006,Complete,Salmonella,Canada: Quebec,,,,,Salmonella gastroenteritis,"Human, Homo sapiens",,Canada,,Human,,,,,611,C,,,,,,4846,,1,,"NZ_CP016579.1,NZ_CP016580.1",4507,,2,Laboratoire de sante publique du Quebec,143x,Illumina HiSeq; PacBio,,Heidelberg,,SH13-006,,,"Included in the study, passed QC/QA"
567,611.114,collected_by:CIPARS,,,,GCF_001692575.1,MIRA v. 4.9.3,,PRJNA298211,SAMN05263515,,,,,1,2013-09-09,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2016-07-22T00:00:00Z,,,2016-08-27T01:53:25.375Z,2016-08-27T01:53:25.375Z,,,52.06,"CP016569,CP016570,CP016571,CP016572",4890688,Salmonella enterica subsp. enterica serovar Heidelberg strain AMR588-04-00320,Complete,Salmonella,Canada: Ontario,,Unknown,,,,,,Canada,,Chicken feces,,,,,611,37 C,,,,,Facultative,4971,,3,,"NZ_CP016569.1,NZ_CP016570.1,NZ_CP016571.1,NZ_CP016572.1",4618,,4,Laboratory for Foodborne Zoonoses,125x,Illumina HiSeq; PacBio,,Heidelberg,,AMR588-04-00320,Mesophilic,,"Included in the study, passed QC/QA"
568,611.116,collected_by:CIPARS,,,,GCF_001692615.1,MIRA v. 4.9.3,,PRJNA298211,SAMN05263517,,,,,1,2013-10-18,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2016-07-22T00:00:00Z,,,2016-08-27T01:54:11.573Z,2016-08-27T01:54:11.573Z,,,52.11,"CP016576,CP016577,CP016578",4791397,Salmonella enterica subsp. enterica serovar Heidelberg strain AMR588-04-00437,Complete,Salmonella,Canada: Ontario,,Unknown,,,,,,Canada,,Chicken feces,,,,,611,37 C,,,,,Facultative,4852,,2,,"NZ_CP016576.1,NZ_CP016577.1,NZ_CP016578.1",4508,,3,Laboratory for Foodborne Zoonoses,130x,PacBio; Illumina HiSeq,,Heidelberg,,AMR588-04-00437,Mesophilic,,"Included in the study, passed QC/QA"
569,611.119,collected_by:hospital,,,,GCF_001689935.1,MIRA v. 4.9.3,,PRJNA305824,SAMN04334633,,,,,1,2012-05,"This study was conducted to evaluate whole-genome sequencing and phylogenetic analysis as an alternative to conventional pulsed-field gel electrophoresis subtyping for Salmonella enterica serovar Heidelberg isolates. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013 and 2014) supported by strong epidemiological evidence, as well as 13 sporadic isolates (2008-2012) were sequenced.",2016-07-21T00:00:00Z,,,2016-09-11T15:28:59.666Z,2016-09-11T15:28:59.666Z,,,52.11,"CP016504,CP016505,CP016506",4791235,Salmonella enterica subsp. enterica serovar Heidelberg strain SH12-007,Complete,Salmonella,Canada: Quebec,,,,,Salmonella gastroenteritis,"Human, Homo sapiens",,Canada,,Human,,,,,611,C,,,,,,4850,,2,,"NZ_CP016504.1,NZ_CP016505.1,NZ_CP016506.1",4508,,3,Laboratoire de sante publique du Quebec,61x,Illumina HiSeq; Illumina MiSeq,,Heidelberg,,SH12-007,,,"Included in the study, passed QC/QA"
570,611.12,collected_by:hospital,,,,GCF_001690005.1,MIRA v. 4.9.3,,PRJNA305824,SAMN04334629,,,,,1,2012-05,"This study was conducted to evaluate whole-genome sequencing and phylogenetic analysis as an alternative to conventional pulsed-field gel electrophoresis subtyping for Salmonella enterica serovar Heidelberg isolates. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013 and 2014) supported by strong epidemiological evidence, as well as 13 sporadic isolates (2008-2012) were sequenced.",2016-07-21T00:00:00Z,,,2016-09-11T15:28:50.826Z,2016-09-11T15:28:50.826Z,,,52.11,"CP016507,CP016508,CP016509",4791235,Salmonella enterica subsp. enterica serovar Heidelberg strain SH12-003,Complete,Salmonella,Canada: Quebec,,,,,Salmonella gastroenteritis,"Human, Homo sapiens",,Canada,,Human,,,,,611,C,,,,,,4843,,2,,"NZ_CP016507.1,NZ_CP016508.1,NZ_CP016509.1",4505,,3,Laboratoire de sante publique du Quebec,75x,Illumina MiSeq; Illumina HiSeq,,Heidelberg,,SH12-003,,,"Included in the study, passed QC/QA"
571,611.121,collected_by:ministe_re de l'Agriculture des Pe_cheries et de l'Alimentation du Que_bec,,,,GCF_001690035.1,MIRA v. 4.9.5_2,,PRJNA305824,SAMN04334672,,,,,1,2014-08,"This study was conducted to evaluate whole-genome sequencing and phylogenetic analysis as an alternative to conventional pulsed-field gel electrophoresis subtyping for Salmonella enterica serovar Heidelberg isolates. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013 and 2014) supported by strong epidemiological evidence, as well as 13 sporadic isolates (2008-2012) were sequenced.",2016-07-21T00:00:00Z,,,2016-09-11T15:31:28.845Z,2016-09-11T15:31:28.845Z,,,52.1,"CP016510,CP016511,CP016512,CP016513",4793963,Salmonella enterica subsp. enterica serovar Heidelberg strain SH14-028,Complete,Salmonella,Canada: Quebec,,,,,,,,Canada,,Food,,,,,611,C,,,,,,4847,,3,,"NZ_CP016510.1,NZ_CP016511.1,NZ_CP016512.1,NZ_CP016513.1",4512,,4,Laboratoire de sante publique du Quebec,123x,PacBio; Illumina HiSeq,,Heidelberg,,SH14-028,,,"Included in the study, passed QC/QA"
572,611.122,collected_by:CNET,,,,GCF_001690075.1,MIRA v. 4.9.3,,PRJNA298211,SAMN05263538,,,,,1,2011,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2016-07-21T00:00:00Z,,,2016-09-11T15:32:20.041Z,2016-09-11T15:32:20.041Z,,,52.06,"CP016517,CP016518,CP016519,CP016520",4888003,Salmonella enterica subsp. enterica serovar Heidelberg strain CE-R2-11-0435,Complete,Salmonella,Canada: Ontario,,Unknown,,,,,,Canada,,Chicken Meat,,,,,611,37 C,,,,,Facultative,4970,,3,,"NZ_CP016517.1,NZ_CP016518.1,NZ_CP016519.1,NZ_CP016520.1",4607,,4,Laboratory for Foodborne Zoonoses,66x,Illumina HiSeq; PacBio,,Heidelberg,,CE-R2-11-0435,Mesophilic,,"Included in the study, passed QC/QA"
573,611.123,collected_by:CIPARS,,,,GCF_001690095.1,MIRA v. 4.9.3,,PRJNA298211,SAMN05263504,,,,,1,2009,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2016-07-21T00:00:00Z,,,2016-09-11T15:32:11.990Z,2016-09-11T15:32:11.990Z,,,52.07,"CP016530,CP016531,CP016532,CP016533",4885371,Salmonella enterica subsp. enterica serovar Heidelberg strain SA01AB09084001,Complete,Salmonella,Canada,,Unknown,,,,,,Canada,,Chicken Cecal Content,,,,,611,37 C,,,,,Facultative,4973,,3,,"NZ_CP016530.1,NZ_CP016531.1,NZ_CP016532.1,NZ_CP016533.1",4609,,4,Laboratory for Foodborne Zoonoses,61x,PacBio; Illumina MiSeq,,Heidelberg,,SA01AB09084001,Mesophilic,,"Included in the study, passed QC/QA"
574,611.124,collected_by:University of Guelph - Animal Health Laboratory,,,,GCF_001690135.1,MIRA v. 4.9.3,,PRJNA298211,SAMN05263546,,,,,1,2009,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2016-07-21T00:00:00Z,,,2016-09-11T15:31:16.005Z,2016-09-11T15:31:16.005Z,,,51.82,"CP016525,CP016526,CP016527,CP016528,CP016529",5062479,Salmonella enterica subsp. enterica serovar Heidelberg strain 09-036813-1A,Complete,Salmonella,Canada: Ontario,,Unknown,,,,Equus ferus caballus,,Canada,,Equine Body Fluid/Excretion,,,,,611,37 C,,,,,Facultative,5191,,4,,"NZ_CP016525.1,NZ_CP016526.1,NZ_CP016527.1,NZ_CP016528.1,NZ_CP016529.1",4796,,5,Laboratory for Foodborne Zoonoses,34x,Illumina MiSeq,,Heidelberg,,09-036813-1A,Mesophilic,,"Included in the study, passed QC/QA"
575,611.125,collected_by:BCPHMRL,,,,GCF_001692495.1,MIRA v. 4.9.3,,PRJNA298211,SAMN05277890,,,,,1,2003,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2016-07-22T00:00:00Z,,,2016-09-11T16:11:21.462Z,2016-09-11T16:11:21.462Z,,,52.11,"CP016563,CP016564",4788924,Salmonella enterica subsp. enterica serovar Heidelberg strain A3EZ223,Complete,Salmonella,Canada: British Columbia,,Unknown,,,,"Human, Homo sapiens",,Canada,,human,,,,,611,37 C,,,,,Facultative,4853,,1,,"NZ_CP016563.1,NZ_CP016564.1",4505,,2,Laboratory for Foodborne Zoonoses,63x,PacBio; Illumina MiSeq,,Heidelberg,,A3EZ223,Mesophilic,,"Included in the study, passed QC/QA"
576,611.126,collected_by:BCPHMRL,,,,GCF_001692555.1,MIRA v. 4.9.3,,PRJNA298211,SAMN05277889,,,,,1,2003,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2016-07-22T00:00:00Z,,,2016-09-11T16:12:54.827Z,2016-09-11T16:12:54.827Z,,,52.11,"CP016561,CP016562",4788923,Salmonella enterica subsp. enterica serovar Heidelberg strain A3ES40,Complete,Salmonella,Canada: British Columbia,,Unknown,,,,,,Canada,,food,,,,,611,37 C,,,,,Facultative,4850,,1,,"NZ_CP016561.1,NZ_CP016562.1",4504,,2,Laboratory for Foodborne Zoonoses,52x,PacBio; Illumina MiSeq,,Heidelberg,,A3ES40,Mesophilic,,"Included in the study, passed QC/QA"
577,611.127,collected_by:CIPARS,,,,GCF_001692595.1,MIRA v. 4.9.3,,PRJNA298211,SAMN05263514,,,,,,2013-09-09,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2016-07-22T00:00:00Z,1,,2016-09-11T16:13:33.698Z,2016-09-11T16:13:33.698Z,,,52.06,"CP016565,CP016566,CP016567,CP016568",4890403,Salmonella enterica subsp. enterica serovar Heidelberg strain AMR588-04-00318,Complete,Salmonella,Canada: Ontario,,Unknown,,,,,,Canada,,Chicken feces,,,,,611,37 C,,,,,Facultative,4969,,3,,"NZ_CP016565.1,NZ_CP016566.1,NZ_CP016567.1,NZ_CP016568.1",4616,,4,Laboratory for Foodborne Zoonoses,127x,Illumina HiSeq; PacBio,,Heidelberg,,AMR588-04-00318,Mesophilic,,"Included in the study, passed QC/QA"
578,611.128,collected_by:hospital,,,,GCF_001692635.1,MIRA v. 4.9.3,,PRJNA305824,SAMN04334640,,,,,1,2013-11,"This study was conducted to evaluate whole-genome sequencing and phylogenetic analysis as an alternative to conventional pulsed-field gel electrophoresis subtyping for Salmonella enterica serovar Heidelberg isolates. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013 and 2014) supported by strong epidemiological evidence, as well as 13 sporadic isolates (2008-2012) were sequenced.",2016-07-22T00:00:00Z,,,2016-09-11T16:14:05.893Z,2016-09-11T16:14:05.893Z,,,52.1,"CP016586,CP016587",4788027,Salmonella enterica subsp. enterica serovar Heidelberg strain SH13-004,Complete,Salmonella,Canada: Quebec,,,,,Salmonella gastroenteritis,"Human, Homo sapiens",,Canada,,Human,,,,,611,C,,,,,,4850,,1,,"NZ_CP016586.1,NZ_CP016587.1",4507,,2,Laboratoire de sante publique du Quebec,143x,Illumina HiSeq; PacBio,,Heidelberg,,SH13-004,,,"Included in the study, passed QC/QA"
579,611.129,collected_by:hospital,,,,GCF_001692655.1,MIRA v. 4.9.3,,PRJNA305824,SAMN04334653,,,,,1,2014-08,"This study was conducted to evaluate whole-genome sequencing and phylogenetic analysis as an alternative to conventional pulsed-field gel electrophoresis subtyping for Salmonella enterica serovar Heidelberg isolates. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013 and 2014) supported by strong epidemiological evidence, as well as 13 sporadic isolates (2008-2012) were sequenced.",2016-07-22T00:00:00Z,,,2016-09-11T16:14:25.546Z,2016-09-11T16:14:25.546Z,,,52.09,"CP016581,CP016582,CP016583,CP016584,CP016585",4893437,Salmonella enterica subsp. enterica serovar Heidelberg strain SH14-009,Complete,Salmonella,Canada: Quebec,,,,,Salmonella gastroenteritis,"Human, Homo sapiens",,Canada,,Human,,,,,611,C,,,,,,4982,,4,,"NZ_CP016581.1,NZ_CP016582.1,NZ_CP016583.1,NZ_CP016584.1,NZ_CP016585.1",4620,,5,Laboratoire de sante publique du Quebec,61x,Illumina HiSeq; PacBio,,Heidelberg,,SH14-009,,,"Included in the study, passed QC/QA"
580,611.64,collected_by:Laboratory for Foodborne Zoonoses,,,,GCA_001441205.1,MIRA v. 4.9.3,,PRJNA298211,SAMN04156749,,,,,1,2010,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2015-11-09T00:00:00Z,,,2016-01-17T17:47:30.798Z,2016-01-17T17:47:30.798Z,,,52.06,"CP012921,CP012922,CP012923",4888155,Salmonella enterica subsp. enterica serovar Heidelberg strain SA02DT10168701,Complete,Salmonella,Canada: Quebec,,Unknown,,,,,,Canada,,chicken meat,,,,,611,37 C,,,,,Facultative,4965,,2,,"NZ_CP012921.1,NZ_CP012922.1,NZ_CP012923.1",4588,,3,Laboratory for Foodborne Zoonoses,85.0x,Illumina MiSeq; PacBio,,Heidelberg,,SA02DT10168701,Mesophilic,,"Included in the study, passed QC/QA"
581,611.65,collected_by:CIPARS,,,,GCA_001441225.1,MIRA v. 4.9.3,,PRJNA298211,SAMN04156727,,,,,1,2012,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2015-11-09T00:00:00Z,,,2016-01-17T17:47:31.190Z,2016-01-17T17:47:31.190Z,,,52.05,"CP012924,CP012925,CP012927,CP012926,CP012928,CP012929",4992458,Salmonella enterica subsp. enterica serovar Heidelberg strain 12-4374,Complete,Salmonella,Canada: Quebec,,Unknown,,,Salmonella gastroenteretis,"Human, Homo sapiens",,Canada,,human stool,,,,,611,37 C,,,,,Facultative,5098,,5,,"NZ_CP012924.1,NZ_CP012925.1,NZ_CP012927.1,NZ_CP012926.1,NZ_CP012928.1,NZ_CP012929.1",4719,,6,Laboratory for Foodborne Zoonoses,133.0x,Illumina MiSeq; PacBio,,Heidelberg,,12-4374,Mesophilic,,"Included in the study, passed QC/QA"
582,611.66,collected_by:CIPARS,,,,GCA_001441245.1,MIRA v. 4.9.3,,PRJNA298211,SAMN04156715,,,,,1,2012-01,Develop molecular sub typing scheme based on whole genome sequencing data of Salmonella Heidelberg,2015-11-09T00:00:00Z,,,2016-01-17T17:47:31.499Z,2016-01-17T17:47:31.499Z,,,51.86,"CP012930,CP012932,CP012931,CP012933,CP012934,CP012935,CP012936",5157495,Salmonella enterica subsp. enterica serovar Heidelberg strain N13-01290,Complete,Salmonella,Canada: Quebec,,Unknown,,,,,,Canada,,turkey meat,,,,,611,37 C,,,,,Facultative,5302,,6,,"NZ_CP012930.1,NZ_CP012932.1,NZ_CP012931.1,NZ_CP012933.1,NZ_CP012934.1,NZ_CP012935.1,NZ_CP012936.1",4889,,7,Laboratory for Foodborne Zoonoses,70.0x,Illumina MiSeq; PacBio,,Heidelberg,,N13-01290,Mesophilic,,"Included in the study, passed QC/QA"
583,70803.13,collected_by:FDA,,,,,HGAP v. 3.0,,PRJNA186035,SAMN02800603,,,,,1,2014-05-12,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,2017-06-15T00:00:00Z,,,2017-07-22T19:23:47.552Z,2017-07-22T19:23:47.552Z,,,52.24,"CP017720,CP017721,CP017722",5004825,Salmonella enterica subsp. enterica serovar Minnesota strain CFSAN017963,Complete,Salmonella,USA:TX,,,,,,,,United States,,mangoes,,,,,70803,,,,,,,5148,,2,,,4747,,3,Center for Food Safety and Applied Nutrition,135,PacBio,,Minnesota,,CFSAN017963,,,"Included in the study, passed QC/QA"
584,718274.8,,,,,GCA_000283735.1,,,PRJNA45951,,,,,Rod,1,2000,Salmonella enterica subsp. enterica serovar Typhimurium str. T000240. This strain was isolated in Japan in 2000. It is of definitive phage type 12 (DT12) and resistant against mulitple antimicrobials including fluoroquinolones.,2010-11-29T00:00:00Z,,,2014-12-08T22:12:52.910Z,2015-03-16T03:17:09.594Z,,Gastroenteritis;Food poisoning,52.25,"AP011957,AP011958,AP011959",5069994,Salmonella enterica subsp. enterica serovar Typhimurium str. T000240,Complete,Salmonella,Japan,-,Multiple,,,,,isolated in Japan in 2000,Japan,,,,,MLST.Salmonella_enterica.19,Yes,718274,-,Salmonella enterica subsp. enterica serovar Typhimurium str. T000240,,,,Facultative,5071,,2,,"NC_016860.1,NC_016861.1,NC_016862.1",4871,,3,National Institute of Technology and Evaluation|National Institute of Infectious Diseases,,,complete,serovar Typhimurium,No,T000240,Mesophilic,,"Included in the study, passed QC/QA"
585,85569.7,,,,,GCA_000493675.1,,,PRJEB1666,,,,,,2,,Generation of a high-quality finished reference sequence of Salmonella enterica subsp. enterica serovar Typhimurium Definitive Type (DT) 104 for use in a comparative study of DT104 isolates from humans and other animals.,2013-09-21T00:00:00Z,, ,2014-12-08T22:12:52.641Z,2015-03-16T03:17:09.594Z,,,52.1187,"HF937208.1,HF937209.1",5027665,Salmonella enterica subsp. enterica serovar Typhimurium str. DT104,Complete,Salmonella,,,,,,,,,,,,,,,,85569,,Salmonella enterica subsp. enterica serovar Typhimurium str. DT104,,,,,5106,,,24030491,"NC_022569.1,NC_022570.1",4656,,2,WTSI,,,complete,serovar Typhimurium,,DT104,,,"Included in the study, passed QC/QA"
586,866913.3,,,,,GCA_000430165.1,SMRT Analysis v. 1.3.3,,PRJNA50689,SAMN02212496,,,,,1,,Salmonella is an important foodborne pathogen.,2013-07-16T00:00:00Z,,,2014-12-08T22:12:47.032Z,2015-03-16T03:17:09.594Z,,,52.2,CP006602.1,4822189,"Salmonella enterica subsp. enterica serovar 4,[5],12:i:- str. 08-1736",Complete,Salmonella,,,,,,,,,,,,,,,,866913,,"Salmonella enterica subsp. enterica serovar 4,[5],12:i:- str. 08-1736",,,,,4815,,,,NC_021820.1,4489,,1,FDA,80X,PacBio RS,complete,4,,08-1736,,,"Included in the study, passed QC/QA"
587,877468.3,,,,,GCA_000442415.1,Celera v. 7.0,,PRJNA51643,SAMN02297856,,,,,1,2005,This serovar is an important foodborne pathogen that causes disease in humans and cattle. Isolates are frequently observed to be resistant to multiple antimicrobial agents.  This strain will be used for comparative analysis.,2013-07-31T00:00:00Z,,,2014-12-08T22:12:51.583Z,2015-03-16T03:17:09.594Z,,,52.1,CP006631.1,4915960,Salmonella enterica subsp. enterica serovar Newport str. USMARC-S3124.1,Complete,Salmonella,USA: BIFSCo Region 2,,,,,,Bos taurus,,United States,,,,,MLST.Salmonella_enterica.45,,877468,,Salmonella enterica subsp. enterica serovar Newport str. USMARC-S3124.1,,,,,4947,,,,NC_021902.1,4828,,1,USMARC-ARS-USDA,complete : 22X coverage : reads >= 5000,454 Titanium : PacBio C2 Long Read,complete,Newport,,USMARC-S3124.1,,,"Included in the study, passed QC/QA"
588,90105.102,collected_by:Ye Htut Zwe,,,,GCA_002290205.1,Celera Assembler v. v1,,PRJNA401082,SAMN07594151,,,,,1,2016,The chromosome and plasmid sequences of a pathogen that can cause foodborne illness.,2017-09-12T00:00:00Z,,,2017-09-28T22:02:53.771Z,2017-09-28T22:02:53.771Z,,,51.96,"CP023166,CP023167",5046426,Salmonella enterica subsp. enterica serovar Saintpaul strain SGB23,Complete,Salmonella,Singapore,,,,,,,,Singapore,,Wet market,,,,,90105,,,,,,,5240,,1,,,5038,,2,Nanyang Technological University,90.4x,PacBio,,Saintpaul,,SGB23,,,"Included in the study, passed QC/QA"
589,90105.125,collected_by:Geroge Washington University,,,,GCA_002386325.1,"SMRT v. 2.3.0, HGAP v. 3",,PRJNA231221,SAMN07312417,,,,,1,01-Jul-2014,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-09-28T00:00:00Z,,FDA:FDAARGOS_373,2017-11-23T02:36:11.785Z,2017-11-23T02:36:11.785Z,,,52.17,CP023512,4838098,Salmonella enterica subsp. enterica serovar Saintpaul strain FDAARGOS_373 strain Not applicable,Complete,Salmonella,USA:DC,,,,,,"Human, Homo sapiens",,United States,,clinical isolate,,,,,90105,,,,,,,5025,,,,,4818,,1,US Food and Drug Administration,11.58x,PacBio; Illumina,,Saintpaul,,Not applicable,,,"Included in the study, passed QC/QA"
590,90105.85,collected_by:CA,,,,,HGAP v. v. 3.0,,PRJNA186035,SAMN05915913,,,,,1,2/15/2013,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,2017-01-18T00:00:00Z,,,2017-05-27T07:22:03.974Z,2017-05-27T07:22:03.974Z,,,52.17,"CP019204,CP019205",4858999,Salmonella enterica subsp. enterica serovar Saintpaul strain CFSAN004173,Complete,Salmonella,USA:CA,,,,,,"Human, Homo sapiens",,United States,,stool,,,,,90105,,,,,,,4999,,1,,,4773,,2,Center for Food Safety and Applied Nutrition,157,PacBio,,Saintpaul,,CFSAN004173,,,"Included in the study, passed QC/QA"
591,90105.86,collected_by:CA,,,,,HGAP v. v. 3.0,,PRJNA186035,SAMN05915912,,,,,1,2/25/2013,Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses,2017-01-18T00:00:00Z,,,2017-05-27T07:27:48.281Z,2017-05-27T07:27:48.281Z,,,52.17,"CP019206,CP019207",4859001,Salmonella enterica subsp. enterica serovar Saintpaul strain CFSAN004174,Complete,Salmonella,USA:CA,,,,,,"Human, Homo sapiens",,United States,,stool,,,,,90105,,,,,,,5006,,1,,,4774,,2,Center for Food Safety and Applied Nutrition,140,PacBio,,Saintpaul,,CFSAN004174,,,"Included in the study, passed QC/QA"
592,90370.2206,,,,,,,,PRJEB21155,SAMEA104109193,,,,,1,2017,Outbreak of Ceftriaxone resistant H58 Salmonella Typhi in Pakistan,2017-06-03T00:00:00Z,,,2017-07-27T23:11:01.971Z,2017-07-27T23:11:01.971Z,,,52.04,"LT882486,LT882487",4812943,Salmonella enterica subsp. enterica serovar Typhi strain BL60006,Complete,Salmonella,,,,,,,"Human, Homo sapiens",,,,blood,,,,,90370,,,host_health_state:diseased,,,,5028,,1,,,,,2,WTSI,,,,Typhi,,BL60006,,,"Included in the study, passed QC/QA"
593,90370.2249,,,,,,,,PRJEB5919,SAMEA2564026,,,,,1,,"http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2017-08-04T00:00:00Z,,,2017-09-29T15:12:40.747Z,2017-09-29T15:12:40.747Z,,,51.84,"LT905060,LT905061",5008887,Salmonella enterica subsp. enterica serovar Typhi strain ISP_03_07467_SGB110-sc-1979083,Complete,Salmonella,,,,,,,,,,,,,,,,90370,,,,,,,5311,,1,,,,,2,SC,,,,,,ISP_03_07467_SGB110-sc-1979083,,,"Included in the study, passed QC/QA"
594,90370.225,,,,,GCA_900205255.1,,,PRJEB5919,SAMEA3109638,,,,,1,,"http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2017-08-04T00:00:00Z,,,2017-09-29T15:12:38.033Z,2017-09-29T15:12:38.033Z,,,52.05,LT905064,4765638,Salmonella enterica subsp. enterica serovar Typhi strain 1554-sc-2165329,Complete,Salmonella,,,,,,,,,,,,,,,,90370,,,,,,,4982,,,,,,,1,SC,,,,,,1554-sc-2165329,,,"Included in the study, passed QC/QA"
595,90370.2251,,,,,GCA_900205265.1,,,PRJEB5919,SAMEA2564024,,,,,1,,"http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2017-08-04T00:00:00Z,,,2017-09-29T15:12:43.210Z,2017-09-29T15:12:43.210Z,,,52.05,LT905063,4795199,Salmonella enterica subsp. enterica serovar Typhi strain lupe_GEN0059-sc-1979081,Complete,Salmonella,,,,,,,,,,,,,,,,90370,,,,,,,5025,,,,,,,1,SC,,,,,,lupe_GEN0059-sc-1979081,,,"Included in the study, passed QC/QA"
596,90370.2252,,,,,GCA_900205275.1,,,PRJEB5919,SAMEA2564027,,,,,1,,"http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2017-08-04T00:00:00Z,,,2017-09-29T15:12:45.137Z,2017-09-29T15:12:45.137Z,,,52.19,LT905062,4676595,Salmonella enterica subsp. enterica serovar Typhi strain 403Ty-sc-1979084,Complete,Salmonella,,,,,,,,,,,,,,,,90370,,,,,,,4893,,,,,,,1,SC,,,,,,403Ty-sc-1979084,,,"Included in the study, passed QC/QA"
597,90370.2253,,,,,GCA_900205295.1,,,PRJEB5919,SAMEA2467787,,,,,1,,"http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2017-08-04T00:00:00Z,,,2017-09-29T15:13:22.033Z,2017-09-29T15:13:22.033Z,,,52.18,LT905143,4618754,Salmonella enterica subsp. enterica serovar Typhi strain E98_3139-sc-1927833,Complete,Salmonella,,,,,,,,,,,,,,,,90370,,,,,,,4764,,,,,,,1,SC,,,,,,E98_3139-sc-1927833,,,"Included in the study, passed QC/QA"
598,90370.929,collected_by:Institute for Research in Molecular Medicine (INFORMM),,,,GCA_001302605.1,Celera Assembler v. HGAP.2,,PRJNA286155,SAMN03765654,,,,,1,Apr-2013,Genome sequencing of Salmonella enterica subsp. enterica serovar Typhi str. PM016/13,2015-11-24T00:00:00Z,,,2016-01-17T17:12:24.255Z,2016-01-17T17:12:24.255Z,,,52.03,CP012091,4793553,Salmonella enterica subsp. enterica serovar Typhi strain PM016/13,Complete,Salmonella,Malaysia: Kelantan,,,,,Typhoid fever,"Human, Homo sapiens",,Malaysia,,Well water,,,,,90370,C,,,,,,5073,,,26564032,NZ_CP012091.1,4460,,1,Universiti Sains Malaysia,256.0x,PacBio,,Typhi,,PM016/13,,,"Included in the study, passed QC/QA"
599,90370.93,collected_by:Kelantan Health Department,,,,GCA_001302625.1,Celera Assembler v. HGAP.2,,PRJNA286162,SAMN03765689,,,,,1,Apr-2013,Genome sequencing of Salmonella enterica subsp. enterica serovar Typhi str. B/SF/13/03/195,2015-09-29T00:00:00Z,,,2016-01-17T17:12:24.621Z,2016-01-17T17:12:24.621Z,,,52.03,CP012151,4798993,Salmonella enterica subsp. enterica serovar Typhi strain B/SF/13/03/195,Complete,Salmonella,Malaysia: Kelantan,,,,,Typhoid fever,"Human, Homo sapiens",,Malaysia,,carrier foodhandler,,,,,90370,C,,,,,,5141,,,,,4352,,1,Universiti Sains Malaysia,184.0x,PacBio,,Typhi,,B/SF/13/03/195,,,"Included in the study, passed QC/QA"
600,90371.1185,collected_by:Mussaret Zaidi,,,,GCF_001576255.1,HGAP2 v. 2.3.0.139497,,PRJNA288151,SAMN03795199,,,,,1,2000,Complete genome sequencing of a Salmonella Typhimurium strain of the ST19 genotype harboring the chromosomal Salmonella genomic island (SGI-1) and the Salmonella virulence plasmid (pSTV),2016-02-26T00:00:00Z,,,2016-03-18T08:53:14.644Z,2016-03-18T08:53:14.644Z,,,52.13,"CP014358,CP014359",5027649,Salmonella enterica subsp. enterica serovar Typhimurium strain YU15,Complete,Salmonella,Mexico:Yucatan,,,,,diarrhoea,"Human, Homo sapiens",,Mexico,,stool,,,MLST.Salmonella_enterica.19,,90371,C,,host_disease_outcome:recovered,,genotype:ST19,,5118,,1,,"NZ_CP014358.1,NZ_CP014359.1",4725,,2,"Instituto de Biotecnologia, UNAM",181x,PacBio RS,,Typhimurium,,YU15,,,"Included in the study, passed QC/QA"
601,90371.1186,collected_by:Mussaret Zaidi,,,,GCF_001576275.1,HGAP2 v. 2.3.0.139497,,PRJNA288330,SAMN03798428,,,,,1,2002,Complete genome sequencing of a Salmonella Typhimurium strain of the ST302 genotype harboring the Salmonella virulence plasmid (pSTV),2016-02-26T00:00:00Z,,,2016-03-18T08:55:51.553Z,2016-03-18T08:55:51.553Z,,,52.19,"CP014356,CP014357",5010007,Salmonella enterica subsp. enterica serovar Typhimurium strain SO2,Complete,Salmonella,Mexico:Sonora,,,five years,,asymptomatic,"Human, Homo sapiens",,Mexico,,stool,,,,,90371,C,,,,genotype:ST302,,5105,,1,,"NZ_CP014356.1,NZ_CP014357.1",4690,,2,"Instituto de Biotecnologia, UNAM",175x,PacBio RS,,Typhimurium,,SO2,,,"Included in the study, passed QC/QA"
602,90371.1187,collected_by:Mussaret Zaidi,,,,GCF_001577505.1,HGAP2 v. 2.3.0.139497,,PRJNA304181,SAMN04296382,,,,,1,2002,Complete genome sequence of Salmonella enterica serovar Typhimurium ST302 strain SO3 isolated from a baby with meningitis in Mexico.,2016-02-26T00:00:00Z,,,2016-03-18T09:20:49.519Z,2016-03-18T09:20:49.519Z,,,52.19,"CP014536,CP014537",5006803,Salmonella enterica subsp. enterica serovar Typhimurium strain SOHS 02-68,Complete,Salmonella,Mexico:Sonora,,,1 month,male,Meningitis,"Human, Homo sapiens",isolated from a baby with meningitis in Mexico,Mexico,,Cerebrospinal fluid,,,,,90371,C,,host_disease_outcome:Death,,genotype:ST302,,5076,,1,,"NZ_CP014536.1,NZ_CP014537.1",4685,,2,"Instituto de Biotecnologia, UNAM",missing,PacBio RS and Illumina HiSeq,,Typhimurium,,SOHS 02-68,,,"Included in the study, passed QC/QA"
603,90371.1188,sample_type:Cell culture,,,,GCA_001587055.1,Velvet v. 1.2.07,,PRJNA227206,SAMN03448627,,,,,,15-Aug-2008,"We performed transcriptome abundance analysis of Salmonella Typhimurium strain SL1344 swap which has been genetically engineered to express the hns open-reading frame from the stpA promoter and the stpA open reading frame from the hns promoter. This strain is designated SL1344(swap). Transcript abundance was compared with that of wild-type SL1344. This comparison was performed to determine the effect of chromosome location of the expression of two related global regulators and how alterations to their expression patterns would impact on their regulons. Overall design: Three independent RNA samples were harvested from wild-type SL1344 and SL1344(swap) grown to exponential phase (OD600nm = 0.3) and hybridized to a microarray containing multiple probes for each of the SL1344 open reading frames. Please note that the original raw data file for the 'SL1344_wildtype_BR2' sample is unavailable, however, the 'wildtype SL1344 BR2.gpr' contains the raw data missing only the header information.",2016-03-11T00:00:00Z,1,,2016-03-18T15:13:42.746Z,2016-03-18T15:13:42.746Z,,,51.82,CP011233,4882689,Salmonella enterica subsp. enterica serovar Typhimurium strain SL1344RX,Complete,Salmonella,Ireland,,,,,,Bos taurus,,Ireland,,Lab Strain,,,MLST.Salmonella_enterica.19,,90371,,,,,,,4960,,,26631971,,4576,,1,"Department of Microbiology, Moyne Institute of Preventive Medicine",225X,Illumina,,,,SL1344RX,,,"Excluded from the study, failed QC/QA."
604,90371.1871,collected_by:Colorado Department of Health,,,,GCA_001617585.1,Newbler v. 2.3,,PRJNA245324,SAMN04038553,,,,,1,2009,"To better understand the genomic relationship of Salmonella enterica subsp. enterica serovar Typhimurium, we sequenced and analyzed the whole genome shotgun assemblies of strains that were isolated across the United States.",2016-04-08T00:00:00Z,,,2016-04-28T09:37:49.123Z,2016-04-28T09:37:49.123Z,,,52.11,"CP012985,CP014577",5052184,Salmonella enterica subsp. enterica serovar Typhimurium strain RM9437,Complete,Salmonella,USA: Colorado,,,,,,Bos taurus,isolated across the United States,United States,,ground beef,,,MLST.Salmonella_enterica.19,,90371,,,,,,,5183,,1,,"NZ_CP012985.1,NZ_CP014577.1",4687,,2,USDA ARS,>100x,454; Illumina,,Typhimurium,,RM9437,,,"Included in the study, passed QC/QA"
605,90371.1922,"collected_by:Department of Microbiology, North Carolina State University",,,,GCF_001705365.1,"HGAP v. 3/SMRT Analysis v. 2.2, MIRA v.",,PRJNA317167,SAMN04600271,,,,,1,15-Jun-2004,"The NC983 isolate is a construct of ATCC 14028s, where the Fumarate Nitrate Reductase gene (fnr) has been inactivated by the insertion of transposon Tn10. The Fnr mutant was then treated with fusaric acid to eliminate the transposon. Thus, the NC983 isolate is tetracycline sensitive and FNR negative.",2016-08-16T00:00:00Z,,ATCC 14028s,2016-09-11T20:16:00.339Z,2016-09-11T20:16:00.339Z,,,52.22,"CP015157,CP015158",4940133,Salmonella enterica subsp. enterica serovar Typhimurium strain NC983,Complete,Salmonella,USA: North Carolina State University: Microbiology Research Laboratory,,,,,,,,United States,,A laboratory derivative of ATCC 14028s,,,,,90371,,,,,,,5064,,1,,"NZ_CP015157.1,NZ_CP015158.1",4679,,2,North Carolina State University,"298x (PB), 19x (IT)","PacBio, Ion Torrent",,Typhimurium,,NC983,,,"Included in the study, passed QC/QA"
606,90371.194,collected_by:Bruce McCollister,,,,GCF_001729225.1,Geneious de novo v. 6.7.1,,PRJNA327740,SAMN05356919,,,,,1,2013,patient samples from an invasive infection,2016-09-16T00:00:00Z,,,2016-11-16T10:13:56.928Z,2016-11-16T10:13:56.928Z,,,52.05,"CP016385,CP016386,CP016387,CP016388,CP016389,CP016390",5172494,Salmonella enterica subsp. enterica serovar Typhimurium strain ST931R,Complete,Salmonella,USA:Colorado,,,,,Sepsis due to Salmonella,"Human, Homo sapiens",,United States,,blood culture,,,,,90371,,,,,,,5365,,5,,"NZ_CP016385.1,NZ_CP016386.1,NZ_CP016387.1,NZ_CP016388.1,NZ_CP016389.1,NZ_CP016390.1",4937,,6,University of Colroado Anschutz Medical Campus,61x,Illumina MiSeq,,Typhimurium,,ST931R,,,"Included in the study, passed QC/QA"
607,90371.2024,sample_type:field sample,,,,GCA_001886995.1,Newbler assembler software v. version 2.6;,,PRJNA344760,SAMN05832834,,,,,1,2007,To carry out genome sequencing of Salmonella isolates from wild birds,2016-11-28T00:00:00Z,,,2017-01-16T05:44:26.714Z,2017-01-16T05:44:26.714Z,,,52.2,"CP017617,CP017618,CP017619",4912568,Salmonella enterica subsp. enterica serovar Typhimurium strain 22495,Complete,Salmonella,Canada,,,,,,gull,,Canada,,,,,,,90371,,,,,,,5201,,2,,"NZ_CP017617.1,NZ_CP017618.1,NZ_CP017619.1",4696,,3,Canadian Food Inspection Agency,missing,454; Illumina,,Typhimurium,,22495,,,"Included in the study, passed QC/QA"
608,90371.2025,sample_type:field sample,,,,GCF_001887015.1,Newbler v. version 2.6; CLC Genomics,,PRJNA344760,SAMN05832872,,,,,1,2007,To carry out genome sequencing of Salmonella isolates from wild birds,2016-11-28T00:00:00Z,,,2017-01-16T05:46:36.580Z,2017-01-16T05:46:36.580Z,,,52.14,"CP017621,CP017620",4900559,Salmonella enterica subsp. enterica serovar Typhimurium strain 22792,Complete,Salmonella,Canada,,,,,,cormorant,,Canada,,,,,,,90371,,,,,,,5084,,1,,"NZ_CP017621.1,NZ_CP017620.1",4639,,2,Canadian Food Inspection Agency,missing,454; Illumina,,Typhimurium,,22792,,,"Included in the study, passed QC/QA"
609,90371.2026,collected_by:USDA,,,,GCF_001922185.1,Newbler v. v2.3,,PRJNA245322,SAMN04125698,,,,,1,26-Jan-2010,"To better understand the genomic relationship of Salmonella enterica subsp. enterica serovar Typhimurium isolates, we sequenced and analyzed the whole genome shotgun assemblies of isolates that were isolated across the United States.",2016-12-27T00:00:00Z,,,2017-01-17T18:57:08.604Z,2017-01-17T18:57:08.604Z,,,52.15,CP013702,4856460,Salmonella enterica subsp. enterica serovar Typhimurium strain RM10961,Complete,Salmonella,USA:California,,,,,,,isolated across the United States,United States,,Gabilan Creek water,,,,,90371,,,,,,,4900,,,,NZ_CP013702.1,4720,,1,USDA ARS,>100x,454,,Typhimurium,,RM10961,,,"Included in the study, passed QC/QA"
610,90371.2143,collected_by:The Clinical Laboratory of the first people's Hospital of Foshan,,,,GCF_001989635.1,HGAP v. 2.0,,PRJNA358799,SAMN06185755,,,,,1,15-Aug-2015,study on the mechanism of antibiotic resistance of this strain,2017-02-07T00:00:00Z,,,2017-03-20T07:34:13.251Z,2017-03-20T07:34:13.251Z,,,51.86,"CP019442,CP019443,CP019444",5293223,Salmonella enterica subsp. enterica serovar Typhimurium strain 81741,Complete,Salmonella,China:Guangdong,,,,,diarrhea,"Human, Homo sapiens",,China,,stool,,,,,90371,,,,,,,5614,,2,,"NZ_CP019442.1,NZ_CP019443.1,NZ_CP019444.1",5336,,3,The forth affiliated hospital of Guangzhou medical university,134.09,PacBio,,Typhimurium,,81741,,,"Included in the study, passed QC/QA"
611,90371.2145,collected_by:California Dept. Fish and Game,,,,GCF_002009155.1,Newbler v. v2.3,,PRJNA294303,SAMN04125827,,,,,1,08-Mar-2009,"To better understand the genomic relationship of Salmonella enterica subsp. enterica serovar Typhimurium isolates, we sequenced and analyzed the whole genome shotgun assemblies of isolates that were isolated across the United States.",2017-03-02T00:00:00Z,,,2017-03-20T08:32:34.267Z,2017-03-20T08:32:34.267Z,,,52.17,"CP013720,CP013721",4983631,Salmonella enterica subsp. enterica serovar Typhimurium strain RM10607,Complete,Salmonella,USA:California,,,,,,,isolated across the United States,United States,,White-crowned sparrow,,,MLST.Salmonella_enterica.19,,90371,C,,,,,,5117,,1,,"NZ_CP013720.1,NZ_CP013721.1",5012,,2,USDA ARS,>100x,454,,Typhimurium,,RM10607,,,"Included in the study, passed QC/QA"
612,90371.2552,collected_by:FDA CVM < CDC,,,,,CA v. 8.2,,PRJNA231221,SAMN06173334,,,,,1,2012,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-06-27T00:00:00Z,,FDA:FDAARGOS_321,2017-07-23T01:23:00.977Z,2017-07-23T01:23:00.977Z,,,52.14,"CP022070,CP022071,CP022072",5020124,Salmonella enterica subsp. enterica serovar Typhimurium strain FDAARGOS_321,Complete,Salmonella,,,,,,,"Human, Homo sapiens",,,,Stool,,,MLST.Salmonella_enterica.19,,90371,,,,,,,5462,,2,,,5077,,3,US Food and Drug Administration,24.12x,PacBio,,Typhimurium,,Not applicable,,,"Included in the study, passed QC/QA"
613,90371.2554,collected_by:Tom Weaver,,,,,Unicycler v. 0.2.0,,PRJNA371529,SAMN06309456,,,,,1,19-Jun-2014,Genome sequencing of Salmonella isolates recovered from livestock in Australia.,2017-06-28T00:00:00Z,,,2017-07-23T01:46:24.113Z,2017-07-23T01:46:24.113Z,,,51.89,"CP019649,CP019647,CP019648",5279746,Salmonella enterica subsp. enterica serovar Typhimurium strain TW-Stm6,Complete,Salmonella,Australia,,,,,none in pigs,"Pig, Sus scrofa domesticus",recovered from livestock in Australia,Australia,,pooled feces,,,MLST.Salmonella_enterica.34,,90371,,,host_disease_outcome:no disease;host_health_state:Victoria,,,,5489,,2,,,5106,,3,University of Melbourne,99.0x,PacBio; illumina,,Typhimurium,,TW-Stm6,,,"Included in the study, passed QC/QA"
614,90371.2564,,,,,,,,PRJEB20926,SAMEA104087369,,,,,1,,Salmonella enterica serovar Typhimurium ST313 responsible for gastroenteritis in the UK are genetically distinct from isolates causing bloodstream infections in Africa,2017-05-24T00:00:00Z,,,2017-07-27T23:17:16.720Z,2017-07-27T23:17:16.720Z,,,52.24,"LT855376,LT855377",4905261,Salmonella enterica subsp. enterica serovar Typhimurium strain STMU2UK,Complete,Salmonella,,,,,,,,,,,,,,,,90371,,,,,,,4948,,1,,,4563,,2,UNIVERSITY OF LIVERPOOL,,,,Typhimurium,,STMU2UK,,,"Included in the study, passed QC/QA"
615,90371.2618,sample_type:cell culture,,,,GCA_002313125.1,HGAP v. 3.0,,PRJNA391357,SAMN07267217,,,,,1,2016,"Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhimurium, a mcr-1 harboring bacterium isolated from Prepared pork in China",2017-09-19T00:00:00Z,,,2017-09-29T01:45:01.813Z,2017-09-29T01:45:01.813Z,,,51.93,"CP022168,CP022169",5142776,Salmonella enterica subsp. enterica serovar Typhimurium strain WW012,Complete,Salmonella,China,,,,,,,,China,,Instant pork,,,,,90371,,,,,,,5227,,1,,,,,2,China National Center for Food Safety Risk Assessment,169.0x,PacBio,,Typhimurium,,WW012,,,"Included in the study, passed QC/QA"
616,90371.2644,collected_by:NCYU,,,,GCA_002762135.1,Velvet v. 1.2.10,,PRJNA416238,SAMN07945789,,,,,1,2011,antibiotic resistant survey,2017-11-08T00:00:00Z,,,2017-11-24T17:23:46.249Z,2017-11-24T17:23:46.249Z,,,52.11,CP024619,4835517,Salmonella enterica subsp. enterica serovar Typhimurium strain BL10,Complete,Salmonella,Taiwan,,,,,Salmonella gastroenteritis,sus scrofa domesticus,,Taiwan,,necropsy,,,,,90371,,,,,,,4973,,,,,4815,,1,"Centers for Disease Control, R.O.C (Taiwan)",100.0x,Illumina MiSeq,,Typhimurium,,BL10,,,"Included in the study, passed QC/QA"
617,90371.2724,,,,,GCA_900166885.1,,,PRJEB19424,SAMEA3448233,,,,,1,,Genome assembly of Salmonella enterica subspecies enterica serovar Typhimurium,2017-10-14T00:00:00Z,,,2017-11-24T17:34:26.841Z,2017-11-24T17:34:26.841Z,,,51.84,"LT795114,LT795115,LT795116",5236057,Salmonella enterica subsp. enterica serovar Typhimurium strain VNB151-sc-2315230,Complete,Salmonella,,,,,,,,,,,,,,,,90371,,,,,,,5323,,2,,,,,3,WTSI,,,,Typhimurium,,VNB151-sc-2315230,,,"Included in the study, passed QC/QA"
618,90371.2827,collected_by:Samsung Seoul Hospital,,,,GCA_002813935.1,SMRT Analysis v. 2.3.0,,PRJNA357860,SAMN06161238,,,,,1,01-Jan-2016,"As a food-borne pathogen, Salmonella exhibits profound food-poisoning activates with high prevalence, every year. This sample was isolated from the blood of a food-poisoned patient in Seoul, Korea.",2017-12-07T00:00:00Z,,,2018-01-01T04:19:35.551Z,2018-01-01T04:19:35.551Z,,,52.18,CP019383,4673894,Salmonella enterica subsp. enterica serovar Typhimurium strain FORC50,Complete,Salmonella,South Korea: Seoul,,,,,Salmonella gastroenteritis,"Human, Homo sapiens","isolated from the blood of a food-poisoned patient in Seoul, Korea",South Korea,,stool,,,,,90371,,,,,,,4694,,,,,4713,,1,Seoul National University,265.58x,PacBio,,Typhimurium,,FORC50,,,"Included in the study, passed QC/QA"
619,90371.686,collected_by:Ohad Gal-Mor,,,,GCF_000636135.1,HGAP v. 2,,PRJNA242139,SAMN02692256,,,,,1,Jun-2011,"Comparative genomics , molecular serotyping , evolution and epidemiology.",2014-04-23T00:00:00Z,,,2016-01-17T15:34:56.020Z,2016-01-17T15:34:56.020Z,,,52.13,"CP007581,CP007582",5025357,Salmonella enterica subsp. enterica serovar Typhimurium strain 138736,Complete,Salmonella,Israel,,,,,Salmonella gastroenteritis.,"Human, Homo sapiens",,Israel,,stool sample from patient with gastroenteritis,,,,,90371,,,,,,,5181,,1,,"NZ_CP007581.1,NZ_CP007582.1",4548,,2,University of California,55.0x,PacBio,,Typhimurium,,138736,,,"Included in the study, passed QC/QA"
620,90371.687,,,,,GCF_000715155.1,Newbler v. 2.6; Ray v. 2.2.0; Geneious,,PRJNA242737,SAMN02798502,,,,Bacilli,1,,"Attenuated Salmonella enterica subsp. enterica Serovar Typhimurium strain VNP 20009 has been employed as an anticancer agent for targeted therapy due to its selective accumulation in tumors. VNP 20009 is a derivative of 14028S and was selected after UV and chemical mutagenesis for its tumor-colonizing and growth-inhibiting properties. To gain a deeper understanding of the genetic and physiological properties of VNP 20009, its entire genome was sequenced.",2014-07-29T00:00:00Z,,ATCC:202165,2016-01-17T15:36:14.361Z,2016-01-17T15:36:14.361Z,,,52.21,"CP007804,CP008745",4857390,Salmonella enterica subsp. enterica serovar Typhimurium strain VNP20009,Complete,Salmonella,,Negative,,,,,,,,,,,,,Yes,90371,,,,,,,4954,,1,,,4805,,2,Virginia Tech,254,Illumina MiSeq,,Typhimurium,,VNP20009,,,"Included in the study, passed QC/QA"
621,90371.688,biomaterial_provider:ATCC;collected_by:Castellani and Chalmers,,,,GCF_000743055.1,HGAP2 v. 2.2.0,,PRJNA256479,SAMN02943517,,,,,1,1911,"We are establishing a methodology for determining a variety of difficult-to-sequence regions in genome available for environmental, medical, or agricultural species.",2014-10-21T00:00:00Z,,,2016-01-17T15:38:55.543Z,2016-01-17T15:38:55.543Z,,,52.11,"CP009102,CP009103",4831756,Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 13311,Complete,Salmonella,,,,,,,,,,,not isolated,,,,,90371,,,,,,,4844,,1,25278532,"NZ_CP009102.1,NZ_CP009103.1",4361,,2,Okinawa Institute of Advanced Sciences,356x,PacBio,,Typhimurium,,ATCC 13311,,,"Included in the study, passed QC/QA"
622,90371.883,collected_by:Juan J. Calva,,,,GCF_001293505.1,HGAP2 v. 2.3.0.139497,,PRJNA288148,SAMN03795193,,,,,1,2011,Complete genome sequencing of a multidrug-resistant and human-invasive Salmonella Typhimurium strain of the emerging ST213 genotype harboring a blaCMY-2-carrying IncF plasmid,2015-09-17T00:00:00Z,,,2016-01-17T17:09:39.319Z,2016-01-17T17:09:39.319Z,,,52.13,"CP012681,CP012683,CP012684,CP012682",5088186,Salmonella enterica subsp. enterica serovar Typhimurium strain 33676,Complete,Salmonella,Mexico: Mexico City,,,fifteen years,female,Salmonellosis,"Human, Homo sapiens",,Mexico,,blood,,,,,90371,C,,host_disease_outcome:recovered;host_disease_stage:febrile illness with invasive severe pancolitis,,genotype:ST213,,5189,,3,,"NZ_CP012681.1,NZ_CP012683.1,NZ_CP012684.1,NZ_CP012682.1",4767,,4,"Instituto de Biotecnologia, UNAM",119x,PacBio RS,,Typhimurium,,33676,,,"Included in the study, passed QC/QA"
623,90371.903,"sample_type:blood culture;biomaterial_provider:125 Gwak-ro, Yuseoung-gu",,,,GCF_000993725.1,SMRT Analysis v. 2.3.0,,PRJNA282346,SAMN03568791,,,,,1,01-Oct-2013,A strain (FORC_015) of Salmonella enterica subsp. enterica serovar Typhimurium was isolated from human blood in South Korea. The complete genome sequence for this strain was obtained by PacBio RS II sequencing technology.,2015-05-07T00:00:00Z,,,2016-01-17T15:58:23.212Z,2016-01-17T15:58:23.212Z,,pathogen infecting humans,52.14,CP011365,4759372,Salmonella enterica subsp. enterica serovar Typhimurium strain FORC_015,Complete,Salmonella,South Korea,,HostAssociated,,,,"Human, Homo sapiens",isolated from human blood in South Korea,South Korea,,blood,,,,,90371,37 C,,,,,Facultative,4787,,,,NZ_CP011365.1,4288,,1,Korea Research Institute of Bioscience and Biotechnology,161x,PacBio RS II,,Typhimurium,,FORC_015,Mesophilic,,"Included in the study, passed QC/QA"
624,90371.906,collected_by:National Culture and Collection for Pathogen in Korea,,,,GCF_001454965.1,CLC Genomics Workbench v. 7.0.4; PacBio,,PRJNA288835,SAMN03839051,,,,,1,2014-08-07,Salmonella Typhimurium is one of the well-known food-borne pathogen. It was isolated from the contaminated food in South Korea.,2015-11-30T00:00:00Z,,,2016-01-30T10:53:41.056Z,2016-01-30T10:53:41.056Z,,,52.26,CP012144,4799793,Salmonella enterica subsp. enterica serovar Typhimurium strain FORC_020,Complete,Salmonella,South Korea,,,,,,,isolated from the contaminated food in South Korea,South Korea,,veinous blood,,,MLST.Salmonella_enterica.166,,90371,C,,,,,,4785,,,,NZ_CP012144.1,4671,,1,"Food-borne Pathogen Omics Research Center, FORC",,Illumina; PacBio,,,,FORC_020,,,"Included in the study, passed QC/QA"
625,90371.991,,,,,GCF_001540845.1,,,PRJEB10340,SAMEA3506109,,,,,1,2009,Microevolutionary events associated with the emergence and clonal expansion of new epidemic clones of bacterial pathogens hold the key to understanding the drivers of epidemiological success. We describe a comparative whole genome sequence and phylogenomic analysis of S. Typhimurium and monophasic Typhimurium strains from the UK associated with an epidemic over the past decade. The monophasic Typhimurium strains from the UK isolated since 2005 are not part of other recent epidemics reported in Spain and North America. Whole genome sequence revealed a large novel genomic island encoding resistance to heavy metals (SGI-3) is characteristic of the monophasic epidemic strains from other Typhimurium isolates in the current epidemic and may have contributed to the epidemiological success. We report a remarkable degree of genotypic variation that accumulated during clonal expansion of an epidemic including acquisition of the virulence-asscoiated sopE effector protein and novel prophage and hyper variability in the phase II flagellum locus.,2016-01-22T00:00:00Z,,,2016-02-05T14:48:46.290Z,2016-02-05T14:48:46.290Z,,,52.17,LN999997,5037238,Salmonella enterica subsp. enterica serovar Typhimurium isolate SO4698-09,Complete,Salmonella,UK,,,,,,Bos taurus,isolated since 2005 are not part of other recent epidemics reported in Spain and North America,United Kingdom,,,,,MLST.Salmonella_enterica.34,,90371,,,,,,,5107,,,,NZ_LN999997.1,,,1,INSTITUTE OF FOOD RESEARCH,,,,,,,,,"Included in the study, passed QC/QA"
626,909946.3,,,,,GCA_000188735.1,,,PRJNA56087,SAMN02602988,,,,,1,,No description available.,2011-02-10T00:00:00Z,,,2014-12-08T22:12:52.765Z,2015-03-16T03:17:09.594Z,,,52.18,"CP002487,CP002488,CP002489,CP002490",5067451,Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74,Complete,Salmonella,,,,,,,,,,,,,,MLST.Salmonella_enterica.19,,909946,-,Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74,,,,,5137,,3,21478351,"NC_016857.1,NC_016858.1,NC_017675.1,NC_016859.1",4842,,4,Ark Genomics,,,complete,serovar Typhimurium,,Apr-74,,,"Included in the study, passed QC/QA"
627,932733.3,"collected_by:Animal Health Laboratory, University of Guelph, Guelph, ON",,,,GCF_001975305.1,SMRT Analysis v. 1.3.3,,PRJNA242810,SAMN04160803,,,,Bacilli,1,22-Jun-2011,Genome sequence of Salmonella Bardo,2017-01-30T00:00:00Z,,,2017-03-20T06:30:55.197Z,2017-03-20T06:30:55.197Z,,,52.2,CP019404,4849139,Salmonella enterica subsp. enterica serovar Bardo strain SA20113257,Complete,Salmonella,Canada: Ontario,Negative,,,,,,,Canada,,Meleagris,,,,Yes,932733,,,,,,,5036,,,,NZ_CP019404.1,4804,,1,Laboratory for Foodborne Zoonoses,98.0x,Illumina MiSeq; PacBio,,Bardo,,SA20113257,,,"Included in the study, passed QC/QA"
628,936157.8,,,,,GCF_000230505.1,,,PRJEA61197,SAMEA2272073,,,,,66,,-,2015-02-27T00:00:00Z,,,2016-01-17T15:28:33.104Z,2016-01-17T15:28:33.104Z,,,52.12,"FR775255,FR775253,FR775252,FR775251,FR775250,FR775249,FR775248,FR775247,FR775246,FR775245,FR775244,FR775243,FR775242,FR775241,FR775240,FR775239,FR775238,FR775237,FR775236,FR775235,FR775234,FR775233,FR775232,FR775231,FR775230,FR775229,FR775228,FR775227,FR775226,FR775225,FR775224,FR775223,FR775222,FR775221,FR775220,FR775219,FR775218,FR775217,FR775216,FR775215,FR775214,FR775213,FR775212,FR775211,FR775210,FR775209,FR775208,FR775207,FR775206,FR775205,FR775204,FR775203,FR775202,FR775201,FR775200,FR775199,FR775198,FR775197,FR775196,FR775195,FR775194,FR775193,FR775192,FR775191,FR775190,FR775189,FR775188",4920331,Salmonella enterica subsp. enterica serovar Weltevreden str. 2007-60-3289-1,Complete,Salmonella,,,,,,,,,,,,,,,,936157,,,,,,,5129,,1,21296964,,4866,,67,"Cebitec, Bielefeld University",,,,Weltevreden,,2007-60-3289-1,,,"Included in the study, passed QC/QA"
629,98360.51,,,,,GCA_000953175.1,,,PRJEB5985,SAMEA724381,,,,,1,,"Many bacterial pathogens are specialised, infecting only one, or a few, hosts, and this is often associated with more acute disease presentation. By looking at specific genomes we can see markers of this specialisation, which often reflect a balance between gene acquisition and functional gene loss. Within Salmonella enterica subspecies enterica, a single lineage exists that includes human and animal pathogens adapted to cause infection in different hosts, including S. enterica serovar Enteritidis (multiple hosts), S. Gallinarum (birds) and S. Dublin (cattle). This provides an excellent evolutionary context in which differences between these pathogen genomes can be related to host range. Genome sequences were obtained from ~60 isolates selected to represent the known diversity of this lineage. Examination and comparison of the clades within the phylogeny of this lineage revealed signs of host restriction as well as evolutionary events that mark a path to host generalism. We have identified the nature and order of events for both evolutionary trajectories. The impact of functional gene loss was predicted based upon position within metabolic pathways and confirmed with phenotyping assays. In the host adapted clades, loss of particular traits such as tetrathionate reduction and adenosylcobalamin biosynthesis could be related to their role in host infection. The structure of S. Enteritidis is more complex than previously known, as a second clade of S. Enteritidis was revealed that is distinct from those commonly seen to cause disease in humans or animals, and which are more closely related to S. Gallinarum. Isolates from this novel clade were tested in a chick model of infection, and exhibited a reduced colonisation phenotype, which we postulate represents an intermediate stage in pathogen-host adaptation.",2014-11-01T00:00:00Z,,,2016-02-29T18:10:53.472Z,2016-02-29T18:10:53.472Z,,,52.14,LK931502,4814038,Salmonella enterica subsp. enterica serovar Dublin strain SC50,Complete,Salmonella,,,,,,,,,,,,,,MLST.Salmonella_enterica.10,,98360,,,,,,,4956,,,,,4505,,1,SC,,,,serovar Enteritidis,,SC50,,,"Included in the study, passed QC/QA"
630,990282.4,,,,,GCA_000213635.1,,,PRJNA63211,SAMN02602986,,,,,1,,"Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University",2011-05-13T00:00:00Z,,,2014-12-08T22:12:52.939Z,2015-03-16T03:17:09.594Z,,,52.22,"CP002614,CP002615",4911145,Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1,Complete,Salmonella,,,,,,,,,,,,,,MLST.Salmonella_enterica.19,,990282,-,Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1,,,,,4928,,1,,"NC_016863.1,NC_016864.1",4555,,2,Arizona State University,,,complete,serovar Typhimurium,,UK-1,,,"Included in the study, passed QC/QA"
631,99287.12,,,,,GCA_000006945.1,,,PRJNA241,SAMN02604315,,,,Rod,1,1940," Salmonella enterica subsp. enterica serovar typhimurium strain LT2. This strain was first isolated in the 1940s by Lilleengen, and typed based on phage sensitivity. It became the principle laboratory strain and many important biochemical and genetic experiments were performed using this strain, including classical phage transduction studies. LT2 contains a plasmid, pSLT, that encodes additional virulence functions. Numerous prophages, some of which contain virulence genes, are inserted into the chromosome of LT2 as compared to related Salmonella.",2001-10-26T00:00:00Z,,,2014-12-08T22:12:52.716Z,2015-03-16T03:17:09.594Z,,Gastroenteritis;Food poisoning,52.2,"AE006468,AE006471",4951371,Salmonella enterica subsp. enterica serovar Typhimurium str. LT2,Complete,Salmonella,,-,Host-associated,,,,,"isolated in the 1940s by Lilleengen, and typed based on phage sensitivity",,,,,,MLST.Salmonella_enterica.19,Yes,99287,37,Salmonella enterica subsp. enterica serovar Typhimurium str. LT2,,,,Facultative,4972,,1,11677609,"NC_003197,NC_003277",4525,,2,Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine,,,complete,serovar Typhimurium,,LT2,Mesophilic,,"Included in the study, passed QC/QA"
632,996633.3,,,,,GCA_000828595.1,CLC De Novo Assembler v. 6.5,,PRJDA63645,-,,,,,2,,This strain will be used for comparative genome analysis.,2014-06-27T00:00:00Z,2,,2015-03-12T14:02:51.747Z,2015-03-16T03:17:09.594Z,,,52.19,"AP014565.1,AP014566.1",5184452,Salmonella enterica subsp. enterica serovar Typhimurium str. L-3553,Complete,Salmonella,,,,,,,,,,,,,,,,996633,,,,,,,5202,,1,-,"NZ_AP014565.1,NZ_AP014566.1",5106,,2,National Institute of Infectious Diseases,200x,MiSeq; Illumina GAII; ABI 3730xl,,serovar Typhimurium,,L-3553,,,"Included in the study, passed QC/QA"
633,1035377.4,,,,,GCA_000222975.1,,,PRJNA67155,,,,,,1,,"Centers for Disease Control and Prevention (CDC)Yersinia. This genus consists of 11 species, 3 of which are human pathogens. Specific virulence factors are encoded within pathogenicity islands (PAIs) that are required for the invasive phenotype associated with Yersinia infections. These PAIs may be carried on extrachromosomal plasmids or on the chromosome. One key virulence plasmid contained by the three human-specific pathogens is pCD1/pYv, which encodes a type III secretion system for the delivery of virulence proteins that contribute to internalization into the host cell.Yersinia pestis. This species was originally described by Institut Pasteur scientist Andre Yersin in 1894 in Hong Kong. It is the causative agent of plague (bubonic and pulmonary) a devastating disease which has killed millions worldwide. The organism can be transmitted from rats to humans through the bite of an infected flea or from human-to-human through the air during widespread infection. Yersinia pestis is an extremely pathogenic organism that requires very few numbers in order to cause disease, and is often lethal if left untreated. The organism is enteroinvasive, and can survive and propagate in macrophages prior to spreading systemically throughout the host. Yersinia pestis consists of three biotypes or serovars, Antiqua, Mediavalis, and Orientalis, that are associated with three major pandemics throughout human history. The first occurred during the first millenium, the second occurred from 1300 up to the 19th century (Black Death), and the third started in China during the 19th century and continues to this day. A fourth biovar type has been proposed, Microtus. Yersinia pestis contains multiple copies of insertion elements, especially IS100, as compared to other Yersinia spp., and 2 species-specific plasmids, pMT1 and pPCP1. pMT1 encodes a protein, murine toxin, that aids rat-to-human transmission by enhancing survival of the organism in the flea midgut. Deep tissue invasion is due to the presence of a plasminogen activator encoded on the pPCP1 plasmid. Yersinia pestis also contains a PAI on the chromosome that is similar to the SPI-2 PAI from Salmonella that allows intracellular survival in the organism. A1122. Strain A1122 grows on almost all isolates of Yersinia pestis and is used by the Centers for Disease Control and Prevention as a diagnostic agent for the causative agent of plague. The sample used for this project was obtained from the CDC.",2011-08-05T00:00:00Z,,,2014-12-08T22:13:51.176Z,2015-03-16T03:17:09.594Z,,,47.63,"CP002956,CP002957,CP002958",4658411,Yersinia pestis A1122,Complete,Yersinia,,,,,,,,,,,,,,MLST.Yersinia_spp.79,,1035377,-,Yersinia pestis A1122,,,,,4379,,2,,"NC_017168.1,NC_017169.1,NC_017170.1",4247,,3,Los Alamos National Lab,,,complete,,,A1122,,,"Included in the study, passed QC/QA"
634,1035377.9,,,,,GCF_000834755.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240102,SAMN03074123,,,,Bacilli,1,1939,Genome sequencing of Yersinia pestis A1122,2015-05-28T00:00:00Z,,,2016-01-17T15:43:26.682Z,2016-01-17T15:43:26.682Z,,,47.62,"CP009840,CP009841,CP009839",4674565,Yersinia pestis A1122,Complete,Yersinia,USA: California,Negative,,,,,"California ground squirrel, Otospermophilus beecheyi",,United States,,California Ground Squirrel (Spermophilus beecheyi),,,,,1035377,,,,,,,4477,,2,25931590,"NZ_CP009840.1,NZ_CP009841.1,NZ_CP009839.1",4144,,3,Los Alamos National Laboratory,379s,Illumina; PacBio; 454,,,,A1122,,,"Included in the study, passed QC/QA"
635,1262462.5,,,,,GCF_000968115.1,,,PRJEB661,,,,,,1,,"Yersinia enterocolitica is an important food-borne pathogen causing gastroenteritis in humans. It is also frequently found in animals. The species is currently divided into 6 different bio-serotypes, which have different pathogenic potential and differ also in prevalence around the world. This strain was sequenced for comparative analysis of all bio-serotypes. This strain is from bio-serotype 2A and was isolated from human faecal matter.",2014-01-06T00:00:00Z,,,2016-01-17T15:52:38.193Z,2016-01-17T15:52:38.193Z,,,47.3,HF571988,4940199,Yersinia enterocolitica (type O:5) str. YE53/03,Complete,Yersinia,,,,,,,"Human, Homo sapiens",is from bio-serotype 2A and was isolated from human faecal matter,,,bio-serotype 2A and was isolated from human faecal matter,,,,,1262462,,,,,,,4795,,,,NZ_HF571988.1,4365,,1,WTSI,,,,serovar s,,YE53/03,,,"Included in the study, passed QC/QA"
636,1262463.3,,,,,GCF_001050735.1,,,PRJEB662,,,,,,,,"Yersinia enterocolitica is an important food-borne pathogen causing gastroenteritis in humans. It is also frequently found in animals. The species is currently divided into 6 different bio-serotypes, which have different pathogenic potential and differ also in prevalence around the world. This strain was sequenced for comparative analysis of all bio-serotypes. This genome is of bioserotype O:9 and is isolated from a pig abbatoir.",2013-09-26T00:00:00Z,1,,2016-01-17T16:12:39.347Z,2016-01-17T16:12:39.347Z,,,46.95,CAQD01000000,4565715,Yersinia enterocolitica (type O:9) str. YE212/02,Complete,Yersinia,,,,,,,"Pig, Sus scrofa",isolated from a pig abbatoir,,,pig abbatoir,,,,,1262463,,,,,,,4358,,,,,3923,,1,WTSI,,,,serovar s,,YE212/02,,,"Included in the study, passed QC/QA"
637,1262464.3,,,,,GCF_001050755.1,,,PRJEB663,,,,,,,,"Yersinia enterocolitica is an important food-borne pathogen causing gastroenteritis in humans. It is also frequently found in animals. The species is currently divided into 6 different bio-serotypes, which have different pathogenic potential and differ also in prevalence around the world. This strain was sequenced for comparative analysis of all bio-serotypes. This strain is of bio-serotype O:2 and was isolated from human faecal matter.",2014-05-12T00:00:00Z,1,,2016-01-17T16:12:39.859Z,2016-01-17T16:12:39.859Z,,,46.95,CAQE01000000,4564695,Yersinia enterocolitica (type O:9) str. YE56/03,Complete,Yersinia,,,,,,,"Human, Homo sapiens",isolated from human faecal matter,,,human faecal matter,,,,,1262464,,,,,,,4366,,,24753568,,3917,,1,WTSI,,,,serovar s,,YE56/03,,,"Included in the study, passed QC/QA"
638,1262465.3,,,,,GCF_001050775.1,,,PRJEB664,,,,,,,,"Yersinia enterocolitica is an important food-borne pathogen causing gastroenteritis in humans. It is also frequently found in animals. The species is currently divided into 6 different bio-serotypes, which have different pathogenic potential and differ also in prevalence around the world. This strain was sequenced for comparative analysis of all bio-serotypes. This strain is from bio-serotype O:5,27 and was isolated from a sheep abattoir.",2014-05-12T00:00:00Z,1,,2016-01-17T16:12:40.181Z,2016-01-17T16:12:40.181Z,,,47.04,CAQF01000000,4596919,"Yersinia enterocolitica (type O:5,27) str. YE149/02",Complete,Yersinia,,,,,,,"Sheep, Ovis sp.","is from bio-serotype O:5,27 and was isolated from a sheep abattoir",,,"bio-serotype O:5,27 and was isolated from a sheep abattoir",,,,,1262465,,,,,,,4424,,,24753568,,3978,,1,WTSI,,,,serovar s,,YE149/02,,,"Included in the study, passed QC/QA"
639,1262466.3,,,,,GCF_001050795.1,,,PRJEB665,,,,,,,,"Yersinia enterocolitica is an important food-borne pathogen causing gastroenteritis in humans. It is also frequently found in animals. The species is currently divided into 6 different bio-serotypes, which have different pathogenic potential and differ also in prevalence around the world. This strain was sequenced for comparative analysis of all bio-serotypes. This strain is from bio-serotype O:3 and was isolated from human faecal matter.",2014-05-12T00:00:00Z,1,,2016-01-17T16:12:40.530Z,2016-01-17T16:12:40.530Z,,,47,CAQG01000000,4528241,Yersinia enterocolitica (type O:3) str. YE12/03,Complete,Yersinia,,,,,,,"Human, Homo sapiens",is from bio-serotype O:3 and was isolated from human faecal matter,,,bio-serotype O:3 and was isolated from human faecal matter,,,,,1262466,,,,,,,4362,,,24753568,,3893,,1,WTSI,,,,serovar s,,YE12/03,,,"Included in the study, passed QC/QA"
640,1262467.6,,,,,GCF_001050815.1,,,PRJEB666,,,,,,,,"Yersinia enterocolitica is an important food-borne pathogen causing gastroenteritis in humans. It is also frequently found in animals. The species is currently divided into 6 different bio-serotypes, which have different pathogenic potential and differ also in prevalence around the world. This strain was sequenced for comparative analysis of all bio-serotypes. This strain is of bio-serotype O:2a,2b,3 and is derived from an animal isolate.",2014-05-12T00:00:00Z,1,,2016-01-17T16:12:40.890Z,2016-01-17T16:12:40.890Z,,,46.96,CAQH01000000,4666303,Yersinia enterocolitica (type O:2) str. YE3094/96,Complete,Yersinia,,,,,,,"Human, Homo sapiens",derived from an animal isolate,,,animal isolate,,,,,1262467,,,,,,,4716,,,24753568,,4051,,1,WTSI,,,,serovar s,,YE3094/96,,,"Included in the study, passed QC/QA"
641,1345701.6,,,,,GCF_001188675.1,Velvet v. 1.0.13; Newbler v.,,PRJNA208248,SAMN02769799,,,,Bacilli,,,Finished genome sequence of Yersinia pestis 790 isolated in the Kyrgyz Republic,2015-07-30T00:00:00Z,1,,2016-01-17T16:41:54.350Z,2016-01-17T16:41:54.350Z,,Plague,47.64,"CP006806,CP006807,CP006808",4781906,Yersinia pestis 790,Complete,Yersinia,Kyrgyzstan,Negative,,,,,,,Kyrgyzstan,,,,,,,1345701,,,,,,,4611,,2,,,4242,,3,Los Alamos National Laboratory,56.2X;32X,Illumina GAii; Roche 454,,,,790,,,"Included in the study, passed QC/QA"
642,1345702.11,,,,,GCF_001188815.1,Velvet v. 1.1.05; Newbler v.,,PRJNA208249,SAMN03941711,,,,Bacilli,1,,Finished genome sequence of Yersinia pestis 2944 isolated in Russia,2015-07-30T00:00:00Z,,,2016-01-17T16:41:56.837Z,2016-01-17T16:41:56.837Z,,Plague,47.59,"CP006792,CP006791,CP006790,CP006793",4672740,Yersinia pestis 2944,Complete,Yersinia,Russia: Kabardino-Balkaria,Negative,,,,,,,Russia,,,,,,,1345702,,,,,,,4526,,3,,"NZ_CP006792.1,NZ_CP006791.1,NZ_CP006790.1,NZ_CP006793.1",4153,,4,Los Alamos National Laboratory,68.8; 23.4,Illumina GAii; Roche 454,,,,2944,,,"Included in the study, passed QC/QA"
643,1345703.9,,,,,GCF_001188695.1,Newbler v. 2.3-PreRelease-6/30/2009;,,PRJNA208250,SAMN03782999,,,,Bacilli,1,,Finished genome sequence of Yersinia pestis 1412 isolated in the Republic of Georgia,2015-07-30T00:00:00Z,,,2016-01-17T16:41:54.682Z,2016-01-17T16:41:54.682Z,,Plague,47.71,"CP006783,CP006780,CP006779",4733482,Yersinia pestis 1412,Complete,Yersinia,Georgia: Ninotsminda,Negative,,,,,,,Georgia,,,,,,,1345703,,,,,,,4563,,2,,"NZ_CP006783.1,NZ_CP006780.1,NZ_CP006779.1",4232,,3,Los Alamos National Laboratory,34.1x; 169.7x,Roche 454 FLX Titanium; Illumina GA IIX,,,,1412,,,"Included in the study, passed QC/QA"
644,1345704.8,,,,,GCF_001188935.1,Newbler v. 2.3-PreRelease-6/30/2009;,,PRJNA208251,SAMN03783058,,,,Bacilli,1,,Finished genome sequence of Yersinia pestis 1413 isolated in the Republic of Georgia,2015-07-30T00:00:00Z,,,2016-01-17T16:41:58.930Z,2016-01-17T16:41:58.930Z,,Plague,47.72,"CP006762,CP006761,CP006760",4736923,Yersinia pestis 1413,Complete,Yersinia,Georgia: Ninotsminda,Negative,,,,,,,Georgia,,,,,,,1345704,,,,,,,4575,,2,,"NZ_CP006762.1,NZ_CP006761.1,NZ_CP006760.1",4231,,3,Los Alamos National Laboratory,150.2x,Illumina Roche 454,,,,1413,,,"Included in the study, passed QC/QA"
645,1345705.8,,,,,GCF_001188715.1,Velvet v. 1.0.13; Newbler v.,,PRJNA208252,SAMN03783057,,,,Bacilli,1,,Finished genome sequence of Yersinia pestis 1522 isolated in the Republic of Armenia,2015-07-30T00:00:00Z,,,2016-01-17T16:41:55.069Z,2016-01-17T16:41:55.069Z,,Plague,47.71,"CP006758,CP006757,CP006756",4738644,Yersinia pestis 1522,Complete,Yersinia,Armenia: Shirak Province,Negative,,,,,,,Armenia,,,,,,,1345705,,,,,,,4578,,2,,"NZ_CP006758.1,NZ_CP006757.1,NZ_CP006756.1",4237,,3,Los Alamos National Laboratory,1022x,Illumina Roche 454,,,,1522,,,"Included in the study, passed QC/QA"
646,1345706.3,,,,,GCF_001188795.1,Velvet v. 1.0.13; Newbler v.,,PRJNA208254,SAMN03943655,,,,Bacilli,1,,Finished genome sequence of Yersinia pestis 3067 isolated in the Republic of Georgia.,2015-07-30T00:00:00Z,,,2016-01-17T16:41:56.445Z,2016-01-17T16:41:56.445Z,,Plague,47.71,"CP006754,CP006753,CP006752",4736090,Yersinia pestis 3067,Complete,Yersinia,Georgia: Ninotsminda,Negative,,,,,,isolated in the Republic of Georgia,Georgia,,,,,,,1345706,,,,,,,4556,,2,,"NZ_CP006754.1,NZ_CP006753.1,NZ_CP006752.1",4230,,3,Los Alamos National Laboratory,158.4x,Illumina Roche 454,,,,3067,,,"Included in the study, passed QC/QA"
647,1345707.6,,,,,GCF_001188775.1,Velvet v. 1.0.13; Newbler v.,,PRJNA208257,SAMN03943654,,,,Bacilli,1,,Finished genome sequence of Yersinia pestis 3770 isolated in the Republic of Georgia,2015-07-30T00:00:00Z,,,2016-01-17T16:41:56.089Z,2016-01-17T16:41:56.089Z,,Plague,47.72,"CP006751,CP006750,CP006749",4735667,Yersinia pestis 3770,Complete,Yersinia,Georgia: Ninotsminda,Negative,,,,,,,Georgia,,,,,,,1345707,,,,,,,4578,,2,,"NZ_CP006751.1,NZ_CP006750.1,NZ_CP006749.1",4231,,3,Los Alamos National Laboratory,84.9X,Illumina Roche 454,,,,3770,,,"Included in the study, passed QC/QA"
648,1345708.6,,,,,GCF_001188755.1,Velvet v. 1.0.13; Newbler v.,,PRJNA208258,SAMN03943569,,,,Bacilli,1,,Finished genome sequence of Yersinia pestis 8787 isolated in the Republic of Georgia,2015-07-30T00:00:00Z,,,2016-01-17T16:41:55.786Z,2016-01-17T16:41:55.786Z,,Plague,47.73,"CP006748,CP006747,CP006746",4675987,Yersinia pestis 8787,Complete,Yersinia,Georgia: Ninotsminda,Negative,,,,,,,Georgia,,,,,,,1345708,,,,,,,4530,,2,,"NZ_CP006748.1,NZ_CP006747.1,NZ_CP006746.1",4174,,3,Los Alamos National Laboratory,152x,Illumina Roche 454,,,,8787,,,"Included in the study, passed QC/QA"
649,1345710.7,,,,,GCF_001188735.1,Velvet v. 1.1.05; Newbler v. 2.6; Parallel,,PRJNA208260,SAMN03943674,,,,Bacilli,,,Finished genome sequence of Yersinia pestis 1045 isolated in the Republic of Azerbaijan.,2015-07-30T00:00:00Z,1,,2016-01-17T16:41:55.392Z,2016-01-17T16:41:55.392Z,,Plague,47.6,"CP006794,CP006795,CP006797,CP006796",4684080,Yersinia pestis 1045,Complete,Yersinia,Azerbaijan: Apsheron Pen.,Negative,,,,,,isolated in the Republic of Azerbaijan,Azerbaijan,,,,,,,1345710,,,,,,,4576,,3,,,4169,,4,Los Alamos National Laboratory,57.2;23.5,Illumina GAii; Roche 454,,,,1045,,,"Included in the study, passed QC/QA"
650,1443113.3,,,,,GCA_000597945.1,Newbler v. 2.3; Consed v. 23.0; SOAPdenovo,,PRJNA233451,SAMN03081541,,,,,1,2008,comparative genomic study to analyze the pathogenicity and evolutional relationships with Yersinia enterocolitica.,2014-03-19T00:00:00Z,, ,2014-12-08T22:13:50.951Z,2015-03-16T03:17:09.594Z,,,48.0504,"CP007448.1,CP007449.1,CP007450.1",4900014,Yersinia enterocolitica LC20,Complete,Yersinia,China: Zhejiang,,,,,,"Norway rat, Rattus norvegicus",,China,,feces,,,,,1443113,,Yersinia enterocolitica LC20,,,,,5386,,2,,-,5498,,3,"'Beijing Institute of Genomics, Chinese Academy of Sciences'",14x; 207x,454; Illumina; Sanger dideoxy sequencing,complete,,,LC20,,,"Included in the study, passed QC/QA"
651,1453495.3,,,,,GCA_000834395.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA236105,SAMN03144720,,,,Bacilli,1,,Genome sequencing of Yersinia aldovae 670-83,2015-02-09T00:00:00Z,1,,2015-03-12T13:45:34.541Z,2015-03-16T03:17:09.594Z,,,47.69,CP009781.1,4471090,Yersinia aldovae 670-83,Complete,Yersinia,Norway,Negative,,,,,,,Norway,,Fish,,,,,1453495,,,,,,,4094,,,-,NZ_CP009781.1,3943,,1,Los Alamos National Laboratory,813x,Illumina; PacBio; 454,,,,670-83,,,"Included in the study, passed QC/QA"
652,1454377.3,,,,,GCA_000834215.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA236482,SAMN03010446,,,,Bacilli,1,,Genome sequencing of Yersinia frederiksenii Y225,2015-02-09T00:00:00Z,2,,2015-03-12T13:45:36.508Z,2015-03-16T03:17:09.594Z,,,47.28,"CP009364.1,CP009363.1",4550894,Yersinia frederiksenii Y225,Complete,Yersinia,,Negative,,,,,,,,,,,,,,1454377,,,,,,,4209,,1,-,"NZ_CP009364.1,NZ_CP009363.1",4088,,2,Los Alamos National Laboratory,317x,Illumina; 454,,,,Y225,,,"Included in the study, passed QC/QA"
653,1839800.3,collected_by:USAMRIID,,,,,HGAP v. 3,,PRJNA231221,SAMN04875565,,,,,1,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",2017-03-29T00:00:00Z,,FDA:FDAARGOS_228,2017-05-28T05:07:14.799Z,2017-05-28T05:07:14.799Z,,,47.52,CP020409,4962867,Yersinia sp. FDAARGOS_228 strain FDAARGOS_228,Complete,Yersinia,USA:MD,,,Not applicable,Not applicable,Not applicable,Wildlife,,United States,,Lymph node tissue,,,,,1839800,,,host_description:Not applicable;host_disease_outcome:Not applicable;host_disease_stage:Not applicable;host_health_state:Not applicable,,,,4894,,,,,4473,,1,US Food and Drug Administration,16.5906726411259x,PacBio,,,,Not applicable,,,"Included in the study, passed QC/QA"
654,187410.11,,,,,GCA_000006645.1,,,PRJNA288,SAMN02604093,,,,Rod,1,,Yersinia pestis strain KIM 10. This strain is a Medievalis subtype (biovar) that is widely used in research and is well characterized.,2002-07-27T00:00:00Z,,,2014-12-08T22:13:51.313Z,2015-03-16T03:17:09.594Z,,Bubonic plague,47.7,"AE009952,AF074611",4701745,Yersinia pestis KIM10+,Complete,Yersinia,,-,Multiple,,,,,,,,,,,MLST.Yersinia_spp.79,,187410,28-30,Yersinia pestis KIM 10,,,,Facultative,4567,,1,"9826348,12142430","NC_004088,NC_004838",4202,,2,"Univ. Wisconsin|University of Wisconsin, Genetics, USA, Madison",,,complete,,,KIM 10,Mesophilic,,"Included in the study, passed QC/QA"
655,214092.181,,,,,GCA_001293415.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA235224,SAMN03160774,,,,Bacilli,1,1992,Genome sequencing of Yersinia pestis CO92,2015-05-28T00:00:00Z,,,2016-01-17T17:09:37.901Z,2016-01-17T17:09:37.901Z,,,47.6,"CP009973,CP009972,CP009971",4722852,Yersinia pestis CO92,Complete,Yersinia,USA: Colorado,Negative,,,,,"Human, Homo sapiens",,United States,,Human Clinical Sample (fatal pneumonic plague),,,,,214092,,,,,,,4555,,2,25931590,"NZ_CP009973.1,NZ_CP009972.1,NZ_CP009971.1",4200,,3,Los Alamos National Laboratory,564x,Illumina; PacBio,,,,CO92,,,"Included in the study, passed QC/QA"
656,214092.21,,,,,GCA_000009065.1,,,PRJNA34,SAMEA1705942,,,,Rod,1,,Yersinia pestis strain CO92. This strain is a recent Orientalis subtype isolated in the USA from a patient who died of pneumonic plague after acquiring the disease from an infected cat. This strain is 50 Kbp larger than the Yersinia pestis KIM10+ genome due to numerous insertions.,2001-10-05T00:00:00Z,,,2014-12-08T22:13:51.215Z,2015-03-16T03:17:09.594Z,,Bubonic plague,47.6,"AL590842,AL117189,AL109969,AL117211",4829855,Yersinia pestis CO92,Complete,Yersinia,USA,-,Multiple,,,,"Human, Homo sapiens",isolated in the USA from a patient who died of pneumonic plague after acquiring the disease from an infected cat,United States,,patient who died of pneumonic plague after acquiring the disease from an infected cat,,,MLST.Yersinia_spp.79,,214092,28-30,Yersinia pestis CO92,,,,Facultative,4666,,3,"11586360,12834539,11274119","NC_003143,NC_003131,NC_003132,NC_003134",4066,,4,Wellcome Trust Sanger Institute,,,complete,,,CO92,Mesophilic,,"Included in the study, passed QC/QA"
657,229193.14,,,,,GCA_000007885.1,,,PRJNA10638,SAMN02602970,biovar Microtus,,,Rod,1,,Yersinia pestis biovar Microtus str. 91001. Formerly the Medievalis subtype (biovar) that is widely used in research and is well characterized. The biovar has been renamed to Microtus.,2004-06-04T00:00:00Z,,,2014-12-08T22:13:51.972Z,2015-03-16T03:17:09.594Z,,Bubonic plague,47.7,"AE017042,AE017043,AE017044,AE017045,AE017046",4803217,Yersinia pestis biovar Microtus str. 91001,Complete,Yersinia,,-,Multiple,,,,,,,,,,,MLST.Yersinia_spp.79,,229193,28-30,Yersinia pestis biovar Microtus str. 91001,,,,Facultative,4887,,4,"15262951,15368893","NC_005810,NC_005813,NC_005814,NC_005815,NC_005816",4138,,5,"Academy of Military Medical Sciences, The Institute of Microbiology and Epidemiology, China",,,complete,,,91001,Mesophilic,,"Included in the study, passed QC/QA"
658,263819.4,sample_type:single cell,,,,GCF_001047675.1,Geneious v. 8.1.3,,PRJNA288628,SAMN03801505,,,,,1,1981,Y. aleksiciae: well adapted to warm blooded species but possibly not host-specific. Apathogenicity needs to be confirmed.,2015-09-23T00:00:00Z,,DSM 14987,2016-01-17T16:11:59.124Z,2016-01-17T16:11:59.124Z,,,49.04,CP011975,4000307,Yersinia aleksiciae strain 159,Complete,Yersinia,Finland,,Multiple,,,,"Human, Homo sapiens",,Finland,,feces,,,,,263819,C,,,,,,3742,,,26383649,NZ_CP011975.1,3423,,1,Friedrich-Loeffler-Institut,,PacBio,,O:16,,159,,,"Included in the study, passed QC/QA"
659,273123.1,,,,,GCA_000047365.1,,,PRJNA12950,,,,,Rod,1,,Yersinia pseudotuberculosis strain IP 32953. This strain is a fully virulent serotype I strain isolated from a human patient.,2004-09-11T00:00:00Z,,,2014-12-08T22:13:52.208Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,47.6,"BX936398,BX936400,BX936399",4840898,Yersinia pseudotuberculosis IP 32953,Complete,Yersinia,,-,Multiple,,,,"Human, Homo sapiens",isolated from a human patient,,,human patient,,,MLST.Yersinia_pseudotuberculosis.42,Yes,273123,28-30,Yersinia pseudotuberculosis IP 32953,,,,Facultative,4745,,2,15358858,"NC_006155,NC_006154,NC_006153",4038,,3,Lawrence Livermore National Laboratory|Institut Pasteur,,,complete,serovar I,,IP 32953,Mesophilic,,"Included in the study, passed QC/QA"
660,273123.14,,,,,GCF_000834295.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA239344,SAMN03121000,,,,Bacilli,1,,Genome sequencing of Yersinia pseudotuberculosis IP32953,2015-05-28T00:00:00Z,,,2016-01-17T15:43:25.055Z,2016-01-17T15:43:25.055Z,,,47.55,"CP009712,CP009711,CP009710",4839430,Yersinia pseudotuberculosis IP 32953,Complete,Yersinia,,Negative,,,,,,,,,,,,,Yes,273123,,,,,,,4547,,2,25931590,"NZ_CP009712.1,NZ_CP009711.1,NZ_CP009710.1",4181,,3,Los Alamos National Laboratory,465x,Illumina; PacBio; 454,,1,,IP32953,,,"Included in the study, passed QC/QA"
661,28152.3,,,,,GCA_000750355.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA243532,SAMN02918303,,,,Coccobacilli,1,,Yersinia kristensenii 33639 Genome Assembly,2014-09-09T00:00:00Z,1,,2014-12-09T00:36:51.327Z,2015-03-16T03:17:09.594Z,,,47.4,CP008955.1,4444330,Yersinia kristensenii strain ATCC 33639,Complete,Yersinia,,Negative,,,,,,,,,,,,,,28152,,,,,,,4085,,,25342679,-,3918,,1,Los Alamos National Laboratory,344x,Illumina; 454,,,,ATCC 33639,,,"Included in the study, passed QC/QA"
662,28152.8,sample_type:Microbial isolate culture,,,,GCF_000834865.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240099,SAMN03202900,,,,Bacilli,1,,Genome sequencing of Yersinia kirstensenii Y231,2015-05-28T00:00:00Z,,,2016-01-17T15:43:27.970Z,2016-01-17T15:43:27.970Z,,,47.4,CP009997,4496569,Yersinia kristensenii strain Y231,Complete,Yersinia,,Negative,,,,,,,,,,,,,,28152,,,,,,,4246,,,25931590,NZ_CP009997.1,3988,,1,Los Alamos National Laboratory,554x,Illumina; PacBio; 454,,,,Y231,,,"Included in the study, passed QC/QA"
663,29484.38,collected_by:USAMRIID < MIDI < DCC < ATCC,,,,GCA_002591095.1,"SMRT v. 2.3.0, HGAP v. 3",,PRJNA231221,SAMN07312461,,,,,1,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-10-18T00:00:00Z,,FDA:FDAARGOS_417,2017-11-24T16:45:31.923Z,2017-11-24T16:45:31.923Z,,,47.64,CP023962,5000678,Yersinia frederiksenii strain FDAARGOS_417 strain Not applicable,Complete,Yersinia,,,,,,,"Human, Homo sapiens",,,,,,,,,29484,,,,,,,4781,,,,,4517,,1,US Food and Drug Administration,12.18x,PacBio; Illumina,,,,Not applicable,,,"Included in the study, passed QC/QA"
664,29484.39,collected_by:USAMRIID < MIDI < DCC < ATCC,,,,GCA_002591195.1,Celera v. 8.2,,PRJNA231221,SAMN07312462,,,,,1,,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-10-18T00:00:00Z,,FDA:FDAARGOS_418,2017-11-24T16:44:20.145Z,2017-11-24T16:44:20.145Z,,,46.98,CP023964,4934031,Yersinia frederiksenii strain FDAARGOS_418 strain Not applicable,Complete,Yersinia,Denmark,,,Not applicable,Not applicable,Not applicable,,,Denmark,,Sewage,,,MLST.Yersinia_spp.32,,29484,,,host_disease_outcome:Not applicable;host_health_state:Not applicable;host_description:Not applicable;host_disease_stage:Not applicable,,,,4671,,,,,4416,,1,US Food and Drug Administration,20.11x,PacBio; Illumina,,,,Not applicable,,,"Included in the study, passed QC/QA"
665,29485.3,,,,,GCA_000834455.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240109,SAMN03144976,,,,Bacilli,1,1987,Genome sequencing of Yersinia rohdei YRA,2015-02-09T00:00:00Z,1,,2015-03-12T13:52:58.775Z,2015-03-16T03:17:09.594Z,,,47.03,CP009787.1,4372253,Yersinia rohdei YRA,Complete,Yersinia,Germany,Negative,,,,,,,Germany,,Animal feces,,,,,29485,,,,,,,4025,,,-,NZ_CP009787.1,3781,,1,Los Alamos National Laboratory,611x,Illumina; PacBio; 454,,,,YRA,,,"Included in the study, passed QC/QA"
666,29486.11,"sample_type:cell culture;biomaterial_provider:Department of Primary Industries Parks Water and Environment, PO Box 46, Kings Meadows, Launceston, Tasmania 7249 Australia;identified_by:Jeremy Carson",,,,,not specified v. not specified,,PRJNA310959,SAMN03287980,,,,,1,2014,"This project explores the evolution and diversity of Yersinia ruckeri in Tasmania, Australia isolated from salmonid fish between 1987 and 2014",2017-06-13T00:00:00Z,,,2017-07-22T17:31:20.011Z,2017-07-22T17:31:20.011Z,,Enteric red mouth,47.71,CP017236,3856634,Yersinia ruckeri strain QMA0440,Complete,Yersinia,Australia: Tasmania,,,,,,"Atlantic salmon, Salmo salar",,Australia,,,,,,,29486,C,,,,,,3711,,,28348835,,3474,,1,The University of Queensland,not specified,not specified,,01b,,QMA0440,,,"Included in the study, passed QC/QA"
667,29486.115,sample_type:tissue sample,,,,GCA_002442495.1,HGAP v. v3,,PRJNA401093,SAMN07594326,,,,,1,Feb-1987,PacBio sequencing of the genome of Yersinia ruckeri NHV_3758 to investigate the DNA repeats in the invasin genes.,2017-10-12T00:00:00Z,,,2017-11-23T02:51:48.808Z,2017-11-23T02:51:48.808Z,,,47.61,CP023184,3766700,Yersinia ruckeri strain NHV_3758,Complete,Yersinia,Norway: Nordland county,,,,,,"Atlantic salmon, Salmo salar",,Norway,,Smolt-producing farm,,,,,29486,,,,,,,3581,,,28888816,,,,1,University of Oslo,186.0x,PacBio,,,,NHV_3758,,,"Included in the study, passed QC/QA"
668,29486.14,,,,,GCA_000834255.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA237812,SAMN03010447,,,,Bacilli,1,,Genome sequencing of Yersinia ruckeri YRB,2015-02-09T00:00:00Z,1,,2015-03-12T13:53:00.840Z,2015-03-16T03:17:09.594Z,,,47.5,CP009539.1,3605216,Yersinia ruckeri YRB,Complete,Yersinia,,Negative,,,,,Fish,,,,liver,,,,,29486,,,,,,,3296,,,-,NZ_CP009539.1,3133,,1,Los Alamos National Laboratory,305s,Illumina; 454,,,,YRB,,,"Included in the study, passed QC/QA"
669,29486.45,sample_type:Whole pure organism;biomaterial_provider:Dr. R.M.W. Stevenson;collected_by:unknown,,,,GCF_000964565.1,Celera assembler & DNASTAR SeqmanPro,,PRJNA278621,SAMN03421018,,,,Bacilli,1,1974,Sequence of fish the second serological variety of salmonid fish pathogen of enteric redmouth disease,2015-03-27T00:00:00Z,,,2016-01-17T15:51:40.824Z,2016-01-17T15:51:40.824Z,unknown,Enteric redmouth disease,47.64,CP011078,3699725,Yersinia ruckeri strain Big Creek 74,Complete,Yersinia,USA: Oregon,Negative,Aquatic,,,,"Chinook salmon, Oncorhynchus tshawytscha",,United States,,aquatic,,,,Yes,29486,18,,,,,Facultative,3490,,,,NZ_CP011078.1,3136,,1,"College of Biological Science, University of Guelph",134,PacBio; Sanger dideoxy,,,,Big Creek 74,Mesophilic,,"Included in the study, passed QC/QA"
670,349746.12,sample_type:Microbial isolate culture,,,,GCF_000834845.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240101,SAMN03177051,,,,Bacilli,1,,Genome sequencing of Yersinia pestis Angola,2015-05-28T00:00:00Z,,,2016-01-17T15:43:27.653Z,2016-01-17T15:43:27.653Z,,,47.62,"CP009935,CP009937,CP009934,CP009936",4674610,Yersinia pestis Angola,Complete,Yersinia,,Negative,,,,,,,,,,,,,,349746,,,,,,,4591,,3,25931590,"NZ_CP009935.1,NZ_CP009937.1,NZ_CP009934.1,NZ_CP009936.1",4304,,4,Los Alamos National Laboratory,367x,Illumina; PacBio; 454,,,,Angola,,,"Included in the study, passed QC/QA"
671,349746.9,,,,,GCA_000018805.1,,,PRJNA16067,,,,,Rod,1,,"Yersinia pestis strain Angola. This strain was isolated prior to 1985 and belongs to the antiqua biovar. It can ferment rhamnonse and melibiose which is a property usually associated with Yersinia pseudotuberculosis. Strain Angola belongs to a group of atypical Yersinia pestis strains with genotypic similarities that are intermediate between Y. pestis and Y. pseudotuberuclosis strains. Genotypic studies indicate that strain Angola is the oldest Y. pestis strain analyzed to date. It carries three plasmids that are similar to other Y. pestis plasmids but have aberrant sizes. The critical virulence factor, the V antigen, is different than that encoded by typical strains of Y. pestis and there is a deletion that affects the F1 operon. Strain Angola has been shown to be virulent by aerosol in mice.Genome sequencing was at 8X coverage and was obtained from three libraries- a medium insert library (6-8 kb; 10,694 reads), a large insert library (10-12 kb; 45,354 reads), and a fosmid library (38-50 kb; 16,013 reads). ",2007-12-12T00:00:00Z,,,2014-12-08T22:13:51.187Z,2015-03-16T03:17:09.594Z,,Bubonic plague,47.6,"CP000901,CP000900,CP000902",4687014,Yersinia pestis Angola,Complete,Yersinia,,-,Multiple,,,,,isolated prior to 1985 and belongs to the antiqua biovar,,,,,,MLST.Yersinia_spp.79,,349746,-,Yersinia pestis Angola,,,,Facultative,4874,,2,20061468,"NC_010159,NC_010158,NC_010157",4040,,3,TIGR,,,complete,,,Angola,Mesophilic,,"Included in the study, passed QC/QA"
672,349747.9,,,,,GCA_000016945.1,,,PRJNA16070,SAMN02604043,,,,Rod,1,1966,"Yersinia pseudotuberculosis strain IP 31758. This strain is serotype 1b and was isolated in 1966 from the stools of a patient presenting with scarlet-like fever in the Primorski region of the former USSR. The strain was sent to the Institut Pasteur by Dr Timofeeva (Antiplague Institute, Irkoutsk).Two libraries were constructed: a small insert library (4-5 kb) and a large insert library (10-12 kb) from which 11,818 and 49,665 reads were sequenced respectively. ",2007-07-23T00:00:00Z,,,2014-12-08T22:13:52.198Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,47.2,"CP000720,CP000719,CP000718",4935125,Yersinia pseudotuberculosis IP 31758,Complete,Yersinia,Primorski region of the former USSR,-,Multiple,,,,"Human, Homo sapiens",isolated in 1966 from the stools of a patient presenting with scarlet-like fever in the Primorski region of the former USSR,Russia,,the stools of a patient presenting with scarlet-like fever,,,MLST.Yersinia_pseudotuberculosis.2,Yes,349747,-,Yersinia pseudotuberculosis IP 31758,,,,Facultative,4749,,2,17784789,"NC_009708,NC_009705,NC_009704",4324,,3,TIGR,,,complete,serovar 1b,,IP31758,Mesophilic,,"Included in the study, passed QC/QA"
673,360102.1,,,,,GCA_000013825.1,,,PRJNA16645,,,,,Rod,1,,"Yersinia pestis Nepal516.This strain, isolated from a soil sample from the Republic of Congo, is being sequenced for comparative genome analysis of Yersinia pestis strains isolated from different parts of the world. ",2006-06-09T00:00:00Z,,,2014-12-08T22:13:51.197Z,2015-03-16T03:17:09.594Z,,Bubonic plague,47.7,"CP000308,CP000310,CP000311,CP000309",4879836,Yersinia pestis Antiqua,Complete,Yersinia,Republic of Congo,-,Multiple,,,,,"isolated from a soil sample from the Republic of Congo, is being sequenced for comparative genome analysis of Yersinia pestis strains isolated from different parts of the world",Republic of the Congo,,soil sample from the Republic of Congo,,,MLST.Yersinia_spp.79,,360102,-,Yersinia pestis Antiqua,,,,Facultative,5018,,3,16740952,"NC_008150,NC_008121,NC_008122,NC_008120",4364,Non-halophilic,4,DOE Joint Genome Institute,,,complete,,,Antiqua,Mesophilic,,"Included in the study, passed QC/QA"
674,360102.15,sample_type:Microbial isolate culture,,,,GCF_000834825.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240103,SAMN03174669,,,,Bacilli,1,1965,Genome sequencing of Yersinia pestis Antiqua,2015-05-28T00:00:00Z,,,2016-01-17T15:43:27.271Z,2016-01-17T15:43:27.271Z,,,47.71,"CP009906,CP009905,CP009904,CP009903",4884396,Yersinia pestis Antiqua,Complete,Yersinia,Republic of the Congo,Negative,,,,,"Human, Homo sapiens",,Republic of the Congo,,Human clinical sample,,,,,360102,,,,,,,4780,,3,25931590,"NZ_CP009906.1,NZ_CP009905.1,NZ_CP009904.1,NZ_CP009903.1",4367,,4,Los Alamos National Laboratory,477x,Illumina; PacBio; 454,,,,Antiqua,,,"Included in the study, passed QC/QA"
675,367190.3,,,,,GCA_000582515.1,Bioedit v. 06022014,,PRJNA238010,,,,,Bacilli,1,,Y. similis isolates may cause diagnostic problems as they cannot be biochemically distinguished from Y. pseudotuberculosis by commercial test kits.,2014-02-26T00:00:00Z,, ,2014-12-08T22:13:52.265Z,2015-03-16T03:17:09.594Z,,,47.0098,"CP007230.1,CP007231.1",4964409,Yersinia similis strain 228,Complete,Yersinia,Germany,Negative,Terrestrial,,,,"Rabbit, Oryctolagus cuniculus",,Germany,,feces,,,,Yes,367190,,Yersinia similis,,,,Unknown,4718,,1,,"NZ_CP007230.1,NZ_CP007231.1",4135,Unknown,2,Friedrich-Loeffler-Institut,100x,PacBio,complete,,No,228,Unknown,,"Included in the study, passed QC/QA"
676,377628.1,,,,,GCA_000013805.1,,,PRJNA16646,,,,,Rod,1,,"Yersinia pestis Nepal516.This strain, isolated from a soil sample from Nepal, is being sequenced for comparative genome analysis of Yersinia pestis strains isolated from different parts of the world.",2006-06-09T00:00:00Z,,,2014-12-08T22:13:51.315Z,2015-03-16T03:17:09.594Z,,Bubonic plague,47.6,"CP000305,CP000306,CP000307",4646286,Yersinia pestis Nepal516,Complete,Yersinia,Nepal,-,Multiple,,,,,"isolated from a soil sample from Nepal, is being sequenced for comparative genome analysis of Yersinia pestis strains isolated from different parts of the world",Nepal,,soil sample from Nepal,,,MLST.Yersinia_spp.79,,377628,-,Yersinia pestis Nepal516,,,,Facultative,4684,,2,16740952,"NC_008149,NC_008118,NC_008119",4094,Non-halophilic,3,DOE Joint Genome Institute,,,complete,,,Nepal516,Mesophilic,,"Included in the study, passed QC/QA"
677,386656.14,,,,,GCF_000834315.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA239345,SAMN03121016,,,,Bacilli,1,,Genome sequencing of Yersinia pestis Pestoides F,2015-05-28T00:00:00Z,,,2016-01-17T15:43:25.353Z,2016-01-17T15:43:25.353Z,,,47.73,"CP009715,CP009713,CP009714",4728318,Yersinia pestis Pestoides F,Complete,Yersinia,USSR,Negative,,,,,,,USSR,,,,,,,386656,,,,,,,4549,,2,25931590,"NZ_CP009715.1,NZ_CP009713.1,NZ_CP009714.1",4148,,3,Los Alamos National Laboratory,723x,Illumina; PacBio; 454,,,,Pestoides F,,,"Included in the study, passed QC/QA"
678,386656.9,,,,,GCA_000016445.1,,,PRJNA16700,,,,,Rod,1,,Yersinia pestis Pestoides F.This strain lacks a plasminogen activator and is virulent by the aerosol route. The genome of this organism is being sequenced for a comparative genomics project.,2007-04-13T00:00:00Z,,,2014-12-08T22:13:51.895Z,2015-03-16T03:17:09.594Z,,Bubonic plague,47.7,"CP000668,CP000670,CP000669",4725862,Yersinia pestis Pestoides F,Complete,Yersinia,,-,Multiple,,,,,,,,,,,MLST.Yersinia_spp.79,,386656,-,Yersinia pestis Pestoides F,,,,Facultative,4855,,2,,"NC_009381,NC_009378,NC_009377",4069,Non-halophilic,3,DOE Joint Genome Institute,,,complete,,,Pestoides F,Mesophilic,,"Included in the study, passed QC/QA"
679,393305.7,,,,,GCA_000009345.1,,,PRJNA190,SAMEA1705958,,,,Rod,1,,Yersinia enterocolitica (type 0:8) strain 8081. This isolate (strain 8081; NCTC 13174) is a mouse-lethal serotype of Yersinia enterocolitica that contains a high pathogenicity island (HPI) that encodes an iron uptake system (yersiniabactin) and a type II secretion system.,2007-01-12T00:00:00Z,,NCTC 13174,2014-12-08T22:13:50.971Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,47.2,"AM286415,AM286416",4683620,Yersinia enterocolitica subsp. enterocolitica 8081,Complete,Yersinia,,-,Multiple,,,,,,,,,,,MLST.Yersinia_spp.1,Yes,393305,28-30,Yersinia enterocolitica subsp. enterocolitica 8081,,,,Facultative,4479,,1,"12834539,17173484","NC_008800,NC_008791",4051,,2,Wellcome Trust Sanger Institute,,,complete,,,8081,Mesophilic,,"Included in the study, passed QC/QA"
680,502800.11,,,,,GCF_000834375.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA239354,SAMN03144706,,,,Bacilli,1,,Genome sequencing of Yersinia pseudotuberculosis YPIII,2015-05-28T00:00:00Z,,,2016-01-17T15:43:25.730Z,2016-01-17T15:43:25.730Z,,,47.53,CP009792,4689436,Yersinia pseudotuberculosis YPIII,Complete,Yersinia,,Negative,,,,,,,,,,,,,Yes,502800,,,,,,,4414,,,25931590,NZ_CP009792.1,4054,,1,Los Alamos National Laboratory,391x,Illumina; PacBio; 454,,O3,,YPIII,,,"Included in the study, passed QC/QA"
681,502800.6,,,,,GCA_000019465.1,,,PRJNA28743,,,,,Rod,1,,Yersinia pseudotuberculosis YPIII. This strain is an O3 serotype strain and is unable to survive in mouse J774A.1 macrophages. This strain will be used for comparative analysis.,2008-03-11T00:00:00Z,,,2014-12-08T22:13:52.236Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,47.5,CP000950,4689441,Yersinia pseudotuberculosis YPIII,Complete,Yersinia,,-,Multiple,,,,,,,,,,,MLST.Yersinia_pseudotuberculosis.14,Yes,502800,-,Yersinia pseudotuberculosis YPIII,,,,Facultative,4581,,,,NC_010465,4192,,1,US DOE Joint Genome Institute|DOE Joint Genome Institute|JGI-PSF,,,complete,serovar strain,,YPIII,Mesophilic,Yes,"Included in the study, passed QC/QA"
682,502801.1,,,,,GCF_000834475.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA239343,SAMN03144729,,,,Bacilli,1,,Genome sequencing of Yersinia pseudotuberculosis PB1/+,2015-05-28T00:00:00Z,,,2016-01-17T15:43:26.041Z,2016-01-17T15:43:26.041Z,,,47.49,"CP009780,CP009779",4765387,Yersinia pseudotuberculosis PB1/+,Complete,Yersinia,,Negative,,,,,,,,,,,,,Yes,502801,,,,,,,4462,,1,25931590,"NZ_CP009780.1,NZ_CP009779.1",4099,,2,Los Alamos National Laboratory,617x,Illumina; PacBio; 454,,1,,PB1/+,,,"Included in the study, passed QC/QA"
683,502801.6,,,,,GCA_000020085.1,,,PRJNA28745,,,,,Rod,1,,Yersinia pseudotuberculosis PB1/+. This is a serotype IB strain and will be used for comparative analysis,2008-04-25T00:00:00Z,,,2014-12-08T22:13:52.227Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,47.5,"CP001048,CP001049",4765431,Yersinia pseudotuberculosis PB1/+,Complete,Yersinia,,-,Multiple,,,,,,,,,,,MLST.Yersinia_pseudotuberculosis.42,Yes,502801,-,Yersinia pseudotuberculosis PB1/+,,,,Facultative,4638,,1,,"NC_010634,NC_010635",4237,,2,US DOE Joint Genome Institute|DOE Joint Genome Institute|JGI-PSF,,,complete,serovar IB,,PB1/+,Mesophilic,,"Included in the study, passed QC/QA"
684,547048.4,,,,,GCA_000186725.1,,,PRJNA30505,SAMN02603222,,,,Rod-shaped,1,,"Animal Pathogen, Human Pathogen, Medical, Biothreat",2011-01-25T00:00:00Z,,,2014-12-08T22:13:51.962Z,2015-03-16T03:17:09.594Z,,Bubonic plague;Pneumonic plague,48,"CP001608.1,CP001611.1,CP001609.1,CP001610.1",4709501,Yersinia pestis biovar Medievalis str. Harbin 35,Complete,Yersinia,China,,Host,,,,"Human, Homo sapiens",,China,,human isolate from China,,,MLST.Yersinia_spp.79,Motile,547048,,Yersinia pestis biovar Medievalis str. Harbin 35,,,,Facultative,4996,,3,,"NC_017265.1,NC_017263.1,NC_017266.1,NC_017264.1",,,4,Los Alamos National Lab,,Sanger,complete,Medievalis,Nonsporulating,Harbin 35,Mesophile,,"Included in the study, passed QC/QA"
685,630.128,collected_by:Ministry of Food and Drug Safety,,,,GCA_001304755.1,SMRT Portal v. 2.2.0,,PRJNA260989,SAMN03078687,,,,,1,2014-06-01,Make the compelte genome sequence,2015-10-01T00:00:00Z,,,2016-01-17T17:12:58.912Z,2016-01-17T17:12:58.912Z,,,47.04,"CP009456,CP009457",4837316,Yersinia enterocolitica strain FORC-002,Complete,Yersinia,South Korea,,,,,,,,South Korea,,Food,,,,,630,,,,,,,4575,,1,,"NZ_CP009456.1,NZ_CP009457.1",4190,,2,Seoul National Univerisity,,PacBio,,,,FORC_002,,,"Included in the study, passed QC/QA"
686,630.129,,,,,GCF_001305635.1,CLC Genomics Workbench v. 8.0;,,PRJNA281164,SAMN03490473,,,,,1,1991,-,2015-10-02T00:00:00Z,,,2016-01-17T17:13:09.591Z,2016-01-17T17:13:09.591Z,,,46.95,"CP011286,CP011287",4651078,Yersinia enterocolitica strain KNG22703,Complete,Yersinia,Belgium,,,,,,"Human, Homo sapiens",,Belgium,,,,,,,630,C,,,,,,4428,,1,,"NZ_CP011286.1,NZ_CP011287.1",4015,,2,University of Oxford,190,Illumina,,,,KNG22703,,,"Included in the study, passed QC/QA"
687,630.15,collected_by:Maria Fredriksson-Ahomaa,,,,GCF_001708555.1,PacBio SMRT analysis v. 2.3.0,,PRJNA335326,SAMN05440573,,,,,1,2015,Yersiniosis is an important zoonotic disease that can be transmitted from food animal reservoirs to humans through meat products contaminated with Yersinia enterocolitica. YE7 is a Yersinia enterocolitica strain isolated from a Finnish sheep sampled at the slaughterhouse. The genome sequence of this strain will be determined and used for comparative analysis with genomes of other sequenced Yersinia enterocolitica strains.,2016-08-23T00:00:00Z,,,2016-09-11T21:27:48.745Z,2016-09-11T21:27:48.745Z,,,46.81,"CP016935,CP016934,CP016936",4850821,Yersinia enterocolitica strain YE7,Complete,Yersinia,Finland,,,,,,Sheep,isolated from a Finnish sheep sampled at the slaughterhouse,Finland,,Fecal samples from slaughtered sheep,,,,,630,,,,,,,4983,,2,,"NZ_CP016935.1,NZ_CP016934.1,NZ_CP016936.1",4408,,3,"University of Zurich, Vetsuisse Faculty",215,PacBio,,O:3,,YE7,,,"Included in the study, passed QC/QA"
688,630.151,"collected_by:Institute fro Food Safety and Hygiene, University of Zurich",,,,GCF_001708575.1,PacBio SMRT analysis v. 2.3.0,,PRJNA329498,SAMN05413581,,,,,1,2011-09,Yersiniosis is an important zoonotic disease that can be transmitted from food animal reservoirs to humans through meat products contaminated with Yersinia enterocolitica. YE 165 is a Yersinia enterocolitica strain isolated from a Swiss alpine Ibex. The genome sequence of this strain will be determined and used for comparative analysis with genomes of other sequenced Yersinia enterocolitica strains.,2016-08-23T00:00:00Z,,,2016-09-11T21:26:35.745Z,2016-09-11T21:26:35.745Z,,,46.82,"CP016931,CP016932,CP016933",4885782,Yersinia enterocolitica strain YE165,Complete,Yersinia,Switzerland,,,,,,,isolated from a Swiss alpine Ibex,Switzerland,,Swiss alpine Ibex feces,,,,,630,,,,,,,5017,,2,,"NZ_CP016931.1,NZ_CP016932.1,NZ_CP016933.1",4445,,3,"University of Zurich, Vetsuisse Faculty",203,PacBio,,"O:1,2,3",,YE165,,,"Included in the study, passed QC/QA"
689,630.152,collected_by:Maria Fredriksson-Ahomaa,,,,GCF_001708595.1,PacBio SMRT analysis v. 2.3.0,,PRJNA335325,SAMN05440514,,,,,1,2015,Yersiniosis is an important zoonotic disease that can be transmitted from food animal reservoirs to humans through meat products contaminated with Yersinia enterocolitica. YE6 is a Yersinia enterocolitica strain isolated from a Finnish sheep sampled at the slaughterhouse. The genome sequence of this strain will be determined and used for comparative analysis with genomes of other sequenced Yersinia enterocolitica strains.,2016-08-23T00:00:00Z,,,2016-09-11T21:30:42.723Z,2016-09-11T21:30:42.723Z,,,46.8,"CP016937,CP016938",4923138,Yersinia enterocolitica strain YE6,Complete,Yersinia,Finland,,,,,,Sheep,isolated from a Finnish sheep sampled at the slaughterhouse,Finland,,Fecal samples from slaughtered sheep,,,,,630,,,,,,,5061,,1,,"NZ_CP016937.1,NZ_CP016938.1",4471,,2,"University of Zurich, Vetsuisse Faculty",212,PacBio,,O:3,,YE6,,,"Included in the study, passed QC/QA"
690,630.153,collected_by:Maria Fredriksson-Ahomaa,,,,GCF_001708615.1,PacBio SMRT analysis v. 2.3.0,,PRJNA335324,SAMN05440511,,,,,1,2015,Yersiniosis is an important zoonotic disease that can be transmitted from food animal reservoirs to humans through meat products contaminated with Yersinia enterocolitica. YE5 is a Yersinia enterocolitica strain isolated from a Finnish sheep sampled at the slaughterhouse. The genome sequence of this strain will be determined and used for comparative analysis with genomes of other sequenced Yersinia enterocolitica strains.,2016-08-23T00:00:00Z,,,2016-09-11T21:31:51.899Z,2016-09-11T21:31:51.899Z,,,46.8,"CP016940,CP016939,CP016941",4787042,Yersinia enterocolitica strain YE5,Complete,Yersinia,Finland,,,,,,Sheep,isolated from a Finnish sheep sampled at the slaughterhouse,Finland,,Fecal samples from slaughtered sheep,,,,,630,,,,,,,4897,,2,,"NZ_CP016940.1,NZ_CP016939.1,NZ_CP016941.1",4339,,3,"University of Zurich, Vetsuisse Faculty",198,PacBio,,O:3,,YE5,,,"Included in the study, passed QC/QA"
691,630.154,collected_by:Maria Fredriksson-Ahomaa,,,,GCF_001708635.1,PacBio SMRT analysis v. 2.3.0,,PRJNA339119,SAMN05440467,,,,,1,2015,Yersiniosis is an important zoonotic disease that can be transmitted from food animal reservoirs to humans through meat products contaminated with Yersinia enterocolitica. YE1 is a Yersinia enterocolitica strain isolated from a Finnish sheep sampled at the slaughterhouse. The genome sequence of this strain will be determined and used for comparative analysis with genomes of other sequenced Yersinia enterocolitica strains,2016-08-23T00:00:00Z,,,2016-09-11T21:33:45.834Z,2016-09-11T21:33:45.834Z,,,46.82,"CP016945,CP016946,CP016947",4841962,Yersinia enterocolitica strain YE1,Complete,Yersinia,Finland,,,,,,Sheep,isolated from a Finnish sheep sampled at the slaughterhouse,Finland,,Sheep fecal sample,,,,,630,,,,,,,4958,,2,,"NZ_CP016945.1,NZ_CP016946.1,NZ_CP016947.1",4393,,3,"University of Zurich, Vetsuisse Faculty",280,PacBio,,O:3,,YE1,,,"Included in the study, passed QC/QA"
692,630.155,collected_by:Maria Fredriksson-Ahomaa,,,,GCF_001708655.1,PacBio SMRT analysis v. 2.3.0,,PRJNA335321,SAMN05440502,,,,,1,2015,Yersiniosis is an important zoonotic disease that can be transmitted from food animal reservoirs to humans through meat products contaminated with Yersinia enterocolitica. YE3 is a Yersinia enterocolitica strain isolated from a Finnish sheep sampled at the slaughterhouse. The genome sequence of this strain will be determined and used for comparative analysis with genomes of other sequenced Yersinia enterocolitica strains.,2016-08-23T00:00:00Z,,,2016-09-11T21:32:26.422Z,2016-09-11T21:32:26.422Z,,,46.82,"CP016944,CP016942,CP016943",4838744,Yersinia enterocolitica strain YE3,Complete,Yersinia,Finland,,,,,,Sheep,isolated from a Finnish sheep sampled at the slaughterhouse,Finland,,Fecal samples from slaughtered sheep,,,,,630,,,,,,,4970,,2,,"NZ_CP016944.1,NZ_CP016942.1,NZ_CP016943.1",4390,,3,"University of Zurich, Vetsuisse Faculty",196,PacBio,,O:3,,YE3,,,"Included in the study, passed QC/QA"
693,630.16,,,,,GCA_000834195.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240087,SAMN03010445,,,,Bacilli,1,,Genome sequencing of Yersinia enterocolitica WA,2015-02-09T00:00:00Z,2,,2015-03-12T14:01:01.061Z,2015-03-16T03:17:09.594Z,,,47.23,"CP009367.1,CP009366.1",4615412,Yersinia enterocolitica WA,Complete,Yersinia,USA: New York,Negative,,,,,"Human, Homo sapiens",,United States,,,,,,,630,,,,,,,4337,,1,-,"NZ_CP009367.1,NZ_CP009366.1",4118,,2,Los Alamos National Laboratory,388x,Illumina; 454,,,,WA,,,"Included in the study, passed QC/QA"
694,630.17,,,,,GCA_000834735.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240088,SAMN03161068,,,,Bacilli,1,,Genome sequencing of Yersinia enterocolitica 2516-87,2015-02-09T00:00:00Z,2,,2015-03-12T14:01:01.818Z,2015-03-16T03:17:09.594Z,,,46.97,"CP009838.1,CP009837.1",4603945,Yersinia enterocolitica 2516-87,Complete,Yersinia,,Negative,,,,,,,,,,,,,,630,,,,,,,4316,,1,-,"NZ_CP009838.1,NZ_CP009837.1",4067,,2,Los Alamos National Laboratory,488x,Illumina; PacBiol 454,,,,2516-87,,,"Included in the study, passed QC/QA"
695,630.18,,,,,GCA_000834795.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240089,SAMN03160540,,,,Bacilli,1,,Genome sequencing of Yersinia enterocolitica 8081,2015-02-09T00:00:00Z,2,,2015-03-12T14:01:02.146Z,2015-03-16T03:17:09.594Z,,,47.2,"CP009846.1,CP009845.1",4685386,Yersinia enterocolitica 8081,Complete,Yersinia,USA: Ohio,Negative,,,,,"Human, Homo sapiens",,United States,,Fatal septicemia (human clinicalisolate),,,,,630,,,,,,,4393,,1,-,"NZ_CP009846.1,NZ_CP009845.1",4203,,2,Los Alamos National Laboratory,538x,Illumina; PacBio; 454,,,,8081,,,"Included in the study, passed QC/QA"
696,630.33,biomaterial_provider:USAMRIID,,,,GCF_000755055.1,Newbler v. 2.6; Velvet v. 1.2.08; AllPaths,,PRJNA243535,SAMN02887290,,,,Coccobacilli,,,Yersinia enterocolitica ATCC 9610 Genome Assembly,2014-09-16T00:00:00Z,1,ATCC:9610,2016-01-17T15:40:02.222Z,2016-01-17T15:40:02.222Z,,,47.28,JPDV01000000,4538553,Yersinia enterocolitica strain ATCC 9610,Complete,Yersinia,USA: New York,Negative,,,,,"Human, Homo sapiens",,United States,,,,,,,630,,,,,,,4367,,,,,4084,,1,Los Alamos National Laboratory,200.0x,454; Illumina,,,,ATCC 9610,,,"Included in the study, passed QC/QA"
697,630.34,collected_by:Seoul National University,,,,GCF_000987925.1,HGAP assembly v. 2.2,,PRJNA279015,SAMN03434891,,,,,1,2013,Genome would be useful to elucidate virulence factors that might be useful for development of new biomarkers for rapid detection of this pathogen in foods,2015-05-05T00:00:00Z,,,2016-01-17T15:56:51.929Z,2016-01-17T15:56:51.929Z,,,47.04,"CP011118,CP011119",4837317,Yersinia enterocolitica strain FORC_002,Complete,Yersinia,,,,,,,Flatfish,,,,gill of flatfish,,,,,630,,,,,,,4580,,1,,"NZ_CP011118.1,NZ_CP011119.1",4236,,2,Seoul National University,13.3x,PacBio,,,,FORC_002,,,"Included in the study, passed QC/QA"
698,631.3,,,,,GCA_000834515.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240097,SAMN03160554,,,,Bacilli,1,,Genome sequencing of Yersinia intermedia Y228,2015-02-09T00:00:00Z,1,,2015-03-12T14:01:02.475Z,2015-03-16T03:17:09.594Z,,,47.47,CP009801.1,4859749,Yersinia intermedia Y228,Complete,Yersinia,,Negative,,,,,,,,,,,,,Yes,631,,,,,,,4472,,,-,NZ_CP009801.1,4300,,1,Los Alamos National Laboratory,487x,Illumina; PacBio; 454,,,,Y228,,,"Included in the study, passed QC/QA"
699,632.125,,,,,GCA_000834235.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240104,SAMN03074081,,,,Bacilli,1,,Genome sequencing of Yersinia pestis PBM19,2015-02-09T00:00:00Z,4,,2015-03-12T14:01:02.847Z,2015-03-16T03:17:09.594Z,,,47.64,"CP009492.1,CP009491.1,CP009490.1,CP009489.1",4861517,Yersinia pestis PBM19,Complete,Yersinia,,Negative,,,,,,,,,,,,,,632,,,,,,,4686,,3,-,"NZ_CP009492.1,NZ_CP009491.1,NZ_CP009490.1,NZ_CP009489.1",4351,,4,Los Alamos National Laboratory,626x,Illumina; PacBio,,,,PBM19,,,"Included in the study, passed QC/QA"
700,632.126,,,,,GCA_000834275.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240100,SAMN02769655,,,,Bacilli,1,1940,Genome sequencing of Yersinia pestis Harbin35,2015-02-09T00:00:00Z,4,,2015-03-12T14:01:03.171Z,2015-03-16T03:17:09.594Z,,,47.59,"CP009704.1,CP009701.1,CP009703.1,CP009702.1",4709246,Yersinia pestis Harbin35,Complete,Yersinia,China: Manchuria,Negative,,,,,,,China,,,,,,,632,,,,,,,4544,,3,-,"NZ_CP009704.1,NZ_CP009701.1,NZ_CP009703.1,NZ_CP009702.1",4286,,4,Los Alamos National Laboratory,366x,Illumina; PacBio,,,,Harbin35,,,"Included in the study, passed QC/QA"
701,632.127,,,,,GCA_000834335.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA239341,SAMN03120838,,,,Bacilli,1,1954,Genome sequencing of Yersinia pestis Shasta,2015-02-09T00:00:00Z,4,,2015-03-12T14:01:03.511Z,2015-03-16T03:17:09.594Z,,,47.63,"CP009723.1,CP009721.1,CP009722.1,CP009724.1",4835409,Yersinia pestis Shasta,Complete,Yersinia,USA: California,Negative,,,,,"Human, Homo sapiens",,United States,,Human clinical,,,,,632,,,,,,,4592,,3,-,"NZ_CP009723.1,NZ_CP009721.1,NZ_CP009722.1,NZ_CP009724.1",4288,,4,Los Alamos National Laboratory,562x,Illumina; PacBio; 454,,,,Shasta,,,"Included in the study, passed QC/QA"
702,632.128,,,,,GCA_000834495.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240085,SAMN03145064,,,,Bacilli,1,2002,Genome sequencing of Yersinia pestis El Dorado,2015-02-09T00:00:00Z,4,,2015-03-12T14:01:04.319Z,2015-03-16T03:17:09.594Z,,,47.64,"CP009785.1,CP009784.1,CP009782.1,CP009783.1",4838262,Yersinia pestis El Dorado,Complete,Yersinia,USA,Negative,,,,,,,United States,,Human clinical sample,,,,,632,,,,,,,4591,,3,-,"NZ_CP009785.1,NZ_CP009784.1,NZ_CP009782.1,NZ_CP009783.1",4293,,4,Los Alamos National Laboratory,688x,Illumina; PacBio; 454,,,,El Dorado,,,"Included in the study, passed QC/QA"
703,632.129,,,,,GCA_000834775.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240106,SAMN03161124,,,,Bacilli,1,1967,Genome sequencing of Yersinia pestis Dodson,2015-02-09T00:00:00Z,3,,2015-03-12T14:01:04.636Z,2015-03-16T03:17:09.594Z,,,47.6,"CP009844.1,CP009842.1,CP009843.1",4777968,Yersinia pestis Dodson,Complete,Yersinia,"USA: Tuba City, AZ",Negative,,,,,"Human, Homo sapiens",,United States,,Clinical Sample,,,,,632,,,,,,,4552,,2,-,"NZ_CP009844.1,NZ_CP009842.1,NZ_CP009843.1",4257,,3,Los Alamos National Laboratory,522x,Illumina; PacBio; 454,,,,Dodson,,,"Included in the study, passed QC/QA"
704,632.13,,,,,GCA_000834885.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240108,SAMN03216612,,,,Bacilli,4,,Genome sequencing of Yersinia pestis Nicholisk 41,2015-02-09T00:00:00Z,4,,2015-03-12T14:01:04.962Z,2015-03-16T03:17:09.594Z,,,47.59,"CP009991.1,CP009990.1,CP009988.1,CP009989.1",4700481,Yersinia pestis Nicholisk 41,Complete,Yersinia,,Negative,,,,,,,,,,,,,,632,,,,,,,4516,,3,-,"NZ_CP009991.1,NZ_CP009990.1,NZ_CP009988.1,NZ_CP009989.1",4160,,4,Los Alamos National Laboratory,534x,Illumina; PacBio; 454,,,,Nicholisk 41,,,"Included in the study, passed QC/QA"
705,632.131,,,,,GCA_000834905.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240107,SAMN03216587,,,,Bacilli,1,,Genome sequencing of Yersinia pestis Java9,2015-02-09T00:00:00Z,5,,2015-03-12T14:01:05.674Z,2015-03-16T03:17:09.594Z,,,47.54,"CP009996.1,CP009994.1,CP009992.1,CP009995.1,CP009993.1",4830559,Yersinia pestis Java9,Complete,Yersinia,Indonesia,Negative,,,,,Rat,,Indonesia,,,,,,,632,,,,,,,4588,,4,-,"NZ_CP009996.1,NZ_CP009994.1,NZ_CP009992.1,NZ_CP009995.1,NZ_CP009993.1",4288,,5,Los Alamos National Laboratory,590x,Illumina; PacBio; 454,,,,Java9,,,"Included in the study, passed QC/QA"
706,632.132,,,,,GCA_000835005.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240084,SAMN03256395,,,,Bacilli,1,1985,Genome sequencing of Yersinia pestis Nairobi,2015-02-09T00:00:00Z,1,,2015-03-12T14:01:06.628Z,2015-03-16T03:17:09.594Z,,,46.7,"CP010293.1,CP010294.1",4572683,Yersinia pestis Nairobi,Complete,Yersinia,Kenya: Nairobi,Negative,,,,,,,Kenya,,Wild Rat,,,,,632,,,,,,,4161,,1,-,"NZ_CP010293.1,NZ_CP010294.1",3973,,2,Los Alamos National Laboratory,595x,Illumina; PacBio; 454,,,,Nairobi,,,"Excluded from the study, failed QC/QA."
707,632.152,,,,,GCF_000970105.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240083,SAMN03160723,,,,Bacilli,1,2007,Genome sequencing of Yersinia pestis KIM,2015-05-28T00:00:00Z,,,2016-01-17T15:53:07.508Z,2016-01-17T15:53:07.508Z,,,47.65,"CP009836,CP009835,CP009834,CP009833",4787503,Yersinia pestis strain KIM5,Complete,Yersinia,USA: Kentucky,Negative,,,,,,,United States,,Electroporation of Y pestis Kim6+ in pCD1Ap+,,,,,632,,,,,,,4598,,3,25931590,,4222,,4,Los Alamos National Laboratory,489x,Illumina; PacBio; 454,,,,KIM5,,,"Included in the study, passed QC/QA"
708,632.175,collected_by:USAMRIID DSD,,,,GCF_001693595.1,HGAP v. 2.3,,PRJNA326509,SAMN05282282,,,,,1,06-Jun-2016,Investigation of AMR in Yersinia pestis,2016-07-26T00:00:00Z,,,2016-09-11T16:27:38.948Z,2016-09-11T16:27:38.948Z,,,47.59,"CP016273,CP016274,CP016275,CP016276",4778555,Yersinia pestis strain Cadman,Complete,Yersinia,"USA: Gallup, NM",,,,,Plague,"Human, Homo sapiens",,United States,,,,,,,632,,,,,,,4734,,3,,"NZ_CP016273.1,NZ_CP016274.1,NZ_CP016275.1,NZ_CP016276.1",4359,,4,USAMRIID,450x,PacBio,,,,Cadman,,,"Included in the study, passed QC/QA"
709,632.205,sample_type:cell culture,,,,GCA_002005285.1,Canu v. 1.3,,PRJNA357858,SAMN06161235,,,,,1,2015-12-08,Yersinia pestis 195/P nanopore assembly and sequencing benchmarking,2017-02-21T00:00:00Z,,,2017-03-20T08:24:35.039Z,2017-03-20T08:24:35.039Z,,,47.65,"CP019708,CP019710,CP019709,CP019711",4831198,Yersinia pestis strain 195/P,Complete,Yersinia,,,,,,,,,,,lab strain,,,MLST.Yersinia_spp.79,,632,,,,,,,4918,,3,,,,,4,NHGRI/NIH,40.0x,Oxford Nanopore,,,,195/P,,,"Included in the study, passed QC/QA"
710,633.36,,,,,GCA_000834355.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA239351,SAMN03140242,,,,Bacilli,1,,Genome sequencing of Yersinia pseudotuberculosis MD67,2015-02-09T00:00:00Z,1,,2015-03-12T14:01:06.972Z,2015-03-16T03:17:09.594Z,,,47.54,CP009757.1,4729753,Yersinia pseudotuberculosis MD67,Complete,Yersinia,,Negative,,,,,,,,,,,,,Yes,633,,,,,,,4363,,,-,NZ_CP009757.1,4054,,1,Los Alamos National Laboratory,552x,Illumina; PacBio; 454,,,No,MD67,,,"Included in the study, passed QC/QA"
711,633.37,,,,,GCA_000834415.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA239350,SAMN03140184,,,,,1,,Genome sequencing of Yersinia pseudotuberculosis EP2/+,2015-02-09T00:00:00Z,2,,2015-03-12T14:01:07.274Z,2015-03-16T03:17:09.594Z,,,47.43,"CP009759.1,CP009758.1",4774559,Yersinia pseudotuberculosis EP2/+,Complete,Yersinia,,Negative,,,,,,,,,,,,,Yes,633,,,,,,,4446,,1,-,"NZ_CP009759.1,NZ_CP009758.1",4099,,2,Los Alamos National Laboratory,567x,Illumina; PacBio; 454,,,No,EP2/+,,,"Included in the study, passed QC/QA"
712,633.38,,,,,GCA_000834435.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA239355,SAMN03144835,,,,Bacilli,1,,Genome sequencing of Yersinia pseudotuberculosis 1,2015-02-09T00:00:00Z,1,,2015-03-12T14:01:08.074Z,2015-03-16T03:17:09.594Z,,,47.62,CP009786.1,4728337,Yersinia pseudotuberculosis 1,Complete,Yersinia,,Negative,,,,,,,,,,,,,Yes,633,,,,,,,4353,,,-,NZ_CP009786.1,4032,,1,Los Alamos National Laboratory,461x,Illumina; PacBio; 454,,,No,1,,,"Included in the study, passed QC/QA"
713,633.44,biomaterial_provider:USAMRIID,,,,GCF_000750315.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA243514,SAMN02906921,,,,,1,,Genome sequencing of Yersinia pseudotuberculosis 6904,2014-10-30T00:00:00Z,,ATCC:6904,2016-01-17T15:39:20.164Z,2016-01-17T15:39:20.164Z,,,47.6,CP008943,4806594,Yersinia pseudotuberculosis strain 6904,Complete,Yersinia,,,,,,,,,,,,,,,,633,,,,,,,4540,,,25342679,NZ_CP008943.1,4113,,1,Los Alamos National Laboratory,232x,Illumina; 454,,,,ATCC 6904,,,"Included in the study, passed QC/QA"
714,633.88,,,,,GCF_900092345.1,,,PRJEB14046,SAMEA3988158,,,,,1,2014,This study performed comparative genomics a large temporal and geographically diverse collection of isolates belonging to the Y. pseudotuberculosis complex to explore the genomic epidemiology of a sustained outbreak of yersiniosis in New Zealand.,2017-01-02T00:00:00Z,,,2017-01-18T15:50:02.526Z,2017-01-18T15:50:02.526Z,,,47.51,"LT596221,LT596222",4794091,Yersinia pseudotuberculosis strain NZYP4713,Complete,Yersinia,,,,,,,"Human, Homo sapiens",,,,Faeces,,,,,633,,,,,,,4514,,1,,"NZ_LT596221.1,NZ_LT596222.1",,,2,UNIVERSITY OF MELBOURNE,,,,,,NZYP4713,,,"Included in the study, passed QC/QA"
715,637382.3,,,,,GCA_000022805.1,,,PRJNA36507,SAMN02603871,,,,Rod,1,2006,"Yersinia pestis D106004.Strain D106004 was isolated from a new plague focus in Yulong County, China, in 2006.This strain will be used for comparative genome analysis.",2009-11-04T00:00:00Z,,,2014-12-08T22:13:51.224Z,2015-03-16T03:17:09.594Z,,Bubonic plague,47.6,"CP001585,CP001587,CP001588,CP001586",4812922,Yersinia pestis D106004,Complete,Yersinia,Yulong County China,,,,,,,"isolated from a new plague focus in Yulong County, China, in 2006",China,,new plague focus,,,MLST.Yersinia_spp.79,Yes,637382,-,Yersinia pestis D106004,,,,Facultative,5044,,3,19815893,"NC_017154.1,NC_017153.1,NC_017155.1,NC_017156.1",3783,,4,"State Key Laboratory for Infectious Disease Prevention and Control, Institute for Communicable Disease Control and Prevention",,,complete,,No,D106004,Mesophilic,,"Included in the study, passed QC/QA"
716,637385.3,,,,,GCA_000022825.1,,,PRJNA36545,SAMN02603872,,,,Rod,1,,"Yersinia pestis D182038. This strain belongs to Antiqua biovar of Yersinia pestis. It was isolated from Apodemus chevrieri (Chevrier's field mouse) in Yunnan province, China. ",2009-11-04T00:00:00Z,,,2014-12-08T22:13:51.234Z,2015-03-16T03:17:09.594Z,,Bubonic plague,47.6,"CP001589,CP001591,CP001592,CP001590",4802263,Yersinia pestis D182038,Complete,Yersinia,"Yunnan province, China",,,,,,"Chevrier's field mouse, Apodemus chevrieri","isolated from Apodemus chevrieri (Chevrier's field mouse) in Yunnan province, China",China,,Apodemus chevrieri (Chevrier's field mouse),,,MLST.Yersinia_spp.79,Yes,637385,-,Yersinia pestis D182038,,,,Facultative,5061,,3,19815893,"NC_017160.1,NC_017157.1,NC_017158.1,NC_017159.1",3787,,4,"State Key Laboratory for Infectious Disease Prevention and Control, Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention",,,complete,,No,D182038,Mesophilic,,"Included in the study, passed QC/QA"
717,637386.3,,,,,GCA_000022845.1,,,PRJNA36547,SAMN02603873,,,,Rod,1,,"Yersinia pestis Z176003.This strain belongs to Antiqua biovar of Yersinia pestis. It was isolated from a dead marmot in Tibet Autonomous Region, China. ",2010-04-08T00:00:00Z,,,2014-12-08T22:13:51.914Z,2015-03-16T03:17:09.594Z,,Bubonic plague,47.7,"CP001595,CP001596,CP001594,CP001593",4725788,Yersinia pestis Z176003,Complete,Yersinia,Tibet Autonomous Region China,,,,,,,"isolated from a dead marmot in Tibet Autonomous Region, China",China,,dead marmot,,,MLST.Yersinia_spp.79,Yes,637386,-,Yersinia pestis Z176003,,,,Facultative,4838,,3,20453098,"NC_014029,NC_014022,NC_014017,NC_014027",3693,,4,"State Key Laboratory for Infectious Disease Prevention and Control, Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention",,,complete,,No,Z176003,Mesophilic,,"Included in the study, passed QC/QA"
718,649716.3,,,,,GCA_000834985.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240082,SAMN03202985,,,,Bacilli,1,,Genome sequencing of Yersinia pestis Pestoides G,2015-02-09T00:00:00Z,3,,2015-03-12T14:01:15.203Z,2015-03-16T03:17:09.594Z,,,47.73,"CP010247.1,CP010246.1,CP010248.1",4738142,Yersinia pestis Pestoides G,Complete,Yersinia,USSR,Negative,,,,,,,USSR,,,,,,,649716,,,,,,,4499,,2,-,"NZ_CP010247.1,NZ_CP010246.1,NZ_CP010248.1",4169,,3,Los Alamos National Laboratory,586x,Illumina; PacBio; 454,,,,Pestoides G,,,"Included in the study, passed QC/QA"
719,748672.3,,,,,GCA_000834945.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA239349,SAMN03223176,,,,Bacilli,1,2009,Genome sequencing of Yersinia pseudotuberculosis Pa3606,2015-02-09T00:00:00Z,3,,2015-03-12T14:02:15.604Z,2015-03-16T03:17:09.594Z,,,47.51,"CP010067.1,CP010068.1,CP010069.1",4830299,Yersinia pseudotuberculosis str. PA3606 Pa3606,Complete,Yersinia,Japan: Fukushima,Negative,,,,,"Human, Homo sapiens",,Japan,,,,,,Yes,748672,,,,,,,4462,,2,-,"NZ_CP010067.1,NZ_CP010068.1,NZ_CP010069.1",4111,,3,Los Alamos National Laboratory,471x,Illumina; PacBio; 454,,,No,Pa3606,,,"Included in the study, passed QC/QA"
720,748678.3,,,,,GCA_000834925.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA240105,SAMN03218157,,,,Bacilli,1,,Genome sequencing of Yersinia pestis Pestoides B,2015-02-09T00:00:00Z,4,,2015-03-12T14:02:15.924Z,2015-03-16T03:17:09.594Z,,,47.66,"CP010023.1,CP010020.1,CP010022.1,CP010021.1",4794427,Yersinia pestis str. Pestoides B,Complete,Yersinia,USSR,Negative,,,,,,,USSR,,,,,,,748678,,,,,,,4555,,3,-,"NZ_CP010023.1,NZ_CP010020.1,NZ_CP010022.1,NZ_CP010021.1",4215,,4,Los Alamos National Laboratory,386x,Illumina; PacBio; 454,,,,Pestoides B,,,"Included in the study, passed QC/QA"
721,930944.6,,,,,GCA_000253175.1,,,PRJNA60483,SAMEA2271938,,,,,1,,"Yersiniosis is the third most common bacterial enteric disease in Europe and Yersinia enterocolitica subsp. palearctica O:3/4 is the most common bioserotype isolated from humans and asymptomatic slaughter pigs in Europe, Northern Asia and Australia. Thus, deciphering of Yersinia enterocolitica subsp. palearctica O:3/4 genome will help to uncover the mechanisms behind is host adaptation strategy and successful worldwide dissemination.",2011-01-14T00:00:00Z,,,2014-12-08T22:13:51.032Z,2015-03-16T03:17:09.594Z,,,46.97,"FR729477,FR745874",4625880,Yersinia enterocolitica subsp. palearctica Y11,Complete,Yersinia,Europe Northern Asia,,,,,,"Human, Homo sapiens","isolated from humans and asymptomatic slaughter pigs in Europe, Northern Asia and Australia",Germany,,humans and asymptomatic slaughter pigs,,,,,930944,-,Yersinia enterocolitica subsp. palearctica Y11,,,,,4424,,1,21296963,"NC_017564.1,NC_017565.1",4459,,2,Max von Pettenkofer-Institute,,,complete,,,Y11,,,"Included in the study, passed QC/QA"
722,935293.3,sample_type:bacteria colonies,,,,GCF_001656035.1,Velvet v. Nov-2013,,PRJNA267025,SAMN03177402,,,,,,1-May-96,Yersinia entomophaga is a pathogen for some agricultural pests.,2016-06-03T00:00:00Z,1,,2016-07-05T20:14:57.884Z,2016-07-05T20:14:57.884Z,,,48.58,CP010029,4275406,Yersinia entomophaga strain MH96,Complete,Yersinia,New Zealand: Canterbury,,,,,,,,New Zealand,,grass grub,,,,,935293,,,,,,,4105,,,27187466,,3738,,1,AgResearch,100x,Illumina,,,,MH96,,,"Included in the study, passed QC/QA"
723,994476.3,,,,,GCA_000192105.1,,,PRJNA53341,SAMN02603637,,,,,1,,Yersinia enterocolitica strain 105.5R(r).This strain will be used for comparative genome analysis.,2011-03-10T00:00:00Z,,,2014-12-08T22:13:50.992Z,2015-03-16T03:17:09.594Z,,,46.96,"CP002246,CP002247",4621811,Yersinia enterocolitica subsp. palearctica 105.5R(r),Complete,Yersinia,,,,,,,,,,,,,,MLST.Yersinia_spp.145,,994476,-,Yersinia enterocolitica subsp. palearctica 105.5R(r),,,,,4378,,1,,"NC_015224,NC_015475",4021,,2,Nankai University|Tianjin Biochip Corporation,,,complete,,,105.5R(r),,,"Included in the study, passed QC/QA"
724,1006551.4,,,,,GCA_000240325.1,,,PRJNA65523,SAMN02603580,,,,,1,,Source DNA available from Dr Kap-Seok Yang  (ksyang@macrogen.com) at Macrogen Inc.,2011-12-29T00:00:00Z,1,,2014-12-08T22:11:48.653Z,2015-03-16T03:17:09.594Z,,,56.05,CP003218,5974109,Klebsiella oxytoca KCTC 1686,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_oxytoca.28,,1006551,-,Klebsiella oxytoca KCTC 1686,,,,,5553,,,,NC_016612,5488,,,Macrogen Inc.,,,unfinished,,,KCTC 1686,,,"Included in the study, passed QC/QA"
725,1028307.3,,,,,GCA_000215745.1,,,PRJNA66537,SAMN02603581,,,,,1,,Project description not provided.,2011-06-03T00:00:00Z,1,,2014-12-08T22:11:10.422Z,2015-03-16T03:17:09.594Z,,,54.85,CP002824,5280350,Enterobacter aerogenes KCTC 2190,Complete,Klesiella,,,,,,,,,,,,,,,,1028307,-,Enterobacter aerogenes KCTC 2190,,,,,4907,,,,NC_015663,4912,,,Macrogen Inc.,,,complete,,,KCTC 2190,,,"Included in the study, passed QC/QA"
726,1049565.4,,,,,GCA_000220485.1,,,PRJNA67293,SAMN02603582,,,,,1,,-,2011-07-12T00:00:00Z,2,,2014-12-08T22:11:49.468Z,2015-03-16T03:17:09.594Z,,,57.28,"CP002910,CP002911",5462423,Klebsiella pneumoniae KCTC 2242,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.375,,1049565,-,Klebsiella pneumoniae KCTC 2242,,,,,5189,,1,,"NC_017540.1,NC_017541.1",5152,,,Macrogen Inc.,,,complete,,,KCTC 2242,,,"Included in the study, passed QC/QA"
727,1123862.3,,,,,GCA_000512165.1,,,PRJNA78291,SAMN02641520,,,,,1,2009,The emergence and global spread of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae are a significant threat to public health. This study aims to sequence and analyze one such isolate.,2013-12-30T00:00:00Z,7, ,2014-12-08T22:11:50.898Z,2015-03-16T03:17:09.594Z,,,56.8079,"CP003999.1,CP003998.1,CP004000.1,CP003997.1,CP003994.1,CP003996.1,CP003995.1",5739888,Klebsiella pneumoniae subsp. pneumoniae Kp13,Complete,Klesiella,Brazil,,,,,,"Human, Homo sapiens",,Brazil,,blood,,,MLST.Klebsiella_pneumoniae.442,,1123862,,Klebsiella pneumoniae subsp. pneumoniae Kp13,,,,,5453,,6,,"NZ_CP003999.1,NZ_CP003996.1,NZ_CP003994.1,NZ_CP003995.1,NZ_CP003997.1,NZ_CP003998.1,NZ_CP004000.1",5736,,,Laborat¿¿¿¿¿¿rio Nacional de Computa¿¿¿¿¿¿¿¿¿¿o Cient¿¿¿¿¿¿fica,,,complete,,,Kp13,,,"Included in the study, passed QC/QA"
728,1125630.4,,,,,GCA_000240185.2,,,PRJNA78789,SAMN02602959,,,,,1,,Comparative genome analysis,2011-12-21T00:00:00Z,7,,2014-12-08T22:11:50.630Z,2015-03-16T03:17:09.594Z,,,57.12,"CP003223,CP003200,CP003224,CP003225,CP003226,CP003227,CP003228",5682322,Klebsiella pneumoniae subsp. pneumoniae HS11286,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.11,,1125630,,Klebsiella pneumoniae subsp. pneumoniae HS11286,,,,,5523,,6,,"NC_016845.1,NC_016838.1,NC_016846.1,NC_016839.1,NC_016840.1,NC_016847.1,NC_016841.1",5779,,,"Bioinformatics & Microbial Genomics, State Key Laboratory of Microbial Metabolism, Shanghai Jiaotong University",,,,,,HS11286,,,"Included in the study, passed QC/QA"
729,1134687.22,collected_by:Beiwen Zheng,,,,,HGAP v. 3,,PRJNA393093,SAMN07315162,,,,,1,2017-01-09,"Detection and characterization of a Klebsiella michiganensis isolate carrying NDM-1-encoding plasmid, NDM-5-carrying plasmid and KPC-2-harbouring",2017-07-12T00:00:00Z,4,,2017-07-23T05:54:42.172Z,2017-07-23T05:54:42.172Z,,,55.83,"CP022348,CP022349,CP022350,CP022351",6418740,Klebsiella michiganensis strain K516,Complete,Klesiella,China: The First Affiliated Hospital of Zhejiang University,,,,,"acute leukemia, pneumonia","Human, Homo sapiens",,China,,feces,,,,,1134687,,,,,,,6526,,3,,,6246,,,State Key Laboratory for Diagnosis and Treatment of Infectious Disease,150.0x,PacBio,,,,K516,,,"Included in the study, passed QC/QA"
730,1134687.24,collected_by:Beiwen Zheng,,,,GCA_002290285.1,HGAP3 v. 3.10.1,,PRJNA393093,SAMN07551913,,,,,1,2017-01-13,"Detection and characterization of a Klebsiella michiganensis isolate carrying NDM-1-encoding plasmid, NDM-5-carrying plasmid and KPC-2-harbouring",2017-09-12T00:00:00Z,4,,2017-09-28T22:03:32.897Z,2017-09-28T22:03:32.897Z,,,55.83,"CP023185,CP023186,CP023187,CP023188",6418567,Klebsiella michiganensis strain K518,Complete,Klesiella,China: Zhejiang,,,,,"acute leukemia, pneumonia",patient,,China,,China: The First Affiliated Hospital of Zhejiang University,,,,,1134687,,,,,,,6546,,3,,,6256,,,State Key Laboratory for Diagnosis and Treatment of Infectious Disease,200.0x,PacBio,,,,K518,,,"Included in the study, passed QC/QA"
731,1134687.4,sample_type:cell culture,,,,GCF_000963575.1,SMRT Analysis v. 2.2.1,,PRJNA278789,SAMN03431443,,,,,1,2013-01,"Klebsiella michiganensis is a rod-shaped, Gram-negative bacterium which was newly classified in 2012 and closely related to K. michiganensis cluster. In 2013, we isolated RC10, which showed strong growth promoting ability from a rice field in Zhejiang Province, China.",2015-03-26T00:00:00Z,1,,2016-01-17T15:51:24.701Z,2016-01-17T15:51:24.701Z,,,54.89,CP011077,5107633,Klebsiella michiganensis strain RC10,Complete,Klesiella,China:Zhejiang,,,,,,,"isolated RC10, which showed strong growth promoting ability from a rice field in Zhejiang Province, China",China,,rice field,,,,,1134687,,,,,,,4900,,,,NZ_CP011077.1,4536,,,China National Rice Research Institute,,PacBio,,,,RC10,,,"Included in the study, passed QC/QA"
732,1134687.63,,,Susceptible;Resistant;Susceptible-dose dependent;Not defined,AMR Panel,GCA_003074075.1,SMRT v. 2.3.0; HGAP v. 3.0; SPAdes v.,,PRJNA316321,SAMN07291518,,,,,1,,"The AR Isolate Bank is a centralized repository of microbial pathogens with well-characterized resistance profiles that are assembled by CDC in collaboration with the Food and Drug Administration (FDA). The AR Bank is available to support and advance development of diagnostic devices and antimicrobial drug products. The AR Isolate Bank also supports the National Action Plan for Combating Antibiotic Resistance Bacteria by advancing the development of diagnostic tests to identify and characterize resistant bacteria, and by accelerating research and development for new antibiotics.The AR Isolate Bank includes collections of bacterial pathogens that are associated with known or emerging resistance mechanisms. Since its launch in July 2015, the AR Bank continues to grow and will eventually include genera and species such as Enterobacteriaceae, Pseudomonas aeruginosa, Staphylococcus, Enterococcus, Streptococcus, Salmonella, and Neisseria gonorrhoeae.Each pathogen listed on this web site includes information regarding its susceptibility and/or resistance profile(s), known resistance biomarkers, isolate characteristics, and associated data in PDF.Use this web site to search through pathogen panels, find additional information about the available isolates, and find procedures for requesting panels.",2018-04-30T00:00:00Z,5,,2018-05-30T17:12:15.966Z,2018-05-30T17:12:15.966Z,,,55.60779,"CP029141,CP029140,CP029142,CP029143,CP029144",6525490,Klebsiella michiganensis strain AR375,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_oxytoca.52,,1134687,,,,,,,6483,,4,,,6417,,,FDA/CDC,15.65x,Pacbio; Illumina,,,,AR375,,,"Included in the study, passed QC/QA"
733,1191061.3,,,,,GCA_000276705.2,,,PRJNA167370,SAMN02603642,,,,Bacilli,1,2010,"Genomic sequencing of an NDM-1 positive antimicrobial resistance Klebsiella oxytoca strain.  A K. oxytoca clinical isolated in 2010, from a patient underwent renal transplantation in China then presented to a hospital in Taiwan 7 days later. Culture from the pelvic abscess fluid found this strain producing NDM-1 metallo beta-lactamase. ",2012-07-09T00:00:00Z,2,,2014-12-08T22:11:48.635Z,2015-03-16T03:17:09.594Z,,,55.5337,"CP003683.1,CP003684.1",6450897,Klebsiella oxytoca E718,Complete,Klesiella,China,Negative,,,,,"Human, Homo sapiens","isolated in 2010, from a patient underwent renal transplantation in China then presented to a hospital in Taiwan 7 days later",China,,patient underwent renal transplantation,,,MLST.Klebsiella_oxytoca.27,,1191061,,Klebsiella oxytoca E718,,,,,6111,,1,,"NC_018106.1,NC_021501.1,NC_018107.1",5909,,,National Chung Hsing University,,,complete,,,E718,,,"Included in the study, passed QC/QA"
734,1193292.6,,,,,GCA_000294365.1,,,PRJNA167369,SAMN02603641,,,,Bacilli,1,,"'Complete genome sequencing of K. pneumoniae 1084, a hypermucoviscosity-negative clinical isloate strain.'",2012-08-29T00:00:00Z,1,,2014-12-08T22:11:50.580Z,2015-03-16T03:17:09.594Z,,,57.4,CP003785.1,5386705,Klebsiella pneumoniae subsp. pneumoniae 1084,Complete,Klesiella,,Negative,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.23,,1193292,,Klebsiella pneumoniae subsp. pneumoniae 1084,,,,,5045,,,,NC_018522.1,4962,,,National Chung Hsing University,,,complete,,,1084,,,"Included in the study, passed QC/QA"
735,1199150.3,,,,,GCA_000714635.1,GS De Novo Assembler v. 2.7,,PRJNA168515,SAMN02746181,,,,,1,2005,"The genome sequence of a bacterial cotton pathogen was generated for the purpose of defining the genetics of the pathogenicity. Novel gene products involved in boll diseases are expected to be identified. These data will likely illuminate basic mechanisms that relate to the infection process interference with cell wall or other cellular metabolism, and seed and fiber development. This investigation will accelerate our goal of developing technology to alert producers of potential pathogen reservoirs and the presence of infectious agents in stink bugs as well as determine whether there is an increased probability for stink bugs to carry pathogens.",2014-06-27T00:00:00Z,2,,2014-12-08T22:33:01.185Z,2015-03-16T03:17:09.594Z,,,57.2718,"CP008700.1,CP008701.1",5551470,Klebsiella pneumoniae subsp. pneumoniae KP5-1,Complete,Klesiella,USA,,,,,,"Southern green stink bug, Nezara viridula",,United States,,,,,,,1199150,,,,,,,5410,,1,25146146,-,4918,,,USDA-ARS,16.0x,454,,,,KP5-1,,,"Included in the study, passed QC/QA"
736,1225181.3,,,,,GCA_000714675.1,HGAP v. 2,,PRJNA173233,SAMN02786855,,,,,1,2012,Whole genome sequencing of carbapenem-resistant Klebsiella pneumoniae.,2014-06-27T00:00:00Z,4,,2014-12-08T22:33:27.644Z,2015-03-16T03:17:09.594Z,,,57.1176,"CP008797.1,CP008800.1,CP008799.1,CP008798.1",5734560,Klebsiella pneumoniae subsp. pneumoniae KPNIH24,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,throat/groin,,,,,1225181,,,,,,,5550,,1,-,"NZ_CP008797.1,NZ_CP008798.1,NZ_CP008799.1,NZ_CP008800.1",5344,,,NISC,173x,Pacific Biosciences RS II,,,,KPNIH24,,,"Included in the study, passed QC/QA"
737,1244085.3,,,,,GCA_000474015.1,ABySS v. V,,PRJNA177782,SAMN02603668,,,,Bacilli,1,,Complete genome sequence of Klebsiella pneumoniae CG43.  Clinical isolates from Chang-Gung Memorial Hospital.,2013-10-18T00:00:00Z,1, ,2014-12-08T22:11:49.278Z,2015-03-16T03:17:09.594Z,,,57.6,CP006648.1,5166857,Klebsiella pneumoniae CG43,Complete,Klesiella,"Taiwan: Chang-Gung Memorial Hospital, Keelung City",Negative,,,,,"Human, Homo sapiens",,Taiwan,,liver abscess,,,MLST.Klebsiella_pneumoniae.86,Nonmotile,1244085,,Klebsiella pneumoniae CG43,,,,,4855,,,,NC_022566.1,4791,,,National Tsing Hua University,200X,Illumina; Sanger,complete,,,CG43,,,"Included in the study, passed QC/QA"
738,1263871.1,collected_by:CDC,,,,GCF_000364385.2,Newbler GS De Novo Assembler v. 2.8,,PRJNA183901,SAMN02152539,,,,Bacilli,1,2010,"First Klebsiella strain isolated in the U.S. to be reported as a 'superbug', i.e., positive for the NDM1 antibiotic resistance gene.",2014-06-13T00:00:00Z,5,ATCC:BAA-2146,2016-01-17T15:30:26.813Z,2016-01-17T15:30:26.813Z,,nosocomial infections,56.97,APNN01000000,5781127,Klebsiella pneumoniae ATCC BAA-2146,Complete,Klesiella,USA,Negative,HostAssociated,,,urinary tract infection,"Human, Homo sapiens",isolated in the U.S,United States,,urine,,,,No,1263871,37C,,,,,Aerobic,5824,,4,24905728,,5653,,,Sandia National Laboratories,85X (Illumina),Illumina MiSeq; Pacific Biosystems,,,,ATCC BAA-2146,Mesophilic,,"Included in the study, passed QC/QA"
739,1308980.3,,,,,GCA_000632415.1,Newbler v. 2.7; Laser Gene v. 7.0,,PRJNA194061,SAMN03081460,,,,,1,,Study the cellulose digestion of Giant Panda.,2014-04-15T00:00:00Z,1,,2014-12-08T22:36:19.420Z,2015-03-16T03:17:09.594Z,,,55.9,CP004887.1,5914410,Klebsiella oxytoca HKOPL1,Complete,Klesiella,,,,,,,"Giant panda, Ailuropoda melanoleuca",,,,fecal sample,,,,,1308980,,,,,,,5601,,,-,NZ_CP004887.1,5389,,,"Bioinformatics Center,Nanjing Agricultural University",23x,Sanger dideoxy sequencing; 454,,,,HKOPL1,,,"Included in the study, passed QC/QA"
740,1316582.3,,,,,GCF_001373075.1,,,PRJEB8210,SAMEA3207734,,,,,,,Klebsiella pneumoniae 45T1-2A genome,2015-06-14T00:00:00Z,1,,2016-01-17T17:28:17.563Z,2016-01-17T17:28:17.563Z,,,57.91,CDMU01000000,5228056,Klebsiella pneumoniae ATCC 43816,Complete,Klesiella,,,,,,,,,,,,,,,,1316582,,,,,,,5085,,,,,4876,,,URMITE,,,,,,45T1-2A,,,"Included in the study, passed QC/QA"
741,1328324.3,,,,,GCA_000695935.1,HGAP v. 2,,PRJNA198783,SAMN02713685,,,,,1,2012,Whole genome sequencing of carbapenem-resistant Klebsiella pneumoniae.,2014-05-27T00:00:00Z,6,,2014-12-08T22:38:18.902Z,2015-03-16T03:17:09.594Z,,,56.7058,"CP007731.1,CP007734.1,CP007735.1,CP007736.1,CP007732.1,CP007733.1",6132440,Klebsiella pneumoniae subsp. pneumoniae KPNIH27,Complete,Klesiella,USA,,,,,,,,United States,,groin,,,,,1328324,,,,,,,5974,,1,-,"NZ_CP007731.1,NZ_CP007732.1,NZ_CP007733.1,NZ_CP007734.1,NZ_CP007735.1,NZ_CP007736.1",5699,,,NISC,116x,Pacific Biosciences RS II,,,,KPNIH27,,,"Included in the study, passed QC/QA"
742,1328325.3,,,,,GCA_000717515.1,HGAP v. 2,,PRJNA198784,SAMN02786856,,,,,1,2012,Whole genome sequencing of carbapenem-resistant Klebsiella pneumoniae.,2014-07-02T00:00:00Z,3,,2014-12-08T22:38:19.406Z,2015-03-16T03:17:09.594Z,,,57.3174,"CP008831.1,CP008832.1,CP008833.1",5436790,Klebsiella pneumoniae subsp. pneumoniae KPR0928,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,sputum,,,,,1328325,,,,,,,5237,,1,-,"NZ_CP008831.1,NZ_CP008832.1,NZ_CP008833.1",5055,,,NISC,170x,Pacific Biosciences RS II,,,,KPR0928,,,"Included in the study, passed QC/QA"
743,1333852.3,,,,,GCA_000714655.1,HGAP v. 2,,PRJNA202895,SAMN02786843,,,,,1,2012,Whole genome sequencing of Klebsiella oxytoca.,2014-06-27T00:00:00Z,4,,2014-12-08T22:39:03.482Z,2015-03-16T03:17:09.594Z,,,55.6381,"CP008788.1,CP008790.1,CP008789.1,CP008791.1",6684900,Klebsiella oxytoca KONIH1,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,perirectal swab,,,,,1333852,,,,,,,6374,,1,-,"NZ_CP008788.1,NZ_CP008789.1,NZ_CP008790.1,NZ_CP008791.1",6155,,,NISC,136x,Pacific Biosciences RS II,,,,KONIH1,,,"Included in the study, passed QC/QA"
744,1380908.3,,,,,GCA_000445405.1,Newbler v. 2.7,,PRJNA213804,SAMN02603607,,,,,1,2010,"Infections caused by K. pneumoniae are discovered throughout the world. This organism is a major cause of urinary tract infection and an important source of nosocomial infection. To date, the spread of multidrug-resistant, even pandrug-resistant, K. pneumoniae has developed into a serious clinical threat. Furthermore, carbapenemases production has recently emerged as an important mechanism for carbapenems resistance. Disturbingly, more and more novel carbapenemases and their variants were continuously discovered. In 2011, we also reported a carbapenem-resistant strain of K. pneumoniae which carried a KPC-2 variant4. In 2010, we isolated another carbapenem-resistant K. pneumoniae strain and then performed bacteriological experiments, PCR and whole-genome sequencing. The genomic sequence data provided us the cause of the carbapenem resistance of this strain.K. pneumoniae JM45 was an isolate from the blood of a 72-year-old male with cerebral infarction after colon carcinoma resection hospitalized in the intensive care unit, the Second Affiliated Hospital of ZheJiang University School of Medcine on April 7, 2010. Species identification was carried out by using Vitek Gram-negative identification cards (bioM¿¿¿¿¿rieux, Marcy l¿¿¿¿¿¿¿Etoile, France) and by 16S rDNA and gyrA sequencing for BLAST searches on Genbank. The minimum inhibitory concentrations(MICs) were determined by Etest (AB bioMe¿¿¿¿rieux, Solna, Sweden) with the results interpreted according to Clinical and Laboratory Standards Institute(CLSI) guidelines. For rapid detection of the presence of AmpC-derepressed, extended-spectrum ¿¿¿¿¿-lactamases(ESBL) and metallo-¿¿¿¿¿-lactamases(MBL), a new system (Cica-Beta-Test, Kanto Chemical, Japan) was utilized. The Modified Hodge Test was carried out to detect carbapenemases.We isolated a pandrug-resistant K. pneumoniae strain from the blood of a patient with cerbral infarction after colon carcinoma resection in the intensive care unit. According to Cica-Beta-Test and Modified Hodge Test, it was considered to harbor various kinds of ¿¿¿¿¿-lactamases including carbapenemase. However, we only detected four class A ¿¿¿¿¿-lactamase genes with no carbapenemase genes by PCR unexpectedly. To explain the inconsistency of these results, we subsequently conducted whole-genome sequencing for K. pneumoniae JM45. As a result, we also detected four homologous class A ¿¿¿¿¿-lactamase genes, and in addition, discovered two novel genes encoding metallo-¿¿¿¿¿-lactamase domain protein locating on the chromosome simultaneously. This is the first report of two non-cassette-mediated metallo-¿¿¿¿¿-lactamase domain protein sequences for carbapenem resistance in the same strain. We will carry out further research on these two novel genes by cloning and expression analysis followed by enzyme kinetics analysis.",2013-08-12T00:00:00Z,3,,2014-12-08T22:11:49.455Z,2015-03-16T03:17:09.594Z,,,57.2405,"CP006656.1,CP006657.1,CP006658.1",5603174,Klebsiella pneumoniae JM45,Complete,Klesiella,,,,,,,"Human, Homo sapiens","isolated another carbapenem-resistant K. pneumoniae strain and then performed bacteriological experiments, PCR and whole-genome sequencing",,,72-year-old male with cerebral infarction after colon carcinoma resection,,,MLST.Klebsiella_pneumoniae.11,,1380908,,Klebsiella pneumoniae JM45,,,,,5508,,2,,"NC_022082.1,NC_022078.1,NC_022083.1",5141,,,"Microbiology Laboratory, Hangzhou Yuhang Hospital of Traditional Chinese Medicine, Hangzhou, PR China",30X,454,complete,,,JM45,,,"Included in the study, passed QC/QA"
745,1392499.4,,,,,GCA_000814805.1,CLC genomic workbench v. 5.5,,PRJNA217288,SAMN03097203,,,,,1,Apr-2002,Complete sequencing of a serotype K2 Klebsiella pneumoniae strain in Taiwan.,2015-01-06T00:00:00Z,1,,2015-03-12T13:43:06.829Z,2015-03-16T03:17:09.594Z,,,57.23,CP006722.1,5341039,Klebsiella pneumoniae subsp. pneumoniae 1158,Complete,Klesiella,Taiwan,,,,,,"Human, Homo sapiens",,Taiwan,,,,,,,1392499,,,,,,,4983,,,-,NZ_CP006722.1,4989,,,National Chung Hsing University,18X; 213X,454 GS Junior; Illumina Miseq; Sanger ABI,,serovar K2,,1158,,,"Included in the study, passed QC/QA"
746,1392500.3,,,,,GCA_000813205.1,Newbler v. 2.7,,PRJNA217289,SAMN03274239,,,,,1,,Complete sequencing of Klebsiella pneumoniae K2 strain HK787,2015-01-02T00:00:00Z,1,,2015-03-12T13:43:07.135Z,2015-03-16T03:17:09.594Z,,,57.49,CP006738.1,5329385,Klebsiella pneumoniae HK787,Complete,Klesiella,,,,,,,,,,,,,,,,1392500,,,,,,,5007,,,-,NZ_CP006738.1,5017,,,National Health Research Institutes,23X (454),454 GS Junior; ABI3730; Illulmina Miseq,,,,HK787,,,"Included in the study, passed QC/QA"
747,1406314.3,,,,,GCA_000733255.1,SMRT Pipe v. v2.0.1,,PRJNA221868,SAMN03081487,,,,Bacilli,1,,Whole genome sequence of a Klebsiella pneumoniae strain co-producing NDM-1 and OXA-232,2014-07-24T00:00:00Z,5,,2014-12-09T00:45:45.509Z,2015-03-16T03:17:09.594Z,,Urine colonization,56.7812,"CP006798.1,CP006800.1,CP006802.1,CP006801.1,CP006799.1",5812300,Klebsiella pneumoniae subsp. pneumoniae PittNDM01,Complete,Klesiella,USA,Negative,HostAssociated,,,,,,United States,,urine,,,,No,1406314,37C,,,,,Aerobic,5452,,1,25070096,"NZ_CP006798.1,NZ_CP006799.1,NZ_CP006800.1,NZ_CP006801.1,NZ_CP006802.1",5420,NonHalophilic,,University of Pittsburgh,333,PacBio,,,No,PittNDM01,Thermophilic,,"Included in the study, passed QC/QA"
748,1420012.3,,,,,GCA_000598005.1,,,PRJNA226698,SAMN03081502,,,,,1,2010,Towards an understanding of the success of the pandemic ST258 carbapenem-resistant Klebsiella pneumoniae strain,2014-03-19T00:00:00Z,6, ,2014-12-08T22:11:48.788Z,2015-03-16T03:17:09.594Z,,,57.146,"CP006923.1,CP006924.1,CP006927.1,CP006928.1,CP006925.1,CP006926.1",5540936,Klebsiella pneumoniae 30660/NJST258_1,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,urinary tract infection,,,MLST.Klebsiella_pneumoniae.258,,1420012,,Klebsiella pneumoniae 30660/NJST258_1,,,,,5385,,5,24639510,"NZ_CP006923.1,NZ_CP006927.1,NZ_CP006926.1,NZ_CP006925.1,NZ_CP006928.1,NZ_CP006924.1",5799,,,Igenbio Inc,,,complete,,,30660/NJST258_1,,,"Included in the study, passed QC/QA"
749,1420013.3,,,,,GCA_000597905.1,,,PRJNA226699,SAMN03081501,,,,,1,2010,Towards an understanding of the success of the pandemic ST258 carbapenem-resistant Klebsiella pneumoniae strain,2014-03-19T00:00:00Z,4, ,2014-12-08T22:11:48.797Z,2015-03-16T03:17:09.594Z,,,57.4316,"CP006918.1,CP006919.1,CP006921.1,CP006922.1",5417216,Klebsiella pneumoniae 30684/NJST258_2,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,urinary tract infection,,,MLST.Klebsiella_pneumoniae.258,,1420013,,Klebsiella pneumoniae 30684/NJST258_2,,,,,5233,,3,24639510,"NZ_CP006918.1,NZ_CP006919.1,NZ_CP006922.1,NZ_CP006921.1",5591,,,Igenbio Inc,,,complete,,,30684/NJST258_2,,,"Included in the study, passed QC/QA"
750,1463165.21,sample_type:fecal sample,,,,GCA_002240295.1,Newbler v. 2.7,,PRJNA309571,SAMN04436401,,,,,1,2013-09,A single strain of bacterium isolated from the Giant Panda feces that is capable of degrading cellulose,2017-08-03T00:00:00Z,1,,2017-09-28T19:43:18.141Z,2017-09-28T19:43:18.141Z,,,58.04,CP014154,5089790,Klebsiella quasipneumoniae strain HKUOPA4,Complete,Klesiella,China:Hong Kong,,,,,,giant panda,,China,,feces,,,,,1463165,C,,,,,,4939,,,,,4854,,,The University of Hong Kong,60x,Illumina MiSeq,,,,HKUOPA4,,,"Included in the study, passed QC/QA"
751,1463165.22,sample_type:fecal sample,,,,GCA_002240315.1,Newbler v. 2.7,,PRJNA309572,SAMN04436402,,,,,1,2013-09,A single strain of bacterium isolated from the Giant Panda feces that is capable of degrading cellulose,2017-08-03T00:00:00Z,1,,2017-09-28T19:43:28.269Z,2017-09-28T19:43:28.269Z,,,58.04,CP014155,5088626,Klebsiella quasipneumoniae strain HKUOPJ4,Complete,Klesiella,China:Hong Kong,,,,,,giant panda,,China,,feces,,,,,1463165,C,,,,,,4937,,,,,4856,,,The University of Hong Kong,60x,Illumina MiSeq,,,,HKUOPJ4,,,"Included in the study, passed QC/QA"
752,1463165.23,sample_type:fecal sample,,,,GCA_002240335.1,Newbler v. 2.7,,PRJNA309573,SAMN04436403,,,,,1,2013-09,A single strain of bacterium isolated from the Giant Panda feces that is capable of degrading cellulose,2017-08-03T00:00:00Z,1,,2017-09-28T19:43:24.466Z,2017-09-28T19:43:24.466Z,,,58.04,CP014156,5087945,Klebsiella quasipneumoniae strain HKUOPL4,Complete,Klesiella,China:Hong Kong,,,,,,giant panda,,China,,feces,,,,,1463165,C,,,,,,4936,,,,,4856,,,The University of Hong Kong,60x,Illumina MiSeq,,,,HKUOPL4,,,"Included in the study, passed QC/QA"
753,1463165.4,collected_by:H Dalton,,,,GCF_001596075.1,HGAP v. May 2015,,PRJNA307517,SAMN04382091,,,,,1,1994,"This project aims to sequence, assemble and annotate the genomes of multidrug resistant pathogens.",2016-03-22T00:00:00Z,3,ATCC:700603,2016-04-27T18:42:25.023Z,2016-04-27T18:42:25.023Z,,,57.7,"CP014696,CP014697,CP014698",5586672,Klebsiella quasipneumoniae strain ATCC 700603,Complete,Klesiella,USA: VA,,,,,,"Human, Homo sapiens",,United States,,Urine from hospitalized patient,,,MLST.Klebsiella_pneumoniae.489,,1463165,,,,,,,5594,,2,,,5394,,,The Unniversity of Queensland,380x,PacBio,,,,K6,,,"Included in the study, passed QC/QA"
754,1463165.7,collected_by:ATCC <-- JM Swenson <-- MJ Ferraro <-- G Jacoby <-- H Dalton,,,,GCA_002953295.1,Celera v. 8.2,,PRJNA231221,SAMN03996259,,,,,1,1994,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2018-02-20T00:00:00Z,3,ATCC:700603,2018-05-26T02:10:23.602Z,2018-05-26T02:10:23.602Z,,,57.73627,"CP014071,CP014072,CP014073",5513032,Klebsiella quasipneumoniae strain ATCC 700603 strain Not Applicable,Complete,Klesiella,USA:VA,,,,,Urinary tract infection,"Human, Homo sapiens",,USA,,urine,,,MLST.Klebsiella_pneumoniae.489,,1463165,,,,,,,5572,ESBL,2,,,5451,,,US Food and Drug Administration,25.45x,PacBio; Illumina,,,,Not Applicable,,,"Included in the study, passed QC/QA"
755,1463165.74,sample_type:whole organism,,,,GCA_003020825.1,Newbler v. 3.0,,PRJNA383559,SAMN06767172,,,,,1,2011,Whole genome sequencing of carbapenem-resistant Klebsiella quasipneumoniae isolate recovered after nosocomial infections in the Brazilian southeast region.,2018-03-27T00:00:00Z,3,,2018-05-31T00:19:25.315Z,2018-05-31T00:19:25.315Z,,,57.59541,"CP023478,CP023479,CP023480",5418654,Klebsiella quasipneumoniae strain KPC142,Complete,Klesiella,"Brazil: City of Belo Horizonte, State of Minas Gerais",,,,,,"Human, Homo sapiens",,Brazil,,tracheal secretion isolated from an uncertain age woman,,,,,1463165,,,,,,,5268,,2,,,4945,,,LNCC,115.0x,Illumina MiSeq,,,,KPC142,,,"Included in the study, passed QC/QA"
756,1715259.3,isolate:G5;sample_type:Monoculture;collected_by:Chen Jian Woon;identified_by:Chen Jian Woon,,,,GCA_001461805.1,HGAP v. 2,,PRJNA297567,SAMN04074888,,,,,1,01-Aug-2010,Complete genome sequencing of Klebsiella sp. strain G5 isolated from tropical soil,2015-12-07T00:00:00Z,1,,2016-01-30T17:10:59.587Z,2016-01-30T17:10:59.587Z,,,57.28,CP012871,4702949,Klebsiella sp. G5,Complete,Klesiella,Malaysia: Rimba Ilmu,,,,,,,,Malaysia,,soil,,,,,1715259,C,,,,,,4487,,,,NZ_CP012871.1,4245,,,University of Malaya,99.55x,PacBio RSII,,,,G5,,,"Included in the study, passed QC/QA"
757,1905288.3,sample_type:Whole organism;collected_by:Lei Zhang,,,,GCF_001753185.1,HGAP v. 2.3.0,,PRJNA344738,SAMN05832682,,,,,1,2014-09,Complete genome sequence of the plant growth promoting endophyte Klebsiella sp. LTGPAF-6F,2016-10-06T00:00:00Z,3,,2016-11-16T23:18:33.039Z,2016-11-16T23:18:33.039Z,,,55.28,"CP017450,CP017451,CP017452",6790399,Klebsiella sp. LTGPAF-6F,Complete,Klesiella,China: Xinjiang Province,,,,,,Alhagi sparsifolia Shap.,,China,,,,,,,1905288,,,,,,,6816,,2,,"NZ_CP017450.1,NZ_CP017451.1,NZ_CP017452.1",6273,,,Northwest A&F University,53.0x,Illumina HiSeq; PacBio,,,,LTGPAF-6F,,,"Included in the study, passed QC/QA"
758,1934254.3,sample_type:Microbe,,,,,SMRT analysis v. v2.3.0,,PRJNA361010,SAMN06219347,,,,,1,,"M5al is a model strain for studying molecular genetics of nitrogen fixation and production of 1,3-propanediol and 2,3-butanediol.",2017-04-13T00:00:00Z,1,,2017-05-28T17:23:25.644Z,2017-05-28T17:23:25.644Z,,,55.92,CP020657,5800138,Klebsiella sp. M5al strain M5al,Complete,Klesiella,,,,,,,,,,,,,,,,1934254,,,,,,,5683,,,,,5476,,,Zhejiang University,307,PacBio,,,,M5al,,,"Included in the study, passed QC/QA"
759,2026240.3,collected_by:Houston Methodist Hospital,,,,GCA_002269255.1,Unicycler v. 0.4.0; SPAdes v. 3.10.0,,PRJNA376414,SAMN06438648,,,,,1,26-Aug-14,"A collection of 1,777 clinical K. pneumoniae isolates from Houston, Texas.",2017-08-24T00:00:00Z,4,,2017-09-28T21:12:02.015Z,2017-09-28T21:12:02.015Z,,,56.66,"CP022823,CP022824,CP022825,CP022826",5946706,Klebsiella sp. KPN1705,Complete,Klesiella,USA: Houston,,,,,Klebsiella Infections,"Human, Homo sapiens",,United States,,WOUND,,,,,2026240,,,host_description:HMH:KPN:1705,,genotype:STNF*; Capsule locus KL153,,6151,,3,,,5940,,,Houston Methodist Hospital,88.0x,Illumina NextSeq; Oxford Nanopore MinION,,,,KPN1705,,,"Included in the study, passed QC/QA"
760,244366.16,,,,,GCA_000812205.1,HGAP in smrtanalysis v. 2.1.1,,PRJNA259590,SAMN03018135,,,,,1,,Klebsiella variicola DX120E is an endophytic nitrogen-fixing bacterium and can promote plant growth.,2014-12-31T00:00:00Z,3,,2015-03-12T13:49:03.079Z,2015-03-16T03:17:09.594Z,,,57.1,"CP009274.1,CP009275.1,CP009276.1",5718434,Klebsiella variicola DX120E,Complete,Klesiella,,,,,,,,,,,,,,,,244366,,,,,,,5356,,2,-,"NZ_CP009274.1,NZ_CP009276.1,NZ_CP009275.1",5172,,,Zhejiang University,,PacBio,,,,DX120E,,,"Included in the study, passed QC/QA"
761,244366.17,,,,,GCA_000828055.1,HGAP in smrtanalysis v. 2.1.1,,PRJNA272370,SAMN01174581,,,,,1,,The Klebsiella variicola type strain DSM 15968 is a N2-fixing bacterium isolated from banana roots.,2015-01-21T00:00:00Z,1,DSM 15968,2015-03-12T13:49:03.378Z,2015-03-16T03:17:09.594Z,,,57.56,CP010523.1,5521203,Klebsiella variicola DSM 15968,Complete,Klesiella,Mexico,,,,,,"Banana, Musa sp.",isolated from banana roots,Mexico,,banana roots,,,,,244366,,,,,,,5166,,,-,NZ_CP010523.1,4979,,,Zhejiang university,185,PacBio,,,,DSM 15968,,Yes,"Included in the study, passed QC/QA"
762,244366.36,sample_type:Environmental sample;biomaterial_provider:Pokfulam Rd.,,,,GCF_001278905.1,Newbler v. 2.7,,PRJNA291549,SAMN03945398,,,,,1,2013,"Cellulose-degrading bacteria isolated from Giant Panda feces has the potential to convert organic waste into biofules. Researchers have identified multiple cellulose-digesting microbes in the Giant Panda gut, but few have applied such bacteria in converting cellulose into glucose to create biofuel. Cellulosic ethanol, a biofuel, is produced through the fermentation of lignocellulosic biomasses. This anaerobic process is aided by cellulose-digesting enzymes.",2015-09-04T00:00:00Z,1,,2016-01-17T17:05:29.051Z,2016-01-17T17:05:29.051Z,,,58.04,CP012252,5090052,Klebsiella variicola strain HKUOPLA,Complete,Klesiella,Hong Kong,,,,,,,isolated from Giant Panda feces has the potential to convert organic waste into biofules,China,,giant panda feces,,,,,244366,C,,,,,,4855,,,,NZ_CP012252.1,4614,,,University of Hong Kong,43,Illumina,,,,HKUOPLA,,,"Included in the study, passed QC/QA"
763,244366.45,,,Susceptible;Resistant;Intermediate,AMR Panel,GCF_001875745.1,HGAP v. 3,,PRJNA292901,SAMN04014857,,,,,,,Collection of bacterial pathogens that demonstrate a range of carbapenem susceptibility,2016-11-10T00:00:00Z,1,,2016-11-19T14:42:58.207Z,2016-11-19T14:42:58.207Z,,,57.45,MPCI00000000,5516831,Klebsiella variicola strain AR_0016,Complete,Klesiella,,,,,,,,,,,,,,,,244366,,,,,,,5314,,,,,,,,Centers for Disease Control and Prevention,221x,PacBio,,,,AR_0016,,,"Included in the study, passed QC/QA"
764,244366.46,,,,,GCF_001989495.1,"SeqMan Pro, DNASTAR v. 12.1.0(141).421",,PRJNA327903,SAMN05361763,,,,,1,Sep-2014,-,2017-02-07T00:00:00Z,4,,2017-03-20T07:35:22.859Z,2017-03-20T07:35:22.859Z,,,57.08,"CP017284,CP017283,CP017281,CP017282",5860470,Klebsiella variicola strain GJ1,Complete,Klesiella,South Korea,,,,,,,,South Korea,,river water,,,MLST.Klebsiella_pneumoniae.363,,244366,,,,,,,5773,,3,28087584,"NZ_CP017284.1,NZ_CP017283.1,NZ_CP017281.1,NZ_CP017282.1",5405,,,,missing,PacBio,,,,GJ1,,,"Included in the study, passed QC/QA"
765,244366.47,,,,,GCF_001989515.1,"SeqMan Pro, DNASTAR v. 12.1.0(141).421",,PRJNA327903,SAMN05361854,,,,,1,,-,2017-02-07T00:00:00Z,5,,2017-03-20T07:35:13.967Z,2017-03-20T07:35:13.967Z,,,57.05,"CP017849,CP017850,CP017851,CP017852,CP017853",5927027,Klebsiella variicola strain GJ2,Complete,Klesiella,,,,,,,,,,,riverwater,,,,,244366,,,,,,,5874,,4,,"NZ_CP017849.1,NZ_CP017850.1,NZ_CP017851.1,NZ_CP017852.1,NZ_CP017853.1",5478,,,,missing,PacBio,,,,GJ2,,,"Included in the study, passed QC/QA"
766,244366.48,,,,,GCF_001989535.1,"SeqMan Pro, DNASTAR v. 12.1.0(141).421",,PRJNA327903,SAMN05361855,,,,,1,,-,2017-02-07T00:00:00Z,5,,2017-03-20T07:35:42.433Z,2017-03-20T07:35:42.433Z,,,57.04,"CP017289,CP017285,CP017286,CP017287,CP017288",5933065,Klebsiella variicola strain GJ3,Complete,Klesiella,,,,,,,,,,,riverwater,,,MLST.Klebsiella_pneumoniae.363,,244366,,,,,,,5873,,4,28087584,"NZ_CP017289.1,NZ_CP017285.1,NZ_CP017286.1,NZ_CP017287.1,NZ_CP017288.1",5484,,,,missing,PacBio,,,,GJ3,,,"Included in the study, passed QC/QA"
767,272620.9,,,,,GCA_000016305.1,,,PRJNA31,SAMN02603941,,,,Rod,1,1994, Klebsiella pneumoniae  subsp. pneumoniae strain MGH 78578. This strain was isolated from a patient in 1994.,2007-07-05T00:00:00Z,6,,2014-12-08T22:11:51.136Z,2015-03-16T03:17:09.594Z,,Pneumonia;Urinary tract infection,57.1,"CP000647,CP000649,CP000650,CP000651,CP000652,CP000648",5694894,Klebsiella pneumoniae subsp. pneumoniae MGH 78578,Complete,Klesiella,,-,Multiple,,,,"Human, Homo sapiens",isolated from a patient in 1994,,,patient,,,MLST.Klebsiella_pneumoniae.38,Yes,272620,37,Klebsiella pneumoniae subsp. pneumoniae MGH 78578,,,,Facultative,5269,,5,,"NC_009648,NC_009650,NC_009651,NC_009652,NC_009653,NC_009649",5185,,,Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine,,,complete,,,MGH 78578,Mesophilic,,"Included in the study, passed QC/QA"
768,484021.57,,,,,GCF_000009885.1,,,PRJDA21069,,,,,Bacilli,2,,Klebsiella pneumoniae NTUH-K2044. This strain was isolated from a liver abscess and will be used for comparative analysis.,2011-03-01T00:00:00Z,2,,2016-01-17T15:28:07.244Z,2016-01-17T15:28:07.244Z,,Pneumonia and urinary tract infections,57.37,"AP006725,AP006726",5472672,Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044,Complete,Klesiella,,Negative,Multiple,,,,,isolated from a liver abscess and will be used for comparative analysis,,,liver abscess,,,,No,484021,,,,,,Facultative,5387,,,19447910,"NC_012731.1,NC_006625.1",5287,,,National Health Research Institutes,,,,,,NTUH-K2044,Mesophilic,,"Included in the study, passed QC/QA"
769,507522.6,,,,,GCA_000019565.1,,,PRJNA28471,SAMN02603449,,,,Rod,1,,"Klebsiella pneumoniae 342. Klebsiella pneumoniae 342 was isolated from the stem tissue of Zea mays. This strain fixes atmospheric nitrogen and may be able to provide nitrogen, in the form of ammonia, to plant cells. This organism will be used for comparative analysis with endophytic and pathogenic Klebsiella pneumoniae strains. ",2008-09-24T00:00:00Z,3,,2014-12-08T22:11:48.805Z,2015-03-16T03:17:09.594Z,,,56.9,"CP000964,CP000966,CP000965",5920257,Klebsiella pneumoniae 342,Complete,Klesiella,,-,Host-associated,,,,"Maize, Zea mays",isolated from the stem tissue of Zea mays,,,the stem tissue of Zea mays,,,MLST.Klebsiella_pneumoniae.146,Yes,507522,-,Klebsiella pneumoniae 342,,,,Facultative,5414,,2,18654632,"NC_011283,NC_011281,NC_011282",5768,,,J. Craig Venter Institute|JCVI,,,complete,,,342,Mesophilic,,"Included in the study, passed QC/QA"
770,548.115,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001021995.1,HGAP3 v. 2.2.0,,PRJNA246471,SAMN03733745,,,,,1,2010-11,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2015-06-09T00:00:00Z,2,,2016-01-17T16:05:39.233Z,2016-01-17T16:05:39.233Z,,,55,"CP011574,CP011573",5138968,Enterobacter aerogenes strain CAV1320,Complete,Klesiella,USA:Virginia,,,,,not applicable,"Human, Homo sapiens",,United States,,Perirectal,,,,,548,,,,,,,4917,,1,,"NZ_CP011574.1,NZ_CP011573.1",4646,,,University of Oxford,75X,PacBio,,,,CAV1320,,,"Included in the study, passed QC/QA"
771,548.154,collected_by:Children's National Hospital,,,,GCF_001559215.1,HGAP3 v. Oct 2014,,PRJNA231221,SAMN03996296,,,,,1,4/23/2014,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",2016-02-11T00:00:00Z,1,FDA:FDAARGOS_152,2016-03-01T20:05:09.727Z,2016-03-01T20:05:09.727Z,,,55,CP014029,5317047,Enterobacter aerogenes strain FDAARGOS_152,Complete,Klesiella,USA:DC,,,19Y,female,Urinary tract infection,"Human, Homo sapiens",,United States,,Urine,,,,,548,,,,,,,5174,,,,NZ_CP014029.1,4843,,,US Food and Drug Administration,23.754x,Pacbio,,,,not applicable,,,"Included in the study, passed QC/QA"
772,548.155,passage_history:not collected;specimen_voucher:not collected,,,,GCF_001571545.2,HGAP v. unspecified,,PRJNA279469,SAMN03448049,,,,,1,1997,Identification of putative mutations responsible for the emrgence of multidrug resistance within series of clinical isolates.,2016-02-24T00:00:00Z,1,not applicable,2016-03-18T06:17:32.823Z,2016-03-18T06:17:32.823Z,,,54.92,CP011539,5452368,Enterobacter aerogenes strain G7,Complete,Klesiella,France,,,,female,,"Human, Homo sapiens",,France,,,,,MLST.Enterobacter_cloacae.248,,548,,,host_subject_id:G;host_description:not collected;host_disease_outcome:death;host_disease_stage:not applicable;host_health_state:not applicable,,genotype:not applicable,,5320,not applicable,,26398358,"NZ_CP011539.1,NZ_CP011540.1",5247,,,Aix Marseille Universite,99.73,PacBio RS,,not applicable,,G7,,,"Included in the study, passed QC/QA"
773,548.156,collected_by:Children's National Hospital,,,,GCF_001593585.1,Celera v. 8.2,,PRJNA231221,SAMN03996283,,,,,1,2/25/2014,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",2016-03-17T00:00:00Z,2,FDA:FDAARGOS_139,2016-04-27T17:17:07.274Z,2016-04-27T17:17:07.274Z,,,55.05,"CP014748,CP014747",5297782,Enterobacter aerogenes strain FDAARGOS_139,Complete,Klesiella,USA:DC,,,3M,male,Colonization,"Human, Homo sapiens",,United States,,Rectal swab,,,MLST.Enterobacter_cloacae.248,,548,,,,,,,5084,,1,,"NZ_CP014748.1,NZ_CP014747.1",4797,,,US Food and Drug Administration,19.65x,Pacbio,,,,not applicable,,,"Included in the study, passed QC/QA"
774,548.223,collected_by:Children's National Hospital,,,,GCA_002591115.1,"SMRT v. 2.3.0, HGAP v. 3",,PRJNA231221,SAMN07312407,,,,,1,12-May-2014,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-10-18T00:00:00Z,1,FDA:FDAARGOS_363,2017-11-24T16:44:15.726Z,2017-11-24T16:44:15.726Z,,,55.06,CP023963,5245455,Klebsiella aerogenes strain FDAARGOS_363 strain Not applicable,Complete,Klesiella,USA:DC,,,6M,male,Colonization/Enteritis,"Human, Homo sapiens",,United States,,stool,,,,,548,,,,,,,5152,,,,,5034,,,US Food and Drug Administration,15.89x,PacBio; Illumina,,,,Not applicable,,,"Included in the study, passed QC/QA"
775,548.234,,,Susceptible;Resistant;Intermediate;Not defined,AMR Panel,GCA_002796405.1,canu v. 1.6,,PRJNA292901,SAMN04014859,,,,,1,,Collection of bacterial pathogens that demonstrate a range of carbapenem susceptibility,2017-11-27T00:00:00Z,1,,2018-01-01T00:35:10.529Z,2018-01-01T00:35:10.529Z,,,55.16,CP024880,5087312,Klebsiella aerogenes strain AR_0018,Complete,Klesiella,,,,,,,,,,,,,,,,548,,,,,,,4974,,,,,4898,,,Centers for Disease Control and Prevention,350x,PacBio RSII,,,,AR_0018,,,"Included in the study, passed QC/QA"
776,548.235,,,Susceptible;Resistant;Not defined;Intermediate,AMR Panel,GCA_002796425.1,canu v. 1.6,,PRJNA292901,SAMN04014848,,,,,1,,Collection of bacterial pathogens that demonstrate a range of carbapenem susceptibility,2017-11-27T00:00:00Z,1,,2018-01-01T00:33:17.613Z,2018-01-01T00:33:17.613Z,,,55.12,CP024883,5118619,Klebsiella aerogenes strain AR_0007,Complete,Klesiella,,,,,,,,,,,,,,,,548,,,,,,,5021,,,,,4918,,,Centers for Disease Control and Prevention,195x,PacBio RSII,,,,AR_0007,,,"Included in the study, passed QC/QA"
777,548.32,collected_by:Beijing Institute of Microbiology and Epidemiology,,,,GCA_002946615.1,Newbler v. 2.6,,PRJNA433314,SAMN08474658,,,,,1,2014-05-22,Klebsiella aerogenes E20 chromosome,2018-02-18T00:00:00Z,1,,2018-05-26T01:22:21.238Z,2018-05-26T01:22:21.238Z,,,54.940655,CP026722,3802693,Klebsiella aerogenes strain E20,Complete,Klesiella,China: Beijing,,,,,Cerebral contusion,"Human, Homo sapiens",,China,,sputum,,,,,548,,,,,,,3777,,,,,3698,,,Beijing Institute of Microbiology and Epidemiology,22.0x,Illumina MiSeq,,,,E20,,,"Included in the study, passed QC/QA"
778,548.321,,,Susceptible;Resistant;Intermediate;Not defined,AMR Panel,GCA_002948835.1,canu v. 1.6,,PRJNA292904,SAMN04014903,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2018-02-19T00:00:00Z,5,,2018-05-26T01:37:17.044Z,2018-05-26T01:37:17.044Z,,,54.866947,"CP026756,CP026757,CP026758,CP026759,CP026760",5444378,Klebsiella aerogenes strain AR_0062,Complete,Klesiella,,,,,,,,,,,,,,,,548,,,,,,,5433,,4,,,5324,,,Centers for Disease Control and Prevention,255x,PacBio RSII,,,,AR_0062,,,"Included in the study, passed QC/QA"
779,548.324,,,Susceptible;Resistant;Not defined;Intermediate,AMR Panel,GCA_003071285.1,HGAP v. 2.3,,PRJNA292902,SAMN04015002,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2018-04-25T00:00:00Z,2,,2018-05-30T17:42:08.723Z,2018-05-30T17:42:08.723Z,,,54.62248,"CP028951,CP028952",5537473,Klebsiella aerogenes strain AR_0161,Complete,Klesiella,,,,,,,,,,,,,,,,548,,,,,,,5541,,1,,,5403,,,Centers for Disease Control and Prevention,275x,PacBio RSII,,,,AR_0161,,,"Included in the study, passed QC/QA"
780,571.108,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001022115.1,HGAP3 v. 2.2.0,,PRJNA246471,SAMN03733750,,,,,1,2010-12,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2015-06-09T00:00:00Z,6,,2016-01-17T16:05:41.374Z,2016-01-17T16:05:41.374Z,,,54.72,"CP011618,CP011617,CP011616,CP011613,CP011614,CP011615",6673117,Klebsiella oxytoca strain CAV1335,Complete,Klesiella,USA:Virginia,,,,,,"Human, Homo sapiens",,United States,,Urine/Genitourinary,,,,,571,,,,,,,6667,,5,,"NZ_CP011618.1,NZ_CP011617.1,NZ_CP011616.1,NZ_CP011613.1,NZ_CP011614.1,NZ_CP011615.1",6130,,,University of Oxford,51X,PacBio,,,,CAV1335,,,"Included in the study, passed QC/QA"
781,571.11,,,,,GCA_001548355.1,GS Assembler software v. 2.6,,PRJDB4173,SAMD00039250,,,,,5,,"The genus Klebsiella belongs to the family Enterobacteriaceae, and contains non-motile, rod-shaped, and gram-negative bacteria. The genus consists of 7 species, including K. oxytoca, with evident DNA homology. K. oxytoca is a free-living bacterium that can be isolated from plants, animals including humans. The species can be either pathogenic or beneficial depending on conditions, because it can cause colitis in rare cases but can also promote the growth of plants and insects as an endophytic diazotroph. These bilateral characteristics of the species require further elucidation. The aim of the project is to provide information for deep understanding of the bacteria.",2015-09-15T00:00:00Z,5,,2016-03-01T08:21:05.655Z,2016-03-01T08:21:05.655Z,,,55.45,"AP014951,AP014952,AP014953,AP014954,AP014955",6343376,Klebsiella oxytoca strain JKo3,Complete,Klesiella,,,,,,,"Human, Homo sapiens","isolated from plants, animals including humans",,,"plants, animals including humans",,,,,571,,,,,,,6373,,,,"NZ_AP014951.1,NZ_AP014952.1,NZ_AP014953.1,NZ_AP014954.1,NZ_AP014955.1",6070,,,The Jikei University School of Medicine,27x,454 GS FLX; Illumina MiSeq,,,,JKo3,,,"Included in the study, passed QC/QA"
782,571.199,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001870185.1,HGAP v. unspecified,,PRJNA246471,SAMN03733631,,,,,1,2007-08,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2016-11-07T00:00:00Z,6,,2016-11-19T10:54:44.349Z,2016-11-19T10:54:44.349Z,,,54.75,"CP017928,CP017931,CP017930,CP017933,CP017932,CP017929",6582387,Klebsiella oxytoca strain CAV1015,Complete,Klesiella,USA:Virginia,,,,,Bacteremia,"Human, Homo sapiens",,United States,,Blood,,,,,571,,,,,,,6564,,5,25561339,"NZ_CP017928.1,NZ_CP017931.1,NZ_CP017930.1,NZ_CP017933.1,NZ_CP017932.1,NZ_CP017929.1",6111,,,University of Oxford,120x,PacBio,,,,CAV1015,,,"Included in the study, passed QC/QA"
783,571.213,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001970835.1,HGAP v. unspecified,,PRJNA246471,SAMN03733848,,,,,1,2012-12,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2016-12-13T00:00:00Z,6,,2017-03-20T06:09:17.337Z,2017-03-20T06:09:17.337Z,,,55.9,"CP018362,CP018360,CP018361,CP018357,CP018358,CP018359",6394387,Klebsiella oxytoca strain CAV1752,Complete,Klesiella,USA:Virginia,,,,,not applicable,"Human, Homo sapiens",,United States,,Perirectal,,,MLST.Klebsiella_oxytoca.144,,571,,,,,,,6415,,5,,"NZ_CP018362.1,NZ_CP018360.1,NZ_CP018361.1,NZ_CP018357.1,NZ_CP018358.1,NZ_CP018359.1",6144,,,University of Oxford,110x,PacBio,,,,CAV1752,,,"Included in the study, passed QC/QA"
784,571.217,,,Susceptible;Resistant;Not defined;Intermediate,AMR Panel,,HGAP v. 2.3,,PRJNA292902,SAMN04014988,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-03-27T00:00:00Z,2,,2017-05-28T04:38:02.860Z,2017-05-28T04:38:02.860Z,,,55.55,"CP020358,CP020359",6461325,Klebsiella oxytoca strain AR_0147,Complete,Klesiella,,,,,,,,,,,,,,,,571,,,,,,,6471,,1,,,6199,,,Centers for Disease Control and Prevention,108x,PacBio RSII,,,,AR_0147,,,"Included in the study, passed QC/QA"
785,571.309,,,,,GCA_002906395.1,canu v. 1.5,,PRJNA430813,SAMN04287054,,,,,1,2015,"Carbapenem Resistant Enterobacteriaceae strains including Klebsiella, Escherichia, Enterobacter, Citrobacter and Pantoea species isolated from patients and hospital environment.",2018-01-30T00:00:00Z,6,,2018-05-25T20:58:34.639Z,2018-05-25T20:58:34.639Z,,,55.314438,"CP026269,CP026271,CP026273,CP026274,CP026272,CP026270",6938447,Klebsiella oxytoca strain KONIH4,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",isolated from patients and hospital environment,,,patients and hospital environment,,,MLST.Klebsiella_oxytoca.151,,571,,,,,,,7247,,5,,,6892,,,NIH,104x,PacBio RSII,,,,KONIH4,,,"Included in the study, passed QC/QA"
786,571.31,,,,,GCA_002906415.1,HGAP v. 2.3,,PRJNA430813,SAMN03456001,,,,,1,2015,"Carbapenem Resistant Enterobacteriaceae strains including Klebsiella, Escherichia, Enterobacter, Citrobacter and Pantoea species isolated from patients and hospital environment.",2018-01-30T00:00:00Z,8,,2018-05-25T20:57:33.044Z,2018-05-25T20:57:33.044Z,,,55.205364,"CP026285,CP026281,CP026278,CP026284,CP026279,CP026282,CP026283,CP026280",7173160,Klebsiella oxytoca strain KONIH2,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",isolated from patients and hospital environment,,,patients and hospital environment,,,MLST.Klebsiella_oxytoca.143,,571,,,,,,,7478,,7,,,7151,,,NIH,156x,PacBio RSII,,,,KONIH2,,,"Included in the study, passed QC/QA"
787,571.311,,,,,GCA_002906435.1,canu v. 1.3,,PRJNA430813,SAMN06040382,,,,,1,2015,"Carbapenem Resistant Enterobacteriaceae strains including Klebsiella, Escherichia, Enterobacter, Citrobacter and Pantoea species isolated from patients and hospital environment.",2018-01-30T00:00:00Z,3,,2018-05-25T20:56:57.219Z,2018-05-25T20:56:57.219Z,,,55.59658,"CP026275,CP026276,CP026277",6518214,Klebsiella oxytoca strain KONIH5,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",isolated from patients and hospital environment,,,patients and hospital environment,,,MLST.Klebsiella_oxytoca.85,,571,,,,,,,6606,,2,,,6331,,,NIH,187x,PacBio RSII,,,,KONIH5,,,"Included in the study, passed QC/QA"
788,571.318,,,Susceptible;Resistant;Not defined,AMR Panel,GCA_002947505.1,HGAP v. 2.3,,PRJNA292901,SAMN04014869,,,,,1,,Collection of bacterial pathogens that demonstrate a range of carbapenem susceptibility,2018-02-18T00:00:00Z,4,,2018-05-26T01:29:34.679Z,2018-05-26T01:29:34.679Z,,,55.843544,"CP026715,CP026716,CP026717,CP026718",6245141,Klebsiella oxytoca strain AR_0028,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_oxytoca.146,,571,,,,,,,6213,,3,,,5957,,,Centers for Disease Control and Prevention,142x,PacBio RSII,,,,AR_0028,,,"Included in the study, passed QC/QA"
789,571.319,collected_by:Children's National Hospital,,,,GCA_002984395.1,"SMRT v. 2.3.0, HGAP v. 3.0",,PRJNA231221,SAMN06173348,,,,,1,11-Feb-2015,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2018-03-09T00:00:00Z,2,FDA:FDAARGOS_335,2018-05-26T05:54:14.438Z,2018-05-26T05:54:14.438Z,,,55.082916,"CP027426,CP027425",6049823,Klebsiella oxytoca strain FDAARGOS_335 strain Not Applicable,Complete,Klesiella,USA:DC,,,4Y,female,Urinary tract infection,"Human, Homo sapiens",,USA,,urine catheter,,,MLST.Klebsiella_oxytoca.147,,571,,,,,,,5935,,1,,,5710,,,US Food and Drug Administration,15.9487981715526x,PacBio; Illumina,,,,Not Applicable,,,"Included in the study, passed QC/QA"
790,571.32,,,Susceptible;Resistant;Intermediate;Not defined,AMR Panel,GCA_003073975.1,canu v. 1.4,,PRJNA316321,SAMN07291523,,,,,1,,"The AR Isolate Bank is a centralized repository of microbial pathogens with well-characterized resistance profiles that are assembled by CDC in collaboration with the Food and Drug Administration (FDA). The AR Bank is available to support and advance development of diagnostic devices and antimicrobial drug products. The AR Isolate Bank also supports the National Action Plan for Combating Antibiotic Resistance Bacteria by advancing the development of diagnostic tests to identify and characterize resistant bacteria, and by accelerating research and development for new antibiotics.The AR Isolate Bank includes collections of bacterial pathogens that are associated with known or emerging resistance mechanisms. Since its launch in July 2015, the AR Bank continues to grow and will eventually include genera and species such as Enterobacteriaceae, Pseudomonas aeruginosa, Staphylococcus, Enterococcus, Streptococcus, Salmonella, and Neisseria gonorrhoeae.Each pathogen listed on this web site includes information regarding its susceptibility and/or resistance profile(s), known resistance biomarkers, isolate characteristics, and associated data in PDF.Use this web site to search through pathogen panels, find additional information about the available isolates, and find procedures for requesting panels.",2018-04-30T00:00:00Z,2,,2018-05-27T22:32:12.635Z,2018-05-27T22:32:12.635Z,,,54.800858,"CP029128,CP029127",6003751,Klebsiella oxytoca strain AR380,Complete,Klesiella,,,,,,,,,,,,,,,,571,,,,,,,5868,,1,,,5849,,,FDA/CDC,19.98x,Pacbio; Illumina,,,,AR380,,,"Included in the study, passed QC/QA"
791,571.33,,,,,GCA_000724525.1,Newbler v. 2.8; SOAPdenovo v. 2.04,,PRJNA253752,SAMN02887315,,,,,1,2012,"We performed whole genome sequencing to compare the genome of Klebsiella oxytoca M1, isolated from Manripo area of South Korea, with the genome of K.oxytoca KCTC1686 (GenBank accession number CP003218). The strain K.oxytoca KCTC1686 is only able to produce 2,3-BDO at 30℃ and 37℃, whereas K.oxytoca M1 is able to produce either 2,3-BDO or acetoin selectively by controlling the pH and temperature.",2014-07-09T00:00:00Z,5,,2014-12-08T23:17:41.869Z,2015-03-16T03:17:09.594Z,,,55.85,"CP008841.1,CP008844.1,CP008845.1,CP008843.1,CP008842.1",6311380,Klebsiella oxytoca strain M1,Complete,Klesiella,South Korea: Maripo beach,,,,,,"Human, Homo sapiens","isolated from Manripo area of South Korea, with the genome of K.oxytoca KCTC1686 (GenBank accession number CP003218)",South Korea,,"Manripo area of South Korea, with the genome of K",,,,,571,,,,,,,5988,,1,-,"NZ_CP008841.1,NZ_CP008842.1,NZ_CP008843.1,NZ_CP008844.1,NZ_CP008845.1",5634,,,Macrogen Inc.,327.0x,454; Illumina HiSeq; ABI3730,,,,M1,,,"Included in the study, passed QC/QA"
792,571.62,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001022195.1,HGAP3 v. 2.2.0,,PRJNA246471,SAMN03733738,,,,,1,2010-08,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2015-06-09T00:00:00Z,12,,2016-01-17T16:05:42.704Z,2016-01-17T16:05:42.704Z,,,55.3,"CP011636,CP011627,CP011633,CP011628,CP011625,CP011634,CP011629,CP011630,CP011631,CP011626,CP011632,CP011635",7227285,Klebsiella oxytoca strain CAV1374,Complete,Klesiella,USA:Virginia,,,,,not applicable,"Human, Homo sapiens",,United States,,Perirectal,,,,,571,,,,,,,7362,,11,,"NZ_CP011636.1,NZ_CP011627.1,NZ_CP011633.1,NZ_CP011628.1,NZ_CP011625.1,NZ_CP011634.1,NZ_CP011629.1,NZ_CP011630.1,NZ_CP011631.1,NZ_CP011626.1,NZ_CP011632.1,NZ_CP011635.1",6622,,,University of Oxford,57X,PacBio,,,,CAV1374,,,"Included in the study, passed QC/QA"
793,571.63,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001022295.1,HGAP3 v. 2.2.0,,PRJNA246471,SAMN03733663,,,,,1,2009-04,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2015-06-09T00:00:00Z,6,,2016-01-17T16:05:44.498Z,2016-01-17T16:05:44.498Z,,,54.71,"CP011597,CP011594,CP011596,CP011592,CP011593,CP011595",6630537,Klebsiella oxytoca strain CAV1099,Complete,Klesiella,USA:Virginia,,,,,not applicable,"Human, Homo sapiens",,United States,,Perirectal,,,,,571,,,,,,,6614,,5,,"NZ_CP011597.1,NZ_CP011594.1,NZ_CP011596.1,NZ_CP011592.1,NZ_CP011593.1,NZ_CP011595.1",6079,,,University of Oxford,96X,PacBio,,,,CAV1099,,,"Included in the study, passed QC/QA"
794,573.12457,,,Resistant;Susceptible,Computational Prediction,,HGAP v. v2,,PRJNA376414,SAMN06701573,,,,,1,2004,"A collection of 1,777 clinical K. pneumoniae isolates from Houston, Texas.",2017-05-23T00:00:00Z,4,,2017-07-21T20:25:15.647Z,2017-07-21T20:25:15.647Z,,,56.99,"CP020837,CP020838,CP020839,CP020840",5896654,Klebsiella pneumoniae strain BK13043,Complete,Klesiella,"USA: New York, New York City",,,,,,"Human, Homo sapiens",,United States,,,,,MLST.Klebsiella_pneumoniae.258,,573,,,,,,,6053,,3,,,5881,,,Houston Methodist Hospital,121x,PacBio,,,,BK13043,,,"Included in the study, passed QC/QA"
795,573.12458,collected_by:Houston Methodist Hospital,,Resistant;Susceptible,Computational Prediction,,HGAP v. v2,,PRJNA376414,SAMN06438459,,,,,1,11-Jun-2014,"A collection of 1,777 clinical K. pneumoniae isolates from Houston, Texas.",2017-05-23T00:00:00Z,6,,2017-07-21T20:26:37.754Z,2017-07-21T20:26:37.754Z,,,56.71,"CP020841,CP020842,CP020843,CP020844,CP020846,CP020845",5965284,Klebsiella pneumoniae strain KPN1482,Complete,Klesiella,USA: Houston,,,,,Klebsiella Infections,"Human, Homo sapiens",,United States,,respiratory,,,MLST.Klebsiella_pneumoniae.37,,573,,,host_description:HMH:KPN:1482,,genotype:ST37; Capsule locus KL105,,6244,,5,,,6014,,,Houston Methodist Hospital,201x,PacBio,,,,KPN1482,,,"Included in the study, passed QC/QA"
796,573.12459,collected_by:Houston Methodist Hospital,,Susceptible;Resistant,Computational Prediction,,HGAP v. v2,,PRJNA376414,SAMN06438458,,,,,1,10-Jun-2014,"A collection of 1,777 clinical K. pneumoniae isolates from Houston, Texas.",2017-05-23T00:00:00Z,6,,2017-07-21T20:29:58.313Z,2017-07-21T20:29:58.313Z,,,56.73,"CP020847,CP020848,CP020851,CP020852,CP020850,CP020849",6106127,Klebsiella pneumoniae strain KPN1481,Complete,Klesiella,USA: Houston,,,,,Klebsiella Infections,"Human, Homo sapiens",,United States,,urine,,,,,573,,,host_description:HMH:KPN:1481,,genotype:ST906; Capsule locus KL10,,6291,,5,,,6026,,,Houston Methodist Hospital,95x,PacBio,,,,KPN1481,,,"Included in the study, passed QC/QA"
797,573.1246,collected_by:Houston Methodist Hospital,,Resistant;Susceptible,Computational Prediction,,HGAP v. v2,,PRJNA376414,SAMN06437491,,,,,1,02-Dec-2012,"A collection of 1,777 clinical K. pneumoniae isolates from Houston, Texas.",2017-05-23T00:00:00Z,4,,2017-07-21T20:29:33.854Z,2017-07-21T20:29:33.854Z,,,56.7,"CP020853,CP020854,CP020855,CP020856",5973075,Klebsiella pneumoniae strain KPN528,Complete,Klesiella,USA: Houston,,,,,Klebsiella Infections,"Human, Homo sapiens",,United States,,respiratory,,,MLST.Klebsiella_pneumoniae.14,,573,,,host_description:HMH:KPN:528,,genotype:ST14; Capsule locus KL2,,6186,,3,,,5898,,,Houston Methodist Hospital,232x,PacBio,,,,KPN528,,,"Included in the study, passed QC/QA"
798,573.12771,,,Susceptible;Resistant;Not defined;Intermediate,AMR Panel,,canu v. 1.3,,PRJNA292902,SAMN04014967,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-13T00:00:00Z,4,,2017-07-22T17:29:48.231Z,2017-07-22T17:29:48.231Z,,,57.26,"CP021740,CP021741,CP021742,CP021743",5598174,Klebsiella pneumoniae strain AR_0126,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5677,,3,,,5522,,,Centers for Disease Control and Prevention,82x,PacBio RSII,,,,AR_0126,,,"Included in the study, passed QC/QA"
799,573.12772,,,Resistant;Susceptible;Intermediate;Not defined,AMR Panel,,HGAP v. 2.3,,PRJNA292902,SAMN04014954,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-13T00:00:00Z,6,,2017-07-22T17:30:27.801Z,2017-07-22T17:30:27.801Z,,,56.96,"CP021751,CP021752,CP021753,CP021754,CP021755,CP021756",5849839,Klebsiella pneumoniae strain AR_0113,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,6041,,5,,,5865,,,Centers for Disease Control and Prevention,169x,PacBio RSII,,,,AR_0113,,,"Included in the study, passed QC/QA"
800,573.12773,,,Resistant;Susceptible;Not defined;Intermediate,AMR Panel,,canu v. 1.3,,PRJNA292902,SAMN04014979,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-13T00:00:00Z,5,,2017-07-22T17:31:29.094Z,2017-07-22T17:31:29.094Z,,,57.02,"CP021757,CP021758,CP021759,CP021760,CP021761",5708112,Klebsiella pneumoniae strain AR_0138,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5794,,4,,,5634,,,Centers for Disease Control and Prevention,84x,PacBio RSII,,,,AR_0138,,,"Included in the study, passed QC/QA"
801,573.12777,,,Resistant;Susceptible;Not defined,AMR Panel,,canu v. 1.3,,PRJNA292902,SAMN04014961,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-16T00:00:00Z,5,,2017-07-22T19:49:02.969Z,2017-07-22T19:49:02.969Z,,,56.91,"CP021833,CP021834,CP021835,CP021836,CP021837",5995730,Klebsiella pneumoniae strain AR_0120,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,6189,,4,,,6005,,,Centers for Disease Control and Prevention,90x,PacBio RSII,,,,AR_0120,,,"Included in the study, passed QC/QA"
802,573.12778,,,Resistant;Susceptible;Intermediate;Not defined,AMR Panel,,canu v. 1.3,,PRJNA292902,SAMN04014966,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-16T00:00:00Z,6,,2017-07-22T19:58:18.830Z,2017-07-22T19:58:18.830Z,,,57.1,"CP021859,CP021856,CP021857,CP021858,CP021860,CP021861",5726558,Klebsiella pneumoniae strain AR_0125,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.258,,573,,,,,,,5884,,5,,,5725,,,Centers for Disease Control and Prevention,85x,PacBio RSII,,,,AR_0125,,,"Included in the study, passed QC/QA"
803,573.12779,,,Susceptible;Resistant;Not defined,AMR Panel,,canu v. 1.3,,PRJNA292902,SAMN04014980,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-20T00:00:00Z,5,,2017-07-22T22:20:38.788Z,2017-07-22T22:20:38.788Z,,,56.57,"CP021960,CP021958,CP021959,CP021961,CP021962",6054276,Klebsiella pneumoniae strain AR_0139,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.37,,573,,,,,,,6319,,4,,,6302,,,Centers for Disease Control and Prevention,128x,PacBio RSII,,,,AR_0139,,,"Included in the study, passed QC/QA"
804,573.1278,,,Susceptible;Resistant;Not defined,AMR Panel,,canu v. 1.3,,PRJNA292902,SAMN04014986,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-20T00:00:00Z,5,,2017-07-22T22:21:58.229Z,2017-07-22T22:21:58.229Z,,,57.09,"CP021939,CP021940,CP021941,CP021942,CP021943",5656270,Klebsiella pneumoniae strain AR_0145,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.147,,573,,,,,,,5697,,4,,,5524,,,Centers for Disease Control and Prevention,100x,PacBio RSII,,,,AR_0145,,,"Included in the study, passed QC/QA"
805,573.12781,,,Susceptible;Resistant;Not defined,AMR Panel,,canu v. 1.3,,PRJNA292902,SAMN04014993,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-20T00:00:00Z,6,,2017-07-22T22:22:51.483Z,2017-07-22T22:22:51.483Z,,,57.02,"CP021944,CP021945,CP021946,CP021947,CP021948,CP021949",5782129,Klebsiella pneumoniae strain AR_0152,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.147,,573,,,,,,,5859,,5,,,5686,,,Centers for Disease Control and Prevention,208x,PacBio RSII,,,,AR_0152,,,"Included in the study, passed QC/QA"
806,573.12782,,,Resistant;Susceptible;Not defined,AMR Panel,,canu v. 1.3,,PRJNA292902,SAMN04014989,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-20T00:00:00Z,5,,2017-07-22T22:22:19.965Z,2017-07-22T22:22:19.965Z,,,56.81,"CP021950,CP021951,CP021952,CP021953,CP021954",5798614,Klebsiella pneumoniae strain AR_0148,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.11,,573,,,,,,,5996,,4,,,5803,,,Centers for Disease Control and Prevention,120x,PacBio RSII,,,,AR_0148,,,"Included in the study, passed QC/QA"
807,573.12783,,,Susceptible;Resistant;Not defined,AMR Panel,,HGAP v. 2.3,,PRJNA292904,SAMN04014948,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2017-06-20T00:00:00Z,3,,2017-07-22T22:32:33.943Z,2017-07-22T22:32:33.943Z,,,57.04,"CP021955,CP021956,CP021957",5658318,Klebsiella pneumoniae strain AR_0107,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5826,,2,,,5656,,,Centers for Disease Control and Prevention,220x,PacBio RSII,,,,AR_0107,,,"Included in the study, passed QC/QA"
808,573.12792,biomaterial_provider:Beijing Institute of Microbiology and Epidemiology;sample_type:clinical,,Susceptible;Resistant,Computational Prediction,,SOAPdenovo v. 1.0,,PRJNA388820,SAMN07187263,,,,,1,,Klebsiella pneumoniae 19051 chromosome,2017-06-27T00:00:00Z,1,,2017-07-23T01:28:51.867Z,2017-07-23T01:28:51.867Z,,,57.41,CP022023,5332976,Klebsiella pneumoniae strain 19051,Complete,Klesiella,,,,62,,,"Human, Homo sapiens",,,,urine,,,,,573,,,,,,,5128,,,,,,,,Beijing Institute of Microbiology and Epidemiology,86.0x,PacBio,,,,19051,,,"Included in the study, passed QC/QA"
809,573.12796,collected_by:Washoe County Health District,,Susceptible;Resistant;Not defined;Intermediate,AMR Panel,,other v. HGAP 3,,PRJNA391323,SAMN07265011,,,,,1,2016-08-19,"Whole genome sequence of a Klebsiella pneumonia isolate, from Washoe County in Nevada, that was non-susceptible to all available antimicrobial drugs.",2017-07-12T00:00:00Z,4,,2017-07-23T03:15:17.194Z,2017-07-23T03:15:17.194Z,,,56.86,"CP022127,CP022126,CP022125,CP022128",5816577,Klebsiella pneumoniae strain MLST-15,Complete,Klesiella,USA: Nevada,,,,,,"Human, Homo sapiens",,United States,,wound,,,MLST.Klebsiella_pneumoniae.15,,573,,,,,,,5902,,3,,,5722,,,Centers for Disease Control and Prevention. Division of Healthcare Quality Promotion,77.48x,PacBio,,,,MLST-15,,,"Included in the study, passed QC/QA"
810,573.1352,collected_by:Julie Segre,,,,GCF_000739495.1,HGAP v. 2,,PRJNA248655,SAMN02777842,,,,,1,2012,Whole genome SMRT sequencing of carbapenem-resistant Klebsiella pneumoniae blaNDM-1.,2015-03-02T00:00:00Z,3,,2016-01-17T15:38:31.930Z,2016-01-17T15:38:31.930Z,,,57.26,"CP009114,CP009116,CP009115",5510332,Klebsiella pneumoniae strain blaNDM-1,Complete,Klesiella,USA: HHS Region 5,,,,,coronary graft,"Human, Homo sapiens",,United States,,clinical urine culture,,,,,573,,,,,,,5460,,2,24798270,"NZ_CP009114.1,NZ_CP009116.1,NZ_CP009115.1",5075,,,FNLCR,150x,PacBio,,,,carbapenem-resistant blaNDM-1,,,"Included in the study, passed QC/QA"
811,573.1358,collected_by:PED Study Team,,,,GCF_000764615.1,Hgap v. 3,,PRJNA253300,SAMN02885365,,,,,1,16-Aug-2011,Suspected NDM-1 outbreak and enviromental Klebsiella pneumoniae isolates,2014-11-26T00:00:00Z,5,,2016-01-17T15:40:24.654Z,2016-01-17T15:40:24.654Z,,,56.57,"CP008929,CP008930,CP008931,CP008932,CP008933",5990738,Klebsiella pneumoniae strain PMK1,Complete,Klesiella,Nepal,,,,,Klebsiella pneumoniae [K. pneumoniae] as the cause of diseases classified elsewhere,"Human, Homo sapiens",,Nepal,,Blood,,,,,573,,,,,,,5904,,4,25267672,"NZ_CP008929.1,NZ_CP008930.1,NZ_CP008931.1,NZ_CP008932.1,NZ_CP008933.1",5594,,,University of Oxford,60x,Illumina; Pacific Biosciences,,,,PMK1,,,"Included in the study, passed QC/QA"
812,573.1361,collected_by:Yunsong Yu,,,,GCF_000775955.1,idba v. 1.1.1; SSPACE v. 3.0,,PRJNA261555,SAMN02649400,,,,,1,2013-12-13,Ref Seq for SNP detection,2015-01-29T00:00:00Z,1,,2016-01-17T15:40:48.965Z,2016-01-17T15:40:48.965Z,,,57.63,CP009461,5118878,Klebsiella pneumoniae strain XH209,Complete,Klesiella,China:Hangzhou,,,,,Pneumonia due to Klebsiella pneumoniae,"Human, Homo sapiens",,China,,blood from patient with pneumonia,,,,,573,,,,,,,4982,,,25540349,NZ_CP009461.1,4881,,,"Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University",200x,Illumina,,,,XH209,,,"Included in the study, passed QC/QA"
813,573.1369,collected_by:Barry Kreiswirth,,,,GCF_000807395.2,HGAP v. 2,,PRJNA259789,SAMN03067420,,,,,1,2010,"Carbapenem resistance in Enterobacteriacae is increasingly due to the presence of the KPC beta-lactamase, which can be transferred on several different plasmids. The project is designed to better understand the spread of the blaKPC gene and the genetic backgrounds in which it is carried.",2015-02-06T00:00:00Z,4,,2016-01-17T15:41:44.100Z,2016-01-17T15:41:44.100Z,,,57.24,"CP010361,JWRN01000000",5620801,Klebsiella pneumoniae strain 32192,Complete,Klesiella,USA,,,,,Urosepsis,"Human, Homo sapiens",,United States,,Urine,,,,,573,,,host_health_state:Diseased,,genotype:258,,5654,,3,,,5495,,,JCVI,5.63x,Pacbio RS,,,,32192,,,"Included in the study, passed QC/QA"
814,573.1374,collected_by:Barry Kreiswirth,,,,GCF_000814305.1,HGAP v. 3,,PRJNA259789,SAMN03067424,,,,,1,2011,"Carbapenem resistance in Enterobacteriacae is increasingly due to the presence of the KPC beta-lactamase, which can be transferred on several different plasmids. The project is designed to better understand the spread of the blaKPC gene and the genetic backgrounds in which it is carried.",2015-01-05T00:00:00Z,5,,2016-01-17T15:41:58.475Z,2016-01-17T15:41:58.475Z,,,57.21,"CP010392,CP010394,CP010393,CP010395,CP010396",5649912,Klebsiella pneumoniae strain 34618,Complete,Klesiella,USA,,,,,pneumonia,"Human, Homo sapiens",,United States,,bronchoalveolar lavage,,,,,573,,,host_health_state:Diseased,,genotype:258,,5642,,4,,"NZ_CP010392.1,NZ_CP010394.1,NZ_CP010393.1,NZ_CP010395.1,NZ_CP010396.1",5550,,,JCVI,8.73x,Pacbio RS,,,,34618,,,"Included in the study, passed QC/QA"
815,573.14839,sample_type:rectal swab,,Resistant;Susceptible,Computational Prediction,GCA_002243445.1,CLC genomic workbench v. 9,,PRJNA396009,SAMN07419044,,,,,1,2009-09-01,whole genome sequence of KPC-producing Klebsiella pneumoniae,2017-08-08T00:00:00Z,4,,2017-09-28T19:50:40.810Z,2017-09-28T19:50:40.810Z,,,57.16,"CP022573,CP022574,CP022575,CP022576",5621950,Klebsiella pneumoniae strain BIC-1,Complete,Klesiella,France: Kremlin-Bicetre,,,,,,"Human, Homo sapiens",,France,,,,,,,573,,,,,,,5762,,3,,,5618,,,"Faculte de Medecine, Universite Paris-Sud",30.0x,PacBio,,,,BIC-1,,,"Included in the study, passed QC/QA"
816,573.1488,,,,,GCF_000968155.1,,,PRJEB99,SAMEA3283117,,,,,3,,Strain Kp52.145 is a laboratory strain used to study Klebsiella pneumoniae pathogenesis. The complete genome sequence of this virulent K2 strain of sequence type ST66 has been determined.,2015-03-07T00:00:00Z,3,,2016-01-17T15:52:38.942Z,2016-01-17T15:52:38.942Z,,,57.1,"FO834906,FO834904,FO834905",5655684,Klebsiella pneumoniae strain CIP 52.145,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5657,,,25341126,"NZ_FO834906.1,NZ_FO834904.1,NZ_FO834905.1",5309,,,Genoscope CEA,,,,,,CIP 52.145,,,"Included in the study, passed QC/QA"
817,573.1493,sample_type:microbe,,,,GCA_001006265.1,Velvet v. MAY-2014,,PRJNA271515,SAMN03274783,,,,,,2007-03-12,The finding might be applicable to the industrial production of Chinese ham,2015-05-13T00:00:00Z,1,,2016-01-17T16:02:06.941Z,2016-01-17T16:02:06.941Z,,,54.93,CP011421,5081069,Klebsiella pneumoniae strain yzusk-4,Complete,Klesiella,China: Jiangsu,,,,,,,,China,,rugao ham,,,,,573,,,,,,,4792,,,,,4587,,,food sience,92.0x,Illumina,,,,yzusk-4,,,"Excluded from the study, failed QC/QA."
818,573.1497,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001022235.1,HGAP3 v. 2.2.0,,PRJNA246471,SAMN03024583,,,,,1,Apr-2012,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2015-06-09T00:00:00Z,5,,2016-01-17T16:05:43.400Z,2016-01-17T16:05:43.400Z,,,57.13,"CP011647,CP011643,CP011644,CP011645,CP011646",5620516,Klebsiella pneumoniae strain CAV1596,Complete,Klesiella,USA:Virginia,,,,,not applicable,"Human, Homo sapiens",,United States,,Perirectal,,,,,573,,,,,,,5607,,4,,"NZ_CP011647.1,NZ_CP011643.1,NZ_CP011644.1,NZ_CP011645.1,NZ_CP011646.1",5507,,,University of Oxford,90X,PacBio,,,,CAV1596,,,"Included in the study, passed QC/QA"
819,573.14988,collected_by:Beijing Institute of Microbiology and Epidemiology,,Susceptible;Resistant,Computational Prediction,GCA_002269295.1,SOAPdenovo v. 1.0,,PRJNA398333,SAMN07508215,,,,,1,2014-09,Klebsiella pneumoniae 911021 chromosome,2017-08-24T00:00:00Z,1,,2017-09-28T21:11:56.962Z,2017-09-28T21:11:56.962Z,,,57.46,CP022882,5456357,Klebsiella pneumoniae strain 911021,Complete,Klesiella,China: Chongqing,,,,,stroke,"Human, Homo sapiens",,China,,urine,,,,,573,,,,,,,5508,,,,,5385,,,Beijing Institute of Microbiology and Epidemiology,73.0x,PacBio,,,,911021,,,"Included in the study, passed QC/QA"
820,573.1499,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001022035.1,HGAP3 v. 2.2.0,,PRJNA246471,SAMN03024610,,,,,1,Mar-2011,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2015-06-09T00:00:00Z,4,,2016-01-17T16:05:39.957Z,2016-01-17T16:05:39.957Z,,,57.26,"CP011578,CP011577,CP011576,CP011575",5552491,Klebsiella pneumoniae strain CAV1392,Complete,Klesiella,USA:Virginia,,,,,Pneumonia,"Human, Homo sapiens",,United States,,Sputum,,,,,573,,,,,,,5551,,3,,"NZ_CP011578.1,NZ_CP011577.1,NZ_CP011576.1,NZ_CP011575.1",5454,,,University of Oxford,49X,PacBio,,,,CAV1392,,,"Included in the study, passed QC/QA"
821,573.15,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001022175.1,HGAP3 v. 2.3.0,,PRJNA246471,SAMN03024590,,,,,1,Dec-2010,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2015-06-09T00:00:00Z,6,,2016-01-17T16:05:42.395Z,2016-01-17T16:05:42.395Z,,,57.08,"CP011624,CP011623,CP011619,CP011620,CP011621,CP011622",5810009,Klebsiella pneumoniae strain CAV1344,Complete,Klesiella,USA:Virginia,,,,,Urinary Tract Infection,"Human, Homo sapiens",,United States,,Urine,,,,,573,,,,,,,5864,,5,,"NZ_CP011624.1,NZ_CP011623.1,NZ_CP011619.1,NZ_CP011620.1,NZ_CP011621.1,NZ_CP011622.1",5668,,,University of Oxford,98X,PacBio,,,,CAV1344,,,"Included in the study, passed QC/QA"
822,573.15001,biomaterial_provider:Beijing Institute of Microbiology and Epidemiology;collected_by:Beijing Institute of Microbiology and Epidemiology,,Susceptible;Resistant,Computational Prediction,GCA_002278055.1,SOAPdenovo v. 1.0,,PRJNA397713,SAMN07484315,,,,,1,2013,Klebsiella pneumoniae 721005 chromosome,2017-08-30T00:00:00Z,1,,2017-09-28T21:31:47.582Z,2017-09-28T21:31:47.582Z,,,57.38,CP022997,5475860,Klebsiella pneumoniae strain 721005,Complete,Klesiella,China: Ningbo,,,,,Paralysis,"Human, Homo sapiens",,China,,urine,,,,,573,,,,,,,5539,,,,,5416,,,Beijing Institute of Microbiology and Epidemiology,165.0x,PacBio,,,,721005,,,"Included in the study, passed QC/QA"
823,573.15042,,,Susceptible;Resistant;Not defined;Intermediate,Computational Prediction,GCA_002180255.1,canu v. 1.3,,PRJNA292902,SAMN04014999,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-08T00:00:00Z,5,,2017-09-29T16:42:00.341Z,2017-09-29T16:42:00.341Z,,,56.65,"CP021696,CP021697,CP021698,CP021699,CP021700",5806817,Klebsiella pneumoniae strain AR_0158,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5952,,4,,,5736,,,Centers for Disease Control and Prevention,183x,PacBio RSII,,,,AR_0158,,,"Included in the study, passed QC/QA"
824,573.15043,,,Intermediate;Resistant;Not defined;Susceptible,Computational Prediction,GCA_002180175.1,canu v. 1.3,,PRJNA292902,SAMN04014987,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-08T00:00:00Z,4,,2017-09-29T16:42:15.777Z,2017-09-29T16:42:15.777Z,,,57.05,"CP021685,CP021686,CP021687,CP021688",5746129,Klebsiella pneumoniae strain AR_0146,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5854,,3,,,5685,,,Centers for Disease Control and Prevention,125x,PacBio RSII,,,,AR_0146,,,"Included in the study, passed QC/QA"
825,573.15044,,,Intermediate;Resistant;Not defined;Susceptible,Computational Prediction,GCA_002180075.1,canu v. 1.3,,PRJNA292904,SAMN04014888,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2017-06-08T00:00:00Z,5,,2017-09-29T16:42:11.098Z,2017-09-29T16:42:11.098Z,,,57.06,"CP021539,CP021540,CP021541,CP021542,CP021543",5774316,Klebsiella pneumoniae strain AR_0047,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5974,,4,,,6059,,,Centers for Disease Control and Prevention,177x,PacBio RSII,,,,AR_0047,,,"Included in the study, passed QC/QA"
826,573.15107,,,Intermediate;Resistant;Not defined;Susceptible,Computational Prediction,GCA_002180295.1,canu v. 1.3,,PRJNA292902,SAMN04014970,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-08T00:00:00Z,6,,2017-10-24T14:07:49.832Z,2017-10-24T14:07:49.832Z,,,56.9,"CP021718,CP021713,CP021714,CP021715,CP021716,CP021717",5835823,Klebsiella pneumoniae strain AR_0129,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5999,,5,,,5829,,,Centers for Disease Control and Prevention,90x,PacBio RSII,,,,AR_0129,,,"Included in the study, passed QC/QA"
827,573.15108,,,Resistant;Not defined;Susceptible,Computational Prediction,GCA_002180315.1,canu v. 1.3,,PRJNA292902,SAMN04014984,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-08T00:00:00Z,5,,2017-10-24T14:09:08.634Z,2017-10-24T14:09:08.634Z,,,56.9,"CP021708,CP021709,CP021710,CP021711,CP021712",5989257,Klebsiella pneumoniae strain AR_0143,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,6094,,4,,,5928,,,Centers for Disease Control and Prevention,117x,PacBio RSII,,,,AR_0143,,,"Included in the study, passed QC/QA"
828,573.15217,,,Susceptible;Resistant;Not defined,Computational Prediction,GCA_002180155.1,canu v. 1.3,,PRJNA292902,SAMN04014953,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-08T00:00:00Z,6,,2017-11-23T01:18:25.934Z,2017-11-23T01:18:25.934Z,,,56.97,"CP021549,CP021544,CP021545,CP021546,CP021547,CP021548",5859680,Klebsiella pneumoniae strain AR_0112,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.258,,573,,,,,,,6070,,5,,,6141,,,Centers for Disease Control and Prevention,167x,PacBio RSII,,,,AR_0112,,,"Included in the study, passed QC/QA"
829,573.15234,collected_by:BC Centre for Disease Control,,Susceptible;Resistant,Computational Prediction,GCA_002386225.1,Celera v. 8.2,,PRJNA231221,SAMN07312489,,,,,1,2013-11,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-09-28T00:00:00Z,2,FDA:FDAARGOS_445,2017-11-23T02:35:01.765Z,2017-11-23T02:35:01.765Z,,,57.28,"CP023502,CP023503",5537327,Klebsiella pneumoniae strain FDAARGOS_445 strain Not applicable,Complete,Klesiella,Canada:BC,,,Not applicable,,,"Human, Homo sapiens",,Canada,,urine,,,MLST.Klebsiella_pneumoniae.340,,573,,,host_description:Not applicable,,,,5645,,1,,,5509,,,US Food and Drug Administration,15.49x,PacBio; Illumina,,,,Not applicable,,,"Included in the study, passed QC/QA"
830,573.15309,collected_by:BC Centre for Disease Control,,Resistant;Susceptible,Computational Prediction,GCA_002587165.1,"SMRT v. 2.3.0, HGAP v. 3, SPAdes v. 3.6.0",,PRJNA231221,SAMN07312488,,,,,1,2013-07,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-10-18T00:00:00Z,5,FDA:FDAARGOS_444,2017-11-24T16:42:59.019Z,2017-11-24T16:42:59.019Z,,,57.07,"CP023941,CP023940,CP023943,CP023942,CP023944",5880984,Klebsiella pneumoniae strain FDAARGOS_444 strain Not applicable,Complete,Klesiella,Canada:BC,,,Not applicable,,,"Human, Homo sapiens",,Canada,,wound,,,MLST.Klebsiella_pneumoniae.11,,573,,,host_description:Not applicable,,,,6118,,4,,,5968,,,US Food and Drug Administration,15.18x,PacBio; Illumina,,,,Not applicable,,,"Included in the study, passed QC/QA"
831,573.1531,collected_by:BC Centre for Disease Control,,Susceptible;Resistant,Computational Prediction,GCA_002587885.1,"SMRT v. 2.3.0, HGAP v. 3, SPAdes v. 3.6.0",,PRJNA231221,SAMN07312490,,,,,1,2014-01,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-10-18T00:00:00Z,4,FDA:FDAARGOS_446,2017-11-24T16:46:00.093Z,2017-11-24T16:46:00.093Z,,,57.06,"CP023946,CP023948,CP023947,CP023945",5769651,Klebsiella pneumoniae strain FDAARGOS_446 strain Not applicable,Complete,Klesiella,Canada:BC,,,Not applicable,,Screening,"Human, Homo sapiens",,Canada,,Rectal,,,,,573,,,host_description:Not applicable,,,,5972,,3,,,5799,,,US Food and Drug Administration,15.99x,PacBio; Illumina,,,,Not applicable,,,"Included in the study, passed QC/QA"
832,573.15312,collected_by:BC Centre for Disease Control,,Resistant;Susceptible,Computational Prediction,GCA_002591075.1,"SMRT v. 2.3.0, HGAP v. 3, SPAdes v. 3.6.0",,PRJNA231221,SAMN07312483,,,,,1,2014-12,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-10-18T00:00:00Z,6,FDA:FDAARGOS_439,2017-11-24T16:44:23.258Z,2017-11-24T16:44:23.258Z,,,57.01,"CP023913,CP023918,CP023917,CP023916,CP023914,CP023915",5752865,Klebsiella pneumoniae strain FDAARGOS_439 strain Not applicable,Complete,Klesiella,Canada:BC,,,Not applicable,,,"Human, Homo sapiens",,Canada,,urine,,,MLST.Klebsiella_pneumoniae.147,,573,,,host_description:Not applicable,,,,5904,,5,,,5741,,,US Food and Drug Administration,12.96x,PacBio; Illumina,,,,Not applicable,,,"Included in the study, passed QC/QA"
833,573.15317,collected_by:BC Centre for Disease Control,,Susceptible;Resistant,Computational Prediction,GCA_002635725.1,"SMRT v. 2.3.0, HGAP v. 3, SPAdes v. 3.6.0",,PRJNA231221,SAMN07312484,,,,,1,2015-01,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-10-18T00:00:00Z,6,FDA:FDAARGOS_440,2017-11-24T16:51:15.524Z,2017-11-24T16:51:15.524Z,,,57.18,"CP023919,CP023920,CP023921,CP023923,CP023922,CP023924",5606744,Klebsiella pneumoniae strain FDAARGOS_440 strain Not applicable,Complete,Klesiella,Canada:BC,,,Not applicable,,,"Human, Homo sapiens",,Canada,,blood,,,MLST.Klebsiella_pneumoniae.16,,573,,,host_description:Not applicable,,,,5762,,5,,,5604,,,US Food and Drug Administration,14.07x,PacBio; Illumina,,,,Not applicable,,,"Included in the study, passed QC/QA"
834,573.15318,collected_by:BC Centre for Disease Control,,Resistant,Computational Prediction,GCA_002636215.1,"SMRT v. 2.3.0, HGAP v. 3",,PRJNA231221,SAMN07312491,,,,,1,2014-05,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-10-18T00:00:00Z,7,FDA:FDAARGOS_447,2017-11-24T16:51:32.831Z,2017-11-24T16:51:32.831Z,,,57.15,"CP023949,CP023954,CP023955,CP023952,CP023953,CP023950,CP023951",5789969,Klebsiella pneumoniae strain FDAARGOS_447 strain Not applicable,Complete,Klesiella,Canada:BC,,,Not applicable,,Screening,"Human, Homo sapiens",,Canada,,Perirectal,,,MLST.Klebsiella_pneumoniae.152,,573,,,host_description:Not applicable,,,,5984,,6,,,5800,,,US Food and Drug Administration,15.33x,PacBio; Illumina,,,,Not applicable,,,"Included in the study, passed QC/QA"
835,573.15319,collected_by:BC Centre for Disease Control,,Resistant;Susceptible,Computational Prediction,GCA_002636095.1,"SMRT v. 2.3.0, HGAP v. 3, SPAdes v. 3.6.0",,PRJNA231221,SAMN07312480,,,,,1,2014-09,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-10-18T00:00:00Z,7,FDA:FDAARGOS_436,2017-11-24T16:53:42.713Z,2017-11-24T16:53:42.713Z,,,57.19,"CP023907,CP023909,CP023911,CP023912,CP023910,CP023908,CP023906",5625903,Klebsiella pneumoniae strain FDAARGOS_436 strain Not applicable,Complete,Klesiella,Canada:BC,,,Not applicable,,,"Human, Homo sapiens",,Canada,,respiratory,,,,,573,,,host_description:Not applicable,,,,5791,,6,,,5645,,,US Food and Drug Administration,16.36x,PacBio; Illumina,,,,Not applicable,,,"Included in the study, passed QC/QA"
836,573.1532,collected_by:BC Centre for Disease Control,,Susceptible;Resistant,Computational Prediction,GCA_002636375.1,"SMRT v. 2.3.0, HGAP v. 3, SPAdes v. 3.6.0",,PRJNA231221,SAMN07312486,,,,,1,2010-11,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-10-18T00:00:00Z,7,FDA:FDAARGOS_442,2017-11-24T16:51:36.565Z,2017-11-24T16:51:36.565Z,,,57.06,"CP023925,CP023926,CP023931,CP023928,CP023929,CP023927,CP023930",5727717,Klebsiella pneumoniae strain FDAARGOS_442 strain Not applicable,Complete,Klesiella,Canada:BC,,,Not applicable,,,"Human, Homo sapiens",,Canada,,blood,,,MLST.Klebsiella_pneumoniae.147,,573,,,host_description:Not applicable,,,,5914,,6,,,5701,,,US Food and Drug Administration,14.26x,PacBio; Illumina,,,,Not applicable,,,"Included in the study, passed QC/QA"
837,573.15321,collected_by:BC Centre for Disease Control,,Susceptible;Resistant,Computational Prediction,GCA_002636515.1,"SMRT v. 2.3.0, HGAP v. 3, SPAdes v. 3.6.0",,PRJNA231221,SAMN07312487,,,,,1,2012-11,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-10-18T00:00:00Z,8,FDA:FDAARGOS_443,2017-11-24T16:51:45.232Z,2017-11-24T16:51:45.232Z,,,57.05,"CP023933,CP023935,CP023939,CP023937,CP023938,CP023934,CP023932,CP023936",5951576,Klebsiella pneumoniae strain FDAARGOS_443 strain Not applicable,Complete,Klesiella,Canada:BC,,,Not applicable,,Screening,"Human, Homo sapiens",,Canada,,Rectal,,,MLST.Klebsiella_pneumoniae.11,,573,,,host_description:Not applicable,,,,6219,,7,,,6048,,,US Food and Drug Administration,15.43x,PacBio; Illumina,,,,Not applicable,,,"Included in the study, passed QC/QA"
838,573.15329,collected_by:University of Melbourne,,Susceptible;Resistant,Computational Prediction,GCA_002741685.1,Unicycler v. 0.4.0,,PRJNA351909,SAMN06112197,,,,,1,2013,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-02T00:00:00Z,7,,2017-11-24T17:09:39.032Z,2017-11-24T17:09:39.032Z,,,57.06,"CP024191,CP024192,CP024193,CP024194,CP024195,CP024196,CP024197",5768890,Klebsiella pneumoniae strain KSB1_5D,Complete,Klesiella,Australia: Melbourne,,,,,carriage,"Human, Homo sapiens",,Australia,,rectal swab,,,,,573,,,,,,,5938,,6,,,5800,,,University of Melbourne,83x,Illumina HiSeq and ONT,,,,KSB1_5D,,,"Included in the study, passed QC/QA"
839,573.1536,,,Susceptible;Resistant,Computational Prediction,GCA_002752775.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357223,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,7,,2017-11-24T17:14:30.110Z,2017-11-24T17:14:30.110Z,,,57.11,"CP024489,CP024490,CP024491,CP024492,CP024493,CP024494,CP024495",5676465,Klebsiella pneumoniae strain INF249,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.29,,573,,,,,,,5760,,6,,,5611,,,University of Melbourne,138x,Illumina HiSeq and ONT,,,,INF249,,,"Included in the study, passed QC/QA"
840,573.15361,,,Susceptible;Resistant,Computational Prediction,GCA_002752815.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357193,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,7,,2017-11-24T17:16:22.855Z,2017-11-24T17:16:22.855Z,,,57.1,"CP024482,CP024483,CP024484,CP024485,CP024486,CP024487,CP024488",5684599,Klebsiella pneumoniae strain INF322,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5752,,6,,,5599,,,University of Melbourne,113x,Illumina HiSeq and ONT,,,,INF322,,,"Included in the study, passed QC/QA"
841,573.15362,,,Susceptible,Computational Prediction,GCA_002752905.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357328,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,3,,2017-11-24T17:14:50.561Z,2017-11-24T17:14:50.561Z,,,57.05,"CP024496,CP024497,CP024498",5448674,Klebsiella pneumoniae strain KSB1_7E,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.323,,573,,,,,,,5428,,2,,,5292,,,University of Melbourne,138x,Illumina HiSeq and ONT,,,,KSB1_7E,,,"Included in the study, passed QC/QA"
842,573.15364,,,Susceptible;Resistant,Computational Prediction,GCA_002752975.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357272,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,7,,2017-11-24T17:14:57.672Z,2017-11-24T17:14:57.672Z,,,57.06,"CP024563,CP024564,CP024565,CP024566,CP024567,CP024568,CP024569",5731216,Klebsiella pneumoniae strain INF278,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.340,,573,,,,,,,5887,,6,,,5754,,,University of Melbourne,115x,Illumina HiSeq and ONT,,,,INF278,,,"Included in the study, passed QC/QA"
843,573.15365,collected_by:AFRIMS,,Susceptible;Resistant,Computational Prediction,GCA_002752955.1,HGAP v. 2.0,,PRJNA414489,SAMN07792166,,,,,1,May-2017,Sequencing of mcr-1 positive Klebsiella pneumonia isolates from Thailand.,2017-11-08T00:00:00Z,8,MRSN<USA>:480738,2017-11-24T17:16:48.075Z,2017-11-24T17:16:48.075Z,,,56.94,"CP024458,CP024459,CP024462,CP024461,CP024465,CP024463,CP024460,CP024464",5717053,Klebsiella pneumoniae strain QS17-0161,Complete,Klesiella,Thailand: Chonburi,,,,,,"Human, Homo sapiens",,Thailand,,sputum,,,,,573,,,,,,,5776,,7,,,5618,,,Walter Reed Army Institute of Research,200.0x,PacBio; Illumina MiSeq,,,,QS17-0161,,,"Included in the study, passed QC/QA"
844,573.15366,,,Susceptible;Resistant,Computational Prediction,GCA_002752995.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357010,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,3,,2017-11-24T17:16:31.758Z,2017-11-24T17:16:31.758Z,,,57.27,"CP024542,CP024543,CP024544",5519452,Klebsiella pneumoniae strain INF042,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5594,,2,,,5450,,,University of Melbourne,121x,Illumina HiSeq and ONT,,,,INF042,,,"Included in the study, passed QC/QA"
845,573.15367,,,Susceptible;Resistant,Computational Prediction,GCA_002753015.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357405,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,11,,2017-11-24T17:17:16.864Z,2017-11-24T17:17:16.864Z,,,56.65,"CP024504,CP024507,CP024506,CP024508,CP024509,CP024510,CP024511,CP024512,CP024513,CP024514,CP024505",6025713,Klebsiella pneumoniae strain KSB2_1B,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,6164,,10,,,5976,,,University of Melbourne,109x,Illumina HiSeq and ONT,,,,KSB2_1B,,,"Included in the study, passed QC/QA"
846,573.15368,,,Susceptible;Resistant,Computational Prediction,GCA_002753035.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357381,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,6,,2017-11-24T17:17:02.139Z,2017-11-24T17:17:02.139Z,,,56.86,"CP024515,CP024516,CP024517,CP024518,CP024519,CP024520",5677989,Klebsiella pneumoniae strain KSB1_10J,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5708,,5,,,5559,,,University of Melbourne,117x,Illumina HiSeq and ONT,,,,KSB1_10J,,,"Included in the study, passed QC/QA"
847,573.15369,,,Susceptible;Resistant,Computational Prediction,GCA_002753055.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357080,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,7,,2017-11-24T17:16:44.370Z,2017-11-24T17:16:44.370Z,,,57.06,"CP024521,CP024522,CP024523,CP024524,CP024525,CP024526,CP024527",5768996,Klebsiella pneumoniae strain INF158,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5941,,6,,,5801,,,University of Melbourne,125x,Illumina HiSeq and ONT,,,,INF158,,,"Included in the study, passed QC/QA"
848,573.1537,,,Susceptible;Resistant,Computational Prediction,GCA_002753075.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357077,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,7,,2017-11-24T17:16:58.455Z,2017-11-24T17:16:58.455Z,,,57.06,"CP024528,CP024529,CP024530,CP024531,CP024532,CP024533,CP024534",5768986,Klebsiella pneumoniae strain INF157,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5934,,6,,,5799,,,University of Melbourne,120x,Illumina HiSeq and ONT,,,,INF157,,,"Included in the study, passed QC/QA"
849,573.15371,collected_by:not collected,,Susceptible;Resistant,Computational Prediction,GCA_002753165.1,Unicycler v. 0.4.0,,PRJNA351909,SAMN07211282,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,7,,2017-11-24T17:17:11.943Z,2017-11-24T17:17:11.943Z,,,57.12,"CP024535,CP024536,CP024537,CP024538,CP024539,CP024540,CP024541",5702263,Klebsiella pneumoniae strain KSB1_9D,Complete,Klesiella,,,,,,not collected,,,,,,,,,,573,,,,,,,5864,,6,,,5722,,,University of Melbourne,88x,Illumina HiSeq and ONT,,,,KSB1_9D,,,"Included in the study, passed QC/QA"
850,573.15372,,,Susceptible;Resistant,Computational Prediction,GCA_002753355.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357043,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,3,,2017-11-24T17:16:39.782Z,2017-11-24T17:16:39.782Z,,,57.27,"CP024545,CP024546,CP024547",5519452,Klebsiella pneumoniae strain INF059,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5591,,2,,,5450,,,University of Melbourne,139x,Illumina HiSeq and ONT,,,,INF059,,,"Included in the study, passed QC/QA"
851,573.15373,,,Susceptible;Resistant,Computational Prediction,GCA_002753375.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357374,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,1,,2017-11-24T17:15:02.669Z,2017-11-24T17:15:02.669Z,,,57.12,CP024548,5354543,Klebsiella pneumoniae strain KSB1_7J,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.37,,573,,,,,,,5379,,,,,5222,,,University of Melbourne,117x,Illumina HiSeq and ONT,,,,KSB1_7J,,,"Included in the study, passed QC/QA"
852,573.15374,collected_by:not collected,,Susceptible;Resistant,Computational Prediction,GCA_002753405.1,Unicycler v. 0.4.0,,PRJNA351909,SAMN07211279,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,7,,2017-11-24T17:16:53.658Z,2017-11-24T17:16:53.658Z,,,57.06,"CP024549,CP024550,CP024551,CP024552,CP024553,CP024554,CP024555",5736111,Klebsiella pneumoniae strain INF163,Complete,Klesiella,,,,,,not collected,,,,,,,,,,573,,,,,,,5904,,6,,,5758,,,University of Melbourne,82x,Illumina HiSeq and ONT,,,,INF163,,,"Included in the study, passed QC/QA"
853,573.15375,collected_by:not collected,,Susceptible;Resistant,Computational Prediction,GCA_002753555.1,Unicycler v. 0.4.0,,PRJNA351909,SAMN07211280,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,7,,2017-11-24T17:17:06.826Z,2017-11-24T17:17:06.826Z,,,57.05,"CP024556,CP024557,CP024558,CP024559,CP024560,CP024561,CP024562",5766429,Klebsiella pneumoniae strain INF164,Complete,Klesiella,,,,,,not collected,,,,,,,,,,573,,,,,,,5939,,6,,,5795,,,University of Melbourne,91x,Illumina HiSeq and ONT,,,,INF164,,,"Included in the study, passed QC/QA"
854,573.15376,,,Susceptible;Resistant,Computational Prediction,GCA_002753605.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357268,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,6,,2017-11-24T17:15:07.011Z,2017-11-24T17:15:07.011Z,,,57.06,"CP024570,CP024571,CP024572,CP024573,CP024574,CP024575",5732200,Klebsiella pneumoniae strain INF274,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.340,,573,,,,,,,5894,,5,,,5753,,,University of Melbourne,133x,Illumina HiSeq and ONT,,,,INF274,,,"Included in the study, passed QC/QA"
855,573.15377,,,Susceptible;Resistant,Computational Prediction,GCA_002754835.1,Unicycler v. 0.4.0,,PRJNA351909,SAMEA3357325,,,,,1,,Klebsiella pneumoniae isolates from carriage screening and infection cases in an Australian hospital for investigation of carriage frequency and population structure.,2017-11-06T00:00:00Z,5,,2017-11-24T17:17:41.791Z,2017-11-24T17:17:41.791Z,,,56.85,"CP024499,CP024500,CP024501,CP024502,CP024503",5698065,Klebsiella pneumoniae strain KSB1_4E,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5729,,4,,,5575,,,University of Melbourne,124x,Illumina HiSeq and ONT,,,,KSB1_4E,,,"Included in the study, passed QC/QA"
856,573.15379,collected_by:Fujian Provincial Hospital,,Susceptible,Computational Prediction,GCA_002761315.1,HGAP v. 2.0,,PRJNA325419,SAMN05231874,,,,,1,2007-09-08,Complete nucleotide sequence of the chromosome of a clinical Klebsiella pneumoniae isolate 1428,2017-11-07T00:00:00Z,1,,2017-11-24T17:22:32.075Z,2017-11-24T17:22:32.075Z,,,57.13,CP017994,5633290,Klebsiella pneumoniae strain P1428,Complete,Klesiella,China: Beijing,,,62,male,pneumonia,"Human, Homo sapiens",,China,,Sputum,,,,,573,,,,,,,5582,,,,,5356,,,Peking University People's Hospital,100.0x,PacBio,,,,P1428,,,"Included in the study, passed QC/QA"
857,573.1542,,,Susceptible;Resistant;Not defined,Computational Prediction,GCA_002180155.1,canu v. 1.3,,PRJNA292902,SAMN04014953,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-08T00:00:00Z,6,,2017-11-28T19:17:38.483Z,2017-11-28T19:17:38.483Z,,,56.97,"CP021549,CP021544,CP021545,CP021546,CP021547,CP021548",5859680,Klebsiella pneumoniae strain AR_0112,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,6070,,5,,,6141,,,Centers for Disease Control and Prevention,167x,PacBio RSII,,,,AR_0112,,,"Included in the study, passed QC/QA"
858,573.1644,collected_by:Fujian Provincial Hospital,,Susceptible;Resistant,Computational Prediction,GCA_002814015.1,not specified v. not specified,,PRJNA325418,SAMN05231873,,,,,1,2008-10-08,Complete nucleotide sequence of the chromosome of a clinical Klebsiella pneumoniae isolate 459,2017-12-07T00:00:00Z,1,,2018-01-01T04:24:09.580Z,2018-01-01T04:24:09.580Z,,,57.4,CP018306,5320942,Klebsiella pneumoniae strain 459,Complete,Klesiella,China,,,49,female,pneumonia,"Human, Homo sapiens",,China,,Sputum,,,MLST.Klebsiella_pneumoniae.37,,573,,,,,,,5401,,,,,5416,,,Peking University People's Hospital,not specified,not specified,,,,459,,,"Included in the study, passed QC/QA"
859,573.16441,collected_by:Columbia University,,Susceptible;Resistant,Computational Prediction,GCA_002833445.1,SPAdes hybrid assembly v. 3.10.1,,PRJNA420753,SAMN08133260,,,,,1,Nov-2016,Identification of distinct genomic adaptations in blaKPC-2-harboring Klebsiella pneumoniae ST307 conferring resistance to Ceftazidime-Avibactam.,2017-12-12T00:00:00Z,3,,2018-01-01T04:45:26.382Z,2018-01-01T04:45:26.382Z,,,57.12,"CP025140,CP025141,CP025142",5745430,Klebsiella pneumoniae strain KP1768,Complete,Klesiella,USA: New York City,,,,,not applicable,"Human, Homo sapiens",,United States,,Pancreatic Fluid,,,MLST.Klebsiella_pneumoniae.307,,573,,,,,genotype:ST307,,5891,,2,,,5744,,,Medini Annavajhala's shared submissions,61X,Illumina MiSeq and Oxford Nanopore,,,,KP1768,,,"Included in the study, passed QC/QA"
860,573.16442,collected_by:Columbia University,,Susceptible;Resistant,Computational Prediction,GCA_002833425.1,SPAdes hybrid assembly v. 3.10.1,,PRJNA420753,SAMN08133261,,,,,1,Dec-2016,Identification of distinct genomic adaptations in blaKPC-2-harboring Klebsiella pneumoniae ST307 conferring resistance to Ceftazidime-Avibactam.,2017-12-12T00:00:00Z,3,,2018-01-01T04:45:38.792Z,2018-01-01T04:45:38.792Z,,,57.12,"CP025143,CP025144,CP025145",5741903,Klebsiella pneumoniae strain NR5632,Complete,Klesiella,USA: New York City,,,,,not applicable,"Human, Homo sapiens",,United States,,bronchoalveolar lavage,,,MLST.Klebsiella_pneumoniae.307,,573,,,,,genotype:ST307,,5891,,2,,,5745,,,Medini Annavajhala's shared submissions,31X,Illumina MiSeq and Oxford Nanopore,,,,NR5632,,,"Included in the study, passed QC/QA"
861,573.16443,collected_by:Columbia University,,Susceptible;Resistant,Computational Prediction,GCA_002833465.1,SPAdes hybrid assembly v. 3.10.1,,PRJNA420753,SAMN08133262,,,,,1,Dec-2016,Identification of distinct genomic adaptations in blaKPC-2-harboring Klebsiella pneumoniae ST307 conferring resistance to Ceftazidime-Avibactam.,2017-12-12T00:00:00Z,3,,2018-01-01T04:45:49.960Z,2018-01-01T04:45:49.960Z,,,57.16,"CP025146,CP025147,CP025148",5751187,Klebsiella pneumoniae strain KP1766,Complete,Klesiella,USA: New York City,,,,,not applicable,"Human, Homo sapiens",,United States,,blood,,,MLST.Klebsiella_pneumoniae.307,,573,,,,,genotype:ST307,,5900,,2,,,5752,,,Medini Annavajhala's shared submissions,71X,Illumina MiSeq and Oxford Nanopore,,,,KP1766,,,"Included in the study, passed QC/QA"
862,573.16472,sample_type:The liver abscess puncture fluid,,Susceptible,Computational Prediction,GCA_002845865.1,A5-miseq v. v20150522,,PRJNA420654,SAMN08117208,,,,,1,18-Apr-2009,High a virulence strains,2017-12-20T00:00:00Z,1,,2018-01-01T06:40:44.553Z,2018-01-01T06:40:44.553Z,,,57.31,CP025089,5478203,Klebsiella pneumoniae strain KP8,Complete,Klesiella,China: Shanghai,,,,,,"Human, Homo sapiens",,China,,,,,,,573,,,,,,,5329,,,,,,,,Department of Laboratory Medicine,99.0x,Illumina MiSeq,,,,KP8,,,"Included in the study, passed QC/QA"
863,573.16473,sample_type:The liver abscess puncture fluid,,Susceptible,Computational Prediction,GCA_002845885.1,A5-miseq v. v20150522,,PRJNA420766,SAMN08117212,,,,,1,18-Apr-2009,have a high virulence strains.,2017-12-20T00:00:00Z,1,,2018-01-01T06:40:23.542Z,2018-01-01T06:40:23.542Z,,,57.55,CP025092,4766628,Klebsiella pneumoniae strain KP11,Complete,Klesiella,China: Shanghai,,,,,,"Human, Homo sapiens",,China,,,,,,,573,,,,,,,4585,,,,,,,,Department of Laboratory Medicine,99.0x,Illumina MiSeq,,,,KP11,,,"Included in the study, passed QC/QA"
864,573.16474,sample_type:The liver abscess puncture fluid,,Susceptible,Computational Prediction,GCA_002845905.1,A5-miseq v. v20150522,,PRJNA420765,SAMN08117209,,,,,1,18-Apr-2009,have High virulence strains,2017-12-20T00:00:00Z,1,,2018-01-01T06:41:06.168Z,2018-01-01T06:41:06.168Z,,,57.42,CP025090,5339613,Klebsiella pneumoniae strain KP9,Complete,Klesiella,China: Shanghai,,,,,,"Human, Homo sapiens",,China,,,,,,,573,,,,,,,5160,,,,,,,,Department of Laboratory Medicine,99.0x,Illumina MiSeq,,,,KP9,,,"Included in the study, passed QC/QA"
865,573.16475,sample_type:The liver abscess puncture fluid,,Susceptible,Computational Prediction,GCA_002845925.1,A5-miseq v. v20150522,,PRJNA420767,SAMN08117210,,,,,1,18-Apr-2009,their have a high virulence strains,2017-12-20T00:00:00Z,1,,2018-01-01T06:42:15.911Z,2018-01-01T06:42:15.911Z,,,57.87,CP025091,5061821,Klebsiella pneumoniae strain KP10,Complete,Klesiella,China: Shanghai,,,,,,"Human, Homo sapiens",,China,,,,,MLST.Klebsiella_pneumoniae.29,,573,,,,,,,4845,,,,,,,,Department of Laboratory Medicine,99.0x,Illumina MiSeq,,,,KP10,,,"Included in the study, passed QC/QA"
866,573.16476,sample_type:The liver abscess puncture fluid,,Susceptible,Computational Prediction,GCA_002845945.1,A5-miseq v. v20150522,,PRJNA420653,SAMN08117217,,,,,1,18-Apr-2009,have low power strains,2017-12-20T00:00:00Z,1,,2018-01-01T06:43:10.876Z,2018-01-01T06:43:10.876Z,,,57.71,CP025093,5187330,Klebsiella pneumoniae strain KP14,Complete,Klesiella,China: Shanghai,,,,,,"Human, Homo sapiens",,China,,,,,,,573,,,,,,,4986,,,,,,,,Department of Laboratory Medicine,99.0x,Illumina MiSeq,,,,KP14,,,"Included in the study, passed QC/QA"
867,573.16477,sample_type:The liver abscess puncture fluid,,Susceptible,Computational Prediction,GCA_002845965.1,A5-miseq v. v20150522,,PRJNA420616,SAMN08117788,,,,,1,18-Apr-2009,High virulence strains,2017-12-20T00:00:00Z,1,,2018-01-01T06:42:20.798Z,2018-01-01T06:42:20.798Z,,,57.38,CP025088,5405065,Klebsiella pneumoniae strain KP7,Complete,Klesiella,China: shanghai,,,,,,"Human, Homo sapiens",,China,,,,,,,573,,,,,,,5195,,,,,,,,Department of Laboratory Medicine,99.0x,Illumina MiSeq,,,,KP7,,,"Included in the study, passed QC/QA"
868,573.1761,collected_by:KEPCO Medical Center,,,,GCA_001307175.1,,,PRJNA295237,SAMN04044480,,,,,1,29-May-2013,"Complete Genome Sequence of OXA-232 and NDM1 producing Klebsiella pneumoniae, Isolated from Korea",2015-10-06T00:00:00Z,3,,2016-01-17T17:13:30.171Z,2016-01-17T17:13:30.171Z,,Bacterial Pneumonia,56.87,"CP012753,CP012754,CP012755",5696051,Klebsiella pneumoniae strain KP617,Complete,Klesiella,Korea: Seoul,,HostAssociated,,,Bacterial Pneumonia,"Human, Homo sapiens",,South Korea,,Burn Patient,,,,,573,C,,,,,Anaerobic,5616,,2,,"NZ_CP012753.1,NZ_CP012754.1,NZ_CP012755.1",5438,,,"Korea National Institute of Health, Korea Centers for Disease Control & Prevention",,,,,,KP617,Unknown,,"Included in the study, passed QC/QA"
869,573.17803,collected_by:Federal University of Uberlandia,,Susceptible;Resistant,Computational Prediction,GCA_002887435.1,CLC v. CLC Genomic Workbench 8,,PRJNA428749,SAMN08298849,,,,,1,29-Jul-2014,The Klebsiella pneumoniae Kp81 is a strain isolated from human urine in 2014. The antibiotic resistance is a main characteristic of this strain.,2018-01-17T00:00:00Z,3,,2018-05-25T18:50:14.869Z,2018-05-25T18:50:14.869Z,,,57.432728,"CP025816,CP025817,CP025818",5314129,Klebsiella pneumoniae strain Kp81,Complete,Klesiella,Brazil:Minas Gerais,,,,,Urinary tract infection,"Human, Homo sapiens",isolated from human urine in 2014,Brazil,,urine,,,MLST.Klebsiella_pneumoniae.340,,573,,,,,,,5466,,2,,,5339,,,Londrina State University,240.0x,Illumina,,,,Kp81,,,"Included in the study, passed QC/QA"
870,573.17821,,,Susceptible;Resistant,Computational Prediction,GCA_002903005.1,canu v. 1.3,,PRJNA430813,SAMN06040389,,,,,1,2016,"Carbapenem Resistant Enterobacteriaceae strains including Klebsiella, Escherichia, Enterobacter, Citrobacter and Pantoea species isolated from patients and hospital environment.",2018-01-29T00:00:00Z,6,,2018-05-25T20:31:12.607Z,2018-05-25T20:31:12.607Z,,,56.354553,"CP026177,CP026175,CP026174,CP026176,CP026172,CP026173",6209759,Klebsiella pneumoniae strain KPNIH50,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",isolated from patients and hospital environment,,,patients and hospital environment,,,MLST.Klebsiella_pneumoniae.252,,573,,,,,,,6676,,5,,,6417,,,NIH,214x,PacBio RSII,,,,KPNIH50,,,"Included in the study, passed QC/QA"
871,573.17822,,,Resistant;Susceptible,Computational Prediction,GCA_002903025.1,canu v. 1.5,,PRJNA430813,SAMN06040388,,,,,1,2016,"Carbapenem Resistant Enterobacteriaceae strains including Klebsiella, Escherichia, Enterobacter, Citrobacter and Pantoea species isolated from patients and hospital environment.",2018-01-29T00:00:00Z,9,,2018-05-25T20:34:01.780Z,2018-05-25T20:34:01.780Z,,,56.209274,"CP026178,CP026179,CP026182,CP026186,CP026181,CP026180,CP026185,CP026184,CP026183",6374553,Klebsiella pneumoniae strain KPNIH49,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",isolated from patients and hospital environment,,,patients and hospital environment,,,MLST.Klebsiella_pneumoniae.359,,573,,,,,,,6853,,8,,,6591,,,NIH,250x,PacBio RSII,,,,KPNIH49,,,"Included in the study, passed QC/QA"
872,573.17904,,,Susceptible;Resistant,Computational Prediction,GCA_002935085.1,canu v. 1.3,,PRJNA430813,SAMN06040387,,,,,1,2016,"Carbapenem Resistant Enterobacteriaceae strains including Klebsiella, Escherichia, Enterobacter, Citrobacter and Pantoea species isolated from patients and hospital environment.",2018-02-04T00:00:00Z,7,,2018-05-26T00:00:12.557Z,2018-05-26T00:00:12.557Z,,,56.31113,"CP026392,CP026394,CP026395,CP026397,CP026393,CP026396,CP026398",6296819,Klebsiella pneumoniae strain KPNIH48,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",isolated from patients and hospital environment,,,patients and hospital environment,,,MLST.Klebsiella_pneumoniae.252,,573,,,,,,,6667,,6,,,6422,,,NIH,226x,PacBio RSII,,,,KPNIH48,,,"Included in the study, passed QC/QA"
873,573.17907,sample_type:tissue sample,,Susceptible;Resistant,Computational Prediction,GCA_002944845.1,HGAP3 v. smrt v2.3 HGAP3,,PRJNA432625,SAMN08455837,,,,,1,24-Oct-2016,a microbe from a male with burn injury,2018-02-12T00:00:00Z,5,,2018-05-26T01:13:38.673Z,2018-05-26T01:13:38.673Z,,,57.045467,"CP026586,CP026587,CP026588,CP026589,CP026590",5782903,Klebsiella pneumoniae strain NUHL30457,Complete,Klesiella,China:Nanchang,,,,,,"Human, Homo sapiens",,China,,,,,MLST.Klebsiella_pneumoniae.86,,573,,,,,,,5988,,4,,,5811,,,"First Affiliated Hospital of Nanchang University, Nanchang University",151.0x,PacBio,,,,NUHL30457,,,"Included in the study, passed QC/QA"
874,573.17908,,,Intermediate;Resistant;Not defined;Susceptible,Computational Prediction,GCA_002948565.1,canu v. 1.6,,PRJNA292904,SAMN04014907,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2018-02-19T00:00:00Z,3,,2018-05-26T01:37:07.716Z,2018-05-26T01:37:07.716Z,,,57.140907,"CP026751,CP026752,CP026753",5733600,Klebsiella pneumoniae strain AR_0066,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.14,,573,,,,,,,5787,,2,,,5668,,,Centers for Disease Control and Prevention,250x,PacBio RSII,,,,AR_0066,,,"Included in the study, passed QC/QA"
875,573.17909,collected_by:Children's National Hospital,,Susceptible;Resistant,Computational Prediction,GCA_002951635.1,HGAP3 v. Oct 2014,,PRJNA231221,SAMN03996301,,,,,1,2014-05-11,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally:  Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases.   The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2018-02-20T00:00:00Z,5,FDA:FDAARGOS_156,2018-05-26T02:02:04.614Z,2018-05-26T02:02:04.614Z,,,57.100292,"CP014123,CP014121,CP014124,CP014125,CP014122",5550639,Klebsiella pneumoniae strain FDAARGOS_156 strain Not Applicable,Complete,Klesiella,USA:DC,,,9M,male,Urinary tract infection,"Human, Homo sapiens",,USA,,urine,,,MLST.Klebsiella_pneumoniae.13,,573,,,,,,,5602,,4,,,5426,,,US Food and Drug Administration,19.325x,PacBio; Illumina,,,,Not Applicable,,,"Included in the study, passed QC/QA"
876,573.1791,collected_by:Chen Qiong,,Susceptible;Resistant,Computational Prediction,GCA_002966875.1,Canu v. V1.5,,PRJNA421241,SAMN08135572,,,,,1,2016-03-05,Klebsiella pneumoniae strain HZW25 isolated from blie of a patient with acute cholangitis,2018-03-02T00:00:00Z,5,,2018-05-26T03:30:21.497Z,2018-05-26T03:30:21.497Z,,,56.98831,"CP025211,CP025212,CP025213,CP025214,CP025215",5604335,Klebsiella pneumoniae strain HZW25,Complete,Klesiella,China: Hangzhou,,,36,,Acute cholangitis,"Human, Homo sapiens",,China,,blie,,,MLST.Klebsiella_pneumoniae.34,,573,,,,,,,5951,,4,,,5650,,,The First Affiliated Hospital College of Medicine Zhejiang University,221.0x,PacBio,,,,HZW25,,,"Included in the study, passed QC/QA"
877,573.17914,,,Intermediate;Resistant;Susceptible;Not defined,Computational Prediction,GCA_002968475.1,SMRT v. 2.3.0; HGAP v. 3.0,,PRJNA316321,SAMN07291506,,,,,1,,"The AR Isolate Bank is a centralized repository of microbial pathogens with well-characterized resistance profiles that are assembled by CDC in collaboration with the Food and Drug Administration (FDA). The AR Bank is available to support and advance development of diagnostic devices and antimicrobial drug products. The AR Isolate Bank also supports the National Action Plan for Combating Antibiotic Resistance Bacteria by advancing the development of diagnostic tests to identify and characterize resistant bacteria, and by accelerating research and development for new antibiotics.The AR Isolate Bank includes collections of bacterial pathogens that are associated with known or emerging resistance mechanisms. Since its launch in July 2015, the AR Bank continues to grow and will eventually include genera and species such as Enterobacteriaceae, Pseudomonas aeruginosa, Staphylococcus, Enterococcus, Streptococcus, Salmonella, and Neisseria gonorrhoeae.Each pathogen listed on this web site includes information regarding its susceptibility and/or resistance profile(s), known resistance biomarkers, isolate characteristics, and associated data in PDF.Use this web site to search through pathogen panels, find additional information about the available isolates, and find procedures for requesting panels.",2018-04-25T00:00:00Z,11,,2018-05-26T03:44:48.514Z,2018-05-26T03:44:48.514Z,,,56.73893,"CP027146,CP027152,CP027151,CP027147,CP027150,CP027156,CP027148,CP027155,CP027153,CP027149,CP027154",5892020,Klebsiella pneumoniae strain AR_0363,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.258,,573,,,,,,,5898,,10,,,5794,,,FDA/CDC,16.41x,Pacbio; Illumina,,,,AR_0363,,,"Included in the study, passed QC/QA"
878,573.17915,,,Intermediate;Resistant;Susceptible;Not defined,Computational Prediction,GCA_002968495.1,SMRT v. 2.3.0; HGAP v. 3.0,,PRJNA316321,SAMN07291504,,,,,1,,"The AR Isolate Bank is a centralized repository of microbial pathogens with well-characterized resistance profiles that are assembled by CDC in collaboration with the Food and Drug Administration (FDA). The AR Bank is available to support and advance development of diagnostic devices and antimicrobial drug products. The AR Isolate Bank also supports the National Action Plan for Combating Antibiotic Resistance Bacteria by advancing the development of diagnostic tests to identify and characterize resistant bacteria, and by accelerating research and development for new antibiotics.The AR Isolate Bank includes collections of bacterial pathogens that are associated with known or emerging resistance mechanisms. Since its launch in July 2015, the AR Bank continues to grow and will eventually include genera and species such as Enterobacteriaceae, Pseudomonas aeruginosa, Staphylococcus, Enterococcus, Streptococcus, Salmonella, and Neisseria gonorrhoeae.Each pathogen listed on this web site includes information regarding its susceptibility and/or resistance profile(s), known resistance biomarkers, isolate characteristics, and associated data in PDF.Use this web site to search through pathogen panels, find additional information about the available isolates, and find procedures for requesting panels.",2018-04-25T00:00:00Z,8,,2018-05-26T03:45:11.804Z,2018-05-26T03:45:11.804Z,,,57.23163,"CP027160,CP027161,CP027158,CP027162,CP027164,CP027163,CP027157,CP027159",5597784,Klebsiella pneumoniae strain AR_0361,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.258,,573,,,,,,,5511,,7,,,5423,,,FDA/CDC,17.81x,Pacbio; Illumina,,,,AR_0361,,,"Included in the study, passed QC/QA"
879,573.17919,"collected_by:Gang Li, Tang Yu,Jiang Xiaofei",,Susceptible,Computational Prediction,GCA_002970895.1,smrtlink v. version 4.1,,PRJNA435632,SAMN08582315,,,,,1,2008-06-11,"Klebsiella pneumoniae subsp. pneumoniae strain KPHS1249, complete genome",2018-03-06T00:00:00Z,1,,2018-05-26T04:08:25.948Z,2018-05-26T04:08:25.948Z,,,57.44346,CP027189,5458646,Klebsiella pneumoniae strain KPHS1249,Complete,Klesiella,China,,,,,wood infection,"Human, Homo sapiens",,,,wound,,,MLST.Klebsiella_pneumoniae.23,,573,,,,,,,5416,,,,,5275,,,"Jinshan Hospital, Shanghai Medical College, Fudan University",124.0x,PacBio; Illumina HiSeq,,,,KPHS1249,,,"Included in the study, passed QC/QA"
880,573.1792,collected_by:Fouzia Nahid,,Susceptible;Resistant,Computational Prediction,GCA_003006175.1,CLC Genomics Workbench v. 10,,PRJNA348457,SAMN05908511,,,,,1,Jun-2015,Whole genome sequencing of a clinical Klebsiella pneumoniae encoding OXA181 beta lactamase.,2018-03-16T00:00:00Z,8,,2018-05-26T06:56:47.030Z,2018-05-26T06:56:47.030Z,,,56.840538,"CP024429,CP024430,CP024431,CP024432,CP024433,CP024434,CP024435,CP024436",5752275,Klebsiella pneumoniae strain DA48896,Complete,Klesiella,Pakistan,,,,,Trachaeal secretion,"Human, Homo sapiens",,,,Trachaeal secretion,,,MLST.Klebsiella_pneumoniae.147,,573,,,,,,,5883,,7,29220374,,5707,,,Uppsala University,50.0x,Illumina MiSeq; PacBio,,,,DA48896,,,"Included in the study, passed QC/QA"
881,573.17927,,,Susceptible;Resistant;Not defined,Computational Prediction,GCA_003010595.1,canu v. 1.6,,PRJNA292904,SAMN04014921,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2018-03-19T00:00:00Z,2,,2018-05-26T07:33:09.408Z,2018-05-26T07:33:09.408Z,,,57.330616,"CP027602,CP027603",5598970,Klebsiella pneumoniae strain AR_0080,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.1224,,573,,,,,,,5634,,1,,,5483,,,Centers for Disease Control and Prevention,122x,PacBio RSII,,,,AR_0080,,,"Included in the study, passed QC/QA"
882,573.17931,collected_by:Nan Hospital,,Susceptible;Resistant,Computational Prediction,GCA_003031325.1,CANU v. SEP-2017,,PRJNA418211,SAMN08022168,,,,,1,Aug-2016,"Extensive drug resistant Klebsiella pneumoniae NH25, clinical isolate",2018-04-03T00:00:00Z,6,,2018-05-26T08:09:20.107Z,2018-05-26T08:09:20.107Z,,,56.754913,"CP024874,CP024875,CP024876,CP024877,CP024878,CP024879",5947820,Klebsiella pneumoniae strain NH25,Complete,Klesiella,Thailand,,,,,Klebsiella pneumoniae,"Human, Homo sapiens",,,,sputum,,,MLST.Klebsiella_pneumoniae.15,,573,,,,,,,6155,,5,,,5965,,,Chiang Mai University,131.0x,PacBio,,,,NH25,,,"Included in the study, passed QC/QA"
883,573.17935,collected_by:Hospital Vall d'Hebron,,Susceptible;Resistant,Computational Prediction,GCA_003056445.1,Unicycler assembly pipeline v. 0.4.4,,PRJNA449447,SAMN08904739,,,,,1,16-Jan-2012,K. pneumoniae KP589 whole Genome Sequencing,2018-04-18T00:00:00Z,10,,2018-05-27T22:09:53.615Z,2018-05-27T22:09:53.615Z,,,56.990215,"CP028816,CP028817,CP028819,CP028820,CP028821,CP028822,CP028823,CP028824,CP028825,CP028818",5778569,Klebsiella pneumoniae strain Kp589,Complete,Klesiella,Spain: Barcelona,,,,,Chorioamnionitis,"Human, Homo sapiens",,Spain,,amniotic fluid,,,MLST.Klebsiella_pneumoniae.405,,573,,,,,,,5851,,9,,,5681,,,Hospital Universitari Vall d'Hebron,1.0x,Illumina MiSeq; MinION,,,,Kp589,,,"Included in the study, passed QC/QA"
884,573.17943,,,Resistant;Not defined;Intermediate;Susceptible,Computational Prediction,GCA_003073315.1,HGAP v. 2.3,,PRJNA292902,SAMN04014983,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2018-04-28T00:00:00Z,4,,2018-05-27T22:30:57.254Z,2018-05-27T22:30:57.254Z,,,57.35094,"CP028990,CP028991,CP028992,CP028993",5479509,Klebsiella pneumoniae strain AR_0142,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.34,,573,,,,,,,5619,,3,,,5473,,,Centers for Disease Control and Prevention,120x,PacBio RSII,,,,AR_0142,,,"Included in the study, passed QC/QA"
885,573.1807,collected_by:XuHao,,Susceptible;Resistant,Computational Prediction,GCA_003112125.1,HGAP v. 2.1,,PRJNA449865,SAMN08932689,,,,,1,2017,Uncovering the gut microbiota of hospitalized patients served as the reservoirs of ST11 KPC-2-producing Klebsiella pneumoniae,2018-05-10T00:00:00Z,6,,2018-05-30T15:50:07.884Z,2018-05-30T15:50:07.884Z,,,56.923367,"CP029220,CP029221,CP029222,CP029223,CP029224,CP029225",5945388,Klebsiella pneumoniae strain L388,Complete,Klesiella,China:Zhejiang,,,,,diarrhea,"Human, Homo sapiens",,China,,feces,,,MLST.Klebsiella_pneumoniae.11,,573,,,,,,,6222,,5,,,6059,,,Zhejiang University,50.0x,PacBio,,,,L388,,,"Included in the study, passed QC/QA"
886,573.18071,collected_by:XuHao,,Resistant;Susceptible,Computational Prediction,GCA_003111885.1,HGAP v. 2.1,,PRJNA449865,SAMN08932690,,,,,1,2017,Uncovering the gut microbiota of hospitalized patients served as the reservoirs of ST11 KPC-2-producing Klebsiella pneumoniae,2018-05-10T00:00:00Z,5,,2018-05-30T15:52:29.305Z,2018-05-30T15:52:29.305Z,,,56.87812,"CP029226,CP029227,CP029228,CP029229,CP029230",5958238,Klebsiella pneumoniae strain L491,Complete,Klesiella,China:Zhejiang,,,,,diarrhea,"Human, Homo sapiens",,China,,feces,,,MLST.Klebsiella_pneumoniae.11,,573,,,,,,,6282,,4,,,6119,,,Zhejiang University,50.0x,PacBio,,,,L491,,,"Included in the study, passed QC/QA"
887,573.18072,collected_by:XuHao,,Resistant;Susceptible,Computational Prediction,GCA_003111805.1,HGAP v. 2.1,,PRJNA449865,SAMN08932688,,,,,1,2017,Uncovering the gut microbiota of hospitalized patients served as the reservoirs of ST11 KPC-2-producing Klebsiella pneumoniae,2018-05-10T00:00:00Z,4,,2018-05-30T15:52:42.577Z,2018-05-30T15:52:42.577Z,,,57.135326,"CP029216,CP029217,CP029218,CP029219",5464028,Klebsiella pneumoniae strain L201,Complete,Klesiella,China:Zhejiang,,,,,diarrhea,"Human, Homo sapiens",,China,,feces,,,MLST.Klebsiella_pneumoniae.11,,573,,,,,,,5734,,3,,,5603,,,Zhejiang University,50.0x,PacBio,,,,L201,,,"Included in the study, passed QC/QA"
888,573.18084,sample_type:Genomic DNA,,Susceptible;Resistant,Computational Prediction,GCA_003076915.1,ETHZ_pipeline v. 10.07.2015,,PRJNA449808,SAMN08918337,,,,,1,,Studying the in vitro evolution of drug resistance in Klebsiella pneumoniae. This is the very first strain where the evolution experiment started and where all evolved strains will be mapped to.,2018-05-02T00:00:00Z,2,NCTC:418,2018-05-30T16:47:01.879Z,2018-05-30T16:47:01.879Z,,,57.331688,"CP028915,CP028916",5475977,Klebsiella pneumoniae strain NCTC 418,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.375,,573,,,,,,,5577,,1,,,5375,,,University of Basel,0.969x,PacBio,,,,NCTC 418,,,"Included in the study, passed QC/QA"
889,573.18085,collected_by:Mohammad Ali Boroumand,,Susceptible;Resistant,Computational Prediction,GCA_003076555.1,Unicycler v. v0.4.4,,PRJNA431464,SAMN08391417,,,,,1,2009,"Whole genome sequencing for Klebsiella pneumoniae 616, a novel reference genome for Klebsiella pneumoniae sequence type 307.",2018-05-01T00:00:00Z,3,,2018-05-30T16:51:19.273Z,2018-05-30T16:51:19.273Z,,,57.406395,"CP026495,CP026496,CP026497",5359558,Klebsiella pneumoniae strain 616,Complete,Klesiella,Iran,,,,,urinary tract infection,"Human, Homo sapiens",,,,urine,,,MLST.Klebsiella_pneumoniae.307,,573,,,,,genotype:ST307,,5333,,2,,,5232,,,University of Melbourne,119.0x,Oxford Nanopore minION; Illumina MiniSeq,,,,616,,,"Included in the study, passed QC/QA"
890,573.18086,,,Susceptible;Resistant;Intermediate;Not defined,Computational Prediction,GCA_003074015.1,canu v. 1.4; SPAdes v. 3.6.0,,PRJNA316321,SAMN07291519,,,,,1,,"The AR Isolate Bank is a centralized repository of microbial pathogens with well-characterized resistance profiles that are assembled by CDC in collaboration with the Food and Drug Administration (FDA). The AR Bank is available to support and advance development of diagnostic devices and antimicrobial drug products. The AR Isolate Bank also supports the National Action Plan for Combating Antibiotic Resistance Bacteria by advancing the development of diagnostic tests to identify and characterize resistant bacteria, and by accelerating research and development for new antibiotics.The AR Isolate Bank includes collections of bacterial pathogens that are associated with known or emerging resistance mechanisms. Since its launch in July 2015, the AR Bank continues to grow and will eventually include genera and species such as Enterobacteriaceae, Pseudomonas aeruginosa, Staphylococcus, Enterococcus, Streptococcus, Salmonella, and Neisseria gonorrhoeae.Each pathogen listed on this web site includes information regarding its susceptibility and/or resistance profile(s), known resistance biomarkers, isolate characteristics, and associated data in PDF.Use this web site to search through pathogen panels, find additional information about the available isolates, and find procedures for requesting panels.",2018-04-30T00:00:00Z,5,,2018-05-30T17:12:27.545Z,2018-05-30T17:12:27.545Z,,,57.107483,"CP029137,CP029135,CP029136,CP029138,CP029139",5675659,Klebsiella pneumoniae strain AR376,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.15,,573,,,,,,,5582,,4,,,5545,,,FDA/CDC,20.43x,Pacbio; Illumina,,,,AR376,,,"Included in the study, passed QC/QA"
891,573.18087,,,Susceptible;Resistant;Not defined,Computational Prediction,GCA_003073675.1,SMRT v. 2.3.0; HGAP v. 3.0,,PRJNA316321,SAMN07291531,,,,,1,,"The AR Isolate Bank is a centralized repository of microbial pathogens with well-characterized resistance profiles that are assembled by CDC in collaboration with the Food and Drug Administration (FDA). The AR Bank is available to support and advance development of diagnostic devices and antimicrobial drug products. The AR Isolate Bank also supports the National Action Plan for Combating Antibiotic Resistance Bacteria by advancing the development of diagnostic tests to identify and characterize resistant bacteria, and by accelerating research and development for new antibiotics.The AR Isolate Bank includes collections of bacterial pathogens that are associated with known or emerging resistance mechanisms. Since its launch in July 2015, the AR Bank continues to grow and will eventually include genera and species such as Enterobacteriaceae, Pseudomonas aeruginosa, Staphylococcus, Enterococcus, Streptococcus, Salmonella, and Neisseria gonorrhoeae.Each pathogen listed on this web site includes information regarding its susceptibility and/or resistance profile(s), known resistance biomarkers, isolate characteristics, and associated data in PDF.Use this web site to search through pathogen panels, find additional information about the available isolates, and find procedures for requesting panels.",2018-04-30T00:00:00Z,5,,2018-05-30T17:16:13.433Z,2018-05-30T17:16:13.433Z,,,57.03879,"CP029099,CP029098,CP029100,CP029101,CP029102",5823933,Klebsiella pneumoniae strain AR438,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.512,,573,,,,,,,5834,,4,,,5832,,,FDA/CDC,15.39x,Pacbio; Illumina,,,,AR438,,,"Included in the study, passed QC/QA"
892,573.18088,,,Resistant;Not defined;Susceptible,Computational Prediction,GCA_003073335.1,canu v. 1.6,,PRJNA292904,SAMN04014920,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2018-04-28T00:00:00Z,7,,2018-05-30T17:20:57.630Z,2018-05-30T17:20:57.630Z,,,56.593235,"CP028994,CP029000,CP028999,CP028998,CP028997,CP028996,CP028995",6131952,Klebsiella pneumoniae strain AR_0079,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.11,,573,,,,,,,6484,,6,,,6299,,,Centers for Disease Control and Prevention,98x,PacBio RSII,,,,AR_0079,,,"Included in the study, passed QC/QA"
893,573.18089,collected_by:AFRIMS,,Susceptible;Resistant,Computational Prediction,GCA_003073235.1,HGAP v. 2.0,,PRJNA414481,SAMN07792096,,,,,1,Apr-2017,Sequencing of mcr-1 carrying Escherichia coli isolates from Thailand.,2017-11-08T00:00:00Z,7,MRSN<USA>:479404,2018-05-30T17:21:23.957Z,2018-05-30T17:21:23.957Z,,,57.098103,"CP024038,CP024040,CP024041,CP024039,CP024042,CP024044,CP024043",5617050,Klebsiella pneumoniae strain QS17-0029,Complete,Klesiella,Thailand: Chonburi,,,,,,"Human, Homo sapiens",,Thailand,,,,,MLST.Klebsiella_pneumoniae.16,,573,,,,,,,5779,,6,,,5619,,,Walter Reed Army Institute of Research,200.0x,PacBio; Illumina MiSeq,,,,QS17-0029,,,"Included in the study, passed QC/QA"
894,573.1809,,,Resistant;Intermediate;Not defined;Susceptible,Computational Prediction,GCA_003071305.1,HGAP v. 2.3,,PRJNA292902,SAMN04014982,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2018-04-25T00:00:00Z,3,,2018-05-30T17:42:36.797Z,2018-05-30T17:42:36.797Z,,,57.267338,"CP028953,CP028954,CP028955",5574787,Klebsiella pneumoniae strain AR_0141,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.34,,573,,,,,,,5741,,2,,,5586,,,Centers for Disease Control and Prevention,99x,PacBio RSII,,,,AR_0141,,,"Included in the study, passed QC/QA"
895,573.18093,,,Resistant;Not defined;Intermediate;Susceptible,Computational Prediction,GCA_003069525.1,canu v. 1.6,,PRJNA292902,SAMN04014994,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2018-04-24T00:00:00Z,4,,2018-05-30T17:55:03.288Z,2018-05-30T17:55:03.288Z,,,56.78757,"CP028932,CP028929,CP028930,CP028931",5799475,Klebsiella pneumoniae strain AR_0153,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.14,,573,,,,,,,5900,,3,,,5734,,,Centers for Disease Control and Prevention,144x,PacBio RSII,,,,AR_0153,,,"Included in the study, passed QC/QA"
896,573.1814,sample_type:Sputum sample,,Susceptible;Resistant,Computational Prediction,GCA_003054385.1,SOAPdenovo v. Dec-2017,,PRJNA448464,SAMN08848079,,,,,1,06-Jul-2017,To identify the antimicrobial resistance genes of Klebsiella pneumonia stain SCM96,2018-04-17T00:00:00Z,3,,2018-05-30T20:11:05.621Z,2018-05-30T20:11:05.621Z,,,57.174225,"CP028716,CP028717,CP028718",5579775,Klebsiella pneumoniae strain SCM96,Complete,Klesiella,China,,,,,,,,,,Sputum sample,,,MLST.Klebsiella_pneumoniae.15,,573,,,,,,,5427,,2,,,,,,SOUTHWEST MEDICAL UNIVERSITY,250.0x,PacBio; Illumina HiSeq,,,,SCM96,,,"Included in the study, passed QC/QA"
897,573.18146,sample_type:Pure Culture,,Susceptible;Resistant,Computational Prediction,GCA_003038215.2,Unicycler v. 0.4.4,,PRJNA353728,SAMN08624619,,,,,1,2016-07-18,Genome sequencing and assembly of Klebsiella strains,2018-04-18T00:00:00Z,6,,2018-05-30T22:15:58.558Z,2018-05-30T22:15:58.558Z,,,56.81741,PWDF01000000,5909803,Klebsiella pneumoniae strain WCHKP020030,Complete,Klesiella,"China: Chengdu, Sichuan",,,,,,"Human, Homo sapiens",,China,,,,,MLST.Klebsiella_pneumoniae.11,,573,,,,,,,6166,,5,,,6019,,,"West China Hospital, Sichuan University",200.0x,Illumina HiSeq; MinION,,,,WCHKP020030,,,"Included in the study, passed QC/QA"
898,573.18187,sample_type:Pure Culture,,Susceptible;Resistant,Computational Prediction,GCA_003037325.2,Unicycler v. 0.4.4,,PRJNA353728,SAMN08624668,,,,,1,2017-06-15,Genome sequencing and assembly of Klebsiella strains,2018-04-18T00:00:00Z,4,,2018-05-30T22:24:21.400Z,2018-05-30T22:24:21.400Z,,,57.279354,PWBT01000000,5533074,Klebsiella pneumoniae strain WCHKP040035,Complete,Klesiella,"China: Chengdu, Sichuan",,,,,,"Human, Homo sapiens",,China,,,,,MLST.Klebsiella_pneumoniae.11,,573,,,,,,,5703,,3,,,5592,,,"West China Hospital, Sichuan University",200.0x,Illumina HiSeq; MinION,,,,WCHKP040035,,,"Included in the study, passed QC/QA"
899,573.18238,collected_by:rectal swab,,Susceptible;Resistant,Computational Prediction,GCA_003031345.1,CANU v. JUL-2017,,PRJNA418370,SAMN08026708,,,,,1,SEP-2016,Whole genome sequencing MDR Klebsiella pneumoniae NH54 clinical isolate,2018-04-03T00:00:00Z,4,,2018-05-30T23:00:24.861Z,2018-05-30T23:00:24.861Z,,,57.102512,"CP024916,CP024917,CP024918,CP024919",5640638,Klebsiella pneumoniae strain NH54,Complete,Klesiella,Thailand,,,,,Klebsiella pneumoniae,"Human, Homo sapiens",,,,rectal swab,,,MLST.Klebsiella_pneumoniae.147,,573,,,,,,,5800,,3,,,5641,,,Chiang Mai University,129.0x,CANU,,,,NH54,,,"Included in the study, passed QC/QA"
900,573.18239,collected_by:DTU National Food Institute,,Susceptible;Resistant,Computational Prediction,GCA_003030145.1,HGAP v. 3.0,,PRJNA243331,SAMN08663449,,,,,1,2012-05-10,Draft and complete genome sequences of foodborne bacterial pathogens collected for research purposes at the FDA's Center for Food Safety and Applied Nutrition.,2018-04-02T00:00:00Z,4,,2018-05-30T23:09:05.405Z,2018-05-30T23:09:05.405Z,,,57.209866,"CP028176,CP028177,CP028178,CP028179",5535332,Klebsiella pneumoniae strain CFSAN054111,Complete,Klesiella,Germany,,,,,,"Human, Homo sapiens",,,,human,,,MLST.Klebsiella_pneumoniae.15,,573,,,,,,,5608,,3,,,5465,,,FDA/CFSAN,430.0x,PacBio,,,,CFSAN054111,,,"Included in the study, passed QC/QA"
901,573.1824,collected_by:DTU National Food Institute,,Resistant;Susceptible,Computational Prediction,GCA_003030045.1,HGAP v. 3.0,,PRJNA243331,SAMN08663443,,,,,1,2013-04-16,Draft and complete genome sequences of foodborne bacterial pathogens collected for research purposes at the FDA's Center for Food Safety and Applied Nutrition.,2018-04-02T00:00:00Z,3,,2018-05-30T23:12:45.238Z,2018-05-30T23:12:45.238Z,,,57.110565,"CP028180,CP028181,CP028182",5709497,Klebsiella pneumoniae strain CFSAN054110,Complete,Klesiella,Denmark,,,,,,"Human, Homo sapiens",,,,human,,,MLST.Klebsiella_pneumoniae.512,,573,,,,,,,5885,,2,,,5751,,,FDA/CFSAN,395.0x,PacBio,,,,CFSAN054110,,,"Included in the study, passed QC/QA"
902,573.1921,,,,,GCF_001455995.1,,,PRJEB7538,SAMEA3257677,,,,,1,Apr-2014,"Using Single Molecule Real Time (SMRT) sequencing we determined the complete genome of a pandrug-resistant Klebsiella pneumoniae isolate, representing the first complete genome sequence of a Carbapenem resistant Enterobacteriaceae (CRE) resistant to all commercially available antibiotics. The precise location of acquired antibiotic resistance elements, including mobile elements carrying genes for the OXA-181 carbapenemase, were defined. Intriguingly, we identified three chromosomal copies of an identical ISEcp1-blaOXA-181 mobile element, one of which has disrupted the mgrB regulatory gene, accounting for resistance to colistin. Our findings reveal the critical role of mobile resistance elements in accelerating the emergence of resistance to other last resort antibiotics.",2015-12-01T00:00:00Z,7,,2016-01-30T11:22:27.445Z,2016-01-30T11:22:27.445Z,,,56.57,"LN824133,LN824139,LN824134,LN824135,LN824136,LN824137,LN824138",5980203,Klebsiella pneumoniae strain MS6671,Complete,Klesiella,United Arab Emirates,,,,,,"Human, Homo sapiens",,United Arab Emirates,,urine,,,MLST.Klebsiella_pneumoniae.147,,573,,,,,,,6030,,6,,"NZ_LN824133.1,NZ_LN824139.1,NZ_LN824134.1,NZ_LN824135.1,NZ_LN824136.1,NZ_LN824137.1,NZ_LN824138.1",5664,,,UQ,,,,,,MS6671,,,"Included in the study, passed QC/QA"
903,573.1922,collected_by:CLS,,,,GCF_001456055.1,SMRT pipeline v. January 2015,,PRJNA298912,SAMN04168649,,,,,1,24-Jun-2013,Investigating nosocomial transmission of Klebsiella pneumoniae containing plasmid with NDM-7,2015-12-03T00:00:00Z,5,,2016-01-30T11:31:27.322Z,2016-01-30T11:31:27.322Z,,,57,"CP012987,CP012988,CP012989,CP012990,CP012991",5690900,Klebsiella pneumoniae strain KpN01,Complete,Klesiella,Canada: Calgary,,,98,male,unknown,"Human, Homo sapiens",,Canada,,urine,,,MLST.Klebsiella_pneumoniae.278,,573,C,,,,,,5727,,4,,,5544,,,Calgary Laboratory Services,75x,Pacific Biosciences,,,,KpN01,,,"Included in the study, passed QC/QA"
904,573.1923,collected_by:CLS,,,,GCF_001456095.1,SMRT pipeline v. January 2015,,PRJNA298912,SAMN04168654,,,,,1,19-Sep-2013,Investigating nosocomial transmission of Klebsiella pneumoniae containing plasmid with NDM-7,2015-12-03T00:00:00Z,4,,2016-01-30T11:32:38.864Z,2016-01-30T11:32:38.864Z,,,57.03,"CP012992,CP012993,CP012994,CP012995",5647266,Klebsiella pneumoniae strain KpN06,Complete,Klesiella,Canada: Calgary,,,68,female,unkown,"Human, Homo sapiens",,Canada,,blood,,,MLST.Klebsiella_pneumoniae.278,,573,C,,,,,,5677,,3,,,5508,,,Calgary Laboratory Services,75x,Pacific Biosciences,,,,KpN06,,,"Included in the study, passed QC/QA"
905,573.1924,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001456135.1,HGAP v. 2.3.0,,PRJNA246471,SAMN03733725,,,,,1,2010-05,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2015-12-03T00:00:00Z,6,,2016-01-30T11:29:22.224Z,2016-01-30T11:29:22.224Z,,,57.07,"CP013322,CP013324,CP013323,CP013321,CP013326,CP013325",5874698,Klebsiella pneumoniae strain CAV1193,Complete,Klesiella,USA:Virginia,,,,,,"Human, Homo sapiens",,United States,,Respiratory,,,MLST.Klebsiella_pneumoniae.941,,573,,,,,,,5940,,5,,"NZ_CP013322.1,NZ_CP013324.1,NZ_CP013323.1,NZ_CP013321.1,NZ_CP013326.1,NZ_CP013325.1",5774,,,University of Oxford,48x,PacBio,,,,CAV1193,,,"Included in the study, passed QC/QA"
906,573.1961,collected_by:H. Magesh,,,,GCF_001463165.1,HGAP v. MAY-2015,,PRJNA288422,SAMN03780451,,,,,,07-Oct-2010,whole genome sequence of a high efflux clinical isolate of Klebsiella pneumoniae from Chennai,2015-12-09T00:00:00Z,1,,2016-01-30T18:47:49.206Z,2016-01-30T18:47:49.206Z,,,57.38,CP012043,5491870,Klebsiella pneumoniae strain U25,Complete,Klesiella,India: Chennai,,,,,UTI,"Human, Homo sapiens",,India,,urine,,,MLST.Klebsiella_pneumoniae.14,,573,C,,,,,,5370,,,,,5228,,,DR MGR Educational and Research Institute,25.0x,PacBio,,,,U25,,,"Included in the study, passed QC/QA"
907,573.1987,sample_type:whole oragnism,,,,GCF_001482345.1,SMRT Analysis v. 2.3.0,,PRJNA306571,SAMN04357099,,,,,1,Oct-2014,Klebsiella pneumoniae J1 has been deposited with the accession number DSM 101559. This strain was isolated from the activated sludge of Harbin Taiping wastewater treatment plant.,2015-12-24T00:00:00Z,3,DSM 101559,2016-01-31T21:02:02.949Z,2016-01-31T21:02:02.949Z,,,57.24,"CP013711,CP013712,CP013713",5406866,Klebsiella pneumoniae strain J1,Complete,Klesiella,China: Harbin,,,,,,,isolated from the activated sludge of Harbin Taiping wastewater treatment plant,China,,the activated sludge of Harbin Taiping wastewater treatment plant,,,MLST.Klebsiella_pneumoniae.111,,573,C,,,,,,5376,,2,,"NZ_CP013711.1,NZ_CP013712.1,NZ_CP013713.1",5198,,,State Key Laboratory of Urban Water Resource and Environment,140x,PacBio,,,,J1,,,"Included in the study, passed QC/QA"
908,573.2202,,,,,GCF_001548315.1,GS Assembler software v. 2.6,,PRJDB4172,SAMD00039249,,,,,1,,"Klebsiella pneumoniae is a gram-negative bacterium that lives in soil, plants, and animals including humans. The species is pathogenic, commensal, and beneficial for hosts because it can cause pneumonia and can also promote the growth of plants as an endophytic diazotrophic bacterium. These opposing characteristics of the species have not been fully elucidated because of a lack of information, including the lack of a genomic analysis. The aim of the project is to provide information for deep understanding of the bacteria.",2015-09-15T00:00:00Z,1,,2016-03-01T08:46:12.774Z,2016-03-01T08:46:12.774Z,,,57.27,AP014950,5520319,Klebsiella pneumoniae strain YH43,Complete,Klesiella,,,,,,,,,,,,,,MLST.Klebsiella_pneumoniae.1216,,573,,,,,,,5332,,,,NZ_AP014950.1,5154,,,The Jikei University School of Medicine,40x,,,,,YH43,,,"Included in the study, passed QC/QA"
909,573.4021,collected_by:SKGH,,,,GCF_001644765.1,HGAP3 v. April 2016,,PRJNA320133,SAMN04917370,,,,,1,2015,"A complete genome of a pandrug-resistant Klebsiella pneumoniae isolate, representing a Carbapenem resistant Enterobacteriaceae (CRE) resistant to all commercially available antibiotics in the UAE.",2016-05-19T00:00:00Z,6,,2016-07-05T01:56:51.254Z,2016-07-05T01:56:51.254Z,,,56.53,"CP015500,CP015501,CP015502,CP015503,CP015504,CP015505",6088457,Klebsiella pneumoniae strain SKGH01,Complete,Klesiella,United Arab Emirates,,,,male,UTI,"Human, Homo sapiens",,United Arab Emirates,,Urine sample,,,MLST.Klebsiella_pneumoniae.147,,573,,,,,,,6199,,5,,"NZ_CP015500.1,NZ_CP015501.1,NZ_CP015502.1,NZ_CP015503.1,NZ_CP015504.1,NZ_CP015505.1",5909,,,Sheikh Khalifa General Hospital(SKGH),missing,PacBio,,,,SKGH01,,,"Included in the study, passed QC/QA"
910,573.4022,sample_type:mixed culture,,,,GCF_001646625.1,RS_HGAP Assembly 3 in SMRT Analysis v.,,PRJNA321220,SAMN04992856,,,,,1,24-Jun-14,A strain with strong alcohol-producing ability,2016-05-18T00:00:00Z,3,,2016-07-05T04:06:02.944Z,2016-07-05T04:06:02.944Z,,,57.13,"CP015753,CP015754,CP015755",5495481,Klebsiella pneumoniae strain W14,Complete,Klesiella,China: Beijing,,,,,,"Human, Homo sapiens",,China,,fecal sample,,,MLST.Klebsiella_pneumoniae.1536,,573,,,,,,,5386,,2,,"NZ_CP015753.1,NZ_CP015754.1,NZ_CP015755.1",5278,,,Institute of Disease Control and Prevention,134X,Illumina Hiseq 4000,,,,W14,,,"Included in the study, passed QC/QA"
911,573.4026,,,,,GCF_001648215.1,SMRT Portal v. 2.3,,PRJNA279650,SAMN03455970,,,,,1,2014,Klebsiella pneumoniae AATZP Genome Sequencing,2016-05-19T00:00:00Z,4,,2016-07-05T07:29:47.089Z,2016-07-05T07:29:47.089Z,,,57.17,"CP014755,CP014758,CP014756,CP014757",5566588,Klebsiella pneumoniae strain AATZP,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,,,,MLST.Klebsiella_pneumoniae.147,,573,,,,,,,5448,,3,,"NZ_CP014755.1,NZ_CP014758.1,NZ_CP014756.1,NZ_CP014757.1",5350,,,NHGRI,200x,PacBio RSII,,,,AATZP,,,"Included in the study, passed QC/QA"
912,573.4029,,,,,GCF_001663195.1,HGAP v. HGAP3,,PRJNA323746,SAMN05188406,,,,,1,2015,"Klebsiellar pneumonia strain BR, complete genome",2016-06-15T00:00:00Z,2,,2016-07-06T03:28:16.343Z,2016-07-06T03:28:16.343Z,,,57.31,"CP015990,CP015991",5420718,Klebsiella pneumoniae strain BR,Complete,Klesiella,China: hangzhou,,,,,,"Human, Homo sapiens",,China,,,,,MLST.Klebsiella_pneumoniae.15,,573,,,,,,,5293,,1,,"NZ_CP015990.1,NZ_CP015991.1",5179,,,Zhejiang Sci-Tech University,missing,PacBio,,,,BR,,,"Included in the study, passed QC/QA"
913,573.403,,,,,GCF_001663295.1,HGAP v. 2,,PRJNA279611,SAMN03455930,,,,,1,2014,Klebsiella pneumoniae KPNIH39 Genome Sequencing,2016-06-15T00:00:00Z,4,,2016-07-06T03:33:36.038Z,2016-07-06T03:33:36.038Z,,,56.94,"CP014762,CP014763,CP014764,CP014765",5779669,Klebsiella pneumoniae strain KPNIH39,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,,,,MLST.Klebsiella_pneumoniae.37,,573,,,,,,,5825,,3,,"NZ_CP014762.1,NZ_CP014763.1,NZ_CP014764.1,NZ_CP014765.1",5618,,,NHGRI,120x,PacBio RSII,,,,KPNIH39,,,"Included in the study, passed QC/QA"
914,573.4031,,,,,GCF_001663435.1,SMRT Portal v. 2.2,,PRJNA279655,SAMN03455975,,,,,1,2013,Klebsiella pneumoniae Kpn223 Genome Sequencing,2016-06-16T00:00:00Z,2,,2016-07-06T03:35:29.559Z,2016-07-06T03:35:29.559Z,,,57.17,"CP015025,CP015026",5536135,Klebsiella pneumoniae strain Kpn223,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,,,,MLST.Klebsiella_pneumoniae.273,,573,,,,,,,5507,,1,,"NZ_CP015025.1,NZ_CP015026.1",5326,,,NHGRI,159x,PacBio RSII,,,,Kpn223,,,"Included in the study, passed QC/QA"
915,573.4032,,,,,GCF_001663455.1,SMRT Portal v. 2.2,,PRJNA279656,SAMN03455976,,,,,1,2014,Klebsiella pneumoniae Kpn555 Genome Sequencing,2016-06-16T00:00:00Z,4,,2016-07-06T03:38:30.685Z,2016-07-06T03:38:30.685Z,,,56.99,"CP015130,CP015131,CP015133,CP015132",5730336,Klebsiella pneumoniae strain Kpn555,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,,,,,,573,,,,,,,5739,,3,,"NZ_CP015130.1,NZ_CP015131.1,NZ_CP015133.1,NZ_CP015132.1",5579,,,NHGRI,91x,PacBio RSII,,,,Kpn555,,,"Included in the study, passed QC/QA"
916,573.4038,,,,,GCF_001675125.1,SMRT Portal v. 2.3,,PRJNA284365,SAMN03701676,,,,,1,2013,Klebsiella pneumoniae KPNIH36 Genome Sequencing,2016-06-22T00:00:00Z,4,,2016-07-06T19:12:11.865Z,2016-07-06T19:12:11.865Z,,,57.23,"CP014647,CP014648,CP014649,CP014650",5681468,Klebsiella pneumoniae strain KPNIH36,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,,,,,,573,C,,,,,,5724,,3,,"NZ_CP014647.1,NZ_CP014648.1,NZ_CP014649.1,NZ_CP014650.1",5649,,,NHGRI/NIH,152x,PacBio RSII,,,,KPNIH36,,,"Included in the study, passed QC/QA"
917,573.4039,sample_type:cell culture,,,,GCF_001676825.1,Celera Assembler v. 8.3,,PRJNA321635,SAMN05170048,,,,,1,6/24/14,Auto-brewery syndrome caused by intestinal Enterobacteriaceae family dysbiosis revealed a probabal mechanism of NASH,2016-06-27T00:00:00Z,3,,2016-07-06T20:18:48.044Z,2016-07-06T20:18:48.044Z,,,57.13,"CP016159,CP016160,CP016161",5495471,Klebsiella pneumoniae strain TH1,Complete,Klesiella,China: Beijing,,,,,,,,China,,human fecal sample,,,MLST.Klebsiella_pneumoniae.1536,,573,,,,,,,5376,,2,,"NZ_CP016159.1,NZ_CP016160.1,NZ_CP016161.1",5283,,,Institute of Disease Control and Prevention,130.0x,Illumina HiSeq,,,,TH1,,,"Included in the study, passed QC/QA"
918,573.5649,collected_by:CA State Health Department,,Resistant;Susceptible;Intermediate,AMR Panel,GCF_001704235.1,HGAP v. 3,,PRJNA296771,SAMN04448219,,,,,1,14-Jun-2010,"OXA-48-like enzymes are a type of beta-lactamase that confers resistance to carbapenems. These enzymes were first discovered in Turkey, they are common in the Middle East and North Africa, and they have spread through out Europe. They are rare in the US. This project aimed to characterize the genotype and phenotype of OXA-48-like Enterobacteriaceae in the US.",2016-08-12T00:00:00Z,3,,2016-08-27T07:41:42.166Z,2016-08-27T07:41:42.166Z,,,57.29,"CP016811,CP016810,CP016812",5558458,Klebsiella pneumoniae strain DHQP1002001,Complete,Klesiella,USA: California,,,,,,"Human, Homo sapiens",,United States,,Urine,,,,,573,,,,,,,5621,,2,,"NZ_CP016811.1,NZ_CP016810.1,NZ_CP016812.1",5453,,,Centers for Disease Control and Prevention. Division of Healthcare Quality Promotion,143.0x,PacBio,,,,DHQP1002001,,,"Included in the study, passed QC/QA"
919,573.5783,collected_by:Daniel Goldenberger,,,,GCF_001705385.1,ETHZ_pipeline v. 10.07.2015,,PRJNA322244,SAMN05149976,,,,,1,28-Jul-2010,"KPC-3 expressing multidrug resistant strain isolated from a patient at the University Hospital of Basel, Switzerland (case 2 from Babouee, B. et al., 2011)",2016-08-16T00:00:00Z,4,,2016-09-11T20:18:15.434Z,2016-09-11T20:18:15.434Z,,,57.04,"CP015822,CP015823,CP015824,CP015825",5803735,Klebsiella pneumoniae strain blood sample 2,Complete,Klesiella,Switzerland: Basel,,,60s,male,septicemia,"Human, Homo sapiens","isolated from a patient at the University Hospital of Basel, Switzerland (case 2 from Babouee, B. et al",Switzerland,,blood,,,,,573,,,"host_description:blood sample 2 patient 2 (Babouee et al., 2011);host_disease_outcome:death;host_disease_stage:intermediate;host_health_state:hospitalised",,,,5882,,3,,"NZ_CP015822.1,NZ_CP015823.1,NZ_CP015824.1,NZ_CP015825.1",5773,,,Swiss Institute of Bioinformatics,missing,PacBio,,,,blood sample 2,,,"Included in the study, passed QC/QA"
920,573.5786,sample_type:whole organism;collected_by:Ya-Lei Chen,,,,GCF_001708245.1,HGAP v. 3,,PRJNA330755,SAMN05425525,,,,,1,2006,Pathogenic mechanism of Klebsiella pneumoniae (ST23),2016-08-19T00:00:00Z,1,,2016-09-11T21:16:27.670Z,2016-09-11T21:16:27.670Z,,,57.42,CP016813,5412960,Klebsiella pneumoniae strain ED2,Complete,Klesiella,Taiwan,,,,,,"Human, Homo sapiens",,Taiwan,,blood,,,,,573,,,,,genotype:ST23,,5243,,,,NZ_CP016813.1,5132,,,National Kaohsiung Normal University,149.59,PacBio,,,,ED2,,,"Included in the study, passed QC/QA"
921,573.6972,sample_type:whole organism;collected_by:Ya-Lei Chen,,,,GCF_001708225.1,HGAP v. 3,,PRJNA330755,SAMN05425526,,,,,1,2006,Pathogenic mechanism of Klebsiella pneumoniae (ST23),2016-08-19T00:00:00Z,2,,2016-11-15T20:18:24.474Z,2016-11-15T20:18:24.474Z,,,57.29,"CP016814,CP016815",5587396,Klebsiella pneumoniae strain ED23,Complete,Klesiella,Taiwan,,,,,,"Human, Homo sapiens",,Taiwan,,blood,,,,,573,,,,,genotype:ST23,,5513,,1,,"NZ_CP016814.1,NZ_CP016815.1",5386,,,National Kaohsiung Normal University,138.19,PacBio,,,,ED23,,,"Included in the study, passed QC/QA"
922,573.6973,collected_by:PA State Health Department,,Resistant;Intermediate;Susceptible,AMR Panel,GCF_001709275.1,HGAP v. v. 3,,PRJNA296771,SAMN04448229,,,,,1,2013-03-14,"OXA-48-like enzymes are a type of beta-lactamase that confers resistance to carbapenems. These enzymes were first discovered in Turkey, they are common in the Middle East and North Africa, and they have spread through out Europe. They are rare in the US. This project aimed to characterize the genotype and phenotype of OXA-48-like Enterobacteriaceae in the US.",2016-08-23T00:00:00Z,5,,2016-11-15T20:27:12.366Z,2016-11-15T20:27:12.366Z,,,56.78,"CP016923,CP016919,CP016922,CP016920,CP016921",5805603,Klebsiella pneumoniae strain 11,Complete,Klesiella,USA: Pennsylvania,,,,,,"Human, Homo sapiens",,United States,,Urine,,,,,573,,,,,,,5762,,4,,"NZ_CP016923.1,NZ_CP016919.1,NZ_CP016922.1,NZ_CP016920.1,NZ_CP016921.1",5582,,,Centers for Disease Control and Prevention. Division of Healthcare Quality Promotion,139.0x,PacBio,,,,11,,,"Included in the study, passed QC/QA"
923,573.6974,collected_by:MN State Health Department,,Resistant;Intermediate;Susceptible,AMR Panel,GCF_001709295.1,HGAP v. v. 3,,PRJNA296771,SAMN04448241,,,,,1,2014-03-08,"OXA-48-like enzymes are a type of beta-lactamase that confers resistance to carbapenems. These enzymes were first discovered in Turkey, they are common in the Middle East and North Africa, and they have spread through out Europe. They are rare in the US. This project aimed to characterize the genotype and phenotype of OXA-48-like Enterobacteriaceae in the US.",2016-08-23T00:00:00Z,4,,2016-11-15T20:26:49.337Z,2016-11-15T20:26:49.337Z,,,57.17,"CP016926,CP016924,CP016927,CP016925",5483848,Klebsiella pneumoniae strain 23,Complete,Klesiella,USA: Minnesota,,,,,,"Human, Homo sapiens",,United States,,Tracheal Aspirate,,,,,573,,,,,,,5382,,3,,"NZ_CP016926.1,NZ_CP016927.1,NZ_CP016924.1,NZ_CP016925.1",5292,,,Centers for Disease Control and Prevention. Division of Healthcare Quality Promotion,137.0x,PacBio,,,,23,,,"Included in the study, passed QC/QA"
924,573.6995,collected_by:UCLA,,,,GCF_001721725.1,HGAP3 v. May-2015,,PRJNA293620,SAMN04008891,,,,,1,2014-10-12,UCLA OXA-232 CRKP Outbreak,2016-09-08T00:00:00Z,1,,2016-11-16T00:44:01.889Z,2016-11-16T00:44:01.889Z,,,57.5,CP012560,5312744,Klebsiella pneumoniae strain UCLAOXA232KP_Pt0,Complete,Klesiella,USA: California,,,,,Aspiration pneumonia,"Human, Homo sapiens",,United States,,Respiratory,,,,,573,C,,,,,,5236,,,,NZ_CP012560.1,5081,,,UCLA Medical Center,50.0x,PacBio,,,,UCLAOXA232KP_Pt0,,,"Included in the study, passed QC/QA"
925,573.6996,collected_by:UCLA,,,,GCA_001741545.1,HGAP3 v. May-2015,,PRJNA293620,SAMN04008893,,,,,1,2015-03-11,UCLA OXA-232 CRKP Outbreak,2016-09-21T00:00:00Z,5,,2016-11-16T12:52:31.260Z,2016-11-16T12:52:31.260Z,,,57.02,"CP012568,CP012569,CP012570,CP012571,CP012572",5798553,Klebsiella pneumoniae strain UCLAOXA232KP,Complete,Klesiella,USA: California,,,,,CRE Colonization,"Human, Homo sapiens",,United States,,Rectal,,,,,573,C,,,,,,5830,,4,,"NZ_CP012568.1,NZ_CP012569.1,NZ_CP012570.1,NZ_CP012571.1,NZ_CP012572.1",5573,,,UCLA Medical Center,50.0x,PacBio,,,,UCLAOXA232KP,,,"Included in the study, passed QC/QA"
926,573.6997,collected_by:UCLA,,,,GCA_001741665.1,HGAP3 v. May-2015,,PRJNA293620,SAMN04008892,,,,,1,2014-10-12,UCLA OXA-232 CRKP Outbreak,2016-09-21T00:00:00Z,7,,2016-11-16T12:53:06.225Z,2016-11-16T12:53:06.225Z,,,56.93,"CP012561,CP012562,CP012563,CP012564,CP012565,CP012566,CP012567",5880491,Klebsiella pneumoniae strain UCLAOXA232KP,Complete,Klesiella,USA: California,,,,,end-stage liver disease,"Human, Homo sapiens",,United States,,abdominal drainage,,,,,573,C,,,,,,5950,,6,,"NZ_CP012561.1,NZ_CP012562.1,NZ_CP012563.1,NZ_CP012564.1,NZ_CP012565.1,NZ_CP012566.1,NZ_CP012567.1",5658,,,UCLA Medical Center,50.0x,PacBio,,,,UCLAOXA232KP,,,"Included in the study, passed QC/QA"
927,573.7004,collected_by:National Cheng Kung University Hospital,,,,GCF_001750805.1,,,PRJNA343398,SAMN05786944,,,,,1,2007-04-12,"Urinary tract infection (UTI) is a serious health problem affecting millions of people each year. In the community setting, K. pneumoniae infection could contribute to diverse diseases, including UTI. We isolated a K. pneumoniae strain KP36 from the urine sample of a clinical patient with community-acquired upper UTI. The complete genome of this K. pneumoniae strain will help understand the molecular mechanisms of UTI contributed by the strain.",2016-10-03T00:00:00Z,4,,2016-11-16T20:21:23.861Z,2016-11-16T20:21:23.861Z,,,57.01,"CP017385,CP017386,CP017387,CP017388",5759206,Klebsiella pneumoniae strain KP36,Complete,Klesiella,Taiwan: Tainan,,,,,acute pyelonephritis,"Human, Homo sapiens",isolated a K. pneumoniae strain KP36 from the urine sample of a clinical patient with community-acquired upper UTI,Taiwan,,urine,,,,,573,,,,,,,5673,,3,,"NZ_CP017385.1,NZ_CP017386.1,NZ_CP017387.1,NZ_CP017388.1",5544,,,National Cheng Kung University,,,,,,KP36,,,"Included in the study, passed QC/QA"
928,573.7015,collected_by:NUH,,,,GCF_001855315.1,HGAP v. 1.0,,PRJNA286828,SAMN03770912,,,,,1,2014,To sequence a Klebsiella pneumoniae isolate using PacBio SMRT sequencing technology.,2016-10-27T00:00:00Z,5,,2016-11-19T05:09:15.109Z,2016-11-19T05:09:15.109Z,,,56.96,"CP012426,CP012427,CP012428,CP012429,CP011839",5718854,Klebsiella pneumoniae strain KP5,Complete,Klesiella,Singapore,,,,,Colonization,"Human, Homo sapiens",,Singapore,,Hospital,,,,,573,C,,,,,,5656,,4,27494913,"NZ_CP012426.1,NZ_CP012427.1,NZ_CP012428.1,NZ_CP012429.1,NZ_CP011839.1",5475,,,Tan Tock Seng Hospital,100x,PacBio,,,,KP5,,,"Included in the study, passed QC/QA"
929,573.702,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001870165.1,HGAP v. unspecified,,PRJNA246471,SAMN03024573,,,,,1,2007-08,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2016-11-07T00:00:00Z,4,,2016-11-19T10:52:25.707Z,2016-11-19T10:52:25.707Z,,,57.26,"CP017934,CP017936,CP017935,CP017937",5597109,Klebsiella pneumoniae strain CAV1016,Complete,Klesiella,USA:Virginia,,,,,Intra-abdominal infection,"Human, Homo sapiens",,United States,,Abdominal Abscess,,,,,573,,,,,,,5576,,3,25561339,"NZ_CP017934.1,NZ_CP017936.1,NZ_CP017935.1,NZ_CP017937.1",5473,,,University of Oxford,92x,PacBio,,,,CAV1016,,,"Included in the study, passed QC/QA"
930,573.7226,collected_by:Andreas Erich Zautner,,,,GCF_001885255.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412444,,,,,1,2013-03-12,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-05T00:00:00Z,1,DSM:103701,2017-01-16T04:27:57.082Z,2017-01-16T04:27:57.082Z,,,57.36,CP018140,5381436,Klebsiella pneumoniae strain Kp_Goe_822579,Complete,Klesiella,Germany: Goettingen,,,22,male,colonization,"Human, Homo sapiens",,Germany,,nose,,,,,573,,,host_description:Refugee from North Africa,,genotype:ST147,,5206,,,,,4943,,,University Medical Center Goettingen,112,PacBio RSII,,,,Kp_Goe_822579,,,"Included in the study, passed QC/QA"
931,573.7238,collected_by:Minnesota Department of Health,,,,GCF_001902195.1,PacBio SMRT Portal v. Nov-2016; Pilon,,PRJNA355274,SAMN06067846,,,,,1,2013-01,Clonal dissemination of KPC-2 positive Klebsiella pneumoniae,2016-12-13T00:00:00Z,5,,2017-01-16T18:09:08.466Z,2017-01-16T18:09:08.466Z,,,56.84,"CP018428,CP018431,CP018429,CP018432,CP018430",5778465,Klebsiella pneumoniae strain MNCRE78,Complete,Klesiella,USA:Minnesota,,,,,,"Human, Homo sapiens",,United States,,Wound,,,,,573,,,,,,,5937,,4,,"NZ_CP018428.1,NZ_CP018431.1,NZ_CP018429.1,NZ_CP018432.1,NZ_CP018430.1",5967,,,University of Minnesota,100x; 20x,PacBio RS II; Illumina MiSeq,,,,MNCRE78,,,"Included in the study, passed QC/QA"
932,573.7239,collected_by:Minnesota Department of Health,,,,GCF_001902215.1,PacBio SMRT Portal v. Nov-2016; Pilon,,PRJNA355274,SAMN06067845,,,,,1,2012-10,Clonal dissemination of KPC-2 positive Klebsiella pneumoniae,2016-12-13T00:00:00Z,5,,2017-01-16T18:09:00.487Z,2017-01-16T18:09:00.487Z,,,56.85,"CP018427,CP018425,CP018423,CP018426,CP018424",5773763,Klebsiella pneumoniae strain MNCRE69,Complete,Klesiella,USA:Minnesota,,,,,,"Human, Homo sapiens",,United States,,Urine,,,,,573,,,,,,,5932,,4,,"NZ_CP018427.1,NZ_CP018425.1,NZ_CP018423.1,NZ_CP018426.1,NZ_CP018424.1",5957,,,University of Minnesota,100x; 20x,PacBio RS II; Illumina MiSeq,,,,MNCRE69,,,"Included in the study, passed QC/QA"
933,573.724,collected_by:Minnesota Department of Health,,,,GCF_001902235.1,PacBio SMRT Portal v. Nov-2016; Pilon,,PRJNA355274,SAMN06067844,,,,,1,2012-05,Clonal dissemination of KPC-2 positive Klebsiella pneumoniae,2016-12-13T00:00:00Z,5,,2017-01-16T18:09:40.017Z,2017-01-16T18:09:40.017Z,,,56.86,"CP018437,CP018433,CP018435,CP018436,CP018434",5811538,Klebsiella pneumoniae strain MNCRE53,Complete,Klesiella,USA:Minnesota,,,,,,"Human, Homo sapiens",,United States,,Wound,,,,,573,,,,,,,5959,,4,,"NZ_CP018437.1,NZ_CP018433.1,NZ_CP018435.1,NZ_CP018436.1,NZ_CP018434.1",5993,,,University of Minnesota,100x; 20x,PacBio RS II; Illumina MiSeq,,,,MNCRE53,,,"Included in the study, passed QC/QA"
934,573.7241,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001902255.1,HGAP v. unspecified,,PRJNA246471,SAMN03733793,,,,,1,2011-10,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2016-12-13T00:00:00Z,4,,2017-01-16T18:11:47.982Z,2017-01-16T18:11:47.982Z,,,57.24,"CP018356,CP018353,CP018355,CP018354",5594981,Klebsiella pneumoniae strain CAV1453,Complete,Klesiella,USA:Virginia,,,,,not applicable,"Human, Homo sapiens",,United States,,Perirectal,,,,,573,,,,,,,5714,,3,,"NZ_CP018356.1,NZ_CP018353.1,NZ_CP018355.1,NZ_CP018354.1",5768,,,University of Oxford,129x,PacBio,,,,CAV1453,,,"Included in the study, passed QC/QA"
935,573.7242,collected_by:Andreas Erich Zautner,,,,GCF_001902335.1,SMRT Analysis Software v. 2.3.0.,,PRJNA329409,SAMN05412805,,,,,1,2014-07-21,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-13T00:00:00Z,7,,2017-01-16T18:15:26.042Z,2017-01-16T18:15:26.042Z,,,56.62,"CP018337,CP018339,CP018338,CP018340,CP018341,CP018342,CP018343",5851286,Klebsiella pneumoniae strain Kp_Goe_154414,Complete,Klesiella,Germany: Goettingen,,,36,male,wound (hand),"Human, Homo sapiens",,Germany,,wound swab,,,,,573,,,host_description:German citizen,,genotype:MLST ST23,,6093,,6,,"NZ_CP018337.1,NZ_CP018339.1,NZ_CP018338.1,NZ_CP018340.1,NZ_CP018341.1,NZ_CP018342.1,NZ_CP018343.1",6039,,,University Medical Center Goettingen,147.0x,PacBio,,,,Kp_Goe_154414,,,"Included in the study, passed QC/QA"
936,573.7243,collected_by:Andreas Erich Zautner,,,,GCF_001902355.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412811,,,,,1,2015-06-22,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-13T00:00:00Z,3,DSM:103698,2017-01-16T18:12:57.738Z,2017-01-16T18:12:57.738Z,,,57.13,"CP018364,CP018365,CP018366",5778578,Klebsiella pneumoniae strain Kp_Goe_62629,Complete,Klesiella,Germany: Goettingen,,,43,male,urinary tract infection,"Human, Homo sapiens",,Germany,,urine,,,,,573,,,host_description:refugee from orth africa,,genotype:MLST ST395,,5971,,2,,"NZ_CP018364.1,NZ_CP018365.1,NZ_CP018366.1",5998,,,University Medical Center Goettingen,153.0x,PacBio,,,,Kp_Goe_62629,,,"Included in the study, passed QC/QA"
937,573.7244,collected_by:Andreas Erich Zautner,,,,GCF_001902395.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412810,,,,,1,2014-09-23,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-13T00:00:00Z,5,DSM:103697,2017-01-16T18:12:30.151Z,2017-01-16T18:12:30.151Z,,,56.97,"CP018458,CP018460,CP018461,CP018462,CP018459",5676522,Klebsiella pneumoniae strain Kp_Goe_39795,Complete,Klesiella,Germany: Goettingen,,,53,male,pneumonia,"Human, Homo sapiens",,Germany,,tracheal secretion,,,,,573,,,host_description:German citizen,,genotype:MLST ST15,,5762,,4,,"NZ_CP018458.1,NZ_CP018460.1,NZ_CP018461.1,NZ_CP018462.1,NZ_CP018459.1",5787,,,University Medical Center Goettingen,139.0x,PacBio,,,,Kp_Goe_39795,,,"Included in the study, passed QC/QA"
938,573.7245,collected_by:Andreas Erich Zautner,,,,GCF_001902415.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412453,,,,,,2013-03-12,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-13T00:00:00Z,9,DSM:103702,2017-01-16T18:14:09.501Z,2017-01-16T18:14:09.501Z,,,57.25,"CP018438,CP018441,CP018443,CP018442,CP018445,CP018444,CP018440,CP018446,CP018439",5584283,Klebsiella pneumoniae strain Kp_Goe_822917,Complete,Klesiella,Germany: Goettingen,,,49,male,colonization,"Human, Homo sapiens",,Germany,,skin swab,,,,,573,,,host_description:Refugee from North Africa,,genotype:MLST ST11,,5698,,8,,"NZ_CP018438.1,NZ_CP018441.1,NZ_CP018443.1,NZ_CP018442.1,NZ_CP018445.1,NZ_CP018444.1,NZ_CP018440.1,NZ_CP018446.1,NZ_CP018439.1",5756,,,University Medical Center Goettingen,117.0x,PacBio,,,,Kp_Goe_822917,,,"Included in the study, passed QC/QA"
939,573.7246,collected_by:Andreas Erich Zautner,,,,GCF_001902435.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412455,,,,,1,2013-04-05,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-13T00:00:00Z,3,DSM:103696,2017-01-16T18:14:15.932Z,2017-01-16T18:14:15.932Z,,,56.95,"CP018447,CP018448,CP018449",5655658,Klebsiella pneumoniae strain Kp_Goe_33208,Complete,Klesiella,Germany: Goettingen,,,31,male,wound infection,"Human, Homo sapiens",,Germany,,wound swab,,,,,573,,,,,genotype:MLST ST101,,5833,,2,,"NZ_CP018447.1,NZ_CP018448.1,NZ_CP018449.1",5802,,,University Medical Center Goettingen,140.0x,PacBio,,,,Kp_Goe_33208,,,"Included in the study, passed QC/QA"
940,573.7247,collected_by:Yingshun Zhou,,,,GCF_001902475.1,SOAPdenovo v. v2.04,,PRJNA354663,SAMN06109054,,,,,1,Mar-2015,Molecular characteristic of a hypermucoviscous Klebsiella pneumoniae strian isolate from the Liver abscess patients,2016-12-13T00:00:00Z,2,,2017-01-16T18:14:45.635Z,2017-01-16T18:14:45.635Z,,,57.4,"CP018454,CP018455",5699058,Klebsiella pneumoniae strain SWU01,Complete,Klesiella,China,,,,,infection,"Human, Homo sapiens",,China,,blood specimen,,,,,573,,,,,,,5654,,1,,"NZ_CP018454.1,NZ_CP018455.1",,,,Southwest Medical University,180.0x,Illumina Miseq and PacBio RS Sequencing,,,,SWU01,,,"Included in the study, passed QC/QA"
941,573.7248,collected_by:Andreas Erich Zautner,,,,GCF_001902515.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412456,,,,,1,2013-04-05,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-13T00:00:00Z,4,DSM:103699,2017-01-16T18:15:23.121Z,2017-01-16T18:15:23.121Z,,,56.95,"CP018450,CP018451,CP018452,CP018453",5658942,Klebsiella pneumoniae strain Kp_Goe_71070,Complete,Klesiella,Germany: Goettingen,,,31,male,Urinary tract infection,"Human, Homo sapiens",,Germany,,urine sample,,,,,573,,,host_description:Refugee from North Africa,,genotype:MLST ST101,,5845,,3,,"NZ_CP018450.1,NZ_CP018451.1,NZ_CP018452.1,NZ_CP018453.1",5809,,,University Medical Center Goettingen,123.0x,PacBio,,,,Kp_Goe_71070,,,"Included in the study, passed QC/QA"
942,573.7249,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCA_001902535.1,HGAP v. unspecified,,PRJNA246471,SAMN03733765,,,,,1,2011-05,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2016-12-13T00:00:00Z,5,,2017-01-16T18:19:05.986Z,2017-01-16T18:19:05.986Z,,,56.95,"CP018352,CP018351,CP018350,CP018348,CP018349",5513536,Klebsiella pneumoniae strain CAV1417,Complete,Klesiella,USA:Virginia,,,,,,"Human, Homo sapiens",,United States,,Urine/Genitourinary,,,,,573,,,,,,,5731,,3,,,5779,,,University of Oxford,133x,PacBio,,,,CAV1417,,,"Included in the study, passed QC/QA"
943,573.7351,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCF_001908515.1,HGAP v. unspecified,,PRJNA246471,SAMN03024576,,,,,1,Apr-2008,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2016-12-19T00:00:00Z,7,,2017-01-17T01:00:47.110Z,2017-01-17T01:00:47.110Z,,,56.83,"CP018671,CP018670,CP018665,CP018666,CP018667,CP018668,CP018669",5752260,Klebsiella pneumoniae strain CAV1042,Complete,Klesiella,USA:Virginia,,,,,Urinary Tract Infection,"Human, Homo sapiens",,United States,,Urine,,,,,573,,,,,,,5944,,6,,"NZ_CP018671.1,NZ_CP018670.1,NZ_CP018665.1,NZ_CP018666.1,NZ_CP018667.1,NZ_CP018668.1,NZ_CP018669.1",5931,,,University of Oxford,170x,PacBio,,,,CAV1042,,,"Included in the study, passed QC/QA"
944,573.7352,collected_by:Andreas Erich Zautner,,,,GCF_001908595.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412458,,,,,,2014-05-07,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-19T00:00:00Z,6,DSM:103708,2017-01-17T01:04:58.066Z,2017-01-17T01:04:58.066Z,,,56.59,"CP018686,CP018687,CP018689,CP018690,CP018691,CP018688",5916317,Klebsiella pneumoniae strain Kp_Goe_149473,Complete,Klesiella,Germany: Goettingen,,,70,male,pneumonia,"Human, Homo sapiens",,Germany,,tracheal secretion,,,,,573,,,host_description:German citizen,,genotype:MLST ST147,,6082,,5,,"NZ_CP018686.1,NZ_CP018687.1,NZ_CP018689.1,NZ_CP018690.1,NZ_CP018691.1,NZ_CP018688.1",6063,,,University Medical Center Goettingen,140.0x,PacBio,,,,Kp_Goe_149473,,,"Included in the study, passed QC/QA"
945,573.7353,collected_by:Andreas Erich Zautner,,,,GCF_001908625.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412797,,,,,1,2014-05-30,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-19T00:00:00Z,6,DSM:103704,2017-01-17T01:05:54.086Z,2017-01-17T01:05:54.086Z,,,56.6,"CP018701,CP018702,CP018704,CP018706,CP018705,CP018703",5907691,Klebsiella pneumoniae strain Kp_Goe_827024,Complete,Klesiella,Germany: Goettingen,,,51,male,peritonitis,"Human, Homo sapiens",,Germany,,abdominal drainage fluid,,,,,573,,,,,genotype:MLST ST147,,6072,,5,,"NZ_CP018701.1,NZ_CP018702.1,NZ_CP018704.1,NZ_CP018706.1,NZ_CP018705.1,NZ_CP018703.1",6061,,,University Medical Center Goettingen,128.0x,PacBio,,,,Kp_Goe_827024,,,"Included in the study, passed QC/QA"
946,573.7354,collected_by:Andreas Erich Zautner,,,,GCF_001908655.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412802,,,,,1,2014-05-30,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-19T00:00:00Z,6,DSM:103705,2017-01-17T01:06:01.557Z,2017-01-17T01:06:01.557Z,,,56.59,"CP018707,CP018708,CP018710,CP018712,CP018711,CP018709",5913496,Klebsiella pneumoniae strain Kp_Goe_827026,Complete,Klesiella,Germany: Goettingen,,,51,male,colonization,"Human, Homo sapiens",,Germany,,nasal swab,,,,,573,,,host_description:German citizen,,genotype:MLST ST147,,6071,,5,,"NZ_CP018707.1,NZ_CP018708.1,NZ_CP018710.1,NZ_CP018712.1,NZ_CP018711.1,NZ_CP018709.1",6059,,,University Medical Center Goettingen,134.0x,PacBio,,,,Kp_Goe_827026,,,"Included in the study, passed QC/QA"
947,573.7355,collected_by:Andreas Erich Zautner,,,,GCF_001908675.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412803,,,,,1,2014-06-13,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-19T00:00:00Z,6,DSM:103710,2017-01-17T01:07:34.714Z,2017-01-17T01:07:34.714Z,,,56.59,"CP018713,CP018714,CP018716,CP018717,CP018718,CP018715",5921376,Klebsiella pneumoniae strain Kp_Goe_152021,Complete,Klesiella,Germany: Goettingen,,,82,female,peritonitis,"Human, Homo sapiens",,Germany,,abdominal drainage fluid,,,,,573,,,host_description:German citizen,,genotype:MLST ST147,,6079,,5,,"NZ_CP018713.1,NZ_CP018714.1,NZ_CP018716.1,NZ_CP018717.1,NZ_CP018718.1,NZ_CP018715.1",6063,,,University Medical Center Goettingen,126.0x,PacBio,,,,Kp_Goe_152021,,,"Included in the study, passed QC/QA"
948,573.7356,collected_by:Andreas Erich Zautner,,,,GCF_001908695.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412804,,,,,1,2014-06-17,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-19T00:00:00Z,6,DSM:103706,2017-01-17T01:08:13.537Z,2017-01-17T01:08:13.537Z,,,56.59,"CP018719,CP018720,CP018722,CP018723,CP018724,CP018721",5914083,Klebsiella pneumoniae strain KP_Goe_828304,Complete,Klesiella,Germany: Goettingen,,,61,male,colonization,"Human, Homo sapiens",,Germany,,anal swab,,,,,573,,,host_description:German citizen,,genotype:MLST ST147,,6080,,5,,"NZ_CP018719.1,NZ_CP018720.1,NZ_CP018722.1,NZ_CP018723.1,NZ_CP018724.1,NZ_CP018721.1",6067,,,University Medical Center Goettingen,98.0x,PacBio,,,,KP_Goe_828304,,,"Included in the study, passed QC/QA"
949,573.7357,collected_by:Clinical Microbiology University of Virginia Health System,,,,GCA_001908715.1,HGAP v. unspecified,,PRJNA246471,SAMN03024585,,,,,1,Aug-2010,"Multi-drug resistant gram negative bacteria (also known as “Superbugs”) are causing infections in vulnerable patients in hospitals around the world. Much of the clinically relevant antibiotic resistance in these bacteria is driven by genes carried on mobile pieces of DNA called plasmids. A particularly significant resistance mechanism called the Klebsiella pneumoniae carbapenemase (KPC) is capable of hydrolyzing all penicillins, cephalosporins and carbapenems leaving very few therapeutic options for patients infected with blaKPC positive Enterobacteriaeceae. Unfortunately, the tools that we use for tracking of hospital transmission of bacteria do not focus on plasmids but rather the genome of the bacterium which has acquired the plasmid. Our project is to explore the blaKPC plasmid transmission across species in a single institution in Virginia where KPC-producing Gammaproteobacteria are endemic over several years using whole genome sequencing to gain insights into plasmid transmission and evolution of genes of drug resistance.",2016-12-19T00:00:00Z,5,,2017-01-17T01:09:40.741Z,2017-01-17T01:09:40.741Z,,,57.11,"CP018676,CP018674,CP018672,CP018675,CP018673",5379063,Klebsiella pneumoniae strain CAV1217,Complete,Klesiella,USA:Virginia,,,,,Urinary Tract Infection,"Human, Homo sapiens",,United States,,Urine,,,,,573,,,,,,,5559,,3,,,5625,,,University of Oxford,200x,PacBio,,,,CAV1217,,,"Included in the study, passed QC/QA"
950,573.7358,collected_by:Andreas Erich Zautner,,,,GCF_001908875.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412459,,,,,1,2014-05-12,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-19T00:00:00Z,6,DSM:103709,2017-01-17T01:17:45.303Z,2017-01-17T01:17:45.303Z,,,56.59,"CP018695,CP018696,CP018698,CP018700,CP018699,CP018697",5920288,Klebsiella pneumoniae strain Kp_Goe_149832,Complete,Klesiella,Germany: Goettingen,,,51,male,peritonitis,"Human, Homo sapiens",,Germany,,abdominal drain fluid,,,,,573,,,host_description:German citizen,,genotype:MLST ST147,,6078,,5,,"NZ_CP018695.1,NZ_CP018696.1,NZ_CP018698.1,NZ_CP018700.1,NZ_CP018699.1,NZ_CP018697.1",6064,,,University Medical Center Goettingen,160.0x,PacBio,,,,Kp_Goe_149832,,,"Included in the study, passed QC/QA"
951,573.7359,collected_by:Andreas Erich Zautner,,,,GCF_001908895.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412457,,,,,,2014-02-11,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-19T00:00:00Z,3,DSM:103700,2017-01-17T01:16:12.653Z,2017-01-17T01:16:12.653Z,,,57.3,"CP018692,CP018693,CP018694",5526153,Klebsiella pneumoniae strain Kp_Goe_821588,Complete,Klesiella,Germany: Goettingen,,,50,male,colonization,"Human, Homo sapiens",,Germany,,anal swab,,,,,573,,,host_description:Refugee from North Africa,,genotype:MLST ST11,,5618,,2,,"NZ_CP018692.1,NZ_CP018693.1,NZ_CP018694.1",5715,,,University Medical Center Goettingen,160.0x,PacBio,,,,Kp_Goe_821588,,,"Included in the study, passed QC/QA"
952,573.736,collected_by:Andreas Erich Zautner,,,,GCF_001913175.1,SMRT Analysis Software v. 2.3.0,,PRJNA329409,SAMN05412452,,,,,1,2013-03-12,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2016-12-21T00:00:00Z,6,DSM:103707,2017-01-17T03:41:23.183Z,2017-01-17T03:41:23.183Z,,,56.97,"CP018735,CP018737,CP018736,CP018738,CP018740,CP018739",5627728,Klebsiella pneumoniae strain Kp_Goe_121641,Complete,Klesiella,Germany: Goettingen,,,32,male,Urinary tract infection,"Human, Homo sapiens",,Germany,,urine sample,,,,,573,,,host_description:Refugee from North Africa,,genotype:MLST ST101,,5612,,5,,"NZ_CP018735.1,NZ_CP018737.1,NZ_CP018736.1,NZ_CP018738.1,NZ_CP018740.1,NZ_CP018739.1",5265,,,University Medical Center Goettingen,308.0x,PacBio,,,,Kp_Goe_121641,,,"Included in the study, passed QC/QA"
953,573.7362,,,Resistant;Not defined,AMR Panel,GCF_001922465.1,HGAP v. 2.3,,PRJNA292904,SAMN04014890,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2016-12-27T00:00:00Z,4,,2017-01-17T19:04:05.144Z,2017-01-17T19:04:05.144Z,,,56.97,"CP018816,CP018817,CP018818,CP018819",5779484,Klebsiella pneumoniae strain AR_0049,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5985,,3,,"NZ_CP018816.1,NZ_CP018817.1,NZ_CP018818.1,NZ_CP018819.1",6017,,,Centers for Disease Control and Prevention,109x,PacBio RSII,,,,AR_0049,,,"Included in the study, passed QC/QA"
954,573.7386,,,,,GCF_001936035.1,SMRT Portal v. 2.2,,PRJNA279657,SAMN03455977,,,,,1,,Klebsiella pneumoniae ATCC 35657 Genome Sequencing,2017-01-05T00:00:00Z,2,ATCC 35657,2017-01-24T01:37:41.261Z,2017-01-24T01:37:41.261Z,,,57.37,"CP015134,CP015135",5387970,Klebsiella pneumoniae strain ATCC 35657,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5305,,1,,"NZ_CP015134.1,NZ_CP015135.1",5211,,,NHGRI,126x,PacBio RSII,,,,ATCC 35657,,,"Included in the study, passed QC/QA"
955,573.9629,sample_type:Clinical isolate,,,,GCF_001952835.1,HGAP version 3.0 v. 2016-05-19,,PRJNA360900,SAMN06216564,,,,,1,2004-10-26,K. pneumoniae strain 1756 is resistant to carbapenems,2017-01-17T00:00:00Z,2,,2017-03-20T04:46:46.170Z,2017-03-20T04:46:46.170Z,,,57.52,"CP019219,CP019220",5269768,Klebsiella pneumoniae strain 1756,Complete,Klesiella,Taiwan,,,,,,"Human, Homo sapiens",,Taiwan,,pus,,,,,573,,,,,,,5268,,1,,"NZ_CP019219.1,NZ_CP019220.1",5321,,,National Yang Ming University,173.0x,PacBio,,,,1756,,,"Included in the study, passed QC/QA"
956,573.963,,,Resistant,Computational Prediction,GCF_001952875.1,SPAdes v. 3.5.0; HGAP Assembly v. 3,,PRJNA319426,SAMN04889855,,,,,1,,To study multidrug-resistant strains and their genome structure,2017-01-17T00:00:00Z,3,,2017-03-20T04:41:26.193Z,2017-03-20T04:41:26.193Z,,,57.28,"CP015382,CP015383,CP015384",5435802,Klebsiella pneumoniae strain CN1,Complete,Klesiella,USA: New York,,,,,,"Human, Homo sapiens",,United States,,,,,MLST.Klebsiella_pneumoniae.392,,573,,,,,,,5377,,2,,"NZ_CP015382.1,NZ_CP015383.1,NZ_CP015384.1",5285,,,New York Medical College,300x,Illumina; PacBio,,,,CN1,,,"Included in the study, passed QC/QA"
957,573.9631,,,Resistant,Computational Prediction,GCF_001952895.1,SPAdes v. 3.5.0; HGAP Assembly v. 3,,PRJNA319426,SAMN04889856,,,,,1,,To study multidrug-resistant strains and their genome structure,2017-01-17T00:00:00Z,7,,2017-03-20T04:40:11.216Z,2017-03-20T04:40:11.216Z,,,57.06,"CP015385,CP015386,CP015387,CP015388,CP015389,CP015390,CP015391",5880908,Klebsiella pneumoniae strain NY9,Complete,Klesiella,USA: New York,,,,,,"Human, Homo sapiens",,United States,,,,,,,573,,,,,,,5952,,6,,"NZ_CP015385.1,NZ_CP015386.1,NZ_CP015387.1,NZ_CP015388.1,NZ_CP015389.1,NZ_CP015390.1,NZ_CP015391.1",5841,,,New York Medical College,300x,Illumina; PacBio,,,,NY9,,,"Included in the study, passed QC/QA"
958,573.9632,,,Resistant,Computational Prediction,GCF_001952915.1,SPAdes v. 3.5.0; HGAP Assembly v. 3,,PRJNA319426,SAMN04889857,,,,,1,,To study multidrug-resistant strains and their genome structure,2017-01-17T00:00:00Z,6,,2017-03-20T04:43:34.650Z,2017-03-20T04:43:34.650Z,,,56.75,"CP015392,CP015393,CP015394,CP015395,CP015396,CP015397",6063895,Klebsiella pneumoniae strain CR14,Complete,Klesiella,USA: New York,,,,,,"Human, Homo sapiens",,United States,,,,,MLST.Klebsiella_pneumoniae.258,,573,,,,,,,6122,,5,,"NZ_CP015392.1,NZ_CP015393.1,NZ_CP015394.1,NZ_CP015395.1,NZ_CP015396.1,NZ_CP015397.1",5956,,,New York Medical College,300x,Illumina; PacBio,,,,CR14,,,"Included in the study, passed QC/QA"
959,573.9643,collected_by:USAMRIID,,Resistant,Computational Prediction,GCA_002009075.1,HGAP v. 2.3,,PRJNA311034,SAMN04457965,,,,,1,01-Dec-2015,Whole genome long-read sequencing of isolates of Klebsiella and Acinetobacter,2017-03-02T00:00:00Z,7,,2017-03-20T08:32:28.572Z,2017-03-20T08:32:28.572Z,,,57.11,"CP014294,CP014295,CP014296,CP014297,CP014298,CP014299,CP014300",5852942,Klebsiella pneumoniae strain KP38731,Complete,Klesiella,,,,,,pneumonia,"Human, Homo sapiens",,,,,,,MLST.Klebsiella_pneumoniae.11,,573,,,,,,,6138,,6,,"NZ_CP014294.1,NZ_CP014295.1,NZ_CP014296.1,NZ_CP014297.1,NZ_CP014298.1,NZ_CP014299.1,NZ_CP014300.1",5802,,,USAMRIID,150,PacBio,,,,KP38731,,,"Included in the study, passed QC/QA"
960,573.9645,collected_by:Andreas Erich Zautner,,Resistant,Computational Prediction,GCF_001956965.1,SMRT Analysis v. 2.3.0,,PRJNA329409,SAMN05412796,,,,,1,2014-05-14,"Klebsiella pneumoniae oxa48 local outbreak in G�ttingen, Lower Saxony, Germany 2013-2014",2017-01-19T00:00:00Z,5,DSM:103703,2017-03-20T09:48:20.361Z,2017-03-20T09:48:20.361Z,,,56.64,"CP017985,CP017986,CP017987,CP017988,CP017989",5869161,Klebsiella pneumoniae strain 825795-1,Complete,Klesiella,Germany: Goettingen,,,73,male,colonization,"Human, Homo sapiens",,Germany,,anal swab,,,MLST.Klebsiella_pneumoniae.147,,573,,,host_description:German citizen,,genotype:MLST ST147,,5815,,4,,"NZ_CP017985.1,NZ_CP017986.1,NZ_CP017987.1,NZ_CP017988.1,NZ_CP017989.1",5472,,,University Medical Center Goettingen,160,Illumina; PacBio,,,,825795-1,,,"Included in the study, passed QC/QA"
961,573.9721,,,Susceptible;Resistant;Intermediate;Not defined,AMR Panel,,HGAP v. 2.3,,PRJNA292902,SAMN04014958,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-03-21T00:00:00Z,6,,2017-05-28T00:11:51.785Z,2017-05-28T00:11:51.785Z,,,56.76,"CP020061,CP020062,CP020063,CP020064,CP020065,CP020066",5838292,Klebsiella pneumoniae strain AR_0117,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5931,,5,,,5950,,,Centers for Disease Control and Prevention,201x,PacBio RSII,,,,AR_0117,,,"Included in the study, passed QC/QA"
962,573.9722,,,Resistant;Susceptible;Not defined;Intermediate,AMR Panel,,HGAP v. 2.3,,PRJNA292904,SAMN04014909,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2017-03-21T00:00:00Z,4,,2017-05-28T00:08:49.491Z,2017-05-28T00:08:49.491Z,,,56.73,"CP020067,CP020068,CP020069,CP020070",5884778,Klebsiella pneumoniae strain AR_0068,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,6033,,3,,,6028,,,Centers for Disease Control and Prevention,220x,PacBio RSII,,,,AR_0068,,,"Included in the study, passed QC/QA"
963,573.9723,,,Resistant;Susceptible;Intermediate;Not defined,AMR Panel,,canu v 1.3,,PRJNA292902,SAMN04014956,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-03-21T00:00:00Z,5,,2017-05-28T00:17:08.574Z,2017-05-28T00:17:08.574Z,,,57.12,"CP020071,CP020072,CP020073,CP020074,CP020075",5666107,Klebsiella pneumoniae strain AR_0115,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5829,,4,,,5927,,,Centers for Disease Control and Prevention,196x,PacBio RSII,,,,AR_0115,,,"Included in the study, passed QC/QA"
964,573.9724,,,Intermediate;Resistant;Not defined;Susceptible,AMR Panel,,canu v. 1.3,,PRJNA292904,SAMN04014939,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2017-03-21T00:00:00Z,5,,2017-05-28T00:19:28.339Z,2017-05-28T00:19:28.339Z,,,57.1,"CP020108,CP020109,CP020110,CP020111,CP020112",5708390,Klebsiella pneumoniae strain AR_0098,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5896,,4,,,5985,,,Centers for Disease Control and Prevention,210x,PacBio RSII,,,,AR_0098,,,"Included in the study, passed QC/QA"
965,573.9779,collected_by:USAMRIID,,,,,HGAP v. 2.3,,PRJNA317547,SAMN04621179,,,,,1,2015,Genomic investigation of drug-resistant isolates of Klebsiella pneumoniae,2017-05-02T00:00:00Z,1,,2017-05-29T10:10:56.599Z,2017-05-29T10:10:56.599Z,,,57.56,CP015120,5264852,Klebsiella pneumoniae strain kp757,Complete,Klesiella,USA,,,,,pneumonia,"Human, Homo sapiens",,United States,,,,,,,573,,,,,,,5174,,,,,5106,,,USAMRIID,215,PacBio,,,,kp757,,,"Included in the study, passed QC/QA"
966,573.9836,,,,,,,,PRJEB12753,SAMEA1920840,,,,,1,,"We have sequenced, assembled and annotated the genome of Klebsiella pneumoniae RH201207.",2016-05-16T00:00:00Z,5,,2017-05-30T04:50:29.793Z,2017-05-30T04:50:29.793Z,,,56.95,"LT216436,LT216437,LT216438,LT216439,LT216440",5870288,Klebsiella pneumoniae strain 207M1D0-sc-2013-04-03T11:21:06Z-1606409,Complete,Klesiella,,,,,,,,,,,,,,,,573,,,,,,,5947,,4,,,5616,,,WTSI,,,,,,207M1D0-sc-2013-04-03T11:21:06Z-1606409,,,"Included in the study, passed QC/QA"
967,574.2,,,Susceptible;Resistant;Not defined,Computational Prediction,GCA_003010735.1,HGAP v. 2.3,,PRJNA292904,SAMN04014937,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2018-03-19T00:00:00Z,6,,2018-05-26T07:33:38.778Z,2018-05-26T07:33:38.778Z,,,56.853188,"CP027612,CP027613,CP027614,CP027615,CP027616,CP027617",5651305,Klebsiella pneumoniae subsp. ozaenae strain AR_0096,Complete,Klesiella,,,,,,,,,,,,,,,,574,,,,,,,5926,,5,,,5760,,,Centers for Disease Control and Prevention,129x,PacBio RSII,,,,AR_0096,,,"Included in the study, passed QC/QA"
968,640131.3,,,,,GCA_000025465.1,,,PRJNA37701,SAMN02598515,,,,,1,,Klebsiella variicola At-22. Project description not provided.,2010-02-16T00:00:00Z,1,,2014-12-08T22:11:51.326Z,2015-03-16T03:17:09.594Z,,,57.6,CP001891,5458505,Klebsiella variicola At-22,Complete,Klesiella,,,,,,,,,,,,,,,,640131,-,Klebsiella variicola At-22,,,,,5073,,,19965433,NC_013850,5057,,,"US DOE Joint Genome Institute|DOE Joint Genome Institute|JGI-PGF|University of Wisconsin-Madison, Department of Bacteriology, USA, Madison",,,complete,,,At-22,,,"Included in the study, passed QC/QA"
969,72407.108,collected_by:Yang Liu,,,,GCF_001521895.1,SMRTAnalysis v. 2.3.0 HGAP2,,PRJNA309157,SAMN04421276,,,,,1,28-Sep-2014,"The strain was a NDM-5-producing K. pneumoniae hypervirulent clone of capsular serotype K2 belonging to sequence type 14,which was isolated from urine with mucoviscosity phenotype.",2016-01-21T00:00:00Z,3,,2016-02-02T23:09:55.560Z,2016-02-02T23:09:55.560Z,,,57.19,"CP014004,CP014005,CP014006",5535187,Klebsiella pneumoniae subsp. pneumoniae strain NUHL24835,Complete,Klesiella,China: Jiangxi,,,,,urine with mucoviscosity phenotype,"Human, Homo sapiens",isolated from urine with mucoviscosity phenotype,China,,urine,,,MLST.Klebsiella_pneumoniae.14,,72407,C,,,,,,5441,,2,,"NZ_CP014004.1,NZ_CP014005.1,NZ_CP014006.1",5339,,,The First Affiliated Hospital of Nanchang University,180x,PacBio RS II system,,serovar K2,,NUHL24835,,,"Included in the study, passed QC/QA"
970,72407.109,"collected_by:Department of Critical Care Medicine and Respiratory Intensive Care Unit, Shanghai Ruijin Hospital Affiliated with Jiaotong University",,,,GCF_001529935.1,Newbler v. 2.3; Celera Assembler v. 8.3,,PRJNA307276,SAMN04377968,,,,,1,26-Jan-2015,Comparative genome analysis,2016-01-22T00:00:00Z,2,,2016-02-04T03:22:57.289Z,2016-02-04T03:22:57.289Z,,,57.14,"CP014010,CP014011",5690826,Klebsiella pneumoniae subsp. pneumoniae strain RJF999,Complete,Klesiella,China: Shanghai,,,,,Coronary heart disease,"Human, Homo sapiens",,China,,blood,,,MLST.Klebsiella_pneumoniae.23,,72407,C,,,,,,5594,,1,,"NZ_CP014010.1,NZ_CP014011.1",5444,,,Shanghai Ruijin Hospital Affiliated with Jiaotong University,124x,PacBio RS II,,,,RJF999,,,"Included in the study, passed QC/QA"
971,72407.11,"collected_by:Department of Critical Care Medicine and Respiratory Intensive Care Unit, Shanghai Ruijin Hospital Affiliated with Jiaotong University",,,,GCF_001530015.1,Newbler v. 2.3; Celera Assembler v. 8.3,,PRJNA307277,SAMN04377969,,,,,1,2014-09-08,comparative genome analysis,2016-01-22T00:00:00Z,2,,2016-02-04T03:58:18.905Z,2016-02-04T03:58:18.905Z,,,57.2,"CP014008,CP014009",5450593,Klebsiella pneumoniae subsp. pneumoniae strain RJF293,Complete,Klesiella,China: Shanghai,,,,,Gastric remnant cancer,"Human, Homo sapiens",,China,,blood,,,MLST.Klebsiella_pneumoniae.374,,72407,C,,,,,,5333,,1,,"NZ_CP014008.1,NZ_CP014009.1",5225,,,Shanghai Ruijin Hospital Affiliated with Jiaotong University,195x,PacBio RS II,,,,RJF293,,,"Included in the study, passed QC/QA"
972,72407.122,collected_by:Olympia,,,,GCF_001611055.1,SPAdes v. 3.1,,PRJNA295651,SAMN04087461,,,,,1,12-Jun-2011,Longitude analysis of ST383,2016-04-05T00:00:00Z,1,,2016-04-28T03:22:58.345Z,2016-04-28T03:22:58.345Z,,,57.03,CP012743,5439720,Klebsiella pneumoniae subsp. pneumoniae strain TGH8,Complete,Klesiella,Greece,,,,male,Bacterial infections,"Human, Homo sapiens",,Greece,,CVC,,,,,72407,C,,,,,,5449,,,26968884,NZ_CP012743.1,5246,,,University of Antwerpen,112,Illumina,,,,TGH8,,,"Included in the study, passed QC/QA"
973,72407.123,collected_by:Olympia,,,,GCF_001611095.1,SPAdes v. 3.1,,PRJNA295651,SAMN04087462,,,,,1,02-Mar-2013,Longitude analysis of ST383,2016-04-05T00:00:00Z,1,,2016-04-28T03:22:54.419Z,2016-04-28T03:22:54.419Z,,,57.25,CP012744,5355459,Klebsiella pneumoniae subsp. pneumoniae strain TGH10,Complete,Klesiella,Greece,,,,,Bacterial infections,"Human, Homo sapiens",,Greece,,wound swab,,,,,72407,C,,,,,,5368,,,26968884,NZ_CP012744.1,5189,,,University of Antwerpen,131,Illumina,,,,TGH10,,,"Included in the study, passed QC/QA"
974,72407.38,,,,,GCA_000742755.1,HGAP SMRT Portal v. 2.2.0,,PRJNA253462,SAMN02982872,,,,Bacilli,1,2000,"Spontaneous rifampin-resistant mutant of strain ATCC 43816, commonly used in animal studies of infection, as well as molecular and genetic characterization of K. pneumoniae",2014-08-21T00:00:00Z,1,ATCC 43816,2014-12-09T00:47:19.991Z,2015-03-16T03:17:09.594Z,,,57.4,CP009208.1,5374830,Klebsiella pneumoniae subsp. pneumoniae strain VK055,Complete,Klesiella,USA,Negative,,,,,,,United States,,Spontaneous rifampin-resistant isolatefrom ATCC 43816,,,,No,72407,,,,,,,5031,,,25291761,NZ_CP009208.1,5081,,,University of North Carolina at Chapel Hill,258x,PacBio RSII,,,No,VK055,,,"Included in the study, passed QC/QA"
975,72407.396,collected_by:Olympia,,,,GCF_001746535.1,SPAdes v. 3.1,,PRJNA295651,SAMN04087463,,,,,1,2013-04-14,Longitude analysis of ST383,2016-09-26T00:00:00Z,1,,2016-11-16T14:29:04.936Z,2016-11-16T14:29:04.936Z,,,57.42,CP012745,5344576,Klebsiella pneumoniae subsp. pneumoniae strain TGH13,Complete,Klesiella,Greece,,,,,Bacterial infections,"Human, Homo sapiens",,Greece,,rectal,,,,,72407,C,,,,,,5261,,,,NZ_CP012745.1,5142,,,University of Antwerpen,128,Illumina,,,,TGH13,,,"Included in the study, passed QC/QA"
976,72407.626,"collected_by:Department of Critical Care Medicine and Respiratory Intensive Care Unit, Shanghai Ruijin Hospital Affiliated with Jiaotong University",,Susceptible,Computational Prediction,,SPAdes v. 3.9,,PRJNA360094,SAMN06200334,,,,,1,04-May-2015,comparative genomic analysis,2017-06-02T00:00:00Z,4,,2017-07-22T03:52:51.664Z,2017-07-22T03:52:51.664Z,,,56.68,"CP019047,CP019048,CP019049,CP019050",5918670,Klebsiella pneumoniae subsp. pneumoniae strain RJA166,Complete,Klesiella,China: Shanghai,,,,,heart disease,"Human, Homo sapiens",,China,,sputum,,,MLST.Klebsiella_pneumoniae.23,,72407,,,,,,,6049,,3,,,6014,,,Shanghai Ruijin Hospital Affiliated with Jiaotong University,400.0x,Illumina MiSeq; PacBio,,,,RJA166,,,"Included in the study, passed QC/QA"
977,72407.693,collected_by:Doherty Applied Microbial Genomics,,Resistant;Susceptible,Computational Prediction,GCA_002249975.1,Canu v. 1.5,,PRJNA397262,SAMN07452764,,,,,1,26-Sep-2012,"Whole-genome sequencing of KPC-producing Enterobacteriaceae from an outbreak in Victoria, Australia",2017-08-14T00:00:00Z,4,,2017-09-28T20:13:02.923Z,2017-09-28T20:13:02.923Z,,,57.02,"CP022691,CP022692,CP022693,CP022694",5814263,Klebsiella pneumoniae subsp. pneumoniae strain AUSMDU00008079,Complete,Klesiella,Australia: Victoria,,,,,Urinary tract infection,"Human, Homo sapiens",,Australia,,Patient urine,,,,,72407,,,,,,,5998,,3,,,5835,,,Doherty Applied Microbial Genomics,85.0x,PacBio; Illumina NextSeq,,,,AUSMDU00008079,,,"Included in the study, passed QC/QA"
978,72407.733,"collected_by:Laboratory Medicine, Peking University People's Hospital",,Susceptible,Computational Prediction,GCA_002761515.1,HGAP v. 2.0,,PRJNA301380,SAMN04244588,,,,,1,08-Jul-2010,study of the complete genome sequence of the strian of Klebsiella pneumoniae H11,2017-11-07T00:00:00Z,1,,2017-11-24T17:23:17.735Z,2017-11-24T17:23:17.735Z,,pneumonia,57.43,CP018056,5316818,Klebsiella pneumoniae subsp. pneumoniae strain H11,Complete,Klesiella,China:Beijing,,HostAssociated,65,male,pneumonia,"Human, Homo sapiens",,China,,separated from patient's sputum,,,,,72407,37 C,,,,,Aerobic,5186,,,,,5121,,,Peking University People's Hospital,100.0x,PacBio,,,,H11,Mesophilic,,"Included in the study, passed QC/QA"
979,72407.75,,,,,GCF_000775375.1,SMRT Portal v. 2.0,,PRJNA243858,SAMN02720898,,,,,1,2013,Whole genome sequencing of Klebsiella pneumoniae,2015-03-02T00:00:00Z,4,,2016-01-17T15:40:45.930Z,2016-01-17T15:40:45.930Z,,,57.19,"CP009771,CP009772,CP009773,CP009774",5695223,Klebsiella pneumoniae subsp. pneumoniae strain KPNIH33,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,,,,,,72407,,,,,,,5649,,3,25232178,"NZ_CP009771.1,NZ_CP009772.1,NZ_CP009773.1,NZ_CP009774.1",5545,,,NIH,,PacBio RSII,,,,KPNIH33,,,"Included in the study, passed QC/QA"
980,72407.76,,,,,GCF_000775395.1,SMRT Portal v. 2.0,,PRJNA251381,SAMN02820981,,,,,1,2013,Whole genome sequencing of Klebsiella pneumoniae,2015-03-02T00:00:00Z,4,,2016-01-17T15:40:46.350Z,2016-01-17T15:40:46.350Z,,,56.99,"CP009775,CP009776,CP009777,CP009778",5858308,Klebsiella pneumoniae subsp. pneumoniae strain KPNIH32,Complete,Klesiella,USA,,,,,,,,United States,,perirectal swab,,,,,72407,,,,,,,5867,,3,25232178,"NZ_CP009775.1,NZ_CP009776.1,NZ_CP009777.1,NZ_CP009778.1",5741,,,NIH,,PacBio RSII,,,,KPNIH32,,,"Included in the study, passed QC/QA"
981,72407.77,,,,,GCF_000784945.1,SMRT Portal v. 2.0,,PRJNA248880,SAMN02803823,,,,,1,2013,Whole genome sequencing of Klebsiella pneumoniae,2015-03-02T00:00:00Z,3,,2016-01-17T15:41:01.629Z,2016-01-17T15:41:01.629Z,,,57.2,"CP009863,CP009864,CP009865",5520596,Klebsiella pneumoniae subsp. pneumoniae strain KPNIH29,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,perirectal swab,,,,,72407,,,,,,,5508,,2,25232178,"NZ_CP009863.1,NZ_CP009864.1,NZ_CP009865.1",5271,,,NIH,,PacBio RSII,,,,KPNIH29,,,"Included in the study, passed QC/QA"
982,72407.78,,,,,GCF_000784985.1,SMRT Portal v. 2.0,,PRJNA251378,SAMN02820977,,,,,1,2013,Whole genome sequencing of Klebsiella pneumoniae,2015-03-02T00:00:00Z,4,,2016-01-17T15:41:02.046Z,2016-01-17T15:41:02.046Z,,,57.3,"CP009872,CP009873,CP009874,CP009875",5484149,Klebsiella pneumoniae subsp. pneumoniae strain KPNIH30,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,perirectal swab,,,,,72407,,,,,,,5477,,3,25232178,"NZ_CP009872.1,NZ_CP009873.1,NZ_CP009874.1,NZ_CP009875.1",5416,,,NIH,,PacBio RSII,,,,KPNIH30,,,"Included in the study, passed QC/QA"
983,72407.79,,,,,GCF_000785005.1,SMRT Portal v. 2.0,,PRJNA251380,SAMN02820980,,,,,1,2013,Whole genome sequencing of Klebsiella pneumoniae,2015-03-02T00:00:00Z,4,,2016-01-17T15:41:02.569Z,2016-01-17T15:41:02.569Z,,,57.27,"CP009876,CP009877,CP009878,CP009879",5473580,Klebsiella pneumoniae subsp. pneumoniae strain KPNIH31,Complete,Klesiella,USA,,,,,,"Human, Homo sapiens",,United States,,urine,,,,,72407,,,,,,,5414,,3,25232178,"NZ_CP009876.1,NZ_CP009877.1,NZ_CP009878.1,NZ_CP009879.1",5246,,,NIH,,PacBio RSII,,,,KPNIH31,,,"Included in the study, passed QC/QA"
984,72407.81,sample_type:cell culture,,,,GCF_000981845.1,HGAP SMRTPortal v. 2.3.0,,PRJNA281780,SAMN03496739,,,,,1,2011,Genome sequencing of medically relevant Klebsiella pneumoniae 234-12,2015-04-29T00:00:00Z,4,,2016-01-17T15:55:31.961Z,2016-01-17T15:55:31.961Z,,,56.8,"CP011313,CP011315,CP011314,CP011316",5648826,Klebsiella pneumoniae subsp. pneumoniae strain 234-12,Complete,Klesiella,Germany,,,,,,"Human, Homo sapiens",,Germany,,blood,,,,,72407,C,,,,,,5607,,3,,"NZ_CP011313.1,NZ_CP011315.1,NZ_CP011314.1,NZ_CP011316.1",5244,,,Leibniz Institute DSMZ,50x,PacBio; Illumina MiSeq,,,,234-12,,,"Included in the study, passed QC/QA"
985,72407.83,sample_type:Environmental sample,,,,GCF_001280925.1,Newbler v. 2.7,,PRJNA291804,SAMN03955386,,,,,1,2013,"Cellulose-degrading bacteria isolated from Giant Panda feces has the potential to convert organic waste into biofules. Researchers have identified multiple cellulose-digesting microbes in the Giant Panda gut, but few have applied such bacteria in converting cellulose into glucose to create biofuel. Cellulosic ethanol, a biofuel, is produced through the fermentation of lignocellulosic biomasses. This anaerobic process is aided by cellulose-digesting enzymes.",2015-09-10T00:00:00Z,1,,2016-01-17T17:06:04.032Z,2016-01-17T17:06:04.032Z,,,58.04,CP012300,5088873,Klebsiella pneumoniae subsp. pneumoniae strain HKUOPLC,Complete,Klesiella,Hong Kong,,,,,,,isolated from Giant Panda feces has the potential to convert organic waste into biofules,China,,giant panda feces,,,,,72407,C,,,,,,4901,,,,NZ_CP012300.1,4764,,,University of Hong Kong,43,Illumina,,,,HKUOPLC,,,"Included in the study, passed QC/QA"
986,72407.9,"collected_by:Ning Dong, Sheng Chen, Rong Zhang",,Susceptible;Resistant,Computational Prediction,GCA_002893825.1,SPAdes v. 3.9.1,,PRJNA422171,SAMN08166690,,,,,1,2015,Genome analysis of Clinical Multilocus Sequence Type 11 Klebsiella pneumoniae from China,2018-01-21T00:00:00Z,2,,2018-05-25T19:27:25.135Z,2018-05-25T19:27:25.135Z,,,57.362274,"CP025951,CP025952",5537629,Klebsiella pneumoniae subsp. pneumoniae strain GD4,Complete,Klesiella,China,,,,,,"Human, Homo sapiens",,,,,,,MLST.Klebsiella_pneumoniae.11,,72407,,,,,,,5668,,1,,,5580,,,The Hong Kong Polytechnic University,30.0x,PacBio,,,,GD4,,,"Included in the study, passed QC/QA"
987,72407.977,collected_by:Federal University of Rio de Janeiro,,Susceptible;Resistant,Computational Prediction,GCA_002951555.1,PacBio v. HGAP.2,,PRJNA358426,SAMN06173548,,,,,1,2009,High-level carbapenem resistance in KPC-producing Klebsiella pneumoniae emerges from subpopulations that undergo distinct stepwise transcriptional programs from a population exposed to a lethal carbapenem dose.,2018-02-02T00:00:00Z,2,,2018-05-26T01:59:31.725Z,2018-05-26T01:59:31.725Z,,,57.391666,"CP018883,CP018884",5431353,Klebsiella pneumoniae subsp. pneumoniae strain BR7,Complete,Klesiella,Brazil: Rio de Janeiro,,,,,bloodstream infection,"Human, Homo sapiens",,Brazil,,blood,,,MLST.Klebsiella_pneumoniae.437,,72407,,,,,,,5537,,1,,,5607,,,University of California,100.0x,PacBio,,,,BR7,,,"Included in the study, passed QC/QA"
988,72407.978,collected_by:Federal University of Rio de Janeiro,,Resistant;Susceptible,Computational Prediction,GCA_002951595.1,PacBio v. HGAP.2,,PRJNA358426,SAMN06173549,,,,,1,2009,High-level carbapenem resistance in KPC-producing Klebsiella pneumoniae emerges from subpopulations that undergo distinct stepwise transcriptional programs from a population exposed to a lethal carbapenem dose.,2018-02-02T00:00:00Z,3,,2018-05-26T02:00:37.477Z,2018-05-26T02:00:37.477Z,,,57.192398,"CP018885,CP018886,CP018887",5708729,Klebsiella pneumoniae subsp. pneumoniae strain BR21,Complete,Klesiella,Brazil: Rio de Janeiro,,,,,urinary tract infection,"Human, Homo sapiens",,Brazil,,urine,,,MLST.Klebsiella_pneumoniae.437,,72407,,,,,,,5887,,2,,,5951,,,University of California,100.0x,PacBio,,,,BR21,,,"Included in the study, passed QC/QA"
989,861365.4,,,,,GCA_000967845.1,,,PRJNA50357,,,,,,1,,"Klebsiella pneumoniae subsp. rhinoscleromatis SB3432.Total DNA of isolateKlebsiella pneumoniae subsp. rhinoscleromatis is the agent of rhinoscleroma, a chronic granulomatous disease of the upper respiratory airways of humans.",2013-05-15T00:00:00Z,2, ,2014-12-08T22:11:48.716Z,2015-03-16T03:17:09.594Z,,,57.105,"FO203501.1,FO203500.1",5384455,Klebsiella pneumoniae strain SB3432,Complete,Klesiella,,Negative,Host Associated,,,,,,,,,,,MLST.Klebsiella_pneumoniae.67,,573,,Klebsiella pneumoniae subsp. rhinoscleromatis SB3432,,,,,5457,,1,21629720,"NC_021232.1,NC_021231.1",5271,,,Institut Pasteur,,,complete,,,SB3432,Mesophilic,,"Included in the study, passed QC/QA"
990,935296.3,,,,,GCA_000334515.1,,,PRJNA61107,SAMEA3138432,,,,,3,,First genome sequence of a Multi-drug Resistant Isolate of Enterobacter aerogenes species. Clinical isolate from blood culture.,2013-01-25T00:00:00Z,3, ,2014-12-08T22:11:10.403Z,2015-03-16T03:17:09.594Z,,,54.9278,"FO203353.1,FO203354.1,FO203355.1",5591105,Enterobacter aerogenes EA1509E,Complete,Klesiella,France:Marseille,,,,,dead,"Human, Homo sapiens",isolate from blood culture,France,,blood culture,,,,,935296,,Enterobacter aerogenes EA1509E,,,,,5298,,,23071100,"NC_020182.1,NC_020180.1,NC_020181.1",5499,,,Unit¿¿¿¿¿ de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE),,,complete,,,EA1509E,,,"Included in the study, passed QC/QA"
991,1086030.5,,,,,GCA_000252895.1,,,PRJNA73131,SAMN02469698,,,,,1,,,2012-03-15T00:00:00Z,1,,2015-03-12T13:39:47.034Z,2015-03-16T03:17:09.594Z,,,47.58,CM001474.1,463270,Shigella flexneri 5a str. M90T,Complete,Shigella,,,,,,,,,,,,,,,,1086030,,,,,,,675,,8,22582379,NZ_CM001474.1,403,,8,Dalhousie University,,,,,,M90T,,,"Excluded from the study, failed QC/QA."
992,1282357.3,,,,,GCA_000743955.1,,,PRJNA186498,SAMN02999960,,,,,1,,Genome announcement,2014-08-27T00:00:00Z,1,,2014-12-08T22:35:51.624Z,2015-03-16T03:17:09.594Z,,,50.9,CP004056.1,4595810,Shigella flexneri 2003036,Complete,Shigella,,,,,,,,,,,,,,,,1282357,,,,,,,4885,,,-,NZ_CP004056.1,4891,,1,Institute for Communicable Disease Control and Prevention,,,,,,2003036,,,"Included in the study, passed QC/QA"
993,1282358.3,,,,,GCA_000743995.1,,,PRJNA186503,SAMN02999961,,,,,1,,genome announcement,2014-08-27T00:00:00Z,1,,2014-12-08T22:35:52.391Z,2015-03-16T03:17:09.594Z,,,50.9,CP004057.1,4620900,Shigella flexneri Shi06HN006,Complete,Shigella,,,,,,,,,,,,,,,,1282358,,,,,,,4949,,,-,NZ_CP004057.1,4941,,1,Institute for Communicable Disease Control and Prevention,,,,,,Shi06HN006,,,"Included in the study, passed QC/QA"
994,1435046.4,,,,,GCF_001021855.1,Velvet v. 1.2.01,,PRJNA231092,SAMN02440121,,,,,1,,To construct evolutionary tree,2015-06-08T00:00:00Z,,,2016-01-17T16:05:36.895Z,2016-01-17T16:05:36.895Z,,,50.7,"CP007037,CP007038",4817311,Shigella flexneri G1663,Complete,Shigella,,,,,,,"Human, Homo sapiens",,,,stool sample,,,,,1435046,,,,,,,5370,,1,,"NZ_CP007037.1,NZ_CP007038.1",4578,,2,TEDA Institute of Biological and Biotechnology,120x,Illumina GAIIx; 454,,,,G1663,,,"Included in the study, passed QC/QA"
995,1617964.3,sample_type:cell culture,,,,GCF_001579965.1,HS HGAP v. 2,,PRJNA288251,SAMN03797408,,,,,1,2012,genome sequence,2016-03-03T00:00:00Z,,,2016-03-18T11:07:24.124Z,2016-03-18T11:07:24.124Z,,,50.42,"CP012140,CP012141,CP012142,CP012143",5196066,Shigella flexneri 4c strain 1205,Complete,Shigella,China,,,,,,"Human, Homo sapiens",,China,,,,,,,1617964,C,,,,,,5947,,3,,,5122,,4,Hangzhou Centrer for Disease Control amd Prevention,100x,PacBio,,,,1205,,,"Included in the study, passed QC/QA"
996,1617964.7,sample_type:cell culture,,,,GCA_002240075.1,HGAP v. 2.0,,PRJNA356350,SAMN06112245,,,,,1,2016,antibiotic resistance study,2017-08-02T00:00:00Z,,,2017-09-28T19:42:57.884Z,2017-09-28T19:42:57.884Z,,,50.71,"CP020336,CP020337,CP020338",4980844,Shigella flexneri 4c,Complete,Shigella,China:Hangzhou,,,,,,,,China,,hospitalized patients,,,,,1617964,,,,,,,5768,,2,,,5374,,3,Hangzhou Normal University,169.12,PacBio,,,,1602,,,"Included in the study, passed QC/QA"
997,1617964.8,sample_type:cell culture,,,,GCA_002240095.1,HGAP v. 2.0,,PRJNA356348,SAMN06112243,,,,,1,2007,antibiotic resistance study,2017-08-02T00:00:00Z,,,2017-09-28T19:43:06.789Z,2017-09-28T19:43:06.789Z,,,50.8,"CP020339,CP020340,CP020341",4767656,Shigella flexneri 4c,Complete,Shigella,China: Hangzhou,,,,,,,,China,,hospitalized patients,,,,,1617964,,,,,,,5491,,2,,,5098,,3,Hangzhou Normal University,78.93,PacBio,,,,702,,,"Included in the study, passed QC/QA"
998,1813821.3,sample_type:single cell,,,,GCF_001596115.1,HGAP v. 2.3 2016-01,,PRJNA315032,SAMN04548868,,,,,,2015-01,Shigella sp. from lichen,2016-03-22T00:00:00Z,1,PAMC:28760,2016-04-27T18:36:31.029Z,2016-04-27T18:36:31.029Z,,,50.84,CP014768,4558287,Shigella sp. PAMC 28760,Complete,Shigella,Antarctica,,,,,,Lichen,,Antarctica,,,,,,,1813821,,,,,,,4582,,,,NZ_CP014768.1,4387,,1,Korea Polar Research Institute,100x,PacBio,,,,28760,,,"Included in the study, passed QC/QA"
999,1935181.3,collected_by:Nils I. A. Carlin,,,,GCA_002442995.1,HGAP3.3 SMRT Pipeline v. 2.3.0; Pilon v.,,PRJNA382451,SAMN06706581,,,,,1,1988,"Shigella species cause bacillary dysentery – a severe form of diarrhoea, characterized by acute colonic and rectal mucosal inflammation leading to fever, abdominal cramps and bloody mucoid stools. Out of four species of Shigella, S. flexneri is the most prevalent enteric pathogen in developing countries. Shigella is transmitted through faecal-oral route and can cause gastrointestinal infection via an exceptionally low infectious dose (as many as 10 bacteria). S. flexneri is classified into different serotypes based on the O-antigen structure of its lipopolysaccharide. The serotype conversion is mediated by bacteriophages and plasmids carrying genes that modify the O-antigen. The S. flexneri serotype 1c is a novel serotype, which has now been found to be prevalent in many developing countries. However, little is known about its virulence signatures and evolution. Here, we provide the unique features of this serotype through the whole genome sequencing and bioinformatics tools. We also identified it as a highly adaptive pathogen with unique O-antigen modification possibly mediated by three different bacteriophages during its evolution. Furthermore, this serotype possesses several hypothetical genes and putative bacteriophage regions that will guide future investigation to identify novel genes involved in pathogen’s virulence and its survival in the host environment.",2017-10-04T00:00:00Z,,,2017-11-23T02:52:19.805Z,2017-11-23T02:52:19.805Z,,,50.91,CP020753,4584634,Shigella flexneri 1c strain Y394,Complete,Shigella,Bangladesh: Matlab,,,,,Shigellosis,"Human, Homo sapiens",,Bangladesh,,Human stool sample,,,,,1935181,,,,,,,5175,,,28899344,,4822,,1,Australian National University,203.0x,PacBio; Illumina MiSeq,,1c,,Y394,,,"Included in the study, passed QC/QA"
1000,198214.7,,,,,GCA_000006925.2,,,PRJNA310,SAMN02603599,,,,Rod,1,1984,"  Shigella flexneri 2a str. 301. This strain was isolated in 1984 from a patient in Beijing, China. It is similar to pathogenic Escherichia coli except for the more numerous insertion sequences and contains a virulence plasmid (pCP301).",2002-10-18T00:00:00Z,,,2014-12-08T22:12:54.946Z,2015-03-16T03:17:09.594Z,,Dysentery,50.7,"AE005674,AF386526",4828821,Shigella flexneri 2a str. 301,Complete,Shigella,China: Beijing,-,Host-associated,,,,"Human, Homo sapiens","isolated in 1984 from a patient in Beijing, China",China,,patient,,,,,198214,37,Shigella flexneri 2a str. 301,,,,Facultative,5527,,1,12384590,"NC_004337,NC_004851",4440,,2,Microbial Genome Center of ChMPH,,,complete,,,301,Mesophilic,,"Included in the study, passed QC/QA"
1001,198215.6,,,,,GCA_000007405.1,,,PRJNA408,,,,,Rod,1,," Shigella flexneri 2a str. 2457T. This is a highly virulent strain that has been widely used for genetic and clinical research. It is similar to pathogenic Escherichia coli except for the more numerous insertion sequences and contains 4 plasmids pINV-2457T, pSf2, and pSf4, and pSf-R27. Plasmid pINV-2457T is similar to plasmids pWR100, pWR501, and pCP301 whereas plasmid pSf-R27 is similar to R27. Plasmids pSf2 and pSf4 are small ColE1-like plasmids. pSf2 is similar to plasmid p2457TS2 found in RefSeq Accession Number NC_002773.",2003-04-22T00:00:00Z,,,2014-12-08T22:12:54.927Z,2015-03-16T03:17:09.594Z,,Dysentery,50.9,AE014073,4599354,Shigella flexneri 2a str. 2457T,Complete,Shigella,,-,Host-associated,,,,,,,,,,,,,198215,37,Shigella flexneri 2a str. 2457T,,,,Facultative,5131,,,,NC_004741,4061,,1,"University of Wisconsin-Madison, USA",,,complete,,,2457T,Mesophilic,,"Included in the study, passed QC/QA"
1002,2049486.3,,,,,GCA_002741635.1,HGAP v. 3,,PRJNA218110,SAMN07702430,,,,,1,,PulseNet STEC genome reference library,2017-11-02T00:00:00Z,,,2017-11-24T17:09:03.595Z,2017-11-24T17:09:03.595Z,,,50.75,"CP024473,CP024474,CP024475,CP024476",4906368,Shigella flexneri 7b strain 94-3007,Complete,Shigella,,,,,,,,,,,,,,,,2049486,,,,,,,5402,,3,,,,,4,CDC,385.0x,PacBio,,7b,,94-3007,,,"Included in the study, passed QC/QA"
1003,216599.12,,,,,GCF_000283715.1,,,PRJEA78129,SAMEA2272161,,,,,5,,-,2015-02-27T00:00:00Z,,,2016-01-17T15:29:05.282Z,2016-01-17T15:29:05.282Z,,,50.72,"HE616528,HE616529,HE616530,HE616531,HE616532",5220473,Shigella sonnei 53G,Complete,Shigella,,,,,,,,,,,,,,,,216599,,,,,,,5483,,,,"NC_016822.1,NC_016833.1,NC_016823.1,NC_016824.1,NC_016834.1",,,5,Wellcome Trust Sanger Insititute,,,,,,53G,,,"Included in the study, passed QC/QA"
1004,300267.13,,,,,GCA_000012005.1,,,PRJNA13145,SAMN02603600,,,,Rod,1,1950, Shigella dysenteriae 1 strain  Sd197 . This strain is an isolate from an epidemic in China in the 1950s.,2005-11-09T00:00:00Z,,,2014-12-08T22:12:54.584Z,2015-03-16T03:17:09.594Z,,Dysentery,51,"CP000034,CP000640,CP000035",4560911,Shigella dysenteriae Sd197,Complete,Shigella,China,-,Host-associated,,,,,isolate from an epidemic in China in the 1950s,China,,epidemic in China in the 1950s,,,,Yes,300267,37,Shigella dysenteriae Sd197,,,,Facultative,5785,,2,16275786,"NC_007606,NC_009344,NC_007607",4502,Non-halophilic,3,Microbial Genome Center of ChMPH,,,complete,,No,Sd197,Mesophilic,,"Included in the study, passed QC/QA"
1005,300268.11,,,,,GCA_000012025.1,,,PRJNA13146,SAMN02603601,,,,Rod,1,1950,Shigella boydii4 strain Sb227. This strain is an isolate from an epidemic that took place in China in the 1950s. ,2005-11-09T00:00:00Z,,,2014-12-08T22:12:54.519Z,2015-03-16T03:17:09.594Z,,Dysentery,51.1,"CP000036,CP000037",4646520,Shigella boydii Sb227,Complete,Shigella,China,-,Host-associated,,,,,isolate from an epidemic that took place in China in the 1950s,China,,epidemic in China in the 1950s,,,,Yes,300268,37,Shigella boydii Sb227,,,,Facultative,5327,,1,16275786,"NC_007613,NC_007608",4282,Non-halophilic,2,Microbial Genome Center of ChMPH,,,complete,,No,Sb227,Mesophilic,,"Included in the study, passed QC/QA"
1006,300269.12,,,,,GCA_000092525.1,,,PRJNA13151,SAMN02603602,,,,Rod,1,1950,Shigella sonnei 1 strain Ss046.This strain is an isolate from an epidemic in China in the 1950s.,2005-08-29T00:00:00Z,,,2014-12-08T22:12:55.336Z,2015-03-16T03:17:09.594Z,,Dysentery,50.8,"CP000038,CP000039,CP000641,CP000642,CP000643",5055316,Shigella sonnei Ss046,Complete,Shigella,China,-,Host-associated,,,,,isolate from an epidemic in China in the 1950s,China,,epidemic in China in the 1950s,,,,Yes,300269,37,Shigella sonnei Ss046,,,,Facultative,5693,,4,"16122562,16275786","NC_007384,NC_007385,NC_009345,NC_009346,NC_009347",4471,Non-halophilic,5,Microbial Genome Center of ChMPH,,,complete,,No,Ss046,Mesophilic,,"Included in the study, passed QC/QA"
1007,344609.11,,,,,GCA_000020185.1,,,PRJNA15637,SAMN02604039,,,,Rod,1,,"Shigella boydii4 strain BS512. This strain (strain BS512; serotype 18) was originally isolated from a 12-year-old boy in Arizona by Dr Nancy Stockbine. It is a member of Group 1 as determined by limited sequence analysis and can invade HeLa cells. Pathogenicity and virulence have been verified during in vitro experimentation, and multiple plasmids are present in this strain.gDNA for sequencing was isolated from a stock culture provided by Dr Anthony Maurelli from Uniformed Services University of Health Sciences. Two libraries were constructed - a small insert library (4-5 kb) and a large insert library (10-12 kb) from which 20,656 and 47,348 reads were sequenced, respectively.",2008-05-05T00:00:00Z,,,2014-12-08T22:12:54.508Z,2015-03-16T03:17:09.594Z,,Dysentery,51,"CP001063,CP001059,CP001060,CP001062,CP001061,CP001058",4874659,Shigella boydii CDC 3083-94,Complete,Shigella,USA: Arizona,-,Host-associated,12,,,"Human, Homo sapiens",isolated from a 12-year-old boy in Arizona by Dr Nancy Stockbine,United States,,12-year-old boy,,,,Yes,344609,37,Shigella boydii CDC 3083-94,,,,Facultative,5696,,5,,"NC_010658,NC_010657,NC_010659,NC_010660,NC_010672,NC_010656",4557,Non-halophilic,6,TIGR,,,complete,serovar 18,No,BS512,Mesophilic,,"Included in the study, passed QC/QA"
1008,373384.11,,,,,GCA_000013585.1,,,PRJNA16375,SAMN02603604,,,,Rod,1,, Shigella flexneri 5 str. 8401. This organism is a strain of serogroup 5 and will be used for comparative analysis. ,2006-07-21T00:00:00Z,,,2014-12-08T22:12:54.965Z,2015-03-16T03:17:09.594Z,,Dysentery,50.9,CP000266,4574284,Shigella flexneri 5 str. 8401,Complete,Shigella,,-,Host-associated,,,,,,,,,,,,,373384,37,Shigella flexneri 5 str. 8401,,,,Facultative,5028,,,16822325,NC_008258,4115,,1,Microbial Genome Center of ChMPH,,,complete,,,8401,Mesophilic,,"Included in the study, passed QC/QA"
1009,374923.3,sample_type:cell culture,,,,GCF_001578125.1,smrtanalysis v. 2.3.0.140936,,PRJNA288250,SAMN03797406,,,,,1,2002,genome sequencing,2016-03-01T00:00:00Z,,,2016-03-18T09:51:26.647Z,2016-03-18T09:51:26.647Z,,,50.73,"CP012735,CP012732,CP012733,CP012734,CP012736",4853344,Shigella flexneri 1a strain 0228,Complete,Shigella,China,,,,,,"Human, Homo sapiens",,China,,,,,,,374923,C,,,,,,5513,,4,,"NZ_CP012735.1,NZ_CP012736.1,NZ_CP012733.1,NZ_CP012734.1,NZ_CP012732.1",4776,,5,Hangzhou Centrer for Disease Control amd Prevention,164.55,PacBio RS,,,,228,,,"Included in the study, passed QC/QA"
1010,374923.6,sample_type:cell culture,,,,GCA_002240115.1,HGAP v. 2.0,,PRJNA356334,SAMN06111927,,,,,1,2004,antibiotic resistance study,2017-08-02T00:00:00Z,,,2017-09-28T19:43:02.508Z,2017-09-28T19:43:02.508Z,,,50.83,"CP020342,CP020343,CP020344",4904083,Shigella flexneri 1a,Complete,Shigella,China: Hangzhou,,,,,,"Human, Homo sapiens",,China,,,,,,,374923,,,,,,,5649,,2,,,5260,,3,Hangzhou Normal University,175.93,PacBio,,,,439,,,"Included in the study, passed QC/QA"
1011,374923.7,sample_type:cell culture,,,,GCA_002240135.1,HGAP v. 2.0,,PRJNA377966,SAMN06478366,,,,,1,2006,Antibiotic resistance study,2017-08-02T00:00:00Z,,,2017-09-28T19:43:11.753Z,2017-09-28T19:43:11.753Z,,,50.61,"CP020086,CP020087,CP020088",4899768,Shigella flexneri 1a,Complete,Shigella,China: Hangzhou,,,,,,"Human, Homo sapiens",,China,,hospitalized patients,,,,,374923,,,,,,,5645,,2,,,5283,,3,Hangzhou Normal University,237.11,PacBio,,1a,,670,,,"Included in the study, passed QC/QA"
1012,42897.19,sample_type:cell culture,,,,GCF_001580175.1,HS HGAP v. 2,,PRJNA288243,SAMN03796074,,,,,1,1998,Genomic Sequence,2016-03-03T00:00:00Z,,,2016-03-18T11:11:49.913Z,2016-03-18T11:11:49.913Z,,,50.78,"CP012137,CP012138,CP012139",4891752,Shigella flexneri 2a strain 981,Complete,Shigella,China,,,,,,"Human, Homo sapiens",,China,,,,,,,42897,C,,,,,,5533,,2,,"NZ_CP012137.1,NZ_CP012138.1,NZ_CP012139.1",4764,,3,Hangzhou Centrer for Disease Control amd Prevention,58x,PacBio,,,,981,,,"Included in the study, passed QC/QA"
1013,591020.3,,,,,GCA_000022245.1,,,PRJNA33639,SAMN02603122,,,,Rod,1,,Shigella flexneri 200217. This strain will be used for comparative analysis with other Shigella species.,2009-12-24T00:00:00Z,,,2014-12-08T22:12:54.720Z,2015-03-16T03:17:09.594Z,,Dysentery,50.6,"CP001383,CP001385,CP001386,CP001387,CP001388,CP001384",4894492,Shigella flexneri 2002017,Complete,Shigella,,-,Multiple,,,,,,,,,,,,Yes,591020,-,Shigella flexneri 2002017,,,,Facultative,5524,,5,19955273,"NC_017328.1,NC_017319.1,NC_017320.1,NC_017329.1,NC_017321.1,NC_017330.1",4706,,6,"Chinese Center for Disease Control and Prevention|TEDA School of Biological Sciences and Biotechnology, Nankai University",,,complete,,No,2002017,Mesophilic,,"Included in the study, passed QC/QA"
1014,621.85,,,,,GCF_001027225.1,HGAP v. SMRT Analysis v2.1,,PRJNA284097,SAMN03699691,,,,,1,,Comparative genomic study for different Shigella species,2015-06-03T00:00:00Z,,ATCC:9210,2016-01-17T16:07:07.051Z,2016-01-17T16:07:07.051Z,,,51.19,CP011511,4574246,Shigella boydii strain ATCC 9210,Complete,Shigella,,,,,,Dysentery,"Human, Homo sapiens",,,,Cases of diarrhea,,,,,621,C,,,,,,5060,,,,NZ_CP011511.1,4485,,1,KRIBB,77.0x,PacBio,,,,ATCC 9210,,,"Included in the study, passed QC/QA"
1015,622.81,,,,,GCA_002741615.1,HGAP v. 3,,PRJNA218110,SAMN07702429,,,,,1,1990,PulseNet STEC genome reference library,2017-11-02T00:00:00Z,,,2017-11-24T17:08:38.323Z,2017-11-24T17:08:38.323Z,,,50.95,"CP024466,CP024468,CP024467,CP024469",4764892,Shigella dysenteriae strain BU53M1,Complete,Shigella,Burundi,,,,,,,,,,,,,,,622,,,,,,,5840,,3,,,,,4,CDC,203.0x,PacBio,,1,,BU53M1,,,"Included in the study, passed QC/QA"
1016,623.158,,,,,GCF_000953035.1,,,PRJEB6778,SAMEA2434358,,,,,1,1915,This is the genome sequence of the first bacteria accessioned into the National Collection of Type Cultures (NCTC1). It is a Shigella flexneri serotype 2a that was isolated in 1915 from the reputed first case of dysentery on the Western Front in WWI.,2014-11-10T00:00:00Z,,NCTC 1,2016-01-17T15:48:57.660Z,2016-01-17T15:48:57.660Z,,,50.9,LM651928,4526576,Shigella flexneri strain NCTC1,Complete,Shigella,WWI,,,,,,,isolated in 1915 from the reputed first case of dysentery on the Western Front in WWI,,,the reputed first case of dysentery on the Western Front,,,,,623,,,,,,,4845,,,,NZ_LM651928.1,4564,,1,SC,,,,serovar 2a,,NCTC1,,,"Included in the study, passed QC/QA"
1017,623.345,,,,,GCA_002741395.1,HGAP v. 3,,PRJNA218110,SAMN07702431,,,,,1,,PulseNet STEC genome reference library,2017-11-02T00:00:00Z,,,2017-11-24T17:08:31.938Z,2017-11-24T17:08:31.938Z,,,50.81,"CP024470,CP024471,CP024472",5090907,Shigella flexneri strain 71-2783,Complete,Shigella,,,,,,,,,,,,,,,,623,,,,,,,5469,,2,,,,,3,CDC,379.0x,PacBio,,3a,,71-2783,,,"Included in the study, passed QC/QA"
1018,624.1184,collected_by:CDC,,,,,other v. 3,,PRJNA218110,SAMN06843643,,,,,1,,PulseNet STEC genome reference library,2017-05-16T00:00:00Z,,,2017-05-29T21:47:39.751Z,2017-05-29T21:47:39.751Z,,,51,CP021144,4935567,Shigella sonnei strain 2015AM-1099,Complete,Shigella,USA,,,,,,"Human, Homo sapiens",,,,,,,,,624,,,,,,,5514,,,,,5308,,1,CDC,78.0x,PacBio,,,,2015AM-1099,,,"Included in the study, passed QC/QA"
1019,624.1185,"collected_by:National Center for Epidemiology, Budapest, Hungary",,,,,CLC Genomics Workbench v. 9.5; Geneious,,PRJNA369464,SAMN06286561,,,,,1,2002,Shigella sonnei strain 75/02 Genome sequencing and assembly,2017-05-19T00:00:00Z,,,2017-05-30T01:52:18.768Z,2017-05-30T01:52:18.768Z,,,50.64,"CP019689,CP019690,CP019691,CP019692,CP019693,CP019694,CP019695,CP019696",5224048,Shigella sonnei strain 75/02,Complete,Shigella,Hungary: Halimba,,,,,shigellosis,"Human, Homo sapiens",,,,feces,,,,,624,,,,,,,5958,,7,,,6087,,8,Seqomics Ltd.,140.0x,Illumina MiSeq,,,,75/02,,,"Included in the study, passed QC/QA"
1020,624.1272,collected_by:CDC,,,,GCA_002224625.1,PacBio Hierarchical Genome Assembly,,PRJNA218110,SAMN06843644,,,,,1,,PulseNet STEC genome reference library,2017-07-24T00:00:00Z,,,2017-09-29T15:23:38.199Z,2017-09-29T15:23:38.199Z,,,51.02,"CP022457,CP022458",4949228,Shigella sonnei strain 2015C-3566,Complete,Shigella,USA,,,,,,"Human, Homo sapiens",,,,,,,,,624,,,,,,,5524,,1,,,5329,,2,CDC,78x,PacBio,,,,2015C-3566,,,"Included in the study, passed QC/QA"
1021,624.1273,collected_by:CDC,,,,GCA_002224605.1,PacBio Hierarchical Genome Assembly,,PRJNA218110,SAMN06843645,,,,,1,,PulseNet STEC genome reference library,2017-07-24T00:00:00Z,,,2017-09-29T15:23:46.800Z,2017-09-29T15:23:46.800Z,,,51,"CP022455,CP022456",4906574,Shigella sonnei strain 2015C-3794,Complete,Shigella,USA,,,,,,"Human, Homo sapiens",,,,,,,,,624,,,,,,,5458,,1,,,5276,,2,CDC,78x,PacBio,,,,2015C-3794,,,"Included in the study, passed QC/QA"
1022,624.1274,collected_by:CDC,,,,GCA_002224465.1,PacBio Hierarchical Genome Assembly,,PRJNA218110,SAMN06843646,,,,,1,,PulseNet STEC genome reference library,2017-07-24T00:00:00Z,,,2017-09-29T15:24:13.249Z,2017-09-29T15:24:13.249Z,,,50.93,"CP022459,CP022460,CP022461",4929151,Shigella sonnei strain 2015C-3807,Complete,Shigella,USA,,,,,,"Human, Homo sapiens",,,,,,,,,624,,,,,,,5691,,2,,,5345,,3,CDC,78x,PacBio,,,,2015C-3807,,,"Included in the study, passed QC/QA"
1023,624.1285,,,,,GCA_002442535.1,HGAP v. v.3.0,,PRJNA273284,SAMN03612247,,,,,1,,Whole genome sequencing of cultured Shigella as part of FDA/CFSAN's surveillance project for rapid source tracking of foodborne illness outbreaks.,2017-10-04T00:00:00Z,,,2017-11-23T02:55:14.659Z,2017-11-23T02:55:14.659Z,,,50.77,"CP023645,CP023646,CP023647,CP023648,CP023649,CP023650,CP023651,CP023652,CP023653",5062953,Shigella sonnei strain CFSAN030807,Complete,Shigella,Somalia,,,,,none,"Human, Homo sapiens",,,,,,,,,624,,,,,,,5712,,8,,,5482,,9,FDA Center for Food Safety and Applied Nutrition,700.0x,PacBio,,Serotype group D,,CFSAN030807,,,"Included in the study, passed QC/QA"
1024,624.635,"isolate:stool;collected_by:National Culture Collection for Pathogens, South Korea",,,,GCF_001518855.1,CLCbio CLC Genomics Workbench v. 7.5;,,PRJNA272666,SAMN03284775,,,,Bacilli,1,1999-03-20,Shigella sonnei is one of the well-known food-borne pathogen. It was isolated from the contaminated food in South Korea.,2016-01-20T00:00:00Z,,,2016-02-02T21:12:13.362Z,2016-02-02T21:12:13.362Z,,,50.76,"CP010829,CP010830,CP010831,CP010832",5132711,Shigella sonnei strain FORC_011,Complete,Shigella,South Korea,Negative,,,,Diarrhea,"Human, Homo sapiens",isolated from the contaminated food in South Korea,South Korea,,Stool,,,,No,624,,,,,,,5479,,3,,"NZ_CP010829.1,NZ_CP010830.1,NZ_CP010831.1,NZ_CP010832.1",5130,,4,"Food-borne Pathogen Omics Research Center, FORC",316.02x,Illumina; PacBio,,,,FORC_011,,,"Included in the study, passed QC/QA"
1025,624.637,collected_by:Children's National Hospital,,,,GCF_001558295.1,HGAP3 v. Oct 2014,,PRJNA231221,SAMN03996263,,,,,1,9/8/2013,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",2016-02-11T00:00:00Z,,FDA:FDAARGOS_90,2016-03-01T19:36:03.859Z,2016-03-01T19:36:03.859Z,,,51,"CP014099,CP014096,CP014097,CP014098,CP014100,CP014101",4988242,Shigella sonnei strain FDAARGOS_90,Complete,Shigella,USA:DC,,,5Y,female,Diarrhea,"Human, Homo sapiens",,United States,,Stool,,,,,624,,,,,,,5424,,5,,"NZ_CP014099.1,NZ_CP014096.1,NZ_CP014097.1,NZ_CP014098.1,NZ_CP014100.1,NZ_CP014101.1",5100,,6,US Food and Drug Administration,23.647x,Pacbio,,,,not applicable,,,"Included in the study, passed QC/QA"
1026,754093.4,,,,,GCF_000497505.1,"Newbler v 2.3, CLC package workbench",,PRJNA218020,,,,,,1,,Comparative genomics of Sd1617 to representative strains in evaluating its pathogenesis.,2015-03-09T00:00:00Z,,,2016-01-17T15:33:51.604Z,2016-01-17T15:33:51.604Z,,,50.98,"CP006736,CP006737",4480198,Shigella dysenteriae 1617,Complete,Shigella,Guatemala,,,,,,"Human, Homo sapiens",,Guatemala,,,,,,,754093,,,,,,,6316,,1,25743074,,6409,,2,Igenbio Inc,20x,"454 GS FLX, Illumina paired end",,,,1617,,,"Included in the study, passed QC/QA"
1027,1033813.3,,,,,GCA_000214765.2,,,PRJNA66975,SAMN02603711,,,,,1,,"Bacterial culture archived with Pathogen Biology Laboratory, Department of Biotechnology, University of Hyderabad, India",2011-05-25T00:00:00Z,,,2014-12-08T22:11:31.206Z,2015-03-16T03:17:09.594Z,,,51.16,CP002797,4935241,Escherichia coli NA114,Complete,Escherichia,,,,,,,,,,,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",,1033813,-,Escherichia coli NA114,,,,,4889,,,,-,4873,,1,"Pathogen Biology Laboratory, Department of Biotechnology, University of Hyderabad",,,complete,,,NA114,,,"Included in the study, passed QC/QA"
1028,1038927.31,collected_by:USAMRIID < CDC-Atlanta,,,,,"SMRT v. 2.3.0, HGAP v. 3.0",,PRJNA231221,SAMN06173361,,,,,1,2009,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-06-27T00:00:00Z,,FDA:FDAARGOS_348,2017-07-23T01:19:19.428Z,2017-07-23T01:19:19.428Z,,,50.58,"CP022086,CP022085,CP022087",5442181,Escherichia coli O104:H4 strain FDAARGOS_348,Complete,Escherichia,USA: Georgia,,,,,Bloody diarrhea complicated hemolytic uremic syndrome (HUS),Homo sapiens,,USA,,Stool,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",,1038927,,,,,,,5899,,2,,,5662,,3,US Food and Drug Administration,18.1565653439553x,PacBio,,O104:H4,,Not applicable,,,"Included in the study, passed QC/QA"
1029,1045010.15,collected_by:Lauren Cowley,,,,GCF_001650275.1,Celera v. 8.1,,PRJNA321984,SAMN05007044,,,,,1,24-Oct-12,A public health investigation into an outbreak of Escherichia coli O157 that involved sequencing of outbreak isolates.,2016-05-24T00:00:00Z,,,2016-07-05T09:47:13.636Z,2016-07-05T09:47:13.636Z,,,50.43,"CP015832,CP015833",5750190,Escherichia coli O157 strain 180-PT54,Complete,Escherichia,United Kingdom,,,,,Diarrhea,"Human, Homo sapiens",,United Kingdom,,fecal sample,,,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,1045010,,,,,,,5958,,1,,"NZ_CP015832.1,NZ_CP015833.1",,,2,Public Health England,30x,Pacific Biosciences,,,,180-PT54,,,"Included in the study, passed QC/QA"
1030,1045010.16,collected_by:Lauren Cowley,,,,GCF_001650295.1,Canu v. 1.1; Celera Assembler v. 8.1,,PRJNA321984,SAMN05007045,,,,,1,30-Aug-12,A public health investigation into an outbreak of Escherichia coli O157 that involved sequencing of outbreak isolates.,2016-05-24T00:00:00Z,,,2016-07-05T09:48:18.250Z,2016-07-05T09:48:18.250Z,,,50.52,CP015831,5831209,Escherichia coli O157 strain 644-PT8,Complete,Escherichia,United Kingdom,,,,,Diarrhea,"Human, Homo sapiens",,United Kingdom,,fecal sample,,,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",,1045010,,,,,,,6090,,,,NZ_CP015831.1,,,1,Public Health England,30x,MinION; Pacific Biosciences,,,,644-PT8,,,"Included in the study, passed QC/QA"
1031,1045010.21,collected_by:George Washington University,,,,,"SMRT v. 2.3.0, HGAP v. 3.0",,PRJNA231221,SAMN06173306,,,,,1,26-Feb-2014,"In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA’s Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: •Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. •Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and Pac Biosequencing platforms at the Institute for Genome Sciences disclaimer icon at the University of Maryland (UMD-IGS). •Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.",2017-06-27T00:00:00Z,,FDA:FDAARGOS_293,2017-07-23T01:14:06.936Z,2017-07-23T01:14:06.936Z,,,50.48,"CP022050,CP022051,CP022052",5686502,Escherichia coli O157 strain FDAARGOS_293,Complete,Escherichia,USA:DC,,,,,,Homo sapiens,,USA,,,,,,,1045010,,,,,,,6234,,2,,,5979,,3,US Food and Drug Administration,17.6648961609863x,PacBio,,,,Not applicable,,,"Included in the study, passed QC/QA"
1032,1048254.4,isolate:368 shch,,,,GCF_000986765.1,HGAP v. 2.0,,PRJNA281410,SAMN03856947,,,,,1,18-May-2011,"To obtain high quality reference assemblies of multiple bacterial genomes and conduct genome-wide analysis of DNA methylation, we sequenced three cultured isolates using a Pacific Biosciences RSII instrument. These long read sequenced isolates include Escherichia coli O104:H4 str. C227-11, Helicobacter pylori J99, and Chromohalobacter salexigens DSM-3043.'",2015-07-13T00:00:00Z,,DSM -3043,2016-01-17T15:56:39.571Z,2016-01-17T15:56:39.571Z,,,50.63,"CP011331,CP011332,CP011333,CP011334,CP011335,CP011336,CP011337,CP011338",5446006,Escherichia coli O104:H4 str. C227-11,Complete,Escherichia,Denmark,,,,,,"Human, Homo sapiens",,Denmark,,stool sample from a 64-year-old woman from Hamburg who presented with bloody diarrhea and did not develop hemolytic uremic syndrome (HUS),,,,,1048254,,,,,,,5664,,7,,"NZ_CP011331.1,NZ_CP011336.1,NZ_CP011337.1,NZ_CP011335.1,NZ_CP011338.1,NZ_CP011334.1,NZ_CP011332.1,NZ_CP011333.1",5275,,8,Icahn School of Medicine at Mount Sinai,100.0x,PacBio,,,,C227-11,,,"Included in the study, passed QC/QA"
1033,1048689.4,,,,,GCA_000245515.1,,,PRJNA68245,SAMN02604278,,,,,1,,"Enteropathogenic Escherichia coli (EPEC) is a leading cause of infant mortality and morbidity in developing countries. In spite of this, only two EPEC genomes have been fully sequenced: the typical, model EPEC strain E2348/69 (O127:H6), and the contemporary, atypical EPEC strain CB9615 (O55:H7, Germany, 2003). This latter serotype has been established as a recent precursor to the virulent, enterohemorrhagic E. coli serotype O157:H7. We chose to sequence strain RM12579 (California, 1974) due to its proximity in time and space to the first O157:H7 isolated in the US, a California isolate from 1975.",2012-02-01T00:00:00Z,, ,2014-12-08T22:11:32.960Z,2015-03-16T03:17:09.594Z,,,50.4328,"CP003109.1,CP003113.1,CP003110.1,CP003111.1,CP003114.1,CP003112.1",5448306,Escherichia coli O55:H7 str. RM12579,Complete,Escherichia,USA,,,,,,,"isolated in the US, a California isolate from 1975",United States,,1975,,,"MLST.Escherichia_coli_1.335,MLST.Escherichia_coli_2.553",,1048689,,Escherichia coli O55:H7 str. RM12579,,,,,5455,,5,,"NC_017656.1,NC_017658.1,NC_017653.1,NC_017657.1,NC_017655.1,NC_017654.1",5128,,6,USDA/ARS,,,complete,serovar has,,RM12579,,,"Included in the study, passed QC/QA"
1034,1050617.5,,,,,GCA_000220005.2,,,PRJNA48455,SAMN02471895,,,,,1,2006,-,2011-11-01T00:00:00Z,,,2014-12-08T22:11:36.205Z,2015-03-16T03:17:09.594Z,,,50.62,AGTD00000000,5635305,Escherichia coli UMNF18,Complete,Escherichia,USA:Iowa,,,,,,,,United States,,lesion swab of diarrheal isolate,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.2",,1050617,-,Escherichia coli UMNF18,,,,,5818,,5,22081385,-,5628,,6,,,,complete,O147,,UMNF18,,,"Included in the study, passed QC/QA"
1035,1072459.4,,,,,GCA_000227625.1,,,PRJNA63597,SAMN02603406,,,,,1,,Project description not provided.,2011-10-06T00:00:00Z,,,2014-12-08T22:11:33.043Z,2015-03-16T03:17:09.594Z,,,50.54,"CP003034,CP003035,CP003036,CP003037,CP003038",5378729,Escherichia coli O7:K1 str. CE10,Complete,Escherichia,,,,,,,,,,,,,,"MLST.Escherichia_coli_1.62,MLST.Escherichia_coli_2.254",,1072459,-,Escherichia coli O157:H7 str. EC10,,,,,5323,,4,,"NC_017646.1,NC_017647.1,NC_017648.1,NC_017649.1,NC_017650.1",5080,,5,"Insitute of Pathogen Biology, CAMS&PUMC|State Key Laboratory for Molecular Virology and Genetic Engineering",,,unfinished,,,CE10,,,"Included in the study, passed QC/QA"
1036,1110693.3,,,,,GCA_000350185.1,Bioscope v. 1.3,,PRJDB193705,,,,,,1,,"Escherichia coli str. K-12 substr. MDS42, complete genome",2011-12-03T00:00:00Z,, ,2014-12-08T22:11:36.804Z,2015-03-16T03:17:09.594Z,,,51.1,AP012306.1,3976195,Escherichia coli str. K-12 substr. MDS42,Complete,Escherichia,,,,,,,,,,,,,,MLST.Escherichia_coli_1.10,,1110693,,Escherichia coli str. K-12 substr. MDS42,,,,,3752,,,,NC_020518.1,3547,,1,Osaka University,300x,SOLiD 3,complete,K12,,MDS42,,,"Included in the study, passed QC/QA"
1037,1133852.3,,,,,GCA_000299455.1,,,PRJNA81095,SAMN01831188,,,,Bacilli,1,,Isolated from US citizen afflicted with HUS after travel to Germany during the 2011 E coli oubreak.,2012-09-27T00:00:00Z,, ,2014-12-08T22:11:31.700Z,2015-03-16T03:17:09.594Z,,Hemolytic uremic syndrome (HUS),50.6346,"CP003289.1,CP003291.1,CP003290.1,CP003292.1",5435858,Escherichia coli O104:H4 str. 2011C-3493,Complete,Escherichia,,Negative,,,,,,Isolated from US citizen afflicted with HUS after travel to Germany during the 2011 E coli oubreak,,,,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",Yes,1133852,,Escherichia coli O104:H4 str. 2011C-3493,,,,,5479,,2,,"NC_018658.1,NC_018666.1,NC_018659.1,NC_018660.1",5150,,4,Los Alamos National Laboratory,,,complete,,No,2011C-3493,,,"Included in the study, passed QC/QA"
1038,1133853.3,,,,,GCA_000299475.1,,,PRJNA81099,SAMN01831190,,,,Bacilli,1,,Isolated from a human patient from a 2009 outbreak of E coli in the Republic of Georgia,2012-09-27T00:00:00Z,, ,2014-12-08T22:11:31.691Z,2015-03-16T03:17:09.594Z,,,50.651,"CP003301.1,CP003303.1,CP003302.1",5388159,Escherichia coli O104:H4 str. 2009EL-2071,Complete,Escherichia,,Negative,,,,,,,,,,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",Yes,1133853,,Escherichia coli O104:H4 str. 2009EL-2071,,,,,5436,,1,,"NC_018661.1,NC_018663.1,NC_018662.1",5126,,3,Los Alamos National Laboratory,,,complete,,No,2009EL-2071,,,"Included in the study, passed QC/QA"
1039,1134782.3,,,,,GCA_000299255.1,,,PRJNA81097,SAMN01831189,,,,Bacilli,1,,Isolated from a human patient from a 2009 outbreak of E coli in the Republic of Georgia,2012-09-25T00:00:00Z,, ,2014-12-08T22:11:31.682Z,2015-03-16T03:17:09.594Z,,,50.5424,"CP003297.1,CP003300.1,CP003299.1,CP003298.1",5436625,Escherichia coli O104:H4 str. 2009EL-2050,Complete,Escherichia,,Negative,,,,,,,,,,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",Yes,1134782,,Escherichia coli O104:H4 str. 2009EL-2050,,,,,5479,,2,,"NC_018650.1,NC_018651.1,NC_018654.1,NC_018652.1",5183,,4,Los Alamos National Laboratory,,,complete,,No,2009EL-2050,,,"Included in the study, passed QC/QA"
1040,1245474.3,,,,,GCA_000800215.1,HGAP v. 2,,PRJNA263007,SAMN03093203,,,,,1,,"Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Laboratory K-12 derivative of Escherichia coli",2014-12-09T00:00:00Z,1,,2015-03-12T13:40:51.030Z,2015-03-16T03:17:09.594Z,,,50.8,CP009644.1,4558663,Escherichia coli ER2796,Complete,Escherichia,,,,,,,,,,,,,,,,1245474,,,,,,,4364,,,-,NZ_CP009644.1,4083,,1,New England Biolabs,300x,PacBio RSII,,,,ER2796,,,"Included in the study, passed QC/QA"
1041,1248823.7,,,,,GCA_000671295.1,Newbler v. v2.3; Geneious v. v5.1; Velvet,,PRJNA178647,SAMN03081527,,,,Bacilli,1,,"Recently there has been an increase in outbreaks associated with non-O157 Shiga-toxin producing Escherichia coli (STEC), most commonly associated with the serotypes O26, O45, O103, O111, O121, and O145. Escherichia coli O145:H28 strain RM12581 was originally isolated from bagged romaine lettuce. It was linked to the 2010 multi-state outbreak of E. coli O145 infection associated with consumption of shredded romaine lettuce in US.",2014-05-01T00:00:00Z,3,,2014-12-09T00:45:12.748Z,2015-03-16T03:17:09.594Z,,Enteric,50.6743,"CP007136.1,CP007137.1,CP007138.1",5737290,Escherichia coli O145:H28 str. RM12581,Complete,Escherichia,USA,Negative,Multiple,,,,,isolated from bagged romaine lettuce,United States,,bagged romaine lettuce,,,,,1248823,37C,,,,,Facultative,5913,,1,24855308,"NZ_CP007136.1,NZ_CP007138.1,NZ_CP007137.1",5769,Mesophilic,3,USDA-ARS-WRRC-PSM,,Sanger dideoxy sequencing; 454; Illumina;,,serovar s,No,RM12581,Mesophilic,,"Included in the study, passed QC/QA"
1042,1248902.3,,,,,GCA_000520035.1,Newbler v. v2.3; Velvet v. v1.0.13;,,PRJNA178648,SAMN02641383,,,,Bacilli,1,,"'Recently there has been an increase in outbreaks associated with non-O157 Shiga-toxin producing Escherichia coli (STEC), most commonly associated with the serotypes O26, O45, O103, O111, O121, and O145. Escherichia coli O145:H28 str. RM13514 was a clinical isolate and linked to the 2010 multi-state outbreak of E. coli O145 infection associated with consumption of shredded romaine lettuce in US.'",2014-01-14T00:00:00Z,, ,2014-12-08T22:11:32.227Z,2015-03-16T03:17:09.594Z,,Enteric,50.6743,"CP006027.1,CP006029.1,CP006028.1",5737294,Escherichia coli O145:H28 str. RM13514,Complete,Escherichia,USA,Negative,Multiple,,,,"Human, Homo sapiens",,United States,,feces; clinical sample,,,MLST.Escherichia_coli_1.32,,1248902,37C,Escherichia coli O145:H28 str. RM13514,,,,Facultative,5979,,2,24410921,"NZ_CP006027.1,NZ_CP006028.1,NZ_CP006029.1",5776,Mesophilic,3,"'USDA, ARS, WRRC, PSM'",,454; Illumina; PacBio,complete,serovar s,Nonsporulating,RM13514,Mesophilic,,"Included in the study, passed QC/QA"
1043,1248903.6,,,,,GCA_000662395.1,Newbler v. v2.3; Geneious v. v5.1; Velvet,,PRJNA178649,SAMN03081526,,,,Bacilli,1,,"Recently there has been an increase in outbreaks associated with non-O157 Shiga-toxin producing Escherichia coli (STECs), most commonly associated with the serotypes O26, O45, O103, O111, O121, and O145. Escherichia coli O145:H28 str. RM12761 was originally isolated from ice cream in Belgium during a 2007 outbreak of STEC infection associated with consumption of ice cream produced in a farm.",2014-05-01T00:00:00Z,3,,2014-12-09T00:45:13.287Z,2015-03-16T03:17:09.594Z,,Enteric,50.5948,"CP007133.1,CP007135.1,CP007134.1",5559010,Escherichia coli O145:H28 str. RM12761,Complete,Escherichia,Belgium,Negative,Multiple,,,,,isolated from ice cream in Belgium during a 2007 outbreak of STEC infection associated with consumption of ice cream produced in a farm,Belgium,,ice cream,,,,,1248903,37C,,,,,Facultative,5610,,1,"21166561,24855308","NZ_CP007133.1,NZ_CP007135.1,NZ_CP007134.1",5493,Mesophilic,3,"USDA, ARS, WRRC, PSM",,Sanger dideoxy sequencing; 454; Illumina;,,serovar s,No,RM12761,Mesophilic,,"Included in the study, passed QC/QA"
1044,1248915.3,,,,,GCA_000520055.1,Newbler v. v2.3; Velvet v. v1.0.13;,,PRJNA178650,SAMN02641384,,,,Bacilli,1,2007,"'Recently there has been an increase in outbreaks associated with non-O157 Shiga-toxin producing Escherichia coli (STECs), most commonly associated with the serotypes O26, O45, O103, O111, O121, and O145. Escherichia coli O145:H28 str. RM13516 was isolated from a patient in Belgium during a 2007 outbreak of STEC infection associated with consumption of ice cream produced in a farm.'",2014-01-14T00:00:00Z,, ,2014-12-08T22:11:32.238Z,2015-03-16T03:17:09.594Z,,Enteric,50.5948,"CP006262.1,CP006264.1,CP006263.1",5559008,Escherichia coli O145:H28 str. RM13516,Complete,Escherichia,Belgium,Negative,Multiple,,,,"Human, Homo sapiens",isolated from a patient in Belgium during a 2007 outbreak of STEC infection associated with consumption of ice cream produced in a farm,Belgium,,feces,,,,,1248915,37C,Escherichia coli O145:H28 str. RM13516,,,,Facultative,5667,,2,24410921,"NZ_CP006262.1,NZ_CP006263.1,NZ_CP006264.1",5513,Mesophilic,3,"'USDA, ARS, WRRC, PSM'",,454; Illumina; PacBio,complete,serovar s,Nonsporulating,RM13516,Mesophilic,,"Included in the study, passed QC/QA"
1045,1274814.3,,,,,GCA_000332755.1,,,PRJNA184588,SAMN02603426,,,,,1,,"Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting turkeys, layers, and broilers. Here we describe the sequence of APEC O78, an O78 strain isolated from the lung of a turkey clinically diagnosed with colibacillosis. Functional analysis of the genome should enhance the community¿¿¿¿¿¿¿s knowledge of the pathogenesis of avian pathogenic E. coli.",2013-01-23T00:00:00Z,, ,2014-12-08T22:11:21.765Z,2015-03-16T03:17:09.594Z,,Colibacillosis,50.7,CP004009.1,4798435,Escherichia coli APEC O78,Complete,Escherichia,,,,,,,"Turkey, Meleagris gallopavo",isolated from the lung of a turkey clinically diagnosed with colibacillosis,,,the lung of a turkey clinically diagnosed with colibacillosis,,,MLST.Escherichia_coli_1.23,,1274814,,Escherichia coli APEC O78,,,,,4716,,,,NC_020163.1,4589,,1,Iowa State University,,,complete,,,APEC O78,,,"Included in the study, passed QC/QA"
1046,1311757.3,,,,,GCF_001051135.1,Newbler v. 2.3,,PRJNA194515,SAMN03852615,,,,,1,,"Avian pathogenic E. coli strains represent potential zoonotic risk and should be worthy of attention. The whole genome sequencing of this avian pathogenic E. coli strain ACN001, including the sequencing of plasmids it contained could provide more information for better understanding the genome diversity and the virulence variation, and contribute to the control and prevention of the plasmid-mediated multidrug resistance.",2015-07-09T00:00:00Z,,,2016-01-17T16:12:46.261Z,2016-01-17T16:12:46.261Z,,,50.67,CP007442,4936576,Escherichia coli ACN001,Complete,Escherichia,,,,,,,,,,,,,,,,1311757,,,,,,,4909,,,,NZ_CP007442.1,4794,,1,Huazhong Agricultural University,23.58x,454,,,,ACN001,,,"Included in the study, passed QC/QA"
1047,1322345.19,biomaterial_provider:USAMRIID,,,,GCF_000743255.1,Newbler v. 2.6; Velvet v. 1.2.08; Allpaths,,PRJNA244551,SAMN02929659,,,,,1,,Genome sequencing of Escherichia coli 25922,2014-10-22T00:00:00Z,,ATCC:25922,2016-01-17T15:38:58.202Z,2016-01-17T15:38:58.202Z,,,50.42,"CP009072,CP009073,CP009074",5203440,Escherichia coli ATCC 25922,Complete,Escherichia,"USA: Seattle, Washington",,,,,,,,United States,,Human,,,,,1322345,,,,,,,5149,,2,25291776,"NZ_CP009072.1,NZ_CP009073.1,NZ_CP009074.1",4808,,3,Los Alamos National Laboratory,332x,Illumina; 454,,,,ATCC 25922,,,"Included in the study, passed QC/QA"
1048,1328859.4,,,,,GCA_000730345.1,DNASTAR SeqMan NGen v. 3.1; Lasergene,,PRJNA200626,SAMN02872945,,,,,1,,This Escherichia coli O157:H7 isolate was obtained from the recto-anal junction of a cow which produced the isolate at &gt; 3x10^6 CFU/g of feces classifying both the cow and the isolate as a super-shedder.,2014-07-17T00:00:00Z,3,,2014-12-08T22:38:21.069Z,2015-03-16T03:17:09.594Z,,,50.385,"CP008805.1,CP008806.1,CP008807.1",5655940,Escherichia coli O157:H7 str. SS17,Complete,Escherichia,,,,,,,,,,,,,,,,1328859,,,,,,,5768,,1,-,"NZ_CP008805.1,NZ_CP008806.1,NZ_CP008807.1",5592,,3,Penn State,100x,Ion Torrent PGM,,,,SS17,,,"Included in the study, passed QC/QA"
1049,1329907.3,,,,,GCA_000813165.1,Newbler v. 2.7,,PRJNA200980,SAMN03274236,,,,,1,,Complete genome sequence of avian pathogenic Escherichia coli strain IMT5155 (O2:K1:H5) isolated from the internal organs of a laying hen with clinical symptoms of septicemia.,2015-01-02T00:00:00Z,3,,2015-03-12T13:41:54.619Z,2015-03-16T03:17:09.594Z,,,50.61,"CP005930.1,CP005931.1,CP005932.1",5126057,Escherichia coli APEC IMT5155,Complete,Escherichia,,,,,,,"Chicken, Gallus gallus",isolated from the internal organs of a laying hen with clinical symptoms of septicemia,,,the internal organs of a laying hen with clinical symptoms of septicemia,,,,,1329907,,,,,,,5073,,2,25397580,"NZ_CP005930.1,NZ_CP005931.1,NZ_CP005932.1",5020,,3,Nanjing Agricultural University,23X,Sanger dideoxy sequencing; 454,,,,APEC IMT5155,,,"Included in the study, passed QC/QA"
1050,1330457.6,,,,,GCA_000803705.1,DNASTAR SeqMan NGen v. 11.0.0;,,PRJNA201344,SAMN03265100,,,,Bacilli,1,,This Escherichia coli O157:H7 isolate was obtained from the recto-anal junction of a cow which produced the isolate at &gt; 6.8X10^5 CFU/g of feces classifying both the cow and the isolate as a super-shedder.,2014-12-18T00:00:00Z,2,,2015-03-12T13:41:55.246Z,2015-03-16T03:17:09.594Z,,,50.47,"CP010304.1,CP010305.1",5583430,Escherichia coli O157:H7 str. SS52,Complete,Escherichia,,Negative,,,,,,,,,,,,,Yes,1330457,,,,,,,5675,,1,-,"NZ_CP010304.1,NZ_CP010305.1",5745,,2,Penn State,168.4x,Ion Torrent PGM sequencer,,,No,SS52,,,"Included in the study, passed QC/QA"
1051,1335916.3,,,,,GCA_000468515.1,Geneious v. Pro 5.5.6,,PRJNA203308,SAMN02604176,,,,,1,,LY180 is an E coli strain engineered to ferment sugars (glucose and xylose) into ethanol. LY180 is derived from the widely used KO11 strain.,2013-09-18T00:00:00Z,, ,2014-12-08T22:11:30.360Z,2015-03-16T03:17:09.594Z,,,50.9,CP006584.1,4835601,Escherichia coli LY180,Complete,Escherichia,,,,,,,,derived from the widely used KO11 strain,,,the widely used KO11 strain,,,"MLST.Escherichia_coli_1.1079,MLST.Escherichia_coli_2.360",,1335916,,Escherichia coli LY180,,,,,4660,,,,NC_022364.1,4463,,1,University of Florida,80X,Illumina GAIIx,complete,,,LY180,,,"Included in the study, passed QC/QA"
1052,1355100.3,,,,,GCA_000493755.1,MIRA v. 3.9.9; ABySS v. 1.3.4; PBJelly v.,,PRJNA218163,SAMN02603887,,,,Bacilli,1,2007,Complete Genome of the Epidemic and Highly Virulent CTX-M-15-Producing H30-Rx Subclone of Escherichia coli ST131.,2013-10-29T00:00:00Z,, ,2014-12-08T22:11:27.555Z,2015-03-16T03:17:09.594Z,,Urosepsis,50.7667,"CP006784.1,CP006789.1,CP006785.1,CP006788.1,CP006786.1,CP006787.1",5306732,Escherichia coli JJ1886,Complete,Escherichia,USA,Negative,Multiple,,,fatal urosepsis,"Human, Homo sapiens",,United States,,Patient,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",Motile,1355100,37C,Escherichia coli JJ1886,,,,Facultative,5323,,4,24309736,"NC_022648.1,NC_022651.1,NC_022661.1,NC_022650.1,NC_022649.1,NC_022662.1",5049,Unknown,6,Statens Serum Institut,50x,454; Illumina; PacBio,complete,,Nonsporulating,JJ1886,Mesophilic,,"Included in the study, passed QC/QA"
1053,1355101.3,collected_by:not applicable,,,,GCF_001593565.1,HGAP v. 3,,PRJNA311313,SAMN04481707,,,,,1,2007,"We report the complete genome sequence, including five plasmid sequences, of Escherichia coli ST131 isolate JJ1887. The isolate was obtained in 2007 in the United States from a patient with recurrent urinary tract infections, whose caregiver died from urosepsis from a nearly identical strain.",2016-03-17T00:00:00Z,,,2016-04-27T17:05:48.674Z,2016-04-27T17:05:48.674Z,,,50.8,"CP014316,CP014317,CP014318,CP014319,CP014321,CP014320",5331521,Escherichia coli JJ1887,Complete,Escherichia,USA,,,,,D014552,"Human, Homo sapiens",is from a nearly identical strain,United States,,not collected,,,,,1355101,C,,,,,,5540,,5,,"NZ_CP014316.1,NZ_CP014317.1,NZ_CP014318.1,NZ_CP014319.1,NZ_CP014321.1,NZ_CP014320.1",5273,,6,Translational Genomics Research Institute,118X,PacBio,,,,JJ1887,,,"Included in the study, passed QC/QA"
1054,1358422.3,,,,,GCF_001029125.1,Newbler v. 2.3,,PRJNA211971,SAMN03765122,,,,,1,,Pathogenic mechanism.,2015-10-01T00:00:00Z,,,2016-01-17T16:07:29.360Z,2016-01-17T16:07:29.360Z,,,50.8,"CP006636,CP006637,CP006638,CP006639,CP006640,CP006641,CP006642",4901825,Escherichia coli PCN061,Complete,Escherichia,,,,,,,,,,,,,,,,1358422,,,,,,,5032,,6,26391348,"NZ_CP006636.1,NZ_CP006637.1,NZ_CP006638.1,NZ_CP006639.1,NZ_CP006640.1,NZ_CP006641.1,NZ_CP006642.1",4843,,7,Huazhong Agricultural University,33X,454,,,,PCN061,,,"Included in the study, passed QC/QA"
1055,1382700.12,,,,,GCF_000493595.2,,,PRJEB4437,,,,,,1,,"Escherichia coli is a highly versatile species, causing diverse intestinal and extra-intestinal infections. Here, we present the complete genome and plasmids sequences of an ExPEC strain that is used as a model for peritonitis in mice and was useful to decipher the innate immune response triggered by ExPEC infections. Plasmids pHUSEC411like and pECOS88like are also included in this genome project.",2013-09-18T00:00:00Z,,,2016-01-17T15:33:42.911Z,2016-01-17T15:33:42.911Z,,,50.74,"HG428755,CBTO010000000,HG428756",5210927,Escherichia coli PMV-1,Complete,Escherichia,,,,,,,,,,,,,,,,1382700,,,,,,,5194,,3,,,4843,,4,ULB,,,,,,PMV-1,,,"Included in the study, passed QC/QA"
1056,1385755.3,,,,,GCA_000474035.1,,,PRJNA215084,,,,,,1,,First Genomically Recoded Organism,2013-10-18T00:00:00Z,, ,2014-12-08T22:11:22.906Z,2015-03-16T03:17:09.594Z,,,50.8,CP006698.1,4643553,Escherichia coli C321.deltaA,Complete,Escherichia,,,,,,,,,,,,,,MLST.Escherichia_coli_1.10,,1385755,,Escherichia coli C321.deltaA,,,,,4545,,,24136966,-,4331,,1,"Church Lab, Department of Genetics, Harvard Medical School",,,complete,,,c321D,,,"Included in the study, passed QC/QA"
1057,1385755.5,,,,,GCA_000826905.1,,,PRJNA272518,SAMN03283144,,,,,1,,"Construction of a series of genomically recoded organisms whose growth is restricted by the expression of essential genes dependent on exogenously supplied synthetic amino acids introduces novel ortho- gonal barriers between these engineered organisms and the environment, thereby creating safer gen- etically modified organisms.",2015-01-21T00:00:00Z,1,,2015-03-12T13:42:55.628Z,2015-03-16T03:17:09.594Z,,,50.76,CP010455.1,4650162,synthetic Escherichia coli C321.deltaA,Complete,Escherichia,,,,,,,,,,,,,,,,1385755,,,,,,,4491,,,25607356,-,,,1,Yale University,,,,,,C321.deltaA,,,"Included in the study, passed QC/QA"
1058,1385755.6,,,,,GCA_000826925.1,,,PRJNA272520,SAMN03283190,,,,,1,,"Construction of a series of genomically recoded organisms whose growth is restricted by the expression of essential genes dependent on exogenously supplied synthetic amino acids introduces novel ortho- gonal barriers between these engineered organisms and the environment, thereby creating safer gen- etically modified organisms.",2015-01-21T00:00:00Z,1,,2015-03-12T13:42:56.051Z,2015-03-16T03:17:09.594Z,,,50.76,CP010456.1,4650152,synthetic Escherichia coli C321.deltaA,Complete,Escherichia,,,,,,,,,,,,,,,,1385755,,,,,,,4489,,,25607356,-,,,1,Yale University,,,,,,C321.deltaA,,,"Included in the study, passed QC/QA"
1059,1401688.5,,,,,,Newbler v. 2.7; Velvet v. 1.1; ELANDv2e v.,,PRJNA219414,SAMN03761813,,,,,1,,"Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting turkeys, layers, and broilers. Here we describe the sequence of first APEC O18 serotype fully complete and closed. This O18 strain was isolated from the pericardium/lung of a chicken. Functional analysis of the genome will enhance the community’s knowledge of the pathogenesis of avian pathogenic E. coli.",2016-06-12T00:00:00Z,,,2017-07-21T16:22:34.551Z,2017-07-21T16:22:34.551Z,,,50.7,CP006830,5006568,Escherichia coli APEC O18 strain APEC O18,Complete,Escherichia,USA,,,,,,chicken,isolated from the pericardium/lung of a chicken,,,pericardium/lung,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",,1401688,,,,,,,4961,,,,,4581,,1,Iowa State University,,454; Illumina,,serovar fully,,APEC O18,,,"Included in the study, passed QC/QA"
1060,1403831.3,,,,,GCA_000499485.1,,,PRJEB4621,SAMEA3138816,,,,,1,,"A related and publicly available reference genome (E. coli K12 strain BW2952, accession: NC_012759) was tailored to represent the sequence of E. coli K12 strain MC4100 as obtained from the Coli Genetic Stock Center. This was done by variant calling, variant incorporation and manual curation of changes to the reference annotation.",2013-11-05T00:00:00Z,, ,2014-12-08T22:11:36.793Z,2015-03-16T03:17:09.594Z,,,50.8,HG738867.1,4527247,Escherichia coli str. K-12 substr. MC4100,Complete,Escherichia,,,,,,,,,,,,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.2",,1403831,,Escherichia coli str. K-12 substr. MC4100,,,,,4378,,,,NZ_HG738867.1,4026,,1,EVOECOGENKIEL,,,complete,,,K-12,,,"Included in the study, passed QC/QA"
1061,1411691.4,isolate:Lac+,,,,GCF_001020945.1,ALLPATHS-LG v. 42411,,PRJNA224130,SAMN02404591,,,,,1,,Escherichia coli K-12 GM4792 Lac+,2015-06-05T00:00:00Z,,,2016-01-17T16:05:26.859Z,2016-01-17T16:05:26.859Z,,,50.81,CP011342,4622332,Escherichia coli K-12 GM4792,Complete,Escherichia,,,,,,,,,,,,,,,,1411691,,,,,,,4504,,,,,3552,,1,"College of Life Sciences, Beijing Normal University",370x,Illumina HiSeq,,,,K12,,,"Included in the study, passed QC/QA"
1062,1412834.4,,,,,GCF_000765435.1,"HGAP (part of Pacific Biosciences, SMRT",,PRJNA260958,SAMN03067748,,,,,,04-Apr-2011,E. coli FAP1 is a pig (faeces) isolate.,2014-10-10T00:00:00Z,1,,2016-01-17T15:40:26.621Z,2016-01-17T15:40:26.621Z,,,50.53,"CP009578,CP009579,CP009580,CP009581,CP009582",5254632,Escherichia coli FAP1,Complete,Escherichia,Netherlands,,,,,,"Pig, Sus scrofa",,Netherlands,,Pig (faeces),,,,,1412834,,,,,,,5403,,4,,,5011,,5,University Medical Center Utrecht,77.0x,PacBio,,,,FAP1,,,"Included in the study, passed QC/QA"
1063,1435461.4,,,,,GCA_000725305.1,Velvet v. 1.2.10,,PRJNA229104,SAMN02440167,,,,Bacilli,1,,Evolution Project,2014-07-14T00:00:00Z,1,,2014-12-09T00:45:54.415Z,2015-03-16T03:17:09.594Z,,,50.7,CP008801.1,4718540,Escherichia coli KLY,Complete,Escherichia,,Negative,,,,,,,,,,,,,,1435461,37C,,,,,,4501,,,25043002,NZ_CP008801.1,4245,,1,Hebrew University - Balaban's Lab,100x,Illumina,,,No,,,,"Included in the study, passed QC/QA"
1064,1440052.3,,,,,GCA_000512125.1,MaSuRCA v. 2.1.0,,PRJNA232181,SAMN02641387,,,,Bacilli,1,,"Escherichia albertii is a new emerging enetric pathogen that has been associated with infections in humans and birds.E. albertii was first isolated from 5 Bangladeshi children with diarrhea. These isolates were initially identified as Hafnia alvei, but further analysis showed that they were more closely related to Escherichia coli and Shigella flexneri, and subsequently reclassified as E. albertii in 2003. E. albertii produces intimin, a virulence factor characteristic for enteropathogenic (EPEC) and enterohemorrhagic E. coli (EHEC) strains. However, its pathogenic potential is currently unknown and it is unclear how common is this new species in food and clinical samples. In addition, its identification is difficult because of the lack of biochemical tests, and exclusively based on molecular methods (e.g. PCR).The project will provide a platform to identify new genes that may contribute to this pathogen's virulence or markers usefull in reliable identification of E. albertii strains. Moreover, it can expand our knowledge about genomic variability, plasticity and mechanisms of evolution of enteropathogenic Escherichia spp. strains.",2013-12-30T00:00:00Z,, ,2014-12-08T22:11:18.855Z,2015-03-16T03:17:09.594Z,,,49.7,CP007025.1,4701875,Escherichia albertii KF1,Complete,Escherichia,Bangladesh,Negative,,,,,"Human, Homo sapiens",isolated from 5 Bangladeshi children with diarrhea,Bangladesh,,5 Bangladeshi children with diarrhea,,,,Nonmotile,1440052,,Escherichia albertii KF1,,,,,4690,,,,NZ_CP007025.1,4422,,1,"Department of Microbiology, Medical University of Bialystok",75x,454; Illumina; IonTorrent,complete,,,KF1,,,"Included in the study, passed QC/QA"
1065,1441627.14,collected_by:Xiancheng Zeng,,,,GCF_001610755.1,HGAP v. 2.3,,PRJNA232611,SAMN02580208,,,,Bacilli,1,Oct-2011,A highly drug resistant strain,2016-04-05T00:00:00Z,,,2016-04-28T03:09:52.509Z,2016-04-28T03:09:52.509Z,,,50.5,"CP011061,CP011067,CP011062,CP011066,CP011065,CP011064,CP011063",5428586,Escherichia coli str. Sanji,Complete,Escherichia,China,Negative,,,,,pheasant,,China,,pheasant duodenum,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.167",No,1441627,,,,,,,5591,,6,,"NZ_CP011061.1,NZ_CP011067.1,NZ_CP011062.1,NZ_CP011066.1,NZ_CP011065.1,NZ_CP011064.1,NZ_CP011063.1",5200,,7,Fujian Agriculture and Forestry University,135x,PacBio,,,,Sanji,,,"Included in the study, passed QC/QA"
1066,155864.42,biomaterial_provider:ATCC 700927,,,,GCF_000732965.1,SMRTAnalysis v. 2.2.0 pl build 134282;,,PRJNA253471,SAMN02905113,,,,,1,,This study is intended to update the genome sequence of E. coli O157:H7 EDL933. This strain is described else where (see Bioproject Accession PRJNA57831),2014-08-19T00:00:00Z,,ATCC:700927,2016-01-17T15:37:59.751Z,2016-01-17T15:37:59.751Z,,,50.43,"CP008957,CP008958",5639399,Escherichia coli O157:H7 str. EDL933,Complete,Escherichia,,,,,,,,,,,,,,,,155864,,,,,,,5873,,1,25125650,"NZ_CP008957.1,NZ_CP008958.1",5772,,2,University of California San Diego,100x; 300x,PacBio; Illumina,,,,EDL933,,,"Included in the study, passed QC/QA"
1067,155864.8,,,,,GCA_000006665.1,,,PRJNA259,,,,,Rod,1,1982,"Escherichia coli O157:H7. This strain is associated with Hamburger disease, which is caused by the contamination of meat products by enterohemorrhagic E. coli (EHEC). The identifier O157:H7 refers to the serotype of EHEC, and reflects the specific antigenic markers found on the surface of the cell. EHEC attaches and effaces to cells in the large intestine.There are numerous differences that distinguish O157:H7 from K-12, hundreds of them associated with genomic islands in either strain, including at least 9 large PAIs in O157:H7 that encode virulence factors. A type III secretion system, the locus of enterocyte effacement, numerous toxins and adhesins, as well as fimbrial gene clusters and iron uptake systems are found in these PAIs. Pathogenicity genes are also found on the plasmid pO157.Escherichia coli O157:H7 strain EDL933. This strain (substrain) is considered a reference strain of O157:H7, which was first isolated during an outbreak in 1982.",2001-02-24T00:00:00Z,,,2014-12-08T22:11:32.746Z,2015-03-16T03:17:09.594Z,,Hemorrhagic colitis,50.4,"AE005174,AF074613",5620522,Escherichia coli O157:H7 str. EDL933,Complete,Escherichia,,-,Host-associated,,,,,isolated during an outbreak in 1982,,,,,,,Yes,155864,25-35,Escherichia coli O157:H7 str. EDL933,,,,Facultative,5680,EHEC,1,"11206551,9722640","NC_002655,NC_007414",5411,,2,"University of Wisconsin-Madison, USA",,,complete,,,O157:H7 EDL933,Mesophilic,,"Included in the study, passed QC/QA"
1068,199310.4,,,,,GCA_000007445.1,,,PRJNA313,SAMN02604094,,,,Rod,1,,"Escherichia coli strain CFT073. This strain (CFT073; O6:K2:H1) is uropathogenic E. coli (UPEC) one of the most common causes of non-hospital-acquired urinary tract infections. There are numerous important differences between EHEC and UPEC, namely the loss of specific virulence factors such as the type III secretion system and plasmid- and phage-associated PAIs. UPEC has gained fimbrial operons, including genes for production of Pap pili, as well as other virulence factors that allow it to colonize the urinary tract.",2002-12-10T00:00:00Z,,,2014-12-08T22:11:23.529Z,2015-03-16T03:17:09.594Z,,Urinary tract infection,50.5,AE014075,5231428,Escherichia coli CFT073,Complete,Escherichia,USA: Maryland,-,Host-associated,,,,"Human, Homo sapiens",isolated at the University of Maryland Hospital,United States,,,,,"MLST.Escherichia_coli_1.73,MLST.Escherichia_coli_2.4",Yes,199310,37,Escherichia coli CFT073,,,,Facultative,5142,UPEC,,"12471157,2182540",NC_004431,5339,,1,"University of Wisconsin-Madison, USA",,,complete,,,CFT073,Mesophilic,,"Included in the study, passed QC/QA"
1069,208962.36,,,,,GCF_001549955.1,Roche 454 GS Assembler v. 2.3,,PRJDB3047,SAMD00026637,,,,Bacilli,1,2006,"We determined 3 complete and 26 draft genome sequence of E. albertii strains by Roche 454, Illumina MiSeq and ABI capillary sequencer.",2015-11-19T00:00:00Z,,,2016-03-01T09:34:43.486Z,2016-03-01T09:34:43.486Z,,,49.76,AP014857,4657167,Escherichia albertii strain EC06-170,Complete,Escherichia,Japan,Negative,,,,,,,Japan,,isolated from diarrheal patient,,,,No,208962,,,,,,,4565,,,26537224,NZ_AP014857.1,4274,,1,University of Miyazaki,29x,454 GS FLX; ABI 3730,,,,EC06-170,,,"Included in the study, passed QC/QA"
1070,208962.5,,,,,GCA_002285475.1,Roche 454 GS Assembler v. 2.3,,PRJDB3047,SAMD00026629,,,,Bacilli,1,2003,"We determined 3 complete and 26 draft genome sequence of E. albertii strains by Roche 454, Illumina MiSeq and ABI capillary sequencer.",2017-04-22T00:00:00Z,,,2017-09-28T21:51:20.677Z,2017-09-28T21:51:20.677Z,,,49.84,AP014856,4598983,Escherichia albertii strain CB9786,Complete,Escherichia,Germany,Negative,,,,,,,,,isolated from diarrheal patient,,,,No,208962,,,,,,,4587,,,26537224,,4283,,1,University of Miyazaki,43x,454 GS FLX; ABI 3730,,,,CB9786,,,"Included in the study, passed QC/QA"
1071,208962.51,,,,,GCA_002285455.1,Roche 454 GS Assembler v. 2.3,,PRJDB3047,SAMD00026650,,,,Bacilli,1,2004,"We determined 3 complete and 26 draft genome sequence of E. albertii strains by Roche 454, Illumina MiSeq and ABI capillary sequencer.",2017-04-22T00:00:00Z,,,2017-09-28T21:51:23.951Z,2017-09-28T21:51:23.951Z,,,49.84,AP014855,4560575,Escherichia albertii strain NIAH_Bird_3,Complete,Escherichia,Japan,Negative,,,,,,,,,isolated from Bird (Puffinus tenuirostris),,,,No,208962,,,,,,,4431,,,26537224,,4125,,1,University of Miyazaki,34x,454 GS FLX; ABI 3730,,,,NIAH_Bird_3,,,"Included in the study, passed QC/QA"
1072,216592.3,,,,,GCA_000027125.1,,,PRJNA40647,SAMEA2272277,,,,Rod,1,,Escherichia coli 042. This genome will be used for comparative analysis.,2010-01-28T00:00:00Z,,,2014-12-08T22:11:18.968Z,2015-03-16T03:17:09.594Z,,Diarrhea,50.5,"FN554766,FN554767",5355323,Escherichia coli 042,Complete,Escherichia,,-,Host-associated,,,,,,,,,,,MLST.Escherichia_coli_1.414,Yes,216592,-,Escherichia coli 042,,,,Facultative,5237,,1,20098708,"NC_017626.1,NC_017627.1",5038,,2,Wellcome Trust Sanger Institute,,,complete,,,42,Mesophilic,,"Included in the study, passed QC/QA"
1073,316385.7,,,,,GCA_000019425.1,,,PRJNA20079,SAMN02604262,,,,Rod,1,,Escherichia coli strain K-12 substrain DH10B. This strain is a substrain of K-12. It was derived from DH10 (which was derived from MC1061 which in turn was derived from M182). It is a common laboratory strain. The source of DNA was commercially competent cells used in BAC library construction at Baylor.,2008-03-14T00:00:00Z,,,2014-12-08T22:11:36.783Z,2015-03-16T03:17:09.594Z,,,50.8,CP000948,4686137,Escherichia coli str. K-12 substr. DH10B,Complete,Escherichia,"Shipyard Creek, Charleston, South Carolina",-,Host-associated,,,,,derived from DH10 (which was derived from MC1061 which in turn was derived from M182),United States,,DH10 (which was derived from MC1061 which,,,MLST.Escherichia_coli_1.1060,Yes,316385,37,Escherichia coli str. K-12 substr. DH10B,,,,Facultative,4606,,,18245285,NC_010473,4126,,1,"University of Wisconsin-Madison|Human Genome Sequencing Center, Baylor College of Medicine",,,complete,,,strain K-12 substrain DH10B,Mesophilic,,"Included in the study, passed QC/QA"
1074,316401.27,,,,,GCF_000210475.1,,,PRJEA42749,SAMEA2272237,,,,Bacilli,1,,Escherichia coli ETEC H10407. This strain will be used for comparative genome analysis.,2015-02-27T00:00:00Z,,,2016-01-17T15:28:29.441Z,2016-01-17T15:28:29.441Z,,Diarrhea,50.69,"FN649414,FN649415,FN649416,FN649417,FN649418",5325888,Escherichia coli ETEC H10407,Complete,Escherichia,,Negative,HostAssociated,,,,,,,,,,,,No,316401,,,,,,Facultative,5451,,4,20802035,"NC_017633.1,NC_017721.1,NC_017723.1,NC_017722.1,NC_017724.1",4974,,5,Wellcome Trust Sanger Institute,,,,,,ETEC H10407,Mesophilic,,"Included in the study, passed QC/QA"
1075,316407.41,sample_type:population,,,,GCF_001878695.1,HGAP v. 2.0,,PRJNA352084,SAMN05965804,,,,,,2014,ZK126 is a sub-strain of Escherichia coli K-12 W3110 used for studying long-term stationary phase.,2016-11-14T00:00:00Z,1,,2017-01-16T02:13:47.093Z,2017-01-16T02:13:47.093Z,,,50.76,CP017979,4541211,Escherichia coli str. K-12 substr. W3110,Complete,Escherichia,USA: Los Angeles,,,,,,,,,,Laboratory,,,,,316407,,,,,,,4544,,,,,4374,,1,University of Southern California,600.0x,PacBio,,,,K-12,,,"Included in the study, passed QC/QA"
1076,316407.9,,,,,GCA_000010245.1,,,PRJNA16351,,,,,Rod,1,,"Escherichia coli strain W3110. This strain is closely related to MG1655 and is descended from K-12 (W1485) which is a derivative of the original K-12 strain (EMG2). It is considered a more wild-type strain than MG1655, although it has also been cured of the lambda prophage and lacks the fertility factor (F+ plasmid) of the original E. coli K-12 (EMG2).Comparison of the two genomes revealed that they are not identical with strain-specific differences reflecting their distinct lineages.",2006-01-23T00:00:00Z,,,2014-12-08T22:11:36.833Z,2015-03-16T03:17:09.594Z,,,50.8,AP009048,4646332,Escherichia coli str. K-12 substr. W3110,Complete,Escherichia,,-,Host-associated,,,,,,,,,,,MLST.Escherichia_coli_1.10,Yes,316407,37,Escherichia coli str. K-12 substr. W3110,,,,Facultative,4454,,,"273224,319453,357433,358189,368797,375010,1325970,1355089,1357528,1396599,1447125,1459951,1474579,1630901,1663890,1670938,1675419,1688424,1695895,1713281,1714590,1721838,1741267,1849492,1850088,1860827,1900346,1943700,1943701,1971619,1987124,1991717,199",AC_000091,4226,,1,Nara Institute of Science and Technology,,,complete,,,W3110,Mesophilic,Yes,"Included in the study, passed QC/QA"
1077,316435.1,collected_by:Alfred Nissle,,,,GCF_000714595.1,Celera Assembler v. Dec. 2013,,PRJNA248167,SAMN02794012,,,,Bacilli,1,1917,Escherichia coli strain Nissle 1917 (EcN) is the active principle of a probiotic preparation (trade name Mutaflor�) used for the treatment of patients with intestinal diseases such as ulcerative colitis and diarrhea.,2015-06-25T00:00:00Z,,,2016-01-17T15:36:10.872Z,2016-01-17T15:36:10.872Z,,,50.58,CP007799,5441200,Escherichia coli Nissle 1917,Complete,Escherichia,,Negative,,,male,dysentery,"Human, Homo sapiens",,,,feces,,,,,316435,,,,,,,5462,,,25093936,NZ_CP007799.1,4821,,1,"Bioifnormatik, Biozentrum, Uni Wuerzburg",115116x,Illumina; Pacific Biosciences,,,,Nissle 1917,,,"Included in the study, passed QC/QA"
1078,331111.12,,,,,GCA_000017745.1,,,PRJNA13960,,,,,Rod,1,,"Escherichia coli strain E24377A. This is an enterotoxigenic E. coli (ETEC) strain (E24377A; serotype O139:H28) and was obtained from Maj. Carl Brinkley at Walter Reed Army Institute of Research. ETEC is the leading cause of traveler's diarrhea, characterized by a large volume of watery diarrhea.  ETEC primarily colonizes  the small intestine by way of the pili. Colonization factor antigens (CFA) in this strain include two pili types (coli surface antigen one and three; CS1 and CS3). Additionally two toxins are thought to be responsible for the virulence, heat stable and heat labile enterotoxins. Other virulence factors include the O139:H28 serotype as well as genes carried on a number of uncharacterized plasmids. The stocks used for genomic DNA preparation were obtained from a master- and  production cGMP cell bank available at WRAIR/NMRC. Pathogenicity has been confirmed in human challenge experiments.",2007-09-11T00:00:00Z,,,2014-12-08T22:11:24.593Z,2015-03-16T03:17:09.594Z,,Diarrhea,50.6,"CP000800,CP000796,CP000797,CP000798,CP000799,CP000801,CP000795",5249288,Escherichia coli E24377A,Complete,Escherichia,,-,Host-associated,,,,,obtained from Maj. Carl Brinkley at Walter Reed Army Institute of Research,,,,,,"MLST.Escherichia_coli_1.1132,MLST.Escherichia_coli_2.468",Yes,331111,37,Escherichia coli E24377A,,,,Facultative,5196,ETEC,6,18676672,"NC_009801,NC_009787,NC_009788,NC_009789,NC_009790,NC_009791,NC_009786",4991,,7,TIGR,,,complete,serovar O139,,E24377A,Mesophilic,,"Included in the study, passed QC/QA"
1079,331112.6,,,,,GCA_000017765.1,,,PRJNA13959,SAMN02604037,,,,Rod,1,1978,"Escherichia coli strain HS. This strain (HS; serotype O9) is a human commensal that was originally isolated from a laboratory scientist at Walter Reed Army Institute of Research in 1978 (Levine, 1978). It was obtained from Drs. Kaper and Nataro at the School of Medicine at the University of Maryland. Strain HS colonizes the human gastrointestinal tract in challenge experiments, but no overt signs of disease occur. Thus, this strain represents a genomic baseline for human gastrointestinal tract colonization. It is competent and amenable to genetic manipulation.",2007-09-10T00:00:00Z,,,2014-12-08T22:11:25.512Z,2015-03-16T03:17:09.594Z,,,50.8,CP000802,4643538,Escherichia coli HS,Complete,Escherichia,Walter Reed Army Institute,-,Host-associated,,,,"Human, Homo sapiens","isolated from a laboratory scientist at Walter Reed Army Institute of Research in 1978 (Levine, 1978)",United States,,laboratory scientist at Walter Reed Army Institute of Research,,,MLST.Escherichia_coli_1.46,Yes,331112,37,Escherichia coli HS,,,,Facultative,4520,Nonpathogenic,,18676672,NC_009800,4378,,1,TIGR,,,complete,serovar O9,,HS,Mesophilic,,"Included in the study, passed QC/QA"
1080,340184.27,,,,,GCF_000725265.1,HGAP v. 1.4,,PRJNA205485,SAMN02918008,,,,,1,1971-07-01,DNA phosphorothioation modified strain Escherichia coli B7A.,2014-07-17T00:00:00Z,,,2016-01-17T15:36:29.135Z,2016-01-17T15:36:29.135Z,,,50.76,"CP005998,CP005999,CP006000,CP006001,CP006002",5230440,Escherichia coli B7A,Complete,Escherichia,Viet Nam,,,,,,,,Vietnam,,stool,,,,,340184,,,,,,,5494,,4,,"NZ_CP005998.1,NZ_CP005999.1,NZ_CP006000.1,NZ_CP006001.1,NZ_CP006002.1",5384,,5,Shanghai Jiao Tong University,80X,SMRT DNA sequencing technology; PacBio,,,,B7A,,,"Included in the study, passed QC/QA"
1081,362663.9,,,,,GCA_000013305.1,,,PRJNA16235,SAMN02604181,,,,Rod,1,,"Escherichia coli strain 536. This strain (536; O6:K15:H31) is a uropathogenic Escherichia coli (UPEC) that was isolated from a patient with acute pyelonephritis (inflammation of the kidney and pelvis). It is a model organism of extraintestinal E. coli, which are among the most common causes of non-hospital-acquired urinary tract infections (UTIs) and UPEC strains are responsible for 40% of nosocomial UTIs. Comparative genomics with other E. coli, especially UPEC strains such as CFT073 will reveal important pathogenicity traits. Studies on strain 536 have revealed at least 5 pathogenicity islands. The project is a collaboration with the group of Prof. Hacker, Institute for Molecular Infection Biology, University of Wurzburg.",2006-07-13T00:00:00Z,,,2014-12-08T22:11:20.299Z,2015-03-16T03:17:09.594Z,,Urinary tract infection,50.5,CP000247,4938920,Escherichia coli 536,Complete,Escherichia,,-,Host-associated,,,acute pyelonephritis (inflammation of the kidney and pelvis),"Human, Homo sapiens",isolated from a patient with acute pyelonephritis (inflammation of the kidney and pelvis),,,patient with acute pyelonephritis (inflammation of the kidney and pelvis),,,"MLST.Escherichia_coli_1.127,MLST.Escherichia_coli_2.261",Yes,362663,-,Escherichia coli 536,,,,Facultative,4773,UPEC,,16879640,NC_008253,4620,,1,University of Goettingen,,,complete,,,536,Mesophilic,,"Included in the study, passed QC/QA"
1082,364106.8,,,,,GCA_000013265.1,,,PRJNA16259,SAMN00000110,,,,Rod,1,,"Escherichia coli strain UTI89. This strain (UTI89) is a uropathogenic strain isolated from a woman with uncomplicated cystitis (bladder inflammation) that has been demonstrated to cause cystitis in a murine urinary tract infection model.The genome of UTI89 showed 4 pathogenicity islands. A plasmid was found that was similar to the F plasmid but which also contained virulence genes. Comparison of a set of orthologs from this organism with other E. coli strains showed positive selection on some genes, including those for iron acquisition. Comparison with additional sequences (found in Accession Numbers DQ389000:DQ389068 and DQ440980:DQ441250) of a subset of genes from a number of isolates from patients with UTI infections and isolates from healthy individuals showed positive selection of fepE and amiA genes and some weakly positive selection for ompC.",2006-04-05T00:00:00Z,,,2014-12-08T22:11:36.454Z,2015-03-16T03:17:09.594Z,,Urinary tract infection,50.6,"CP000243,CP000244",5179971,Escherichia coli UTI89,Complete,Escherichia,,-,Host-associated,,,,"Human, Homo sapiens",isolated from a woman with uncomplicated cystitis (bladder inflammation) that has been demonstrated to cause cystitis in a murine urinary tract infection model,,,woman with uncomplicated cystitis (bladder inflammation) that has been demonstrated to cause cystitis,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",Yes,364106,-,Escherichia coli UTI89,,,,Facultative,5040,UPEC,1,16585510,"NC_007946,NC_007941",5166,,2,Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine,,,complete,,,UTI89,Mesophilic,,"Included in the study, passed QC/QA"
1083,37762.5,sample_type:cell culture,,,,GCF_001559615.1,HGAP.3/Quiver v. 2.3.0,,PRJNA309539,SAMN04435507,,,,,1,,"Complete genome sequences of E. coli SHuffle-K-12 and SHuffle-B and their parental strains, DHB4 and C2566, respectively.",2016-02-11T00:00:00Z,,,2016-03-01T20:06:30.402Z,2016-03-01T20:06:30.402Z,,,50.81,CP014268,4478948,Escherichia coli B strain C2566,Complete,Escherichia,USA,,,,,,,,United States,,laboratory,,,"MLST.Escherichia_coli_1.93,MLST.Escherichia_coli_2.83",,37762,C,,,,,,4491,,,,,4309,,1,New England Biolabs,400x,PacBio,,,,C2566,,,"Included in the study, passed QC/QA"
1084,37762.6,sample_type:cell culture,,,,GCF_001559635.1,HGAP.3/Quiver v. 2.3.0,,PRJNA309540,SAMN04435508,,,,,1,,"Complete genome sequences of E. coli SHuffle-K-12 and SHuffle-B and their parental strains, DHB4 and C2566, respectively.",2016-02-11T00:00:00Z,,,2016-03-01T20:06:44.558Z,2016-03-01T20:06:44.558Z,,,50.82,CP014269,4569185,Escherichia coli B strain C3029,Complete,Escherichia,USA,,,,,,,,United States,,laboratory,,,,,37762,C,,,,,,4626,,,,NZ_CP014269.1,4433,,1,New England Biolabs,240x,PacBio,,,,C3029,,,"Excluded from the study, failed QC/QA."
1085,386585.9,,,,,GCA_000008865.1,,,PRJNA226,SAMN01911278,,,,Rod,1,1997,"Escherichia coli O157:H7. This strain is associated with Hamburger disease, which is caused by the contamination of meat products by enterohemorrhagic E. coli (EHEC). The identifier O157:H7 refers to the serotype of EHEC, and reflects the specific antigenic markers found on the surface of the cell. EHEC attaches and effaces to cells in the large intestine.There are numerous differences that distinguish O157:H7 from K-12, hundreds of them associated with genomic islands in either strain, including at least 9 large PAIs in O157:H7 that encode virulence factors. A type III secretion system, the locus of enterocyte effacement, numerous toxins and adhesins, as well as fimbrial gene clusters and iron uptake systems are found in these PAIs. Pathogenicity genes are also found on the plasmid pO157.Escherichia coli O157:H7 strain Sakai. This strain of O157:H7 was isolated in a 1997 outbreak in Sakai, Japan.",2000-03-29T00:00:00Z,,,2014-12-08T22:11:32.812Z,2015-03-16T03:17:09.594Z,,Hemorrhagic colitis,50.5,"BA000007,AB011549,AB011548",5594477,Escherichia coli O157:H7 str. Sakai,Complete,Escherichia,Sakai Japan,-,Host-associated,,,,,"isolated in a 1997 outbreak in Sakai, Japan",Japan,,,,,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.296",Yes,386585,37,Escherichia coli O157:H7 str. Sakai,,,,Facultative,5602,EHEC,2,"9628576,10734605,11108008,11111050,11258796","NC_002695,NC_002128,NC_002127",5318,,3,Osaka Univ.,,,complete,,,O157:H7,Mesophilic,,"Included in the study, passed QC/QA"
1086,405955.13,,,,,GCA_000014845.1,,,PRJNA16718,SAMN02603424,,,,Rod,1,,"Escherichia coli APEC O1. This strain (serovar O1) is an avian pathogenic strain and causes respiratory, blood, and enteric infections primarily in poultry. ",2006-10-04T00:00:00Z,,,2014-12-08T22:11:21.756Z,2015-03-16T03:17:09.594Z,,Colibacillosis,50.3,"CP000468,DQ517526,DQ381420",5497653,Escherichia coli APEC O1,Complete,Escherichia,,-,Host-associated,,,,"Chicken, Gallus gallus",,,,,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.418",Yes,405955,-,Escherichia coli APEC O1,,,,Facultative,5417,APEC,2,"16940062,17293413,16885466","NC_008563,NC_009838,NC_009837",4851,,3,Iowa State University,,,complete,serovar O1,,O1,Mesophilic,,"Included in the study, passed QC/QA"
1087,409438.11,,,,,GCA_000010385.1,Phred/Phrap/Consed,,PRJNA18057,,,Gastrointestinal tract,,Rod,1,,Escherichia coli SE11.This strain is being sequenced for comparative genome analysis.,2008-10-22T00:00:00Z,,,2014-12-08T22:11:34.523Z,2015-03-16T03:17:09.594Z,,,50.7,"AP009240,AP009245,AP009246,AP009242,AP009243,AP009241,AP009244",5155626,Escherichia coli SE11,Complete,Escherichia,,-,Host-associated,,,,"Human, Homo sapiens",,,,,,,"MLST.Escherichia_coli_1.156,MLST.Escherichia_coli_2.19",,409438,37,Escherichia coli SE11,,,,Facultative,5048,,6,18931093,"NC_011415,NC_011408,NC_011411,NC_011413,NC_011416,NC_011419,NC_011407",5002,Non-halophilic,7,Kitasato Univ.,8x,Sanger,complete,,,SE11,Mesophilic,,"Included in the study, passed QC/QA"
1088,413997.3,,,,,GCA_000017985.1,,,PRJNA18281,SAMN02603421,,,,Rod,1,,"Escherichia coli B. Escherichia coli B has been serving not only as a research model for the study of phage sensitivity, restriction systems, and bacterial evolution, but also as a workhorse for protein expression in life science laboratories and in the biotech industry. Escherichia coli B str. REL606. This strain is unable to use arabinose due to a mutation and has been used in long term evolution experiments to study rates of mutation and adaption. The genome information of E. coli B str. REL606 was determined by an international collaboration, revealing a number of genomic regions unique to either B or K-12 despite very high sequence similarities among the conserved genes.",2009-07-15T00:00:00Z,,,2014-12-08T22:11:21.912Z,2015-03-16T03:17:09.594Z,,,50.8,CP000819,4629812,Escherichia coli B str. REL606,Complete,Escherichia,,-,Multiple,,,,,,,,,,,"MLST.Escherichia_coli_1.93,MLST.Escherichia_coli_2.83",Yes,413997,-,Escherichia coli B str. REL606,,,,Facultative,4524,,,19786035,NC_012967,4205,,1,International E. coli B Consortium|GENOSCOPE / National DNA Sequencing Centre|KRIBB,,,complete,,No,REL606,Mesophilic,,"Included in the study, passed QC/QA"
1089,431946.3,,,,,GCA_000010485.1,Phred/Phrap/Consed,,PRJNA19053,,,Gastrointestinal tract,,Rod,1,,Escherichia coli SE15.This strain is being sequenced for comparative genome analysis.,2009-12-14T00:00:00Z,,,2014-12-08T22:11:34.531Z,2015-03-16T03:17:09.594Z,,,50.7,"AP009378,AP009379",4839683,Escherichia coli SE15,Complete,Escherichia,,-,Host-associated,,,,"Human, Homo sapiens",,,,,,,MLST.Escherichia_coli_1.131,Yes,431946,-,Escherichia coli SE15,,,,Facultative,4664,,1,20008064,"NC_013654.1,NC_013655.1",4488,Non-halophilic,2,Kitasato Univ.,,"454, Sanger",complete,,,SE15,Mesophilic,,"Included in the study, passed QC/QA"
1090,439184.7,,,,,GCA_000800845.2,NGen(DNASTAR) v. 11,,PRJNA228944,SAMN03339595,,,,Cocci,1,,Study objective is to understanding the genetic make up of neonatal meningitis causing E. coli and discovery of novel virulence traits,2015-07-30T00:00:00Z,,,2016-01-17T15:41:13.940Z,2016-01-17T15:41:13.940Z,,,50.66,"CP007149,CP007150",5201869,Escherichia coli RS218,Complete,Escherichia,,Negative,,,,,,,,,,,,,Yes,439184,,,,,,,5380,,1,26205862,"NZ_CP007149.1,NZ_CP007150.1",4658,,2,Penn State University,187x,IonTorrent,,,,RS218,,,"Included in the study, passed QC/QA"
1091,439855.1,,,,,GCA_000019645.1,,,PRJNA19469,SAMN02604066,,,,Rod,1,,"Escherichia coli SMS-3-5. Escherichia coli SMS-3-5 was isolated from a toxic-metal contaminated site, Shipyard Creek, Charleston, South Carolina. This strain is highly resistant to a number of antibiotics and will be used for comparative analysis with other E. coli strains.",2008-03-20T00:00:00Z,,,2014-12-08T22:11:34.555Z,2015-03-16T03:17:09.594Z,,,50.5,"CP000970,CP000973,CP000974,CP000971,CP000972",5215377,Escherichia coli SMS-3-5,Complete,Escherichia,,-,Multiple,,,,,"isolated from a toxic-metal contaminated site, Shipyard Creek, Charleston, South Carolina",,,"toxic-metal contaminated site, Shipyard Creek, Charleston, South Carolina",,,"MLST.Escherichia_coli_1.354,MLST.Escherichia_coli_2.39",Yes,439855,37,Escherichia coli SMS-3-5,,,,Facultative,5051,,4,18708504,"NC_010498,NC_010486,NC_010487,NC_010488,NC_010485",4913,,5,TIGR,,,complete,,No,SMS-3-5,Mesophilic,,"Included in the study, passed QC/QA"
1092,444450.8,,,,,GCA_000021125.1,,,PRJNA27739,SAMN02603441,,,,Rod,1,,"Escherichia coli O157:H7. This strain is associated with Hamburger disease, which is caused by the contamination of meat products by enterohemorrhagic E. coli (EHEC). The identifier O157:H7 refers to the serotype of EHEC, and reflects the specific antigenic markers found on the surface of the cell. EHEC attaches and effaces to cells in the large intestine.There are numerous differences that distinguish O157:H7 from K-12, hundreds of them associated with genomic islands in either strain, including at least 9 large PAIs in O157:H7 that encode virulence factors. A type III secretion system, the locus of enterocyte effacement, numerous toxins and adhesins, as well as fimbrial gene clusters and iron uptake systems are found in these PAIs. Pathogenicity genes are also found on the plasmid pO157.Escherichia coli O157:H7 str. EC4115. This strain will be used for comparative analysis.",2008-10-08T00:00:00Z,,,2014-12-08T22:11:32.407Z,2015-03-16T03:17:09.594Z,,Hemorrhagic colitis,50.4,"CP001164,CP001165,CP001163",5704171,Escherichia coli O157:H7 str. EC4115,Complete,Escherichia,,-,Multiple,,,,,,,,,,,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",Yes,444450,37,Escherichia coli O157:H7 str. EC4115,,,,Facultative,5746,EHEC,2,,"NC_011353,NC_011351,NC_011350",5477,,3,J. Craig Venter Institute|MSC,,,complete,,No,EC4115,Mesophilic,,"Included in the study, passed QC/QA"
1093,469008.15,,,,,GCA_000022665.2,,,PRJNA20713,,,,,Rod,1,,Escherichia coli BL21(DE3). BL21(DE3) is a derivative of E. coli strain B. Deficiency in Lon and OmpT proteases makes it a superior host for recombinant protein expression. It also carries a DE3 recombinant phage harboring the T7 RNA polymerase gene that can direct high-level expression of cloned genes under the control of the T7 promoter.,2009-07-15T00:00:00Z,,,2014-12-08T22:11:22.638Z,2015-03-16T03:17:09.594Z,,,50.8,CP001509,4558953,Escherichia coli BL21(DE3),Complete,Escherichia,,-,Host-associated,,,,,,,,,,,"MLST.Escherichia_coli_1.93,MLST.Escherichia_coli_2.83",Yes,469008,37,Escherichia coli BL21(DE3),,,,Facultative,4399,,,19786035,NC_012971.2,4159,,1,Korea Research Institute of Bioscience and Biotechnology|Genome Encyclopedia of Microbes,,,complete,,No,BL21(DE3),Mesophilic,,"Included in the study, passed QC/QA"
1094,469008.16,,,,,GCA_000009565.2,,,PRJNA28965,,,,,Rod,1,,Escherichia coli BL21. Escherichia coli BL21 is derived from strain B and is commonly used for protein expression and purification.,2009-06-30T00:00:00Z,,,2014-12-08T22:11:22.641Z,2015-03-16T03:17:09.594Z,,,50.8,AM946981,4557041,Escherichia coli BL21(DE3) (Prj:28965),Complete,Escherichia,,-,Specialized,,,,,derived from strain B and is commonly used for protein expression and purification,,,strain B,,,"MLST.Escherichia_coli_1.93,MLST.Escherichia_coli_2.83",Yes,469008,-,Escherichia coli BL21(DE3),,,,Facultative,4466,,,,NC_012892.2,4244,,1,Austrian Center for Biopharmaceutical Technology|Sandoz Austria,,,complete,,No,BL21,Mesophilic,,"Included in the study, passed QC/QA"
1095,469008.4,,,,,GCA_000023665.1,,,PRJNA30681,SAMN00002656,,,,Rod,1,,Escherichia coli BL21-Gold(DE3)pLysS AG.BL21-Gold(DE3)pLysS AG is a derivative of E. coli strain B. Deficiency in Lon and OmpT proteases makes it a superior host for recombinant protein expression. It also carries a DE3 recombinant phage harboring the T7 RNA polymerase gene that can direct high-level expression of cloned genes under the control of the T7 promoter.,2009-06-04T00:00:00Z,,,2014-12-08T22:11:18.938Z,2015-03-16T03:17:09.594Z,,,50.8,CP001665,4570938,Escherichia coli 'BL21-Gold(DE3)pLysS AG',Complete,Escherichia,,_,Multiple,,,,,,,,,,,"MLST.Escherichia_coli_1.93,MLST.Escherichia_coli_2.83",Yes,866768,-,Escherichia coli 'BL21-Gold(DE3)pLysS AG',,,,Anaerobic,4503,,,,NC_012947,4228,,1,US DOE Joint Genome Institute (JGI-PGF)|DOE Joint Genome Institute|JGI-PGF,,,complete,,No,BL21(DE3),Psychrophilic,,"Included in the study, passed QC/QA"
1096,481805.6,,,,,GCA_000019385.1,,,PRJNA18083,SAMN02598405,,,,Rod,1,,"Escherichia coli ATCC 8739.This strain differs from the K-12 strain in having the IS1-13 insertion element associated with an upstream promotor and the first 114 bp of ompC. This deletion also eliminates micF, which negatively controls expression of ompF. The corresponding outer membrane proteins OmpC and OmpF, are the two major porins of K-12. Escherichia coli C str. ATCC 8739 expresses only OmpF.",2008-03-11T00:00:00Z,,ATCC 8739,2014-12-08T22:11:21.835Z,2015-03-16T03:17:09.594Z,,,50.9,CP000946,4746218,Escherichia coli ATCC 8739,Complete,Escherichia,,-,Host-associated,,,,,,,,,,,MLST.Escherichia_coli_1.3021,,481805,-,Escherichia coli ATCC 8739,,,,Facultative,4597,,,,NC_010468,4200,Non-halophilic,1,US DOE Joint Genome Institute (JGI-PGF)|DOE Joint Genome Institute|JGI-PGF,,,complete,,,ATCC 8739,Mesophilic,,"Included in the study, passed QC/QA"
1097,498388.3,sample_type:bacterial culture,,,,,HGAP Assembly v. 2,,PRJNA380607,SAMN06645125,,,,,1,2016-04-01,The last laboratory strain of E. coli to be sequnced. E. coli C is a long time laboratory strain used for phage studies. Recent data shows that it forms much better biofilm than other strains and can be used as a model organism in bacterial biofilm studies.,2017-04-05T00:00:00Z,,,2017-05-28T07:37:09.600Z,2017-05-28T07:37:09.600Z,,,50.96,CP020543,4617024,Escherichia coli C strain C,Complete,Escherichia,USA,,,,,,"Human, Homo sapiens",,,,,,,,,498388,,,,,,,4665,,,,,4581,,1,Drexel University College of Medicine,184.0x,PacBio,,,,C,,,"Included in the study, passed QC/QA"
1098,511145.12,,,,,GCA_000005845.2,,,PRJNA225,,,,,Rod,1,1922,"Escherichia coli strain K-12 substrain MG1655. Non-pathogenic strain MG1655 approximates wild-type E. coli as it has been maintained with very little genetic manipulation except for the curing (removal) of bacteriophage lambda and the F plasmid. MG1655 was derived from strain W1485, which was derived by Joshua Lederberg from the original K-12 isolate obtained from a patient in 1922.",1997-09-05T00:00:00Z,,,2014-12-08T22:11:36.813Z,2015-03-16T03:17:09.594Z,,,50.8,U00096,4639675,Escherichia coli str. K-12 substr. MG1655,Complete,Escherichia,,-,Host-associated,,,,,"derived from strain W1485, which was derived by Joshua Lederberg from the original K-12 isolate obtained from a patient in 1922",,,"derived from strain W1485, which was derived by Joshua Lederberg from the original K-12 isolate obtained from a patient in 1922",,,MLST.Escherichia_coli_1.10,Yes,511145,37,Escherichia coli str. K-12 substr. MG1655,,,,Facultative,4549,,,"2570347,9278503,16397293",NC_000913,4321,,1,"University of Wisconsin-Madison, USA",,,complete,,,K12,Mesophilic,,"Included in the study, passed QC/QA"
1099,511145.18,,,,,GCA_000269645.1,allpaths v. 41303,,PRJNA40075,SAMN02596920,biovar 00000000,,,Bacilli,1,,"To test methods for assembly of very short reads, five microbial genomes were selected which have a finished reference sequence available. Escherichia coli MG1655 was one of these five microbial genomes. At least two libraries (short fragment and jumping) were generated and sequenced using Illumina. Likewise in particular for E. coli, libraries were also generated and run for 454 sequencing. Genomic DNA from Erica Sodergren. Two different genome assemblies are part of this project. The assembly in AKBV00000000 is the complete chromosome assembled from Illumina reads. The assembly in AKVX00000000 is the complete chromosome assembled from reads used to assemble U000096 plus reads from a different isolate of the strain.",2012-07-27T00:00:00Z,,,2016-01-17T15:28:53.936Z,2016-01-17T15:28:53.936Z,,,50.79,AKBV01000000,4638970,Escherichia coli str. K-12 substr. MG1655,Complete,Escherichia,,Negative,HostAssociated,,,,,,,,,,,,No,511145,,,,,,Facultative,4518,,,22829535,,,,1,Broad Institute,92.0x,Illumina/PacBio,,,,K-12,Mesophilic,,"Included in the study, passed QC/QA"
1100,511145.181,,,,,GCF_000273425.1,manual processing,,PRJNA40075,SAMN02597081,biovar 00000000,,,Bacilli,1,,"To test methods for assembly of very short reads, five microbial genomes were selected which have a finished reference sequence available. Escherichia coli MG1655 was one of these five microbial genomes. At least two libraries (short fragment and jumping) were generated and sequenced using Illumina. Likewise in particular for E. coli, libraries were also generated and run for 454 sequencing. Genomic DNA from Erica Sodergren. Two different genome assemblies are part of this project. The assembly in AKBV00000000 is the complete chromosome assembled from Illumina reads. The assembly in AKVX00000000 is the complete chromosome assembled from reads used to assemble U000096 plus reads from a different isolate of the strain.",2014-02-07T00:00:00Z,,,2016-01-17T15:28:58.345Z,2016-01-17T15:28:58.345Z,,,50.79,AKVX01000000,4638970,Escherichia coli str. K-12 substr. MG1655,Complete,Escherichia,,Negative,HostAssociated,,,,,,,,,,,,No,511145,,,,,,Facultative,4517,,,22829535,,,,1,Broad Institute,,Sanger; Illumina,,,,K-12,Mesophilic,,"Included in the study, passed QC/QA"
1101,511145.183,,,,,GCF_000482265.1,allpaths v. 41303,,PRJNA217911,SAMN02596920,,,,,,,Escherichia coli str. K-12 substr. MG1655 reference genome for SNP-calling,2013-10-25T00:00:00Z,1,,2016-01-17T15:33:37.372Z,2016-01-17T15:33:37.372Z,,,50.79,AYEK01000000,4638920,Escherichia coli str. K-12 substr. MG1655,Complete,Escherichia,,,,,,,,,,,,,,,,511145,,,,,,,4518,,,,,,,1,Broad Institute,92.0x,Illumina; PacBio,,,,K-12,,,"Included in the study, passed QC/QA"
1102,511145.185,,,,,GCF_000801205.1,Celera Assembler v. 8.2,,PRJNA237120,SAMN02743420,,,,,1,2014,"DNA from three model organisms (Yeast, Flowering plant, and Fruit Fly) have been sequenced and de novo assembled using the PacBio RS II insrument",2014-12-15T00:00:00Z,,,2016-01-17T15:41:14.602Z,2016-01-17T15:41:14.602Z,,,50.79,CP009685,4636831,Escherichia coli str. K-12 substr. MG1655,Complete,Escherichia,USA: Menlo Park,,,,,,,,United States,,ATCC,,,,,511145,,,,,,,4653,,,,NZ_CP009685.1,4391,,1,Pacific Biosciences,85.0x,PacBio,,,,K-12,,,"Included in the study, passed QC/QA"
1103,511145.186,sample_type:monoisolate,,,,GCF_001308065.1,bowtie v. 2-2.2.3,,PRJNA268139,SAMN03203487,,,,,1,not collected,The E. coli wildtype(strain MG1655) was subjected to lab evolution experiments to study the development of resistance to trimethoprim and the associated genome wide changes,2015-10-08T00:00:00Z,,,2016-01-17T17:13:42.744Z,2016-01-17T17:13:42.744Z,,,50.79,CP012868,4641665,Escherichia coli str. K-12 substr. MG1655,Complete,Escherichia,India,,,,,,,,India,,,,,,,511145,,,,,,,4645,,,,NZ_CP012868.1,4424,,1,Indian Institute of Science,100x,Illumina,,,,K-12,,,"Included in the study, passed QC/QA"
1104,511145.208,sample_type:Cultured isolate,,,,GCF_001544635.1,HGAP2 v. 2.1.0,,PRJNA308372,SAMN04403366,,,,,1,1992,Escherichia coli MRE600 sequencing and assembly,2016-02-02T00:00:00Z,,ATCC:47076,2016-03-01T00:51:59.119Z,2016-03-01T00:51:59.119Z,,,50.78,CP014225,4659625,Escherichia coli str. K-12 substr. MG1655,Complete,Escherichia,USA: Palo Alto,,Unknown,,,,"Human, Homo sapiens",,United States,,stool sample,,,"MLST.Escherichia_coli_2.262,MLST.Escherichia_coli_1.10",,511145,37 C,,,,,Facultative,4683,,,26802429,NZ_CP014225.1,4489,,1,Weill Cornell Medical College,125X,Pacific Biosciences,,,,K-12,Mesophilic,,"Included in the study, passed QC/QA"
1105,511145.209,sample_type:isolated colony,,,,GCF_001566335.1,HGAP v. 2015-02,,PRJNA306781,SAMN04393382,,,,,1,,Genome analysis of cit+ strain of Escherichia coli K12,2016-02-23T00:00:00Z,,,2016-03-01T22:18:20.787Z,2016-03-01T22:18:20.787Z,,,50.75,CP014348,4657541,Escherichia coli str. K-12 substr. MG1655,Complete,Escherichia,not collected,,,,,,,,,,laboratory strain,,,,,511145,C,,,,,,4681,,,,NZ_CP014348.1,4496,,1,University of Idaho,94.0x,PacBio,,,,JW5437-1,,,"Included in the study, passed QC/QA"
1106,536056.19,,,,,GCF_000270105.1,,,PRJDA52077,,,,,,1,,Please refer to the following web page for source information; http://www.shigen.nig.ac.jp/ecoli/strain/nbrpStrainDetailAction.do?strainId=998,2011-06-21T00:00:00Z,,,2016-01-17T15:28:55.161Z,2016-01-17T15:28:55.161Z,,,50.83,AP012030,4621430,Escherichia coli DH1,Complete,Escherichia,,,,,,,,,,,,,,,,536056,,,,,,,4545,,,21611185,NC_017638.1,4260,,1,"Symbiotic Network Design Laboratory, Graduate School of Information Science and Technology, Osaka University",,,,,,DH1,,,"Included in the study, passed QC/QA"
1107,536056.3,,,,,GCA_000023365.1,,,PRJNA30031,SAMN02598470,,,,Rod,1,,Escherichia coli DH1. Escherichia coli DH1 is a plasmid host strain with a high frequency of transformation. It is a common laboratory strain and will be used for comparative analysis.,2009-10-05T00:00:00Z,,,2014-12-08T22:11:24.443Z,2015-03-16T03:17:09.594Z,,,50.8,CP001637,4630707,Escherichia coli DH1,Complete,Escherichia,,-,Multiple,,,,,,,,,,,MLST.Escherichia_coli_1.1060,Yes,536056,35-37,Escherichia coli DH1,,,,Facultative,4535,,,,NC_017625.1,4160,,1,US DOE Joint Genome Institute|DOE Joint Genome Institute|JGI-PGF,,,complete,,No,DH1,Mesophilic,,"Included in the study, passed QC/QA"
1108,544404.4,,,,,GCA_000022225.1,,,PRJNA30045,SAMN02604255,,,,Rod,1,2006,"Escherichia coli O157:H7. This strain is associated with Hamburger disease, which is caused by the contamination of meat products by enterohemorrhagic E. coli (EHEC). The identifier O157:H7 refers to the serotype of EHEC, and reflects the specific antigenic markers found on the surface of the cell. EHEC attaches and effaces to cells in the large intestine.There are numerous differences that distinguish O157:H7 from K-12, hundreds of them associated with genomic islands in either strain, including at least 9 large PAIs in O157:H7 that encode virulence factors. A type III secretion system, the locus of enterocyte effacement, numerous toxins and adhesins, as well as fimbrial gene clusters and iron uptake systems are found in these PAIs. Pathogenicity genes are also found on the plasmid pO157.i&gt;Escherichia coli O157:H7 str. TW14359. This strain was isolated from spinach during the E. coli outbreak in 2006 and will be used for comparative analysis.",2009-07-23T00:00:00Z,,,2014-12-08T22:11:32.822Z,2015-03-16T03:17:09.594Z,,Hemorrhagic colitis,50.5,"CP001368,CP001369",5622737,Escherichia coli O157:H7 str. TW14359,Complete,Escherichia,,-,Multiple,,,,"Spinach, Spinacia oleracea",isolated from spinach during the E. coli outbreak in 2006 and will be used for comparative analysis,,,spinach,,,"MLST.Escherichia_coli_1.11,MLST.Escherichia_coli_2.628",Yes,544404,-,Escherichia coli O157:H7 str. TW14359,,,,Facultative,5658,EHEC,1,19564389,"NC_013008,NC_013010",5372,,2,University of Washington,,,complete,,No,TW14359,Mesophilic,,"Included in the study, passed QC/QA"
1109,562.10006,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_001617565.1,HGAP v. 2.2.0,,PRJNA316786,SAMN04621897,,,,,1,2012,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2016-04-08T00:00:00Z,,,2016-04-28T09:39:18.275Z,2016-04-28T09:39:18.275Z,,,50.88,"CP015138,CP015140,CP015141,CP015142,CP015143,CP015144,CP015139",5418293,Escherichia coli strain Ecol_732,Complete,Escherichia,Thailand: Bangkok,,,,,,"Human, Homo sapiens",,Thailand,,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.43",,562,,,,,,,5611,,6,,"NZ_CP015138.1,NZ_CP015140.1,NZ_CP015141.1,NZ_CP015142.1,NZ_CP015143.1,NZ_CP015144.1,NZ_CP015139.1",5363,,7,University of Oxford,1x,PacBio,,,,Ecol_732,,,"Included in the study, passed QC/QA"
1110,562.10007,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_001618325.1,HGAP v. 2.2.0,,PRJNA316786,SAMN04590096,,,,,1,2012,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2016-04-11T00:00:00Z,,,2016-04-28T09:59:26.887Z,2016-04-28T09:59:26.887Z,,,50.81,"CP015069,CP015070,CP015072,CP015073,CP015071",5140092,Escherichia coli strain Ecol_743,Complete,Escherichia,United Arab Emirates: Dubai,,,,,,"Human, Homo sapiens",,United Arab Emirates,,,,,"MLST.Escherichia_coli_1.131,MLST.Escherichia_coli_2.506",,562,,,,,,,5227,,4,,"NZ_CP015069.1,NZ_CP015070.1,NZ_CP015072.1,NZ_CP015073.1,NZ_CP015071.1",4991,,5,University of Oxford,1x,PacBio,,,,Ecol_743,,,"Included in the study, passed QC/QA"
1111,562.10008,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_001618345.1,HGAP v. 2.2.0,,PRJNA316786,SAMN04590095,,,,,1,2012,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2016-04-11T00:00:00Z,,,2016-04-28T10:00:54.919Z,2016-04-28T10:00:54.919Z,,,50.76,"CP015074,CP015075",5040903,Escherichia coli strain Ecol_745,Complete,Escherichia,Morocco: Rabat,,,,,,"Human, Homo sapiens",,Morocco,,missing,,,MLST.Escherichia_coli_1.131,,562,,,,,,,5111,,1,,,4909,,2,University of Oxford,1x,PacBio,,,,Ecol_745,,,"Included in the study, passed QC/QA"
1112,562.10009,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_001618365.1,HGAP v. 2.2.0,,PRJNA316786,SAMN04590097,,,,,1,2011,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2016-04-11T00:00:00Z,,,2016-04-28T10:04:35.465Z,2016-04-28T10:04:35.465Z,,,50.78,"CP015076,CP015077,CP015078",5212298,Escherichia coli strain Ecol_448,Complete,Escherichia,Argentina: Buenos Aires,,,,,,"Human, Homo sapiens",,Argentina,,,,,"MLST.Escherichia_coli_2.506,MLST.Escherichia_coli_1.131",,562,,,,,,,5366,,2,,"NZ_CP015076.1,NZ_CP015077.1,NZ_CP015078.1",5101,,3,University of Oxford,1x,PacBio,,,,Ecol_448,,,"Included in the study, passed QC/QA"
1113,562.10577,,,,,,,,,,,,,,,,,,1,,2016-05-27T18:55:15.356Z,2016-05-27T18:55:15.356Z,,,46.53,,251493,Escherichia coli pHNSHP45-2,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,326,,,,,,,1,,,,,,,,,,"Excluded from the study, failed QC/QA."
1114,562.10826,collected_by:EDLB-CDC,,,,GCF_001644725.1,PacBio Hierarchical Genome Assembly,,PRJNA218110,SAMN04851092,,,,,1,8/10/11,PulseNet STEC genome reference library,2016-05-19T00:00:00Z,,,2016-07-05T01:51:06.254Z,2016-07-05T01:51:06.254Z,,,50.87,"CP015240,CP015239",4989576,Escherichia coli strain 2011C-3911,Complete,Escherichia,,,,,,,"Human, Homo sapiens",,,,stool,,,MLST.Escherichia_coli_1.1727,,562,,,,,,,5036,STEC,1,,"NZ_CP015240.1,NZ_CP015239.1",4826,,2,CDC,missing,PacBio,,O79:H7,,2011C-3911,,,"Included in the study, passed QC/QA"
1115,562.10827,collected_by:EDLB-CDC,,,,GCF_001644745.1,PacBio Hierarchical Genome Assembly,,PRJNA218110,SAMN04851091,,,,,1,8/20/13,PulseNet STEC genome reference library,2016-05-19T00:00:00Z,,,2016-07-05T01:52:48.658Z,2016-07-05T01:52:48.658Z,,,50.43,"CP015241,CP015242",5494966,Escherichia coli strain 2013C-4465,Complete,Escherichia,,,,,,,"Human, Homo sapiens",,,,stool,,,"MLST.Escherichia_coli_2.553,MLST.Escherichia_coli_1.335",,562,,,,,,,5662,STEC,1,,"NZ_CP015241.1,NZ_CP015242.1",5387,,2,CDC,missing,PacBio,,O55:H7,,2013C-4465,,,"Included in the study, passed QC/QA"
1116,562.10883,sample_type:whole organism,,,,GCF_001660565.1,PacBio SMRT Analysis v. 2.3.0,,PRJNA323827,SAMN05190012,,,,,1,17-Aug-15,Identification of the mcr-1 location,2016-06-09T00:00:00Z,,,2016-07-06T00:13:46.764Z,2016-07-06T00:13:46.764Z,,,50.67,"CP015995,CP015996,CP015997",5186163,Escherichia coli strain S51,Complete,Escherichia,Switzerland,,,,,,,,Switzerland,,poultry meat,,,MLST.Escherichia_coli_2.87,,562,,,,,,,5332,,2,,"NZ_CP015995.1,NZ_CP015996.1,NZ_CP015997.1",5087,,3,University of Zurich,209.0x,PacBio,,,,S51,,,"Included in the study, passed QC/QA"
1117,562.10884,sample_type:organism,,,,GCF_001660585.1,SPAdes v. v3.7.1,,PRJNA324008,SAMN05194365,,,,,1,2014,isolated from the native gut flora of female BALB/c mice (Charles River Laboratories),2016-06-09T00:00:00Z,,,2016-07-06T00:11:19.960Z,2016-07-06T00:11:19.960Z,,,50.58,"CP016007,CP016008,CP016009",5074819,Escherichia coli strain NGF1,Complete,Escherichia,"USA: Massachusetts, Boston",,,,,,"Mouse, Mus musculus",,United States,,gut flora of female BALB/c mice (Charles River Laboratories),,,"MLST.Escherichia_coli_1.998,MLST.Escherichia_coli_2.129",,562,,,,,,,5040,,2,,"NZ_CP016007.1,NZ_CP016008.1,NZ_CP016009.1",4843,,3,Harvard University,22.0x,Illumina HiSeq,,,,NGF1,,,"Included in the study, passed QC/QA"
1118,562.10886,sample_type:laboratory strain;biomaterial_provider:New England Biolabs,,,,GCF_001663075.1,Geneious de novo v. 6.1.7,,PRJNA324607,SAMN05210771,,,,,1,,genome sequence of restrictionless mutant laboratory K12 strain,2016-06-15T00:00:00Z,,,2016-07-06T03:16:27.939Z,2016-07-06T03:16:27.939Z,,,50.83,CP016018,4595577,Escherichia coli strain ER1821R,Complete,Escherichia,,,,,,,,,,,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.10",,562,,,,,genotype:mcrA mcrBC hsdRSM mrr,,4600,,,,NZ_CP016018.1,4418,,1,University of Colroado Anschutz Medical Campus,90x,Illumina MiSeq,,,,ER1821R,,,"Included in the study, passed QC/QA"
1119,562.10887,,,,,GCF_001663475.1,SMRT Portal v. 2.2,,PRJNA279654,SAMN03455974,,,,,1,2014,Escherichia coli Eco889 Genome Sequencing,2016-06-16T00:00:00Z,,,2016-07-06T03:38:26.933Z,2016-07-06T03:38:26.933Z,,,50.75,"CP015159,CP015161,CP015160",5312456,Escherichia coli strain Eco889,Complete,Escherichia,USA,,,,,,"Human, Homo sapiens",,United States,,,,,"MLST.Escherichia_coli_2.506,MLST.Escherichia_coli_1.131",,562,,,,,,,5501,,2,,"NZ_CP015159.1,NZ_CP015161.1,NZ_CP015160.1",5226,,3,NHGRI,150x,PacBio RSII,,,,Eco889,,,"Included in the study, passed QC/QA"
1120,562.10888,,,,,GCF_001672015.1,SPAdes v. 3.8.0,,PRJNA321990,SAMN04963292,,,,,,5/1/15,"We report the first E. coli strain co-producing the two carbapenemases blaNDM-1 and blaOXA-232. While endemic in Greece and India, double-carbapenemase producing enterobacteria are still rare in Germany. The dissemination of these pathogens is worrisome as it potentially further narrows the therapeutic options. Carbapenemase positive strains often display only moderately elevated MICs for at least one carbapenem and high-dose carbapenem therapy with prolonged infusion may be used for treatment in those instances. Double-carbapenemase production likely compromises this therapeutic option. Furthermore, newly developed beta-lactamase inhibitors with activity towards carbapenemases have recently been approved by several drug agencies and hold great promise for currently difficult or even untreatable infections. The presence of diverse beta-lactamases from different molecular groups in one pathogen may result in only partial inhibition and consequently in therapeutic failure. The isolation of nearly identical blaOXA-232 carrying plasmids from geographically and temporally unrelated cases not only from K. pneumoniae but now also from E. coli suggests high mobility of the plasmid, which may be more widespread than currently appreciated. Taken together, we characterized the first blaNDM-1/blaOXA-232 double-carbapenemase producing E. coli, highlighting the constant emergence of novel, highly drug resistant pathogens in central Europe and the necessity to control their spread.",2016-06-20T00:00:00Z,1,,2016-07-06T15:46:33.654Z,2016-07-06T15:46:33.654Z,,,50.54,"CP016034,CP016035,CP016036,CP016037,CP016038,CP016039,CP016040,CP016041,CP016042",5171571,Escherichia coli strain Co6114,Complete,Escherichia,Germany: Hamburg,,,,,,,,Germany,,,,,"MLST.Escherichia_coli_1.448,MLST.Escherichia_coli_2.58",,562,,,,,,,5290,,8,,,5053,,9,University Medical Center Hamburg-Eppendorf,192.0x,Illumina MiSeq; Nanopore,,,,Co6114,,,"Included in the study, passed QC/QA"
1121,562.1089,,,,,GCF_001675145.1,SMRT Portal v. 2.3,,PRJNA279612,SAMN03455931,,,,,1,2014,Escherichia coli ECONIH2 Genome Sequencing,2016-06-22T00:00:00Z,,,2016-07-06T19:14:24.693Z,2016-07-06T19:14:24.693Z,,,50.52,"CP014667,CP014668,CP014669",5331884,Escherichia coli strain ECONIH2,Complete,Escherichia,USA,,,,,,"Human, Homo sapiens",,United States,,,,,"MLST.Escherichia_coli_2.33,MLST.Escherichia_coli_1.127",,562,,,,,,,5391,,2,,"NZ_CP014667.1,NZ_CP014668.1,NZ_CP014669.1",5093,,3,NHGRI,166x,PacBio RSII,,,,ECONIH2,,,"Included in the study, passed QC/QA"
1122,562.11292,,,,,GCF_001677475.1,SMRT Portal HGAP v. 2.1.0,,PRJNA241122,SAMN02808332,,,,,1,2006,PacBio sequencing and assembly of E. coli,2016-07-01T00:00:00Z,,,2016-08-26T17:34:50.760Z,2016-08-26T17:34:50.760Z,,,50.42,"CP015229,CP012498",5712300,Escherichia coli strain 06-00048,Complete,Escherichia,USA:CA,,,,,,,,United States,,alfalfa sprouts,,,,,562,,,,,,,5910,,1,,"NZ_CP015229.1,NZ_CP012498.1",5459,,2,FDA,350X,PacBio RS,,O36:H14,,06-00048,,,"Included in the study, passed QC/QA"
1123,562.11293,,,,,GCF_001677495.1,SMRT Portal HGAP v. 2.3.0,,PRJNA241122,SAMN02808333,,,,,1,2009,PacBio sequencing and assembly of E. coli,2016-07-01T00:00:00Z,,,2016-08-26T16:35:20.106Z,2016-08-26T16:35:20.106Z,,,50.5,"CP015228,CP012500",5511850,Escherichia coli strain 09-00049,Complete,Escherichia,USA:MI,,,,,,,,United States,,lettuce,,,,,562,,,,,,,5784,,1,,"NZ_CP015228.1,NZ_CP012500.1",5393,,2,FDA,169X,PacBio RS,,O168,,09-00049,,,"Included in the study, passed QC/QA"
1124,562.11294,collected_by:MDP,,,,,SMRT Portal HGAP v. 2.3.0,,PRJNA241122,SAMN02688213,,,,,1,,PacBio sequencing and assembly of E. coli,2016-07-01T00:00:00Z,,,2016-08-26T16:30:55.621Z,2016-08-26T16:30:55.621Z,,,50.61,"CP013662,CP012501",5456185,Escherichia coli strain 08-00022,Complete,Escherichia,,,,,,,"Human, Homo sapiens",,,,bagged lettuce,,,,,562,,,,,,,5776,,1,,,5410,,2,FDA,100X,PacBio RS,,,,08-00022,,,"Included in the study, passed QC/QA"
1125,562.11315,collected_by:USDA,,,,GCF_001678965.1,SMRT Portal HGAP v. 2.1.0,,PRJNA241122,SAMN02688215,,,,,1,,PacBio sequencing and assembly of E. coli,2016-07-05T00:00:00Z,,,2016-08-26T17:25:15.140Z,2016-08-26T17:25:15.140Z,,,50.57,"CP013663,CP012499",5457411,Escherichia coli strain GB089,Complete,Escherichia,,,,,,,,,,,ground beef,,,,,562,,,,,,,5729,,1,,"NZ_CP013663.1,NZ_CP012499.1",5362,,2,FDA,350X,PacBio RS,,,,GB089,,,"Included in the study, passed QC/QA"
1126,562.11317,collected_by:UNIVERSITY OF MALAYA,,,,GCF_001682305.1,HGAP v. 2,,PRJNA325730,SAMN05252777,,,,,1,2013-08-18,Complete genome of colistin-resistant strains from Malaysia,2016-07-08T00:00:00Z,,,2016-08-26T18:53:32.150Z,2016-08-26T18:53:32.150Z,,,50.8,CP016182,4617698,Escherichia coli strain EC590,Complete,Escherichia,Malaysia,,,,,,"Human, Homo sapiens",,Malaysia,,Urine,,,,,562,,,,,,,4671,,,,,4445,,1,UNIVERSITY OF MALAYA,156.04 x,PacBio,,,,EC590,,,"Included in the study, passed QC/QA"
1127,562.11318,sample_type:whole organism,,,,GCF_001683435.1,SMRT Analysis v. 2.3.0,,PRJNA326753,SAMN05291917,,,,,1,2015-01-15,Escherichia coli harboring a chromosomal blaCTX-M-15,2016-07-11T00:00:00Z,,,2016-08-26T19:36:00.579Z,2016-08-26T19:36:00.579Z,,,50.37,CP016358,5154641,Escherichia coli strain K-15KW01,Complete,Escherichia,Switzerland,,,,,,"Human, Homo sapiens",,Switzerland,,,,,,,562,,,,,,,5175,,,,NZ_CP016358.1,4947,,1,University of Zurich,212x,PacBio,,,,K-15KW01,,,"Included in the study, passed QC/QA"
1128,562.11327,"collected_by:Chungnam National University Hospital, Daejeon, Korea",,,,GCF_001693315.1,PacBio SMRT Analysis v. 2.3.0,,PRJNA329167,SAMN05392487,,,,,1,27-Oct-2012,"Uropathogenic Escherichia coli (UPEC) are the primary causative of urinary tract infections (UTIs) worldwide. We isolated the strain, UPEC 26-1 from a patient suffering from UTI. The whole genome analysis of the isolate will provide information that will drive further study of UPEC to elucidate the vital factors responsible to cause disease.",2016-07-25T00:00:00Z,,,2016-08-27T02:19:41.307Z,2016-08-27T02:19:41.307Z,,,50.56,"CP016497,CP016498",5329753,Escherichia coli strain UPEC 26-1,Complete,Escherichia,South Korea: Daejeon,,,,,Urinary tract infection,"Human, Homo sapiens","isolated the strain, UPEC 26-1 from a patient suffering from UTI",South Korea,,Urine,,,,,562,,,,,,,5423,,1,,"NZ_CP016497.1,NZ_CP016498.1",5164,,2,"Chungnam National University, College of medicine",70x,PacBio RS,,,,UPEC 26-1,,,"Included in the study, passed QC/QA"
1129,562.11345,"collected_by:CDC, Atlanta",,,,GCF_001705405.1,SMRT v. November-2015,,PRJNA321453,SAMN04966308,,,,,,1982,In Silico and Functional Analysis of Prophage-Encoded 5-N-Acetyl-9-O-Acetyl Neuraminic Acid Esterases of E. coli O157:H7 Strain EDL933,2016-08-16T00:00:00Z,1,,2016-08-27T08:25:07.224Z,2016-08-27T08:25:07.224Z,,,50.43,"CP015855,CP015856",5467086,Escherichia coli strain EDL933-1,Complete,Escherichia,USA,,,,,,,,United States,,ground beef,,,,,562,,,,,,,5777,EHEC,1,,,5434,,2,University of Hohenheim,100.0x,PacBio,,O157:H7,,EDL933-1,,,"Included in the study, passed QC/QA"
1130,562.11469,,,,,GCF_001678925.1,Spades v. 3.0.0,,PRJNA286318,SAMN03768474,,,,,1,,The goal of this study is to compare human and animal E. coli in order to predict zoonotic potential.,2016-07-05T00:00:00Z,,,2016-09-11T10:36:23.347Z,2016-09-11T10:36:23.347Z,,,50.76,CP013031,4731493,Escherichia coli strain H1827/12,Complete,Escherichia,,,,,,bacteremia,"Human, Homo sapiens",,,,blood,,,,,562,C,,,,,,4792,,,,NZ_CP013031.1,4532,,1,Universidade Estadual de Campinas,100x,Illumina and Sanger,,O7:HNT,,H1827/12,,,"Included in the study, passed QC/QA"
1131,562.1147,collected_by:US Department of Agriculture,,,,GCF_001679985.1,CANU v. May-2016; Geneious v. May-2016,,PRJNA323357,SAMN05177221,,,,,1,02-Feb-2016,Isolation of colistin resistant organisms from food animals.,2016-07-06T00:00:00Z,,,2016-09-11T10:48:19.718Z,2016-09-11T10:48:19.718Z,,,50.59,"CP015912,CP015913,CP015914,CP015915,CP015916,CP015917",5424193,Escherichia coli strain 210205630,Complete,Escherichia,USA,,,,,,,,United States,,swine cecum,,,,,562,,,,,,,5566,,5,,"NZ_CP015912.1,NZ_CP015913.1,NZ_CP015914.1,NZ_CP015915.1,NZ_CP015916.1,NZ_CP015917.1",5311,,6,Agricultural Research Service,91x,Illumina; PacBio,,,,210205630,,,"Included in the study, passed QC/QA"
1132,562.11479,"sample_type:whole organisme;biomaterial_provider:Leiden University Medical Center, department Medical microbiology, Albinusdreef 2, 2333ZA Leiden, the Netherlands;collected_by:Leiden University Medical Center, department Medical Microbiology, E.M. Terveer;identified_by:E.M. Terveer",6 m,,,GCF_001693635.1,SMRT analysis v. 2.3.0,,PRJNA329265,SAMN05407982,,,,,1,13-Apr-2015,"The emergence of the newly discovered plasmid-mediated colistin resistance gene, mcr-1, poses a significant threat to hospitalized patients as well as to the community. The aim of this study was to determine the prevalence of mcr-1 mediated colistin resistance gene in fecal samples of patients attending a tertiary care hospital. From November 2014 until July 2015, fecal samples of patients attending the Leiden University Medical Center were collected and retrospectively screened for presence of mcr-1 using real-time PCR. Two of 576 patients were positive for mcr-1, resulting in a prevalence of 0.35%. One sample contained an ESBL negative, AmpC positive and mcr-1 (located on an IncX4 plasmid) containing E.coli. This strain belonged to Sequence Type 359 and serotype O177:H21. The mcr-1 containing E.coli was phenotypically susceptible to colistin with a MIC of ≤ 0.25mg/L, due to a 1329bp transposon IS10R inserted into the mcr-1 gene.",2016-07-26T00:00:00Z,,,2016-09-11T16:31:47.500Z,2016-09-11T16:31:47.500Z,0m,,50.41,"CP016546,CP016547,CP016548,CP016549,CP016550,CP016551",5494878,Escherichia coli strain O177:H21,Complete,Escherichia,Netherlands: Leiden,,,,,,"Human, Homo sapiens",,Netherlands,,faeces,,,,,562,,,,,genotype:ST 359,,5852,,5,,"NZ_CP016546.1,NZ_CP016547.1,NZ_CP016548.1,NZ_CP016549.1,NZ_CP016550.1,NZ_CP016551.1",5467,,6,Leiden University Medical Center,30.0x,PacBio,,O177:H21,,asymptomatic colonization,,,"Included in the study, passed QC/QA"
1133,562.11558,,,,,GCF_900092615.1,,,PRJEB14041,SAMEA3988096,,,,,1,,"In 1885 Theodor Escherich first described Bacillus coli commune. Later this species was renamed Escherichia coli. Here we described the complete genome sequence of the strain of E. coli originally isolated by Escherich over 125 years ago. We performed genomic and phylogenetic comparisons with other E. coli strains. Consistent with Escherich’s observations, these studies revealed Escherich’s original strain is most closely related to the non-pathogenic commensal strains of E. coli and their laboratory derivatives.",2016-07-21T00:00:00Z,,,2016-09-12T11:03:03.228Z,2016-09-12T11:03:03.228Z,,,50.65,LT601384,5144250,Escherichia coli strain NCTC86EC,Complete,Escherichia,,,,,,,,isolated by Escherich over 125 years ago,,,,,,,,562,,,,,,,5150,,,,NZ_LT601384.1,4840,,1,kxd419,,,,,,NCTC86EC,,,"Included in the study, passed QC/QA"
1134,562.12823,collected_by:Korea Center for Disease Control and Prevention,,,,GCF_001721125.1,CLCbio CLC Genomics Workbench v. 7.5.1;,,PRJNA294502,SAMN04026657,,,,,1,2003-01-01,Enterohaemorrhagic Escherichia coli is one of the well-known food-borne pathogen. It was isolated from stool of foodborne poisoning patient in South Korea.,2016-09-07T00:00:00Z,,,2016-11-16T00:10:29.298Z,2016-11-16T00:10:29.298Z,,Foodborne disease,50.62,CP012693,5704396,Escherichia coli strain FORC_028,Complete,Escherichia,South Korea: Gwang-Ju,,HostAssociated,,,Not reported,"Human, Homo sapiens",isolated from stool of foodborne poisoning patient in South Korea,South Korea,,stool,,,,,562,37 C,,,,,Facultative,6027,,,,NZ_CP012693.1,6067,,1,Seoul National University,418.07x,Illumina; PacBio,,,,FORC_028,Mesophilic,,"Included in the study, passed QC/QA"
1135,562.12824,collected_by:CDC,,,,GCF_001721205.1,SMRT Portal HGAP v. 2.3.0,,PRJNA241122,SAMN02688214,,,,,1,2004,PacBio sequencing and assembly of E. coli,2016-09-07T00:00:00Z,,,2016-11-16T00:17:52.394Z,2016-11-16T00:17:52.394Z,,,50.38,"CP014670,CP012494,CP012496,CP012495",5374570,Escherichia coli strain CFSAN004177,Complete,Escherichia,USA,,,,,,"Human, Homo sapiens",,United States,,,,,,,562,,,,,,,5868,,3,,"NZ_CP014670.1,NZ_CP012494.1,NZ_CP012496.1,NZ_CP012495.1",5408,,4,FDA,250,PacBio,,,,CFSAN004177,,,"Included in the study, passed QC/QA"
1136,562.12825,collected_by:CDC,,,,GCF_001721225.1,SMRT Portal HGAP v. 2.3.0,,PRJNA241122,SAMN02688212,,,,,1,2003,PacBio sequencing and assembly of E. coli,2016-09-07T00:00:00Z,,,2016-11-16T00:18:04.021Z,2016-11-16T00:18:04.021Z,,,50.38,"CP014583,CP012493,CP012492,CP012491",5376466,Escherichia coli strain CFSAN004176,Complete,Escherichia,USA,,,,,,"Human, Homo sapiens",,United States,,,,,,,562,,,,,,,5753,,3,,"NZ_CP014583.1,NZ_CP012493.1,NZ_CP012492.1,NZ_CP012491.1",5394,,4,FDA,600,PacBio,,,,CFSAN004176,,,"Included in the study, passed QC/QA"
1137,562.12826,,,,,GCF_001721525.1,HGAP v. 2.0,,PRJNA301656,SAMN04939501,,,,,1,,Complete sequencing of carbapenem resistant uropathogenic E. coli strain MS6198,2016-09-08T00:00:00Z,,,2016-11-16T00:36:02.859Z,2016-11-16T00:36:02.859Z,,,50.5,"CP015834,CP015835,CP015836,CP015837,CP015838",5599783,Escherichia coli strain MS6198,Complete,Escherichia,United Kingdom,,,,,Urinary tract infection,"Human, Homo sapiens",,United Kingdom,,urine,,,,,562,C,,,,,,5644,,4,,"NZ_CP015834.1,NZ_CP015835.1,NZ_CP015836.1,NZ_CP015837.1,NZ_CP015838.1",5275,,5,University of Queensland,120x,PacBio,,,,MS6198,,,"Included in the study, passed QC/QA"
1138,562.12827,sample_type:single cell,,,,GCF_001723505.1,HGAP.3/Quiver v. v2.3.0,,PRJNA341475,SAMN05725120,,,,,1,2016,"Closed and finished genome of NEB 5-alpha, an immediate fhuA derivative of (E. coli K-12) DH5alpha.",2016-09-13T00:00:00Z,,,2016-11-16T02:43:57.125Z,2016-11-16T02:43:57.125Z,,,50.77,CP017100,4583637,Escherichia coli strain K-12 NEB 5-alpha,Complete,Escherichia,"USA: Ipswich, MA",,,,,,,,United States,,laboratory,,,,,562,,,,,,,4600,,,,NZ_CP017100.1,4418,,1,New England Biolabs,314x,PacBio,,,,K-12 NEB 5-alpha,,,"Included in the study, passed QC/QA"
1139,562.1283,sample_type:intestinal contents,,,,GCF_001735705.1,HGAP v. 3; Geneious v. 9.1.5,,PRJNA328481,SAMN05346848,,,,,1,2016-05-17,mcr-1 positive colistin resistant E. coli,2016-09-20T00:00:00Z,,,2016-11-16T12:41:14.335Z,2016-11-16T12:41:14.335Z,,,50.76,"CP016404,CP016405",4731950,Escherichia coli strain 210221272,Complete,Escherichia,USA:Illinois,,,,,,"Pig, Sus scrofa ",,United States,,cecal contents,,,,,562,,,,,,,4791,,1,,"NZ_CP016404.1,NZ_CP016405.1",4577,,2,Agricultural Research Service,98,Illumina; PacBio,,,,210205630,,,"Included in the study, passed QC/QA"
1140,562.12907,collected_by:Korea Center for Disease Control and Prevention,,,,GCF_001750845.1,SMRT Assembly v. 2.3.0,,PRJNA299539,SAMN04209666,,,,,1,2004-01-01,Enterohaemorrhagic Escherichia coli is one of the well-known food-borne pathogen. It was isolated from stool of foodborne poisoning patient in South Korea.,2016-10-03T00:00:00Z,,,2016-11-16T20:13:58.962Z,2016-11-16T20:13:58.962Z,,Foodborne disease,50.56,"CP013190,CP013191,CP013192,CP013193,CP013194",5100852,Escherichia coli strain FORC_031,Complete,Escherichia,Korea: Busan,,HostAssociated,,,Not reported,"Human, Homo sapiens",isolated from stool of foodborne poisoning patient in South Korea,South Korea,,Human Stool,,,,,562,37 C,,,,,Facultative,5304,,4,,"NZ_CP013190.1,NZ_CP013191.1,NZ_CP013192.1,NZ_CP013193.1,NZ_CP013194.1",5252,,5,Seoul National University,missing,PacBio,,,,FORC_031,Mesophilic,,"Included in the study, passed QC/QA"
1141,562.12924,,,,,GCF_001806265.1,smrtanalysis v. 2.3.0; CANU v. 1.3,,PRJNA341860,SAMN05729957,,,,,1,,Whole-genome sequencing of a wild-type E. coli O157:H7 and its mutant isolate to identify genotypic attributes conferring the mutant phenotype,2016-10-21T00:00:00Z,,,2016-11-18T07:55:45.739Z,2016-11-18T07:55:45.739Z,,,50.43,"CP017249,CP017250",5559797,Escherichia coli strain NADC 5570/86-24/6565,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,"genotype:stx2+, eae+, Str-resistant",,5884,EHEC,1,,"NZ_CP017249.1,NZ_CP017250.1",5544,,2,USDA/ARS/National Animal Disease Center,523x,PacBio; Illumina,,O157:H7,,mutant,,,"Included in the study, passed QC/QA"
1142,562.12925,,,,,GCF_001806285.1,smrtanalysis v. 2.3.0; CANU v. 1.3,,PRJNA341860,SAMN05729956,,,,,,,Whole-genome sequencing of a wild-type E. coli O157:H7 and its mutant isolate to identify genotypic attributes conferring the mutant phenotype,2016-10-21T00:00:00Z,1,,2016-11-18T07:58:50.773Z,2016-11-18T07:58:50.773Z,,,50.43,"CP017251,CP017252",5559461,Escherichia coli strain NADC 5570/86-24/6564,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,"genotype:stx2+, eae+, Str-resistant",,5880,EHEC,1,,"NZ_CP017251.1,NZ_CP017252.1",5542,,2,USDA/ARS/National Animal Disease Center,526x,PacBio; Illumina,,O157:H7,,wild type,,,"Included in the study, passed QC/QA"
1143,562.12941,,,,,GCF_001860505.1,SMRT v. unspecified,,PRJNA304360,SAMN04299569,,,,,1,2013-09-28,To reveal characteristics of chromosome-borned blaNDM-1 gene positive Enterobacteriaceae strain,2016-11-01T00:00:00Z,,,2016-11-19T07:30:25.100Z,2016-11-19T07:30:25.100Z,,,50.81,CP013483,4839266,Escherichia coli strain Y5,Complete,Escherichia,China: Zhejiang,,,,,,"Human, Homo sapiens",,China,,urine,,,,,562,C,,,,,,4848,,,,NZ_CP013483.1,4585,,1,"Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China",100,PacBio,,,,Y5,,,"Included in the study, passed QC/QA"
1144,562.12944,sample_type:bacteria,,,,GCF_001865295.1,HGAP v. V3,,PRJNA294158,SAMN04040761,,,,,1,2008,"The project goals are to study DNA sequence, transcriptomic, and phenotypic variations among strains of Shiga toxin producing Escherichia coli in reference to biofilm formation and surface adhesion.",2016-11-03T00:00:00Z,,,2016-11-19T08:38:04.989Z,2016-11-19T08:38:04.989Z,,,50.51,"CP017669,CP017670",5618601,Escherichia coli strain PA20,Complete,Escherichia,USA: Pennsylvania,,,,,,,,United States,,stool,,,,,562,C,,,,,,5961,,1,,"NZ_CP017669.1,NZ_CP017670.1",5646,,2,USDA/ARS/Eastern Regional Research Center,273.59x,PacBio,,,,PA20,,,"Included in the study, passed QC/QA"
1145,562.13544,collected_by:MRSN,,,,GCF_001886535.1,HGAP v. 2.0,,PRJNA353939,SAMN06029893,,,,,1,Jul-2016,Whole genome sequencing of mcr-1 carrying Escherichia coli clinical isolates.,2016-11-28T00:00:00Z,,,2017-01-16T05:21:04.289Z,2017-01-16T05:21:04.289Z,,,50.75,"CP018103,CP018108,CP018107,CP018105,CP018106,CP018104",5200916,Escherichia coli strain MRSN352231,Complete,Escherichia,Germany,,,,,,"Human, Homo sapiens",,,,Clinical,,,,,562,,,,,,,5310,,5,,"NZ_CP018103.1,NZ_CP018108.1,NZ_CP018107.1,NZ_CP018105.1,NZ_CP018106.1,NZ_CP018104.1",5057,,6,Walter Reed Army Institute of Research,300.0x,PacBio; Illumina MiSeq,,,,MRSN352231,,,"Included in the study, passed QC/QA"
1146,562.13545,collected_by:MRSN,,,,GCF_001886555.1,HGAP v. 2.0,,PRJNA353939,SAMN06029895,,,,,1,Jul-2016,Whole genome sequencing of mcr-1 carrying Escherichia coli clinical isolates.,2016-11-28T00:00:00Z,,,2017-01-16T05:21:24.316Z,2017-01-16T05:21:24.316Z,,,50.76,"CP018115,CP018116,CP018120,CP018119,CP018118,CP018117",5116498,Escherichia coli strain MRSN346638,Complete,Escherichia,USA,,,,,,"Human, Homo sapiens",,,,Clinical,,,,,562,,,,,,,5213,,5,,"NZ_CP018115.1,NZ_CP018116.1,NZ_CP018120.1,NZ_CP018119.1,NZ_CP018118.1,NZ_CP018117.1",4964,,6,Walter Reed Army Institute of Research,300.0x,PacBio; Illumina MiSeq,,,,MRSN346638,,,"Included in the study, passed QC/QA"
1147,562.13546,collected_by:MRSN,,,,GCF_001886575.1,HGAP v. 2.0,,PRJNA353939,SAMN06029896,,,,,1,Jul-2016,Whole genome sequencing of mcr-1 carrying Escherichia coli clinical isolates.,2016-11-28T00:00:00Z,,,2017-01-16T05:21:46.698Z,2017-01-16T05:21:46.698Z,,,50.76,"CP018121,CP018122,CP018126,CP018125,CP018124,CP018123",5114354,Escherichia coli strain MRSN346355,Complete,Escherichia,USA,,,,,,"Human, Homo sapiens",,,,Clinical,,,,,562,,,,,,,5208,,5,,"NZ_CP018121.1,NZ_CP018122.1,NZ_CP018126.1,NZ_CP018125.1,NZ_CP018124.1,NZ_CP018123.1",4957,,6,Walter Reed Army Institute of Research,300.0x,PacBio; Illumina MiSeq,,,,MRSN346355,,,"Included in the study, passed QC/QA"
1148,562.13547,collected_by:MRSN,,,,GCF_001886755.1,HGAP v. 2.0,,PRJNA353939,SAMN06029894,,,,,1,Jul-2016,Whole genome sequencing of mcr-1 carrying Escherichia coli clinical isolates.,2016-11-28T00:00:00Z,,,2017-01-16T05:29:10.521Z,2017-01-16T05:29:10.521Z,,,50.76,"CP018109,CP018110,CP018114,CP018113,CP018112,CP018111",5116627,Escherichia coli strain MRSN346595,Complete,Escherichia,USA,,,,,,"Human, Homo sapiens",,,,Clinical,,,,,562,,,,,,,5213,,5,,"NZ_CP018109.1,NZ_CP018110.1,NZ_CP018114.1,NZ_CP018113.1,NZ_CP018112.1,NZ_CP018111.1",4963,,6,Walter Reed Army Institute of Research,300.0x,PacBio; Illumina MiSeq,,,,MRSN346595,,,"Included in the study, passed QC/QA"
1149,562.13548,"collected_by:Centers for Disease Control & Prevention, Korea",,,,GCA_001886895.1,CLC Genomics Workbench v. 7.5.1; BacBio,,PRJNA301212,SAMN04243989,,,,,1,2014-01-01,Complete genome sequencing of Escherichia coli FORC_029,2016-11-28T00:00:00Z,,,2017-01-16T05:35:19.859Z,2017-01-16T05:35:19.859Z,,,50.66,"CP013185,CP013186",5267283,Escherichia coli strain FORC_029,Complete,Escherichia,South Korea,,,,,,,,,,Stool,,,,,562,C,,,,,,5318,,1,,,4999,,2,"Food-borne Pathogen Omics Research Center, FORC",343.97,Illumina; PacBio,,,,FORC_029,,,"Included in the study, passed QC/QA"
1150,562.13549,"collected_by:Ministry of Food and Drug Safety, Republic of Korea",,,,GCF_001886935.1,PacBio SMRT analysis v. 2.3.0,,PRJNA321067,SAMN04965119,,,,,1,2013-05-21,Complete genome sequencing of Escherichia coli FORC_041,2016-11-28T00:00:00Z,,,2017-01-16T05:39:32.569Z,2017-01-16T05:39:32.569Z,,,50.75,CP016628,4867152,Escherichia coli strain FORC_041,Complete,Escherichia,South Korea: Seoul,,,,,,,,,,Bulgogi,,,,,562,,,,,,,4832,EHEC,,,NZ_CP016628.1,4650,,1,"Food-borne Pathogen Omics Research Center, FORC",456.1,PacBio,,,,FORC_041,,,"Included in the study, passed QC/QA"
1151,562.1355,"collected_by:Carlos Eslava Campos, Armando Navarro Ocana, Alejandro Cravioto",,,,GCF_001888075.1,"HGAP_3 in SMRT analysis v. 2.3, Spades v.",,PRJNA350704,SAMN05945146,,,,,1,1987,description og genes involved in pathogenicity,2016-12-02T00:00:00Z,,,2017-01-16T06:24:08.192Z,2017-01-16T06:24:08.192Z,,,50.52,"CP017844,CP017848,CP017845,CP017846,CP017847",5022828,Escherichia coli strain FMU073332,Complete,Escherichia,"Mexico: Tlaltizpan, Morelos",,,730 days,,ETEC infection,"Human, Homo sapiens",,,,faeces,,,,,562,,,host_description:child,,"genotype:st+, lt+, lngA+, cstH+, ecpA+, etpA+, etpB+, tibA-, leoA-, tia-, eatA-, cfAI, cfAIII-, cs1-.",,5217,ETEC,4,,"NZ_CP017844.1,NZ_CP017848.1,NZ_CP017845.1,NZ_CP017846.1,NZ_CP017847.1",4936,,5,Centro de Ciencias Genomicas,290X,Illumina HiSeq and PacBio RSII,,O6:H16,,FMU073332,,,"Included in the study, passed QC/QA"
1152,562.13551,collected_by:Publich Health England,,,,GCF_001890205.1,Celera 8.1 v. Mar-2014,,PRJNA336330,SAMN05544764,,,,,1,2012,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",2016-12-07T00:00:00Z,,,2017-01-16T08:03:48.304Z,2017-01-16T08:03:48.304Z,,,50.5,"CP018237,CP018238",5604428,Escherichia coli strain 155,Complete,Escherichia,United Kingdom,,,,,,"Human, Homo sapiens",,,,Human,,,,,562,,,,,,,6087,EHEC,1,,"NZ_CP018237.1,NZ_CP018238.1",5955,,2,United State Department of Agriculture,103X,PacBio,,O157:H7,,155,,,"Included in the study, passed QC/QA"
1153,562.13552,collected_by:Publich Health England,,,,GCF_001890225.1,Celera 8.1 v. Apr-2014,,PRJNA336330,SAMN05544766,,,,,1,2013,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",2016-12-07T00:00:00Z,,,2017-01-16T08:01:32.213Z,2017-01-16T08:01:32.213Z,,,50.44,"CP018239,CP018240",5568363,Escherichia coli strain 272,Complete,Escherichia,United Kingdom,,,,,,"Human, Homo sapiens",,,,Human,,,,,562,,,,,,,6024,EHEC,1,,"NZ_CP018239.1,NZ_CP018240.1",5909,,2,United State Department of Agriculture,165X,PacBio,,O157:H7,,272,,,"Included in the study, passed QC/QA"
1154,562.13553,collected_by:Publich Health England,,,,GCF_001890245.1,Celera 8.1 v. Jan-2015,,PRJNA336330,SAMN05544767,,,,,1,2012,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",2016-12-07T00:00:00Z,,,2017-01-16T08:04:26.615Z,2017-01-16T08:04:26.615Z,,,50.46,"CP018245,CP018246",5608872,Escherichia coli strain 472,Complete,Escherichia,United Kingdom,,,,,,"Human, Homo sapiens",,,,Human,,,,,562,,,,,,,6101,EHEC,1,,"NZ_CP018245.1,NZ_CP018246.1",5975,,2,United State Department of Agriculture,207X,PacBio,,O157:H7,,472,,,"Included in the study, passed QC/QA"
1155,562.13554,collected_by:Publich Health England,,,,GCF_001890265.1,Celera 8.1 v. Jan-2015,,PRJNA336330,SAMN05544765,,,,,1,2011,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",2016-12-07T00:00:00Z,,,2017-01-16T08:00:53.108Z,2017-01-16T08:00:53.108Z,,,50.49,"CP018243,CP018244",5504345,Escherichia coli strain 350,Complete,Escherichia,United Kingdom,,,,,,"Human, Homo sapiens",,,,Human,,,,,562,,,,,,,5897,EHEC,1,,"NZ_CP018243.1,NZ_CP018244.1",5829,,2,United State Department of Agriculture,283X,PacBio,,O157:H7,,350,,,"Included in the study, passed QC/QA"
1156,562.13555,collected_by:IPRAVE Consortium,,,,GCF_001890285.1,Celera 8.1 v. Aug-2014,,PRJNA336330,SAMN05544760,,,,,1,2002,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",2016-12-07T00:00:00Z,,,2017-01-16T08:02:19.590Z,2017-01-16T08:02:19.590Z,,,50.49,"CP018252,CP018253",5611726,Escherichia coli strain 9000,Complete,Escherichia,United Kingdom,,,,,,,,,,Cattle faeces,,,,,562,,,,,,,6084,EHEC,1,,"NZ_CP018252.1,NZ_CP018253.1",5985,,2,United State Department of Agriculture,297X,PacBio,,O157:H7,,9000,,,"Included in the study, passed QC/QA"
1157,562.13556,collected_by:IPRAVE Consortium,,,,GCF_001890305.1,Celera 8.1 v. Apr-2014,,PRJNA336330,SAMN05544762,,,,,1,2002,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",2016-12-07T00:00:00Z,,,2017-01-16T08:02:28.100Z,2017-01-16T08:02:28.100Z,,,50.46,"CP018247,CP018248",5462063,Escherichia coli strain 7784,Complete,Escherichia,United Kingdom,,,,,,,,,,Cattle faeces,,,,,562,,,,,,,5880,EHEC,1,,"NZ_CP018247.1,NZ_CP018248.1",5781,,2,United State Department of Agriculture,187X,PacBio,,O157:H7,,7784,,,"Included in the study, passed QC/QA"
1158,562.13557,collected_by:Publich Health England,,,,GCF_001890325.1,Celera 8.1 v. Mar-2014,,PRJNA336330,SAMN05544768,,,,,1,2012,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",2016-12-07T00:00:00Z,,,2017-01-16T08:01:01.096Z,2017-01-16T08:01:01.096Z,,,50.49,"CP018241,CP018242",5567385,Escherichia coli strain 319,Complete,Escherichia,United Kingdom,,,,,,"Human, Homo sapiens",,,,Human,,,,,562,,,,,,,5977,EHEC,1,,"NZ_CP018241.1,NZ_CP018242.1",5890,,2,United State Department of Agriculture,132X,PacBio,,O157:H7,,319,,,"Included in the study, passed QC/QA"
1159,562.13558,collected_by:IPRAVE Consortium,,,,GCF_001890345.1,Celera 8.1 v. Feb-2015,,PRJNA336330,SAMN05544761,,,,,1,2002,"Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 strains pose a threat to human health and are usually acquired from ruminants, the environment or fresh produce. Recent whole genome sequencing based on short-read technologies help trace outbreaks and have provided significant insights into the evolution of this pathogen, but these methods don’t capture the genomic variation that underpins differences in zoonotic and pathogenic potential. This variation is, in part, driven by the acquisition of bacteriophages (phages) which contain many similar sequences that require longer read sequencing technologies in order to define their complete composition and position in the genome. This study has used single molecule real time (SMRT) sequencing, a long read technique, to define the integrated phage sequences in a strain set selected to represent the wide diversity of EHEC O157. We demonstrate that the most recent diversification correlates with acquisition of phages encoding specific types of Shiga toxin, responsible for the main damage and life-threatening consequences of EHEC in humans. Smaller phage regions have preferentially lost genes allowing phage production and the density of insertion sequences elements in integrated phage regions supports their involvement in gene deletion and phage entrapment. Profiling of integrated phages will aid identification of virulent strains from short read sequencing currently being adopted more routinely in diagnostic laboratories.",2016-12-07T00:00:00Z,,,2017-01-16T08:06:39.843Z,2017-01-16T08:06:39.843Z,,,50.49,"CP018250,CP018251",5520540,Escherichia coli strain 10671,Complete,Escherichia,United Kingdom,,,,,,,,,,Cattle faeces,,,,,562,,,,,,,5948,EHEC,1,,"NZ_CP018250.1,NZ_CP018251.1",5840,,2,United State Department of Agriculture,134X,PacBio,,O157:H7,,10671,,,"Included in the study, passed QC/QA"
1160,562.13559,collected_by:MRSN,,,,GCF_001890365.1,HGAP v. 2.0,,PRJNA353939,SAMN06067968,,,,,1,Jul-2016,Whole genome sequencing of mcr-1 carrying Escherichia coli clinical isolates.,2016-12-07T00:00:00Z,,,2017-01-16T08:09:52.834Z,2017-01-16T08:09:52.834Z,,,50.62,"CP018206,CP018207,CP018208",5158613,Escherichia coli strain MRSN346647,Complete,Escherichia,USA,,,,,,"Human, Homo sapiens",,,,Clinical,,,,,562,,,,,,,5312,,2,,"NZ_CP018206.1,NZ_CP018207.1,NZ_CP018208.1",5212,,3,Walter Reed Army Institute of Research,200.0x,PacBio; Illumina MiSeq,,,,MRSN346647,,,"Included in the study, passed QC/QA"
1161,562.13736,,,,,GCF_001900295.1,Newbler v. 2.7,,PRJNA269191,SAMN03252409,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T16:53:41.485Z,2017-01-16T16:53:41.485Z,,,50.54,CP010116,4843023,Escherichia coli strain C1,Complete,Escherichia,,,,,,,cow,,,,,,,,,562,,,,,,,4794,,,,NZ_CP010116.1,4546,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,C1,,,"Included in the study, passed QC/QA"
1162,562.13737,,,,,GCF_001900315.1,Newbler v. 2.7,,PRJNA269191,SAMN03252412,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T16:59:14.188Z,2017-01-16T16:59:14.188Z,,,50.56,CP010121,4990476,Escherichia coli strain C4,Complete,Escherichia,,,,,,,cow,,,,,,,,,562,,,,,,,4889,,,,NZ_CP010121.1,4681,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,C4,,,"Included in the study, passed QC/QA"
1163,562.13738,,,,,GCF_001900335.1,Newbler v. 2.7,,PRJNA269191,SAMN03252417,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T16:59:59.731Z,2017-01-16T16:59:59.731Z,,,50.81,CP010132,5021692,Escherichia coli strain C10,Complete,Escherichia,,,,,,,cow,,,,,,,,,562,,,,,,,5023,,,,NZ_CP010132.1,4709,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,C10,,,"Included in the study, passed QC/QA"
1164,562.13739,,,,,GCF_001900355.1,Newbler v. 2.7,,PRJNA269191,SAMN03252418,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:00:32.476Z,2017-01-16T17:00:32.476Z,,,50.83,CP010133,5414571,Escherichia coli strain C11,Complete,Escherichia,,,,,,,cow,,,,,,,,,562,,,,,,,5368,,,,NZ_CP010133.1,5049,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,C11,,,"Included in the study, passed QC/QA"
1165,562.1374,,,,,GCF_001900375.1,Newbler v. 2.7,,PRJNA269191,SAMN03252425,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T16:55:30.910Z,2017-01-16T16:55:30.910Z,,,50.93,CP010150,4827779,Escherichia coli strain D7,Complete,Escherichia,,,,,,,Dog,,,,,,,,,562,,,,,,,4767,,,,NZ_CP010150.1,4557,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,D7,,,"Included in the study, passed QC/QA"
1166,562.13741,,,,,GCF_001900395.1,Newbler v. 2.7,,PRJNA269191,SAMN03252426,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:00:39.256Z,2017-01-16T17:00:39.256Z,,,50.39,CP010151,5130646,Escherichia coli strain D8,Complete,Escherichia,,,,,,,Dog,,,,,,,,,562,,,,,,,5142,,,,NZ_CP010151.1,4831,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,D8,,,"Included in the study, passed QC/QA"
1167,562.13742,,,,,GCF_001900415.1,Newbler v. 2.7,,PRJNA269191,SAMN03252432,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:09:25.506Z,2017-01-16T17:09:25.506Z,,,50.75,CP010169,4833228,Escherichia coli strain H5,Complete,Escherichia,,,,,,,,,,,river water,,,,,562,,,,,,,4817,,,,NZ_CP010169.1,4535,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,H5,,,"Included in the study, passed QC/QA"
1168,562.13743,,,,,GCF_001900435.1,Newbler v. 2.7,,PRJNA269191,SAMN03252433,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:10:29.925Z,2017-01-16T17:10:29.925Z,,,50.75,CP010170,4832567,Escherichia coli strain H6,Complete,Escherichia,,,,,,,,,,,river water,,,,,562,,,,,,,4815,,,,NZ_CP010170.1,4539,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,H6,,,"Included in the study, passed QC/QA"
1169,562.13744,,,,,GCF_001900455.1,Newbler v. 2.7,,PRJNA269191,SAMN03252434,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:02:20.701Z,2017-01-16T17:02:20.701Z,,,50.77,CP010171,4807161,Escherichia coli strain H7,Complete,Escherichia,,,,,,,,,,,river water,,,,,562,,,,,,,4815,,,,NZ_CP010171.1,4524,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,H7,,,"Included in the study, passed QC/QA"
1170,562.13745,,,,,GCF_001900475.1,Newbler v. 2.7,,PRJNA269191,SAMN03252436,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:01:37.959Z,2017-01-16T17:01:37.959Z,,,50.76,CP010176,4805164,Escherichia coli strain H10,Complete,Escherichia,,,,,,,,,,,river water,,,,,562,,,,,,,4758,,,,NZ_CP010176.1,4558,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,H10,,,"Included in the study, passed QC/QA"
1171,562.13746,,,,,GCF_001900495.1,Newbler v. 2.7,,PRJNA269191,SAMN03252410,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:04:20.207Z,2017-01-16T17:04:20.207Z,,,50.73,"CP010117,CP010118",4818237,Escherichia coli strain C2,Complete,Escherichia,,,,,,,cow,,,,,,,,,562,,,,,,,4806,,1,,"NZ_CP010117.1,NZ_CP010118.1",4558,,2,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,C2,,,"Included in the study, passed QC/QA"
1172,562.13747,,,,,GCF_001900515.1,Newbler v. 2.7,,PRJNA269191,SAMN03252411,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:06:41.907Z,2017-01-16T17:06:41.907Z,,,50.61,"CP010119,CP010120",5413266,Escherichia coli strain C3,Complete,Escherichia,,,,,,,cow,,,,,,,,,562,,,,,,,5652,,1,,"NZ_CP010119.1,NZ_CP010120.1",5292,,2,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,C3,,,"Included in the study, passed QC/QA"
1173,562.13748,,,,,GCF_001900535.1,Newbler v. 2.7,,PRJNA269191,SAMN03252413,,,,,3,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:16:08.063Z,2017-01-16T17:16:08.063Z,,,50.45,"CP010122,CP010123,CP010124",5633965,Escherichia coli strain C5,Complete,Escherichia,,,,,,,cow,,,,,,,,,562,,,,,,,5933,,,,"NZ_CP010122.1,NZ_CP010123.1,NZ_CP010124.1",5423,,3,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,C5,,,"Included in the study, passed QC/QA"
1174,562.13749,,,,,GCF_001900555.1,Newbler v. 2.7,,PRJNA269191,SAMN03252415,,,,,4,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:18:21.195Z,2017-01-16T17:18:21.195Z,,,50.66,"CP010125,CP010126,CP010127,CP010128",5096119,Escherichia coli strain C8,Complete,Escherichia,,,,,,,cow,,,,,,,,,562,,,,,,,5140,,,,"NZ_CP010125.1,NZ_CP010126.1,NZ_CP010127.1,NZ_CP010128.1",4795,,4,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,C8,,,"Included in the study, passed QC/QA"
1175,562.1375,,,,,GCF_001900575.1,Newbler v. 2.7,,PRJNA269191,SAMN03252416,,,,,3,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:19:32.332Z,2017-01-16T17:19:32.332Z,,,50.86,"CP010129,CP010130,CP010131",4677457,Escherichia coli strain C9,Complete,Escherichia,,,,,,,cow,,,,,,,,,562,,,,,,,4736,,,,"NZ_CP010129.1,NZ_CP010130.1,NZ_CP010131.1",4394,,3,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,C9,,,"Included in the study, passed QC/QA"
1176,562.13751,,,,,GCF_001900595.1,Newbler v. 2.7,,PRJNA269191,SAMN03252419,,,,,3,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:11:20.399Z,2017-01-16T17:11:20.399Z,,,50.66,"CP010134,CP010135,CP010136",5207335,Escherichia coli strain D1,Complete,Escherichia,,,,,,,Dog,,,,,,,,,562,,,,,,,5330,,,,"NZ_CP010134.1,NZ_CP010135.1,NZ_CP010136.1",4980,,3,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,D1,,,"Included in the study, passed QC/QA"
1177,562.13752,,,,,GCF_001900615.1,Newbler v. 2.7,,PRJNA269191,SAMN03252420,,,,,3,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:16:52.173Z,2017-01-16T17:16:52.173Z,,,50.66,"CP010137,CP010138,CP010139",4876911,Escherichia coli strain D2,Complete,Escherichia,,,,,,,Dog,,,,,,,,,562,,,,,,,4874,,,,"NZ_CP010137.1,NZ_CP010138.1,NZ_CP010139.1",4599,,3,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,D2,,,"Included in the study, passed QC/QA"
1178,562.13753,,,,,GCF_001900635.1,Newbler v. 2.7,,PRJNA269191,SAMN03252421,,,,,3,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:10:48.076Z,2017-01-16T17:10:48.076Z,,,50.69,"CP010140,CP010141,CP010142",5236169,Escherichia coli strain D3,Complete,Escherichia,,,,,,,Dog,,,,,,,,,562,,,,,,,5351,,,,"NZ_CP010140.1,NZ_CP010141.1,NZ_CP010142.1",5033,,3,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,D3,,,"Included in the study, passed QC/QA"
1179,562.13754,,,,,GCF_001900655.1,Newbler v. 2.7,,PRJNA269191,SAMN03252422,,,,,2,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:18:35.545Z,2017-01-16T17:18:35.545Z,,,50.67,"CP010143,CP010144",4935464,Escherichia coli strain D4,Complete,Escherichia,,,,,,,Dog,,,,,,,,,562,,,,,,,4959,,,,"NZ_CP010143.1,NZ_CP010144.1",4638,,2,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,D4,,,"Included in the study, passed QC/QA"
1180,562.13755,,,,,GCF_001900675.1,Newbler v. 2.7,,PRJNA269191,SAMN03252423,,,,,3,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:11:24.187Z,2017-01-16T17:11:24.187Z,,,50.83,"CP010145,CP010146,CP010147",5019088,Escherichia coli strain D5,Complete,Escherichia,,,,,,,Dog,,,,,,,,,562,,,,,,,5064,,,,"NZ_CP010145.1,NZ_CP010146.1,NZ_CP010147.1",4763,,3,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,D5,,,"Included in the study, passed QC/QA"
1181,562.13756,,,,,GCF_001900695.1,Newbler v. 2.7,,PRJNA269191,SAMN03252424,,,,,2,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:10:00.215Z,2017-01-16T17:10:00.215Z,,,50.92,"CP010148,CP010149",4910852,Escherichia coli strain D6,Complete,Escherichia,,,,,,,Dog,,,,,,,,,562,,,,,,,4882,,,,"NZ_CP010148.1,NZ_CP010149.1",4640,,2,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,D6,,,"Included in the study, passed QC/QA"
1182,562.13757,,,,,GCF_001900715.1,Newbler v. 2.7,,PRJNA269191,SAMN03252427,,,,,5,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:19:18.732Z,2017-01-16T17:19:18.732Z,,,50.68,"CP010152,CP010153,CP010154,CP010155,CP010156",4874277,Escherichia coli strain D9,Complete,Escherichia,,,,,,,Dog,,,,,,,,,562,,,,,,,4891,,,,"NZ_CP010152.1,NZ_CP010153.1,NZ_CP010154.1,NZ_CP010155.1,NZ_CP010156.1",4564,,5,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,D9,,,"Included in the study, passed QC/QA"
1183,562.13758,,,,,GCF_001900735.1,Newbler v. 2.7,,PRJNA269191,SAMN03252428,,,,,3,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:15:53.748Z,2017-01-16T17:15:53.748Z,,,50.73,"CP010157,CP010158,CP010159",5247683,Escherichia coli strain D10,Complete,Escherichia,,,,,,,Dog,,,,,,,,,562,,,,,,,5310,,,,"NZ_CP010157.1,NZ_CP010158.1,NZ_CP010159.1",4946,,3,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,D10,,,"Included in the study, passed QC/QA"
1184,562.13759,,,,,GCF_001900775.1,Newbler v. 2.7,,PRJNA269191,SAMN03252429,,,,,3,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:22:52.206Z,2017-01-16T17:22:52.206Z,,,50.89,"CP010160,CP010161,CP010162",4826576,Escherichia coli strain H1,Complete,Escherichia,,,,,,,,,,,river water,,,,,562,,,,,,,4864,,,,"NZ_CP010160.1,NZ_CP010161.1,NZ_CP010162.1",4550,,3,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,H1,,,"Included in the study, passed QC/QA"
1185,562.1376,,,,,GCF_001900795.1,Newbler v. 2.7,,PRJNA269191,SAMN03252430,,,,,4,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:17:05.800Z,2017-01-16T17:17:05.800Z,,,50.8,"CP010163,CP010164,CP010165,CP010166",4577859,Escherichia coli strain H2,Complete,Escherichia,,,,,,,,,,,river water,,,,,562,,,,,,,4689,,,,"NZ_CP010163.1,NZ_CP010164.1,NZ_CP010165.1,NZ_CP010166.1",4326,,4,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,H2,,,"Included in the study, passed QC/QA"
1186,562.13761,,,,,GCF_001900815.1,Newbler v. 2.7,,PRJNA269191,SAMN03252431,,,,,2,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:16:47.802Z,2017-01-16T17:16:47.802Z,,,50.81,"CP010167,CP010168",4679162,Escherichia coli strain H3,Complete,Escherichia,,,,,,,,,,,river water,,,,,562,,,,,,,4638,,,,"NZ_CP010167.1,NZ_CP010168.1",4426,,2,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,H3,,,"Included in the study, passed QC/QA"
1187,562.13762,,,,,GCF_001900835.1,Newbler v. 2.7,,PRJNA269191,SAMN03252435,,,,,4,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:17:10.009Z,2017-01-16T17:17:10.009Z,,,50.67,"CP010172,CP010173,CP010174,CP010175",5137208,Escherichia coli strain H8,Complete,Escherichia,,,,,,,,,,,river water,,,,,562,,,,,,,5208,,,,"NZ_CP010172.1,NZ_CP010173.1,NZ_CP010174.1,NZ_CP010175.1",4863,,4,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,H8,,,"Included in the study, passed QC/QA"
1188,562.13763,,,,,GCF_001900885.1,Newbler v. 2.7,,PRJNA269191,SAMN03252437,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:20:25.547Z,2017-01-16T17:20:25.547Z,,,50.76,CP010177,4735489,Escherichia coli strain H14,Complete,Escherichia,,,,,,,,,,,river water,,,,,562,,,,,,,4667,,,,NZ_CP010177.1,4478,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,H14,,,"Included in the study, passed QC/QA"
1189,562.13764,,,,,GCF_001900905.1,Newbler v. 2.7,,PRJNA269191,SAMN03252450,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:25:40.066Z,2017-01-16T17:25:40.066Z,,,50.66,CP010228,4632368,Escherichia coli strain S3,Complete,Escherichia,,,,,,,,,,,forest soil,,,,,562,,,,,,,4620,,,,NZ_CP010228.1,4409,,1,Nanjing Agricultural University,30-80x,Il;lumina Miseq; Roche 454 GS Junior,,,,S3,,,"Included in the study, passed QC/QA"
1190,562.13765,,,,,GCF_001900925.1,Newbler v. 2.7,,PRJNA269191,SAMN03252452,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:21:01.754Z,2017-01-16T17:21:01.754Z,,,50.76,CP010230,4733615,Escherichia coli strain S21,Complete,Escherichia,,,,,,,,,,,forest soil,,,,,562,,,,,,,4665,,,,NZ_CP010230.1,4475,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,S21,,,"Included in the study, passed QC/QA"
1191,562.13766,,,,,GCF_001900945.1,Newbler v. 2.7,,PRJNA269191,SAMN03252454,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:21:56.933Z,2017-01-16T17:21:56.933Z,,,50.87,CP010235,5399183,Escherichia coli strain S40,Complete,Escherichia,,,,,,,,,,,forest soil,,,,,562,,,,,,,5317,,,,NZ_CP010235.1,5113,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,S40,,,"Included in the study, passed QC/QA"
1192,562.13767,,,,,GCF_001900965.1,Newbler v. 2.7,,PRJNA269191,SAMN03252455,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:23:26.787Z,2017-01-16T17:23:26.787Z,,,50.86,CP010236,4838808,Escherichia coli strain S42,Complete,Escherichia,,,,,,,,,,,forest soil,,,,,562,,,,,,,4804,,,,NZ_CP010236.1,4577,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,S42,,,"Included in the study, passed QC/QA"
1193,562.13768,,,,,GCF_001900985.1,Newbler v. 2.7,,PRJNA269191,SAMN03252456,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:29:35.167Z,2017-01-16T17:29:35.167Z,,,50.64,CP010237,5043711,Escherichia coli strain S43,Complete,Escherichia,,,,,,,,,,,forest soil,,,,,562,,,,,,,5052,,,,NZ_CP010237.1,4693,,1,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,S43,,,"Included in the study, passed QC/QA"
1194,562.13769,,,,,GCF_001901005.1,Newbler v. 2.7,,PRJNA269191,SAMN03252438,,,,,2,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:26:19.399Z,2017-01-16T17:26:19.399Z,,,50.82,"CP010178,CP010179",4857969,Escherichia coli strain H15,Complete,Escherichia,,,,,,,,,,,river water,,,,,562,,,,,,,4838,,,,"NZ_CP010178.1,NZ_CP010179.1",4592,,2,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,H15,,,"Included in the study, passed QC/QA"
1195,562.1377,,,,,GCF_001901025.1,Newbler v. 2.7,,PRJNA269191,SAMN03252439,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:30:20.024Z,2017-01-16T17:30:20.024Z,,,50.66,"CP010180,CP010181,CP010182",5148066,Escherichia coli strain M1,Complete,Escherichia,,,,,,,Mouse,,,,feces,,,,,562,,,,,,,5205,,2,,"NZ_CP010180.1,NZ_CP010181.1,NZ_CP010182.1",4864,,3,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,M1,,,"Included in the study, passed QC/QA"
1196,562.13771,,,,,GCF_001901045.1,Newbler v. 2.7,,PRJNA269191,SAMN03252440,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:29:53.375Z,2017-01-16T17:29:53.375Z,,,50.66,"CP010183,CP010184,CP010185",5146339,Escherichia coli strain M3,Complete,Escherichia,,,,,,,Mouse,,,,feces,,,,,562,,,,,,,5209,,2,,"NZ_CP010183.1,NZ_CP010184.1,NZ_CP010185.1",4858,,3,Nanjing Agricultural University,30-80x,Il;lumina Miseq; Roche 454 GS Junior,,,,M3,,,"Included in the study, passed QC/QA"
1197,562.13772,,,,,GCF_001901065.1,Newbler v. 2.7,,PRJNA269191,SAMN03252441,,,,,5,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:39:09.786Z,2017-01-16T17:39:09.786Z,,,50.46,"CP010186,CP010187,CP010188,CP010189,CP010190",5310163,Escherichia coli strain M6,Complete,Escherichia,,,,,,,Mouse,,,,feces,,,,,562,,,,,,,5369,,,,"NZ_CP010186.1,NZ_CP010187.1,NZ_CP010188.1,NZ_CP010189.1,NZ_CP010190.1",4963,,5,Nanjing Agricultural University,30-80x,Il;lumina Miseq; Roche 454 GS Junior,,,,M6,,,"Included in the study, passed QC/QA"
1198,562.13773,,,,,GCF_001901085.1,Newbler v. 2.7,,PRJNA269191,SAMN03252442,,,,,5,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:32:38.227Z,2017-01-16T17:32:38.227Z,,,50.49,"CP010191,CP010192,CP010193,CP010194,CP010195",5045582,Escherichia coli strain M8,Complete,Escherichia,,,,,,,Mouse,,,,feces,,,,,562,,,,,,,5116,,,,"NZ_CP010191.1,NZ_CP010192.1,NZ_CP010193.1,NZ_CP010194.1,NZ_CP010195.1",4822,,5,Nanjing Agricultural University,30-80x,Il;lumina Miseq; Roche 454 GS Junior,,,,M8,,,"Included in the study, passed QC/QA"
1199,562.13774,,,,,GCF_001901105.1,Newbler v. 2.7,,PRJNA269191,SAMN03252443,,,,,4,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:39:18.509Z,2017-01-16T17:39:18.509Z,,,50.47,"CP010196,CP010197,CP010198,CP010199",5304349,Escherichia coli strain M9,Complete,Escherichia,,,,,,,Mouse,,,,feces,,,,,562,,,,,,,5344,,,,"NZ_CP010196.1,NZ_CP010197.1,NZ_CP010198.1,NZ_CP010199.1",4953,,4,Nanjing Agricultural University,30-80x,Il;lumina Miseq; Roche 454 GS Junior,,,,M9,,,"Included in the study, passed QC/QA"
1200,562.13775,,,,,GCF_001901125.1,Newbler v. 2.7,,PRJNA269191,SAMN03252444,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:31:17.707Z,2017-01-16T17:31:17.707Z,,,50.81,"CP010200,CP010201,CP010202,CP010203,CP010204,CP010205",4954801,Escherichia coli strain M10,Complete,Escherichia,,,,,,,Mouse,,,,feces,,,,,562,,,,,,,4974,,5,,"NZ_CP010200.1,NZ_CP010201.1,NZ_CP010202.1,NZ_CP010203.1,NZ_CP010204.1,NZ_CP010205.1",4726,,6,Nanjing Agricultural University,30-80x,Il;lumina Miseq; Roche 454 GS Junior,,,,M10,,,"Included in the study, passed QC/QA"
1201,562.13776,,,,,GCF_001901145.1,Newbler v. 2.7,,PRJNA269191,SAMN03252445,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:40:09.390Z,2017-01-16T17:40:09.390Z,,,50.48,"CP010206,CP010207,CP010208,CP010209,CP010210,CP010211,CP010212",5306134,Escherichia coli strain M11,Complete,Escherichia,,,,,,,Mouse,,,,feces,,,,,562,,,,,,,5374,,6,,"NZ_CP010206.1,NZ_CP010207.1,NZ_CP010208.1,NZ_CP010209.1,NZ_CP010210.1,NZ_CP010211.1,NZ_CP010212.1",4971,,7,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,M11,,,"Included in the study, passed QC/QA"
1202,562.13777,,,,,GCF_001901165.1,Newbler v. 2.7,,PRJNA269191,SAMN03252446,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:42:19.273Z,2017-01-16T17:42:19.273Z,,,50.5,"CP010213,CP010214,CP010215,CP010216,CP010217,CP010218",5328503,Escherichia coli strain M15,Complete,Escherichia,,,,,,,Mouse,,,,feces,,,,,562,,,,,,,5395,,5,,"NZ_CP010213.1,NZ_CP010214.1,NZ_CP010215.1,NZ_CP010216.1,NZ_CP010217.1,NZ_CP010218.1",4979,,6,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,M15,,,"Included in the study, passed QC/QA"
1203,562.13778,,,,,GCF_001901185.1,Newbler v. 2.7,,PRJNA269191,SAMN03252447,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:34:21.672Z,2017-01-16T17:34:21.672Z,,,50.52,"CP010219,CP010220",5160136,Escherichia coli strain M18,Complete,Escherichia,,,,,,,Mouse,,,,feces,,,,,562,,,,,,,5218,,1,,"NZ_CP010219.1,NZ_CP010220.1",4909,,2,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,M18,,,"Included in the study, passed QC/QA"
1204,562.13779,,,,,GCF_001901215.1,Newbler v. 2.7,,PRJNA269191,SAMN03252448,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:42:48.213Z,2017-01-16T17:42:48.213Z,,,50.5,"CP010221,CP010222,CP010223,CP010224,CP010225",5327147,Escherichia coli strain M19,Complete,Escherichia,,,,,,,Mouse,,,,feces,,,,,562,,,,,,,5403,,4,,"NZ_CP010221.1,NZ_CP010222.1,NZ_CP010223.1,NZ_CP010224.1,NZ_CP010225.1",4977,,5,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,M19,,,"Included in the study, passed QC/QA"
1205,562.1378,,,,,GCF_001901315.1,Newbler v. 2.7,,PRJNA269191,SAMN03252449,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:38:44.075Z,2017-01-16T17:38:44.075Z,,,50.84,"CP010226,CP010227",4707208,Escherichia coli strain S1,Complete,Escherichia,,,,,,,Mouse,,,,forest soil,,,,,562,,,,,,,4760,,1,,"NZ_CP010226.1,NZ_CP010227.1",4447,,2,Nanjing Agricultural University,30-80x,Il;lumina Miseq; Roche 454 GS Junior,,,,S1,,,"Included in the study, passed QC/QA"
1206,562.13781,,,,,GCF_001901365.1,Newbler v. 2.7,,PRJNA269191,SAMN03252453,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:41:03.834Z,2017-01-16T17:41:03.834Z,,,50.67,"CP010231,CP010232,CP010233,CP010234",5072853,Escherichia coli strain S30,Complete,Escherichia,,,,,,,,,,,forest soil,,,,,562,,,,,,,5149,,3,,"NZ_CP010231.1,NZ_CP010232.1,NZ_CP010233.1,NZ_CP010234.1",4790,,4,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,S30,,,"Included in the study, passed QC/QA"
1207,562.13782,,,,,GCF_001901405.1,Newbler v. 2.7,,PRJNA269191,SAMN03252457,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:38:16.083Z,2017-01-16T17:38:16.083Z,,,50.71,"CP010238,CP010239",4981720,Escherichia coli strain S50,Complete,Escherichia,,,,,,,,,,,forest soil,,,,,562,,,,,,,5121,,1,,"NZ_CP010238.1,NZ_CP010239.1",4805,,2,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,S50,,,"Included in the study, passed QC/QA"
1208,562.13783,,,,,GCF_001901425.1,Newbler v. 2.7,,PRJNA269191,SAMN03252414,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:37:06.996Z,2017-01-16T17:37:06.996Z,,,50.67,"CP010240,CP010241",5372411,Escherichia coli strain C7,Complete,Escherichia,,,,,,,cow,,,,,,,,,562,,,,,,,5600,,1,,"NZ_CP010240.1,NZ_CP010241.1",5232,,2,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,C7,,,"Included in the study, passed QC/QA"
1209,562.13784,,,,,GCF_001901445.1,Newbler v. 2.7,,PRJNA269191,SAMN03252458,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:44:57.062Z,2017-01-16T17:44:57.062Z,,,50.84,"CP010242,CP010243,CP010244,CP010245",4992522,Escherichia coli strain S56,Complete,Escherichia,,,,,,,,,,,forest soil,,,,,562,,,,,,,5046,,3,,"NZ_CP010242.1,NZ_CP010243.1,NZ_CP010244.1,NZ_CP010245.1",4755,,4,Nanjing Agricultural University,30-80x,Illumina Miseq; Roche 454 GS Junior,,,,S56,,,"Included in the study, passed QC/QA"
1210,562.13785,,,,,GCF_001901465.1,Newbler v. 2.7,,PRJNA269191,SAMN03252451,,,,,1,2014,Comparative genomic analysis for 50 complete genomes of different E. coli strains isolated from various environments,2016-12-12T00:00:00Z,,,2017-01-16T17:42:56.183Z,2017-01-16T17:42:56.183Z,,,50.77,CP010229,4886210,Escherichia coli strain S10,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4873,,,,NZ_CP010229.1,4631,,1,Nanjing Agricultural University,30-80x,Il;lumina Miseq; Roche 454 GS Junior,,,,S10,,,"Included in the study, passed QC/QA"
1211,562.13792,collected_by:Roger Stephan,,,,GCF_001902735.1,SMRT Analysis v. 2.3.0,,PRJNA352706,SAMN05954729,,,,,,2015,E. coli 256 is a shigatoxin producing Escherichia coli (STEC) strain isolated from a deer faecal sample. It harbours a subAB allele that cannot be typed using the current subAB PCR subtyping scheme. The genome of this strain was sequenced to allow precise delineation of the subAB locus genetic location and design of PCR primers for subtyping the subAB variants harboured in such STEC strains.,2016-12-14T00:00:00Z,1,,2017-01-16T18:29:55.715Z,2017-01-16T18:29:55.715Z,,,50.67,"CM007610,CM007611,MPGT00000000",5543021,Escherichia coli strain 256,Complete,Escherichia,Finland,,,,,,deer,isolated from a deer faecal sample,,,fecal sample,,,,,562,,,,,,,5782,,2,,,5425,,3,"University of Zurich, Vetsuisse Faculty",294.0x,PacBio,,,,256,,,"Included in the study, passed QC/QA"
1212,562.13958,,,,,GCF_900096785.1,,,PRJEB15352,SAMEA4444103,,,,,1,,"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli’s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a ‘trade-up’ is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.",2017-01-02T00:00:00Z,,,2017-01-18T16:00:35.342Z,2017-01-18T16:00:35.342Z,,,50.82,LT615372,4638126,Escherichia coli strain 102,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4512,,,,,,,1,UNIVERSITY OF EXETER,,,,,,102,,,"Included in the study, passed QC/QA"
1213,562.13959,,,,,GCF_900096795.1,,,PRJEB15352,SAMEA4444104,,,,,1,,"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli’s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a ‘trade-up’ is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.",2017-01-02T00:00:00Z,,,2017-01-18T16:00:09.556Z,2017-01-18T16:00:09.556Z,,,50.82,LT615378,4638126,Escherichia coli strain 103,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4516,,,,NZ_LT615378.1,,,1,UNIVERSITY OF EXETER,,,,,,103,,,"Included in the study, passed QC/QA"
1214,562.1396,,,,,GCF_900096805.1,,,PRJEB15352,SAMEA4444108,,,,,1,,"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli’s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a ‘trade-up’ is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.",2017-01-02T00:00:00Z,,,2017-01-18T15:58:58.255Z,2017-01-18T15:58:58.255Z,,,50.83,LT615375,4638126,Escherichia coli strain 107,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4520,,,,,,,1,UNIVERSITY OF EXETER,,,,,,107,,,"Included in the study, passed QC/QA"
1215,562.13961,,,,,GCF_900096815.1,,,PRJEB15352,SAMEA4444106,,,,,1,,"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli’s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a ‘trade-up’ is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.",2017-01-02T00:00:00Z,,,2017-01-18T15:59:39.015Z,2017-01-18T15:59:39.015Z,,,50.83,LT615373,4638126,Escherichia coli strain 105,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4513,,,,,,,1,UNIVERSITY OF EXETER,,,,,,105,,,"Included in the study, passed QC/QA"
1216,562.13962,,,,,GCF_900096825.1,,,PRJEB15352,SAMEA4444105,,,,,1,,"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli’s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a ‘trade-up’ is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.",2017-01-02T00:00:00Z,,,2017-01-18T15:59:56.950Z,2017-01-18T15:59:56.950Z,,,50.39,LT615374,4638126,Escherichia coli strain 104,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4481,,,,,,,1,UNIVERSITY OF EXETER,,,,,,104,,,"Excluded from the study, failed QC/QA."
1217,562.13963,,,,,GCF_900096835.1,,,PRJEB15352,SAMEA4444110,,,,,1,,"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli’s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a ‘trade-up’ is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.",2017-01-02T00:00:00Z,,,2017-01-18T15:59:44.788Z,2017-01-18T15:59:44.788Z,,,50.83,LT615376,4638126,Escherichia coli strain 109,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4512,,,,,,,1,UNIVERSITY OF EXETER,,,,,,109,,,"Included in the study, passed QC/QA"
1218,562.13964,,,,,GCF_900096845.1,,,PRJEB15352,SAMEA4444107,,,,,1,,"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli’s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a ‘trade-up’ is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.",2017-01-02T00:00:00Z,,,2017-01-18T15:59:42.418Z,2017-01-18T15:59:42.418Z,,,50.83,LT615377,4638126,Escherichia coli strain 106,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4520,,,,NZ_LT615377.1,,,1,UNIVERSITY OF EXETER,,,,,,106,,,"Included in the study, passed QC/QA"
1219,562.13965,,,,,GCF_900096855.1,,,PRJEB15352,SAMEA4444109,,,,,1,,"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli’s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a ‘trade-up’ is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.",2017-01-02T00:00:00Z,,,2017-01-18T16:00:53.203Z,2017-01-18T16:00:53.203Z,,,50.83,LT615379,4638126,Escherichia coli strain 108,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4522,,,,,,,1,UNIVERSITY OF EXETER,,,,,,108,,,"Included in the study, passed QC/QA"
1220,562.13966,,,,,GCF_900096865.1,,,PRJEB15352,SAMEA4444102,,,,,1,,"Evolutionary trade-offs arise when mutations that improve one life history trait incur fitness costs in other traits. Trade-offs are thought central to evolution, just as costs are to antibiotic resistance. Since drug resistance by efflux can be associated with a 10%, or more, increase in length of the Escherichia coli chromosome, we sought costs to tetracycline resistance in E. coli. It was, however, difficult to identify costs in evolution experiments because E.coli’s growth rate (r) and maximal population size (K) both increased, as did drug efflux, improvements that remained following drug withdrawal. We sought reasons why resistance mutations would increase r and K, particularly as the latter tradeoff according to rK selection theory. Using prokaryote and eukaryote microbial species, including clinical pathogens, we predicted and subsequently observed that r and K can engage in a tradeoff, but need not do so, because a ‘trade-up’ is present in the parabola constraining r to K. The mechanism supporting the tradeup-tradeoff dichotomy is reduced metabolic efficiency in energy-rich environments. We deployed E. coli ribosomal RNA knockout mutants to show that a specific genetic alteration, a change in rrn operon copy number, can simultaneously optimise r and K within a set of genomes. Moreover, the optimal genome has fewer rrn operons than the ancestral strain. It is, therefore, unsurprising to have observed r-adaptation in the presence of a ribosome-inhibiting antibiotic increase population size. Thus, evolution found resistant bacteria that grew faster to larger population sizes than bacteria that did not encounter the antibiotic; the price E.coli paid for this triple improvement is an elongated lag phase and loss of genes associated with stress protection.",2017-01-02T00:00:00Z,,,2017-01-18T16:01:40.218Z,2017-01-18T16:01:40.218Z,,,50.82,LT615371,4638126,Escherichia coli strain 101,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4511,,,,,,,1,UNIVERSITY OF EXETER,,,,,,101,,,"Included in the study, passed QC/QA"
1221,562.13968,,,,,GCF_900119685.1,,,PRJEB5997,SAMEA2432036,,,,,1,,"http://www.sanger.ac.uk/resources/downloads/bacteria/ These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2016-11-17T00:00:00Z,,,2017-01-18T17:51:48.683Z,2017-01-18T17:51:48.683Z,,,50.87,"LT632320,LT632321",5335700,Escherichia coli strain NCTC 13441,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,5366,,1,,,,,2,SC,,,,,,NCTC 13441,,,"Included in the study, passed QC/QA"
1222,562.14013,collected_by:CDC,,,,GCF_001938625.1,PacBio Hierarchical Genome Assembly,,PRJNA218110,SAMN06159501,,,,,1,,PulseNet STEC genome reference library,2017-01-06T00:00:00Z,,,2017-01-23T21:20:33.020Z,2017-01-23T21:20:33.020Z,,,50.46,"CP018770,CP018773,CP018771,CP018772,CP018774,CP018775",5439080,Escherichia coli strain 2016C-3936C1,Complete,Escherichia,USA: Conneticut,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5704,,5,,,5664,,6,CDC,100.0x,PacBio,,O157:H48,,2016C-3936C1,,,"Included in the study, passed QC/QA"
1223,562.14016,"collected_by:Lili Wang, Qian Chen",,,,GCF_001936315.1,,,PRJNA344951,SAMN05853574,,,,,1,2015-11,An isolate came from a diarrheal patient,2017-01-05T00:00:00Z,,,2017-01-24T01:08:05.153Z,2017-01-24T01:08:05.153Z,,,50.43,"CP017631,CP017632,CP017633",5773662,Escherichia coli strain SLK172,Complete,Escherichia,China: Beijing,,,,,Diarrhea,"Human, Homo sapiens",,,,faeces,,,,,562,,,,,,,6129,,2,,"NZ_CP017631.1,NZ_CP017632.1,NZ_CP017633.1",5746,,3,China National Center For Food Safety and Risk Assessment,,,,,,SLK172,,,"Included in the study, passed QC/QA"
1224,562.14017,sample_type:cell culture,,,,GCF_001932515.1,HGAP SMRTPortal v. 2.3.0,,PRJNA356505,SAMN06115651,,,,,1,1980,Full genome sequence of a native Escherichia coli isolate with a defective TolC efflux pump,2017-01-03T00:00:00Z,,,2017-01-24T02:18:24.386Z,2017-01-24T02:18:24.386Z,,,50.73,CP018801,4792200,Escherichia coli strain tolC-,Complete,Escherichia,Germany: Helmholtz-Centre for Infection Research,,,,,,,,,,laboratory,,,,,562,,,,,,,4741,,,,NZ_CP018801.1,4469,,1,Helmholtz-Centre for Infection Research,137x,PacBio; Illumina MiSeq,,,,tolC-,,,"Included in the study, passed QC/QA"
1225,562.15111,sample_type:Culture,,,,GCF_001969285.1,Canu v. 0.0,,PRJNA275512,SAMN06197014,,,,,1,2015-11,To characterize the genomic sequence of Enterobacteriaceae with acquired resistance to polymyxin and to shed light on the mechamism mediating polymyxin resistance.,2017-01-23T00:00:00Z,,,2017-03-20T06:03:47.536Z,2017-03-20T06:03:47.536Z,,,50.63,"CP019213,CP019215,CP019214,CP019216",5123493,Escherichia coli strain WCHEC1613,Complete,Escherichia,China: Sichuan: Chengdu,,,,,,,,,,Sewage,,,,,562,,,,,,,5408,,3,,"NZ_CP019213.1,NZ_CP019215.1,NZ_CP019214.1,NZ_CP019216.1",5397,,4,"West China Hospital, Sichuan University",85.0x,PacBio; Illumina HiSeq,,,,WCHEC1613,,,"Included in the study, passed QC/QA"
1226,562.15135,sample_type:bacterial culture;biomaterial_provider:Nathalie Balaban Lab,,,,GCF_001999185.1,combination of alignment to reference,,PRJNA361209,SAMN06227049,,,,,1,2014,In vitro evolution experiment shows that tolerance mutations pave the way for the rapid subsequent evolution of resistance.,2017-02-14T00:00:00Z,,,2017-03-20T08:11:28.908Z,2017-03-20T08:11:28.908Z,,,50.79,CP019629,4643284,Escherichia coli strain MGY,Complete,Escherichia,Israel,,,,,,,,,,P1 of YFP-CAM to MG1655 from E. Coli stock center,,,,,562,,,,,,,4792,,,25530806,NZ_CP019629.1,4772,,1,Hebrew University of Jerusalem,100.0x,Illumina HiSeq,,,,MGY,,,"Included in the study, passed QC/QA"
1227,562.15191,sample_type:Bacterial culture,,,,GCF_002007705.1,HGAP3 v. 3,,PRJNA373816,SAMN06314933,,,,,1,1885,PacBio sequencing of the original Theodor Escherich E. coli isolate NCTC86,2017-02-28T00:00:00Z,,NCTC:86,2017-03-20T08:31:08.952Z,2017-03-20T08:31:08.952Z,,,50.66,CP019778,5111920,Escherichia coli strain NCTC86,Complete,Escherichia,Germany,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5347,,,,NZ_CP019778.1,5243,,1,National University of Singapore and Genome Institute of Singapore,200.0x,PacBio,,,,NCTC86,,,"Included in the study, passed QC/QA"
1228,562.15192,,,,,GCF_002009315.1,PacBio Hierarchical Genome Assembly,,PRJNA375745,SAMN06344815,,,,,1,May-2015,Raw sequence reads of Escherichia coli containing MCR-1 gene,2017-03-02T00:00:00Z,,,2017-03-20T08:33:48.128Z,2017-03-20T08:33:48.128Z,,,50.8,"CP019903,CP019908,CP019904,CP019907,CP019909,CP019910,CP019906,CP019905",5465306,Escherichia coli strain MDR_56,Complete,Escherichia,USA:NY,,,,,,"Human, Homo sapiens",,,,Human,,,"MLST.Escherichia_coli_2.641,MLST.Escherichia_coli_1.117",,562,,,,,,,5958,,7,,"NZ_CP019903.1,NZ_CP019908.1,NZ_CP019904.1,NZ_CP019907.1,NZ_CP019909.1,NZ_CP019910.1,NZ_CP019906.1,NZ_CP019905.1",5889,,8,Centers for Disease Control and Prevention,90.0x,PacBio,,,,MDR_56,,,"Included in the study, passed QC/QA"
1229,562.15193,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_002011965.1,HGAP v. unspecified,,PRJNA316786,SAMN05511184,,,,,1,2010,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:37:36.958Z,2017-03-20T08:37:36.958Z,,,50.74,"CP018953,CP018952,CP018951,CP018950,CP018949",5126305,Escherichia coli strain Ecol_276,Complete,Escherichia,USA: Pittsburgh,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5416,,4,,"NZ_CP018953.1,NZ_CP018952.1,NZ_CP018951.1,NZ_CP018950.1,NZ_CP018949.1",5388,,5,University of Oxford,XX,PacBio,,,,Ecol_276,,,"Included in the study, passed QC/QA"
1230,562.15194,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_002011945.1,HGAP v. unspecified,,PRJNA316786,SAMN05511177,,,,,1,2010,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:37:57.824Z,2017-03-20T08:37:57.824Z,,,50.7,"CP018948,CP018947,CP018946,CP018944,CP018943,CP018942,CP018941,CP018940,CP018945",5223096,Escherichia coli strain Ecol_224,Complete,Escherichia,Viet Nam: Hanoi,,,,,,"Human, Homo sapiens",,,,,,,"MLST.Escherichia_coli_2.88,MLST.Escherichia_coli_1.101",,562,,,,,,,5561,,8,,"NZ_CP018948.1,NZ_CP018947.1,NZ_CP018946.1,NZ_CP018944.1,NZ_CP018943.1,NZ_CP018942.1,NZ_CP018941.1,NZ_CP018940.1,NZ_CP018945.1",5521,,9,University of Oxford,XX,PacBio,,,,Ecol_224,,,"Included in the study, passed QC/QA"
1231,562.15195,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_002011985.1,HGAP v. unspecified,,PRJNA316786,SAMN05511183,,,,,1,2011,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:38:02.657Z,2017-03-20T08:38:02.657Z,,,50.82,"CP018957,CP018955,CP018954,CP018956",5471138,Escherichia coli strain Ecol_316,Complete,Escherichia,USA: Caguas,,,,,,"Human, Homo sapiens",,,,,,,"MLST.Escherichia_coli_1.393,MLST.Escherichia_coli_2.494",,562,,,,,,,5699,,3,,"NZ_CP018957.1,NZ_CP018955.1,NZ_CP018954.1,NZ_CP018956.1",5661,,4,University of Oxford,XX,PacBio,,,,Ecol_316,,,"Included in the study, passed QC/QA"
1232,562.15196,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_002012005.1,HGAP v. unspecified,,PRJNA316786,SAMN05511179,,,,,1,2011,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:37:43.013Z,2017-03-20T08:37:43.013Z,,,50.67,"CP018965,CP018964,CP018963",4968096,Escherichia coli strain Ecol_517,Complete,Escherichia,Brazil: Rio de Janeiro,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5230,,2,,"NZ_CP018965.1,NZ_CP018964.1,NZ_CP018963.1",5172,,3,University of Oxford,XX,PacBio,,,,Ecol_517,,,"Included in the study, passed QC/QA"
1233,562.15197,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_002012025.1,HGAP v. unspecified,,PRJNA316786,SAMN05511186,,,,,1,2011,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:37:52.983Z,2017-03-20T08:37:52.983Z,,,50.81,"CP018970,CP018969,CP018967,CP018966,CP018968",5395325,Escherichia coli strain Ecol_542,Complete,Escherichia,Viet Nam: Ho Chi Minh City,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5770,,4,,"NZ_CP018970.1,NZ_CP018969.1,NZ_CP018967.1,NZ_CP018966.1,NZ_CP018968.1",5733,,5,University of Oxford,XX,PacBio,,,,Ecol_542,,,"Included in the study, passed QC/QA"
1234,562.15198,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_002012045.1,HGAP v. unspecified,,PRJNA316786,SAMN05511169,,,,,1,2011,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:37:47.695Z,2017-03-20T08:37:47.695Z,,,50.63,"CP018976,CP018975,CP018973,CP018972,CP018971,CP018974",5276034,Escherichia coli strain Ecol_545,Complete,Escherichia,Viet Nam: Ho Chi Minh City,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5495,,5,,"NZ_CP018976.1,NZ_CP018975.1,NZ_CP018973.1,NZ_CP018972.1,NZ_CP018971.1,NZ_CP018974.1",5440,,6,University of Oxford,XX,PacBio,,,,Ecol_545,,,"Included in the study, passed QC/QA"
1235,562.15199,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_002012065.1,HGAP v. unspecified,,PRJNA316786,SAMN05511161,,,,,1,2012,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:38:15.915Z,2017-03-20T08:38:15.915Z,,,50.8,"CP018979,CP018978,CP018977",5405139,Escherichia coli strain Ecol_656,Complete,Escherichia,USA: Caguas,,,,,,"Human, Homo sapiens",,,,,,,MLST.Escherichia_coli_1.131,,562,,,,,,,5758,,2,,"NZ_CP018979.1,NZ_CP018978.1,NZ_CP018977.1",5690,,3,University of Oxford,XX,PacBio,,,,Ecol_656,,,"Included in the study, passed QC/QA"
1236,562.152,collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,GCF_002012085.1,HGAP v. unspecified,,PRJNA316786,SAMN05511152,,,,,1,2012,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:38:40.476Z,2017-03-20T08:38:40.476Z,,,50.71,"CP018991,CP018990,CP018988,CP018987,CP018986,CP018985,CP018984,CP018989",5727407,Escherichia coli strain Ecol_AZ146,Complete,Escherichia,Italy: Pisa,,,,,,"Human, Homo sapiens",,,,,,,MLST.Escherichia_coli_1.131,,562,,,,,,,6232,,7,,"NZ_CP018991.1,NZ_CP018990.1,NZ_CP018988.1,NZ_CP018987.1,NZ_CP018986.1,NZ_CP018985.1,NZ_CP018984.1,NZ_CP018989.1",6150,,8,University of Oxford,XX,PacBio,,,,Ecol_AZ146,,,"Included in the study, passed QC/QA"
1237,562.15201,collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,GCF_002012105.1,HGAP v. unspecified,,PRJNA316786,SAMN05511182,,,,,1,2012,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:38:54.759Z,2017-03-20T08:38:54.759Z,,,50.89,"CP018995,CP018994,CP018993,CP018992",5090480,Escherichia coli strain Ecol_AZ147,Complete,Escherichia,Israel: Kfar Sava,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5370,,3,,"NZ_CP018995.1,NZ_CP018994.1,NZ_CP018993.1,NZ_CP018992.1",5348,,4,University of Oxford,XX,PacBio,,,,Ecol_AZ147,,,"Included in the study, passed QC/QA"
1238,562.15202,collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,GCF_002012125.1,HGAP v. unspecified,,PRJNA316786,SAMN05511168,,,,,1,2013,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:38:30.656Z,2017-03-20T08:38:30.656Z,,,50.89,"CP019005,CP019002,CP019003,CP019004,CP019001",5090221,Escherichia coli strain Ecol_AZ155,Complete,Escherichia,China: Beijing,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5389,,4,,"NZ_CP019005.1,NZ_CP019002.1,NZ_CP019003.1,NZ_CP019004.1,NZ_CP019001.1",5366,,5,University of Oxford,XX,PacBio,,,,Ecol_AZ155,,,"Included in the study, passed QC/QA"
1239,562.15203,collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,GCF_002012145.1,HGAP v. unspecified,,PRJNA316786,SAMN05511159,,,,,1,2013,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:38:36.360Z,2017-03-20T08:38:36.360Z,,,50.64,"CP019008,CP019007,CP019006",5101928,Escherichia coli strain Ecol_AZ159,Complete,Escherichia,Colombia: Bogota,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5280,,2,,"NZ_CP019008.1,NZ_CP019007.1,NZ_CP019006.1",5258,,3,University of Oxford,XX,PacBio,,,,Ecol_AZ159,,,"Included in the study, passed QC/QA"
1240,562.15204,collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,GCF_002012165.1,HGAP v. unspecified,,PRJNA316786,SAMN05511185,,,,,1,2013,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:38:25.161Z,2017-03-20T08:38:25.161Z,,,50.72,"CP019015,CP019013,CP019014",5351874,Escherichia coli strain Ecol_AZ162,Complete,Escherichia,USA: Boston,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5640,,2,,"NZ_CP019015.1,NZ_CP019013.1,NZ_CP019014.1",5607,,3,University of Oxford,XX,PacBio,,,,Ecol_AZ162,,,"Included in the study, passed QC/QA"
1241,562.15205,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_002012185.1,HGAP v. unspecified,,PRJNA316786,SAMN05511153,,,,,1,2011,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:38:45.424Z,2017-03-20T08:38:45.424Z,,,50.59,"CP018962,CP018961,CP018960,CP018958,CP018959",5215799,Escherichia coli strain Ecol_422,Complete,Escherichia,Ecuador: Quito,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5509,,4,,"NZ_CP018962.1,NZ_CP018961.1,NZ_CP018960.1,NZ_CP018958.1,NZ_CP018959.1",5488,,5,University of Oxford,XX,PacBio,,,,Ecol_422,,,"Included in the study, passed QC/QA"
1242,562.15206,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_002012205.1,HGAP v. unspecified,,PRJNA316786,SAMN05511148,,,,,1,2013,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:38:50.666Z,2017-03-20T08:38:50.666Z,,,50.83,"CP018983,CP018982,CP018980,CP018981",5065803,Escherichia coli strain Ecol_867,Complete,Escherichia,Canada: Toronto,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5282,,3,,"NZ_CP018983.1,NZ_CP018982.1,NZ_CP018980.1,NZ_CP018981.1",5263,,4,University of Oxford,XX,PacBio,,,,Ecol_867,,,"Included in the study, passed QC/QA"
1243,562.15208,collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,GCF_002012245.1,HGAP v. unspecified,,PRJNA316786,SAMN05511160,,,,,1,2013,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:39:02.243Z,2017-03-20T08:39:02.243Z,,,50.9,"CP019000,CP018998,CP018997,CP018996,CP018999",5252746,Escherichia coli strain Ecol_AZ153,Complete,Escherichia,China: Beijing,,,,,,"Human, Homo sapiens",,,,,,,MLST.Escherichia_coli_1.131,,562,,,,,,,5579,,4,,"NZ_CP019000.1,NZ_CP018998.1,NZ_CP018997.1,NZ_CP018996.1,NZ_CP018999.1",5544,,5,University of Oxford,XX,PacBio,,,,Ecol_AZ153,,,"Included in the study, passed QC/QA"
1244,562.15209,collected_by:AstraZeneca global surveillance study of antimicrobial resistance,,,,GCF_002012265.1,HGAP v. unspecified,,PRJNA316786,SAMN05511166,,,,,1,2013,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:39:07.094Z,2017-03-20T08:39:07.094Z,,,50.88,"CP019012,CP019011,CP019009,CP019010",5173038,Escherichia coli strain Ecol_AZ161,Complete,Escherichia,USA: Lafayette,,,,,,"Human, Homo sapiens",,,,,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,562,,,,,,,5424,,3,,"NZ_CP019012.1,NZ_CP019011.1,NZ_CP019009.1,NZ_CP019010.1",5403,,4,University of Oxford,XX,PacBio,,,,Ecol_AZ161,,,"Included in the study, passed QC/QA"
1245,562.1521,collected_by:Merck Study for Monitoring of Antimicrobial Resistance Trends (SMART),,,,GCF_002012305.1,HGAP v. unspecified,,PRJNA316786,SAMN05511157,,,,,1,2010,"Carbapenemase producing Escherichia coli are of clinical concern, commonly resistant to multiple antimicrobial classes as well as carbapenems. This project is focused on providing complete or near-complete genome sequences (chromosome + plasmids) for global E. coli isolates harbouring major carbapenemase genes.",2017-03-03T00:00:00Z,,,2017-03-20T08:39:26.049Z,2017-03-20T08:39:26.049Z,,,50.43,"CP019020,CP019019,CP019018,CP019016,CP019017",5383061,Escherichia coli strain Ecol_244,Complete,Escherichia,Argentina: Buenos Aires,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5701,,4,,"NZ_CP019020.1,NZ_CP019019.1,NZ_CP019018.1,NZ_CP019016.1,NZ_CP019017.1",5592,,5,University of Oxford,XX,PacBio,,,,Ecol_244,,,"Included in the study, passed QC/QA"
1246,562.16323,collected_by:FLI,,,,,HGAP3 v. DEC-2014,,PRJNA378593,SAMN06554468,,,,,1,07-Dec-1998,STEC,2017-03-21T00:00:00Z,,,2017-05-28T00:05:38.047Z,2017-05-28T00:05:38.047Z,,,50.61,CP020092,5112484,Escherichia coli strain 13E0725,Complete,Escherichia,Germany,,,,,,,,,,cattle,,,,,562,,,,,,,5445,STEC,,,,5278,,1,Friedrich-Loeffler-Institut,200.0x,PacBio,,O182:H25,,13E0725,,,"Included in the study, passed QC/QA"
1247,562.16324,,,Resistant;Not defined;Susceptible,AMR Panel,,HGAP v. 2.3,,PRJNA292902,SAMN04014959,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-03-21T00:00:00Z,,,2017-05-28T00:06:22.631Z,2017-05-28T00:06:22.631Z,,,50.65,"CP020048,CP020049,CP020050,CP020051",5365068,Escherichia coli strain AR_0118,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,5666,,3,,,5612,,4,Centers for Disease Control and Prevention,301x,PacBio RSII,,,,AR_0118,,,"Included in the study, passed QC/QA"
1248,562.16325,,,Intermediate;Resistant;Susceptible;Not defined,AMR Panel,,HGAP v. 2.3,,PRJNA292904,SAMN04014902,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2017-03-21T00:00:00Z,,,2017-05-28T00:18:15.432Z,2017-05-28T00:18:15.432Z,,,50.79,"CP020058,CP020059,CP020060",4734219,Escherichia coli strain AR_0061,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4915,,2,,,4884,,3,Centers for Disease Control and Prevention,268x,PacBio RSII,,,,AR_0061,,,"Included in the study, passed QC/QA"
1249,562.16326,,,Susceptible;Resistant;Intermediate;Not defined,AMR Panel,,HGAP v. 2.3,,PRJNA292904,SAMN04014910,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2017-03-21T00:00:00Z,,,2017-05-28T00:19:57.201Z,2017-05-28T00:19:57.201Z,,,50.8,"CP020055,CP020056,CP020057",4826754,Escherichia coli strain AR_0069,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,5017,,2,,,4950,,3,Centers for Disease Control and Prevention,147x,PacBio RSII,,,,AR_0069,,,"Included in the study, passed QC/QA"
1250,562.16327,,,Susceptible;Resistant;Not defined;Intermediate,AMR Panel,,HGAP v. 2.3,,PRJNA292904,SAMN04014945,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2017-03-21T00:00:00Z,,,2017-05-28T00:20:41.335Z,2017-05-28T00:20:41.335Z,,,50.76,"CP020116,CP020117,CP020118,CP020119",5262025,Escherichia coli strain AR_0104,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,5526,,3,,,5476,,4,Centers for Disease Control and Prevention,245x,PacBio RSII,,,,AR_0104,,,"Included in the study, passed QC/QA"
1251,562.16328,collected_by:FLI,,,,,HGAP3 v. DEC-2014,,PRJNA378906,SAMN06563569,,,,,1,06-Jul-1998,STEC,2017-03-21T00:00:00Z,,,2017-05-28T00:32:05.127Z,2017-05-28T00:32:05.127Z,,,50.62,CP020106,5371291,Escherichia coli strain 13E0780,Complete,Escherichia,Germany,,,,,,,,,,cattle,,,,,562,,,,,,,5825,STEC,,,,5654,,1,Friedrich-Loeffler-Institut,200.0x,PacBio,,O156:H25,,13E0780,,,"Included in the study, passed QC/QA"
1252,562.16329,collected_by:FLI,,,,,HGAP3 v. DEC-2014,,PRJNA378908,SAMN06563579,,,,,1,07-Dec-1998,aEPEC,2017-03-21T00:00:00Z,,,2017-05-28T00:32:29.666Z,2017-05-28T00:32:29.666Z,,,50.65,CP020107,4942246,Escherichia coli strain 13E0767,Complete,Escherichia,Germany,,,,,,,,,,Cattle,,,,,562,,,,,,,5122,aEPEC,,,,5026,,1,Friedrich-Loeffler-Institut,200.0x,PacBio,,O156:H8,,13E0767,,,"Included in the study, passed QC/QA"
1253,562.1633,sample_type:cell culture,,,,,HGAP SMRTPortal v. 2.3.0,,PRJNA376490,SAMN06434185,,,,,1,2012,Phage application in poultry farming,2017-03-21T00:00:00Z,,DSM:103246,2017-05-28T00:57:59.277Z,2017-05-28T00:57:59.277Z,,,50.51,CP019944,5445834,Escherichia coli strain DSM 103246,Complete,Escherichia,Germany,,,,,,,,,,chicken carcass,,,,,562,,,,,,,5365,,,,,5058,,1,Leibniz Institute DSMZ,208x,PacBio; Illumina MiSeq,,,,DSM 103246,,,"Included in the study, passed QC/QA"
1254,562.1634,sample_type:single cell;collected_by:Kinga Umenhoffer,,,,,SPAdes v. 3.1.1; CLC Genomics Workbench,,PRJNA312438,SAMN04497926,,,,,1,2012,Engineered variant of Escherichia coli BL21(DE3),2017-04-04T00:00:00Z,,,2017-05-28T07:07:12.719Z,2017-05-28T07:07:12.719Z,,,51.03,CP014641,4165587,Escherichia coli strain BLK9,Complete,Escherichia,Hungary: Szeged,,,,,,,,,,engineered variant of Escherichia coli BL21(DE3),,,,,562,C,,,,,,4095,,,,,3951,,1,Seqomics Ltd.,250.0x,Illumina HiSeq,,,,BLK9,,,"Included in the study, passed QC/QA"
1255,562.16341,sample_type:single cell;collected_by:Kinga Umenhoffer,,,,,SPAdes v. 3.1.1; CLC Genomics Workbench,,PRJNA312746,SAMN04505873,,,,,1,2012,Engineered variant of Escherichia coli BL21(DE3),2017-04-04T00:00:00Z,,,2017-05-28T07:08:26.244Z,2017-05-28T07:08:26.244Z,,,51.03,CP014642,4165783,Escherichia coli strain BLK16,Complete,Escherichia,Hungary: Szeged,,,,,,,,,,Engineered variant of Escherichia coli BL21(DE3),,,,,562,C,,,,,,4096,,,,,3950,,1,Seqomics Ltd.,340.0x,Illumina HiSeq,,,,BLK16,,,"Included in the study, passed QC/QA"
1256,562.16372,sample_type:cell culture,,,,,SMRT v. MAY-2014,,PRJNA379778,SAMN06619924,,,,,1,Dec-2013,"Escherichia coli BLR(DE3) is a commercially available recA-deficient derivative of the widely used BL21(DE3) for recombinant protein expression. Here, we present the full genome sequence of BLR(DE3) and highlight additional differences with its parent strain BL21(DE3) that were previously unreported but may affect its physiology.",2017-04-13T00:00:00Z,,,2017-05-28T17:24:29.484Z,2017-05-28T17:24:29.484Z,,,50.78,CP020368,4550811,Escherichia coli strain BLR(DE3),Complete,Escherichia,,,,,,,,,,,commercial strain obtained from Novagen,,,,,562,,,,,,,4610,,,,,4294,,1,GlaxoSmithKline Vaccines,97.0x,PacBio; Illumina HiSeq,,,,BLR(DE3),,,"Included in the study, passed QC/QA"
1257,562.16414,collected_by:ARL,,,,,HGAP v. v.3.0,,PRJNA312475,SAMN05414625,,,,,1,2014,Whole genome sequencing of cultured E. coli as part of the US Food and Drug Administration surveillance project for the rapid detection of food contamination events.,2017-04-24T00:00:00Z,,,2017-05-29T02:04:47.173Z,2017-05-29T02:04:47.173Z,,,50.95,"CP020835,CP020836",4926135,Escherichia coli strain CFSAN051542,Complete,Escherichia,USA,,,,,,,,,,Blue cheese in wax,,,,,562,C,,,,,,5140,,1,,,5031,,2,FDA,400.0x,PacBio,,O18ac:H14,,CFSAN051542,,,"Included in the study, passed QC/QA"
1258,562.16426,sample_type:single cell,,,,,SMRT portal v. Version 3.2.0,,PRJNA383767,SAMN06819205,,,,,1,2017-04-21,Analysis of assembling and annotation of whole genome of avian multoyage resistant Escherichia,2017-05-01T00:00:00Z,,,2017-05-29T10:06:13.013Z,2017-05-29T10:06:13.013Z,,,50.7,"CP020933,CP020934,CP020935,CP020936",5078176,Escherichia coli strain HB-Coli0,Complete,Escherichia,China: Baoding,,,,,,Chicken,,,,intestine,,,,,562,,,,,,,5259,,3,,,5152,,4,Agricultural University of Hebei Province,300.0x,PacBio,,,,HB-Coli0,,,"Included in the study, passed QC/QA"
1259,562.16427,sample_type:single cell,,,,,HGAP v. 2.3.3,,PRJNA298687,SAMN04396805,,,,,1,27-Nov-2013,SMRT sequencing of E. coli,2017-04-28T00:00:00Z,,,2017-05-29T11:04:28.330Z,2017-05-29T11:04:28.330Z,,,50.79,CP013952,4567242,Escherichia coli strain HST04,Complete,Escherichia,China,,,,,,,,,,TAKARA,,,,,562,C,,,,,,4597,,,28400512,,4405,,1,Wuhan University,180x,SMRT PacBio,,,,HST04,,,"Included in the study, passed QC/QA"
1260,562.16428,,,,,,HGAP 3 (PacBio) v. SEPT-2015,,PRJNA307507,SAMN04381848,,,,,1,2010,Comparative sequencing of ExPEC ST131,2017-05-10T00:00:00Z,,,2017-05-29T12:45:55.838Z,2017-05-29T12:45:55.838Z,,,50.62,"CM007889,LSUP00000000",5277911,Escherichia coli strain G199,Complete,Escherichia,USA: Seattle,,,,,,"Human, Homo sapiens",,,,,,,,,562,C,,,,,,5488,,4,27390780,,5204,,5,University of Minnesota,100.0x,PacBio,,,,G199,,,"Included in the study, passed QC/QA"
1261,562.16465,"collected_by:Affiliated Hospital of Jining Medical University, China",,,,,SmrtPipe v. 2.3.0,,PRJNA386069,SAMN06924979,,,,,1,2014-09-06,"This is a genome of Escherichia coli strain Z1002, isolated from a patient with bloodstream infection. This strain is capable of coproducing MCR-1 and NDM-1.",2017-05-16T00:00:00Z,,,2017-05-29T21:50:28.706Z,2017-05-29T21:50:28.706Z,,,50.54,"CP021202,CP021203,CP021204,CP021205,CP021206",5628524,Escherichia coli strain Z1002,Complete,Escherichia,China:Jining,,,,,bloodstream infection,"Human, Homo sapiens",isolated from a patient with bloodstream infection,,,blood,,,,,562,,,,,,,5934,,4,27506685,,5805,,5,"The First Affiliated Hospital, School of Medicine, Zhejiang University",204.0x,PacBio,,,,Z1002,,,"Included in the study, passed QC/QA"
1262,562.16466,"collected_by:Centers for Disease Control, Taiwan",,Susceptible;Resistant;Not defined,AMR Panel,,Celera Assembler v. HGAP3,,PRJNA384104,SAMN06828737,,,,,1,2016-01,Investigation of colistin resistance gene mcr-1 in clinical isolate,2017-05-16T00:00:00Z,,,2017-05-29T21:49:58.580Z,2017-05-29T21:49:58.580Z,,,50.62,"CP021175,CP021176,CP021177",5256426,Escherichia coli strain 5CRE51,Complete,Escherichia,Taiwan: Tainan,,,,,Urinary tract infection,"Human, Homo sapiens",,,,urine,,,,,562,,,,,,,5520,,2,,,5370,,3,"Centers for Disease Control, Tawian",100x,PacBio,,,,5CRE51,,,"Included in the study, passed QC/QA"
1263,562.16467,"collected_by:Anhui Provincial Hospital, China",,,,,SmrtPipe v. 2.3.0,,PRJNA386074,SAMN06925129,,,,,1,2015-09-11,"This is a genome of Escherichia coli strain Z2474, isolated from a patient with bloodstream infection. This strain is capable of coproducing MCR-1 and NDM-1.",2017-05-16T00:00:00Z,,,2017-05-29T21:51:10.012Z,2017-05-29T21:51:10.012Z,,,50.4,"CP021207,CP021208,CP021209,CP021210",5400073,Escherichia coli strain strain Z247,Complete,Escherichia,China:Hefei,,,,,bloodstream infection,"Human, Homo sapiens",isolated from a patient with bloodstream infection,,,blood,,,,,562,,,,,,,5662,,3,27506685,,5511,,4,"The First Affiliated Hospital, School of Medicine, Zhejiang University",165.0x,PacBio,,,,strain Z247,,,"Included in the study, passed QC/QA"
1264,562.16499,,,,,,,,PRJEB18462,SAMEA19195168,,,,,1,2016,The spread of mcr-1-encoding plasmids into carbapenem-resistant Enterobacteriaceae raises concern about the emergence of untreatable bacteria. We report the acquisition of mcr-1 in a carbapenem resistant E. coli after a 3-week course of colistin in a patient repatriated to France from Portugal.,2017-04-20T00:00:00Z,,,2017-05-30T19:40:30.381Z,2017-05-30T19:40:30.381Z,,,50.79,"LT838196,LT838197,LT838198,LT838199",5008891,Escherichia coli strain WI1 isolate,Complete,Escherichia,,,,,,,"Human, Homo sapiens",,,,clinical isolate,,,,,562,,,host_health_state:diseased,,,,5019,,3,,,4862,,4,CHU Clermont-ferrand,,,,,,WI1 isolate,,,"Included in the study, passed QC/QA"
1265,562.17274,,,,,,Newbler v. 2.9; Velvet v. 1.1,,PRJNA239361,SAMN02666437,,,,,1,,"Escherichia coli causing avian colibacillosis and human neonatal meningitis, urinary tract infections and septicemia are collectively known as extraintestinal pathogenic E. coli (ExPEC). Characterization of ExPEC using various typing techniques has shown that they harbor many similarities despite their isolation from different host species leading to the hypothesis that ExPEC may have zoonotic potential.",2016-06-12T00:00:00Z,,,2017-07-21T16:13:25.364Z,2017-07-21T16:13:25.364Z,,,50.75,CP007275,5002781,Escherichia coli strain NMEC O18,Complete,Escherichia,USA,,,,,,,,,,,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.416",,562,,,,,,,5053,,,,,4782,,1,Iowa State University,,454; Illumina,,,,O18,,,"Included in the study, passed QC/QA"
1266,562.17357,,,,,,HGAP v. 2,,PRJNA383943,SAMN06924970,,,,,1,1995,"In this study we have used Pacific Bioscience single molecule real-time (SMRT) long read sequencing to characterise the complete epigenome (genome and methylome) of 95JB1. Our analysis of the methylome of 95JB1 and a second isolate, 95NR1, identified hemimethylation of a novel motif (5’-CTGCm6AG-3’) in more than 4000 sites in the 95NR1 genome. These sites were entirely unmethalyted in the 95JB1, including at least 180 potential promoter regions that could explain regulatory differences between the strains. We identified a Type IIG methyltransferase encoded in both genomes in association with three additional genes in an operon-like arrangement. IS1203 mediated disruption of this operon in 95JB1 is the likely cause of the observed differential patterns of methylation between 95NR1 and 95JB1. This study demonstrates the enormous potential of SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.",2017-05-23T00:00:00Z,,,2017-07-21T20:36:33.498Z,2017-07-21T20:36:33.498Z,,,50.55,"CP021335,CP021336,CP021337",5517971,Escherichia coli strain 95JB1,Complete,Escherichia,Australia: Adelaide,,,,,,,,Australia,,fecal sample,,,,,562,,,,,,,5712,EHEC,2,,,5319,,3,University of Queensland,200.0x,PacBio,,O111:H-,,95JB1,,,"Included in the study, passed QC/QA"
1267,562.17358,,,,,,HGAP v. 2,,PRJNA383942,SAMN06947002,,,,,1,1995,In this study we have used Pacific Bioscience single molecule real-time (SMRT) long read sequencing to characterise the complete epigenome (genome and methylome) of 95NR1. Using long reads we completely resolved the structure of two tandemly inserted stx2-converting phage in 95NR1. Our analysis of the methylome of 95NR1 identified hemimethylation of a novel motif (5’-CTGCm6AG-3’) in more than 4000 sites in the genome. This study demonstrates the enormous potential of SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.,2017-05-23T00:00:00Z,,,2017-07-21T20:38:14.057Z,2017-07-21T20:38:14.057Z,,,50.54,"CP021339,CP021340,CP021341",5636758,Escherichia coli strain 95NR1,Complete,Escherichia,Australia: Adelaide,,,,,,,,Australia,,fecal sample,,,"MLST.Escherichia_coli_1.294,MLST.Escherichia_coli_2.480",,562,,,,,,,5888,EHEC,2,,,5439,,3,University of Queensland,200.0x,PacBio,,O111:H-,,95NR1,,,"Included in the study, passed QC/QA"
1268,562.17359,collected_by:Sylvia El Kurdi,,Susceptible;Resistant,AMR Panel,,Celera Assembler v. HGAP4,,PRJNA383781,SAMN06808253,,,,,1,25-Oct-2009,"Finished quality genome assembly of Escherichia coli 81009, an ST131-O25b:H4 prototype with multi-drug resistance phenotype",2017-05-24T00:00:00Z,,,2017-07-21T20:56:47.486Z,2017-07-21T20:56:47.486Z,,,50.8,"CP021179,CP021180",5147804,Escherichia coli strain 81009,Complete,Escherichia,"United Arab Emirates: Tawam Hospital, Al Ain",,,76,male,Bacteriuria,Homo sapiens,,United Arab Emirates,,urine,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,562,,,,,,,5116,ExPEC,1,,,4822,,2,Arsanis Biosciences GmbH,275.0x,PacBio,,O25b:H4,,81009,,,"Included in the study, passed QC/QA"
1269,562.17366,sample_type:fecal,,,,,HGAP v. 2; Quiver v. 2016-09-27,,PRJNA355857,SAMN06093946,,,,,1,2014-04-29,Chromosomes and plasmids relevant to copper resistance,2017-06-02T00:00:00Z,,,2017-07-22T03:39:43.040Z,2017-07-22T03:39:43.040Z,,,50.68,CP018323,4855460,Escherichia coli strain 9,Complete,Escherichia,USA,,,,,,,,,,porcine,,,"MLST.Escherichia_coli_1.2480,MLST.Escherichia_coli_2.88",,562,,,,,,,5029,,,,,4962,,1,University of Guelph,254.0x,PacBio,,,,9,,,"Included in the study, passed QC/QA"
1270,562.17367,sample_type:fecal,,,,,HGAP v. 2; Quiver v. 2016-09-27,,PRJNA355857,SAMN06165994,,,,,1,2014-04-29,Chromosomes and plasmids relevant to copper resistance,2017-06-02T00:00:00Z,,,2017-07-22T03:45:58.858Z,2017-07-22T03:45:58.858Z,,,50.64,CP018840,4759716,Escherichia coli strain 64,Complete,Escherichia,USA,,,,,,,,,,porcine,,,"MLST.Escherichia_coli_2.338,MLST.Escherichia_coli_1.154",,562,,,,,,,4879,,,,,4804,,1,University of Guelph,281.0x,PacBio,,,,64,,,"Included in the study, passed QC/QA"
1271,562.17368,sample_type:fecal,,,,,HGAP v. 2; Quiver v. 2016-09-27,,PRJNA355857,SAMN06166007,,,,,1,2014-04-29,Chromosomes and plasmids relevant to copper resistance,2017-06-02T00:00:00Z,,,2017-07-22T03:51:45.753Z,2017-07-22T03:51:45.753Z,,,50.86,"CP019560,CP019561",4855538,Escherichia coli strain 1031,Complete,Escherichia,USA,,,,,,,,,,porcine,,,,,562,,,,,,,4988,,1,,,4964,,2,University of Guelph,281.0x,PacBio,,,,1031,,,"Included in the study, passed QC/QA"
1272,562.17369,sample_type:fecal,,,,,HGAP v. 2; Quiver v. 2016-09-27,,PRJNA355857,SAMN06165999,,,,,1,2014-04-29,Chromosomes and plasmids relevant to copper resistance,2017-06-02T00:00:00Z,,,2017-07-22T03:54:06.390Z,2017-07-22T03:54:06.390Z,,,50.51,"CP019558,CP019559",4984497,Escherichia coli strain 207,Complete,Escherichia,USA,,,,,,,,,,porcine,,,,,562,,,,,,,5112,,1,,,5058,,2,University of Guelph,276.0x,PacBio,,,,207,,,"Included in the study, passed QC/QA"
1273,562.1762,,,Susceptible;Resistant;Not defined;Intermediate,AMR Panel,,HGAP v. 2.3,,PRJNA292902,SAMN04014955,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-13T00:00:00Z,,,2017-07-22T17:28:32.488Z,2017-07-22T17:28:32.488Z,,,50.75,"CP021732,CP021733,CP021734,CP021735",5017345,Escherichia coli strain AR_0114,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,5215,,3,,,5081,,4,Centers for Disease Control and Prevention,138x,PacBio RSII,,,,AR_0114,,,"Included in the study, passed QC/QA"
1274,562.17621,,,Susceptible;Resistant;Not defined,AMR Panel,,canu v. 1.3,,PRJNA292902,SAMN04014991,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-13T00:00:00Z,,,2017-07-22T17:28:19.505Z,2017-07-22T17:28:19.505Z,,,50.82,"CP021736,CP021737,CP021738,CP021739",5078246,Escherichia coli strain AR_0150,Complete,Escherichia,,,,,,,,,,,,,,"MLST.Escherichia_coli_2.2,MLST.Escherichia_coli_1.167",,562,,,,,,,5265,,3,,,5144,,4,Centers for Disease Control and Prevention,225x,PacBio RSII,,,,AR_0150,,,"Included in the study, passed QC/QA"
1275,562.17622,,,,,,HGAP v. 2.3.0,,PRJNA387731,SAMN07162922,,,,,1,,Escherichia coli H105,2017-06-14T00:00:00Z,,,2017-07-22T17:51:54.903Z,2017-07-22T17:51:54.903Z,,,50.78,"CP021454,CP021871",5113241,Escherichia coli strain H105,Complete,Escherichia,Germany,,,,,,Homo sapiens; 55 year old,,,,vaginal swab,,,"MLST.Escherichia_coli_2.43,MLST.Escherichia_coli_1.131",,562,,,,,,,5306,,1,,,5212,,2,"Institute of Medical Microbiology , Justus Liebig University Giessen",86.0x,PacBio,,,,H105,,,"Included in the study, passed QC/QA"
1276,562.1771,collected_by:National Cheng Kung University Hospital,,,,,HGAP version 3.0 v. 3.0,,PRJNA389338,SAMN07192703,,,,,1,2007-08-24,EC974 and EC1515 were isolated from a patient with recurrent urinary tract infection,2017-06-15T00:00:00Z,,,2017-07-22T19:25:44.616Z,2017-07-22T19:25:44.616Z,,,50.53,"CP021840,CP021841,CP021842,CP021843",5457692,Escherichia coli strain EC974,Complete,Escherichia,Taiwan,,,,,Urinary Tract Infection,Homo sapiens,,,,urine; urinary tract infection,,,"MLST.Escherichia_coli_1.219,MLST.Escherichia_coli_2.541",,562,,,,,,,5577,,3,,,5480,,4,National Yang Ming University,143.0x,PacBio,,,,EC974,,,"Included in the study, passed QC/QA"
1277,562.17711,collected_by:National Cheng Kung University Hospital,,,,,HGAP v. 3.0,,PRJNA389338,SAMN07192704,,,,,1,2007-12-10,EC974 and EC1515 were isolated from a patient with recurrent urinary tract infection,2017-06-15T00:00:00Z,,,2017-07-22T19:25:47.950Z,2017-07-22T19:25:47.950Z,,,50.55,"CP021844,CP021845,CP021846,CP021847",5468903,Escherichia coli strain EC1515,Complete,Escherichia,Taiwan,,,,,Urinary Tract Infection,Homo sapiens,,,,urine; urinary tract infection,,,,,562,,,,,,,5590,,3,,,5492,,4,National Yang Ming University,193.0x,PacBio,,,,EC1515,,,"Included in the study, passed QC/QA"
1278,562.17721,,,Resistant;Not defined;Susceptible,AMR Panel,,canu v. 1.3,,PRJNA292902,SAMN04014978,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-20T00:00:00Z,,,2017-07-22T22:10:13.994Z,2017-07-22T22:10:13.994Z,,,50.83,"CP021879,CP021880,CP021881,CP021882",5085165,Escherichia coli strain AR_0137,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,5306,,3,,,5165,,4,Centers for Disease Control and Prevention,87x,PacBio RSII,,,,AR_0137,,,"Included in the study, passed QC/QA"
1279,562.17722,,,Resistant;Not defined;Susceptible,AMR Panel,,HGAP v. 2.3,,PRJNA292904,SAMN04014896,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2017-06-20T00:00:00Z,,,2017-07-22T22:21:04.256Z,2017-07-22T22:21:04.256Z,,,50.88,"CP021935,CP021936,CP021937,CP021938",5506082,Escherichia coli strain AR_0055,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,5857,,3,,,5736,,4,Centers for Disease Control and Prevention,154x,PacBio RSII,,,,AR_0055,,,"Included in the study, passed QC/QA"
1280,562.17727,sample_type:water,,,,,SMRTAnalysis v. 2.3,,PRJNA391287,SAMN07260764,,,,,1,Jan-2016,Full genome sequencing of AMR enterobacteria isolated from food and the environment,2017-06-30T00:00:00Z,,,2017-07-23T03:12:05.798Z,2017-07-23T03:12:05.798Z,,,51,"CP022154,CP022155,CP022156,CP022157,CP022158,CP022159",5466321,Escherichia coli strain ABWA45,Complete,Escherichia,Switzerland:Basel,,,,,,,,Switzerland,,wastewater,,,"MLST.Escherichia_coli_1.635,MLST.Escherichia_coli_2.682",,562,,,,,,,5880,,5,,,5703,,6,University of Zurich,213.0x,PacBio,,,,ABWA45,,,"Included in the study, passed QC/QA"
1281,562.17734,collected_by:Guiqing Wang,,,,,SPAdes v. v3.5.0; HGAP Assembly v. v3,,PRJNA391721,SAMN07273977,,,,,1,2016-11-13,"Escherichia coli harboring mcr-1 on an IncHI2 plasmid in a New York patient returning from Portugal, 2016",2017-07-03T00:00:00Z,,,2017-07-23T04:28:36.316Z,2017-07-23T04:28:36.316Z,,,50.27,"CP022164,CP022165,CP022166,CP022167",5477301,Escherichia coli strain M160133,Complete,Escherichia,USA: New York,,,,,Asymptomatic UTI,Homo sapiens,,USA,,urine,,,,,562,,,,,,,5636,,3,,,5474,,4,New York Medical College,100.0x,Illumina MiSeq; PacBio,,,,M160133,,,"Included in the study, passed QC/QA"
1282,562.17735,collected_by:Korea Center for Disease Control and Prevention,,,,,PacBio SMRT Analysis v. 2.3.0,,PRJNA338095,SAMN05520965,,,,,1,2008-06-03,Enterohaemorrhagic Escherichia coli is one of the well-known food-borne pathogen. It was isolated from stool of foodborne poisoning patient in South Korea.,2017-07-05T00:00:00Z,,,2017-07-23T04:49:19.246Z,2017-07-23T04:49:19.246Z,,,50.75,CP016828,5244443,Escherichia coli strain FORC_043,Complete,Escherichia,South Korea: Gyeonggi-do,,,,,Not reported,Homo sapiens,isolated from stool of foodborne poisoning patient in South Korea,South Korea,,Human Stool,,,,,562,,,,,,,5334,,,,,5328,,1,Seoul National University,124.49x,PacBio,,,,FORC_043,,,"Included in the study, passed QC/QA"
1283,562.17736,"collected_by:Animal Diagnostic Lab, University Park, PA16801, USA",,,,,SMRT v. 2.3.0; DNASTAR SeqMn NGen v.,,PRJNA287563,SAMN03783363,,,,,1,2004,"Layer peritonitis is considered a major cause of morbidity and mortality in laying hens which leads to significant economic losses to the egg industry worldwide. Among the bacterial pathogens, E. coli is the most common bacterial species associated with layer peritonitis. However, the pathogenesis of layer peritonitis has not been elucidated. The objectives of the current study are; 1) to identify potential virulence factors encoded in peritonitis causing E. coli strain using whole genome sequencing, 2) ascertain genotypic homology among avian pathogenic E. coli (APEC) and human extraintestinal pathogenic E. coli (ExPEC) by comparative genomics and 3) to identify potential vaccine targets through antigenome approach",2017-07-06T00:00:00Z,,,2017-07-23T05:01:49.286Z,2017-07-23T05:01:49.286Z,,Layer Peritonitis,50.63,"CP011915,CP011916",5035255,Escherichia coli strain PSUO2,Complete,Escherichia,USA,,,,,Peritonitis,Gallus gallus domesticus,,,,peritoneal cavity,,,,,562,C,,,,,,5045,,1,,,4765,,2,Pennsylvania State University,264x,IonTorrent; PacBio,,,,PSUO2,,,"Included in the study, passed QC/QA"
1284,562.17737,"collected_by:Animal Diagnostic Lab, University Park, PA16801, USA",,,,,SMRT v. 3.2.0,,PRJNA287566,SAMN03783370,,,,,1,2010,"Layer peritonitis is considered a major cause of morbidity and mortality in laying hens which leads to significant economic losses to the table egg industry worldwide. Escherichia coli is the most common bacterial species associated with layer peritonitis. Despite its importance to the poultry industry, pathogenesis of layer peritonitis has not been elucidated. The objectives of the current study are; 1) to identify potential virulence factors encoded in E. coli causing peritonitis using whole genome sequencing, 2) ascertain genotypic homology among avian pathogenic E. coli and human extraintestinal pathogenic E. coli by comparative genomics, and 3) to identify potential vaccine targets through antigenome approaches",2017-07-06T00:00:00Z,,,2017-07-23T05:08:03.144Z,2017-07-23T05:08:03.144Z,,,50.71,"CP012112,CP012113,CP012114",5230570,Escherichia coli strain PSUO78,Complete,Escherichia,USA,,,,,Peritonitis,Gallus gallus domesticus,,,,peritoneal cavity,,,,,562,C,,,,,,5577,,2,,,4617,,3,Pennsylvania State University,14x,PacBio,,,,PSUO78,,,"Included in the study, passed QC/QA"
1285,562.17738,"collected_by:Animal Diagnostic Lab, University Park, PA16801, USA",,,,,DNASTAR NGen v. 12,,PRJNA314794,SAMN04543670,,,,,1,20-Jun-2012,Potential food borne pathogen. Stx1 and eae positive STEC,2017-07-06T00:00:00Z,,,2017-07-23T05:10:58.245Z,2017-07-23T05:10:58.245Z,,,50.7,"CP014752,CP014753",5522653,Escherichia coli strain PSUO103,Complete,Escherichia,USA,,,,,Diarrhoea,Odocoileus virginianus,,,,feces,,,,,562,,,,,,,6212,,1,,,5567,,2,Pennsylvania State University,180x,IonTorrent; PacBio,,,,PSUO103,,,"Included in the study, passed QC/QA"
1286,562.18998,sample_type:not collected,,,,GCA_002237285.1,SMRT Portal HGAP assembly v. 3,,PRJNA292040,SAMN03960341,,,,,1,,Escherichia coli MEM genome sequencing and assembly complete genome,2017-07-31T00:00:00Z,,,2017-09-28T19:40:14.043Z,2017-09-28T19:40:14.043Z,,,50.68,CP012378,4928082,Escherichia coli strain MEM,Complete,Escherichia,China,,,,,,Homo sapiens,,,,human feces of different individuals,,,,,562,C,,,,,,4913,,,,,4824,,1,Nankai University,130x,PacBio; Illumina GAIIx,,,,MEM,,,"Included in the study, passed QC/QA"
1287,562.19087,collected_by:CDC,,,,GCA_002249955.1,HGAP v. 3,,PRJNA218110,SAMN03256350,,,,,1,,PulseNet STEC genome reference library,2017-08-14T00:00:00Z,,,2017-09-28T20:12:20.979Z,2017-09-28T20:12:20.979Z,,,50.45,"CP022689,CP022688",5498101,Escherichia coli strain CDC#03-98,Complete,Escherichia,USA,,,,,,,,,,,,,,,562,,,,,,,5879,,1,,,5718,,2,CDC,160.0x,PacBio,,,,CDC#03-98,,,"Included in the study, passed QC/QA"
1288,562.19131,"collected_by:Labolatory of Food Hygiene and Control, Faculty of Veterinary Medicine, University of Sadat City",,,,GCA_002278115.2,HGAP v. v.3.0,,PRJNA230969,SAMN06928086,,,,,1,2016,Whole genome sequencing of cultured E. coli as part of the US Food and Drug Administration surveillance project for the rapid detection of foodborne contamination events.,2017-09-05T00:00:00Z,,,2017-09-28T21:32:03.423Z,2017-09-28T21:32:03.423Z,,,50.46,"CP023142,CP023143,CP023144,CP023145",5711651,Escherichia coli strain CFSAN061770,Complete,Escherichia,Egypt,,,,,,,,,,Raw milk cheese,,,,,562,,,,,,,6046,,3,,,5904,,4,FDA/CFSAN,286.0x,PacBio,,,,CFSAN061770,,,"Included in the study, passed QC/QA"
1289,562.19158,sample_type:whole organism,,,,GCA_002285755.1,HGAP v. 2.0,,PRJNA385892,SAMN06920354,,,,,1,2010,"Uropathogenic Escherichia coli (UPEC) are responsible for the majority of urinary tract infections (UTIs). UPEC strains possess an array of virulence-associated factors that aid in their colonization, survival and persistence in the urinary tract. One such factor is the polysaccharide K capsule, which provides protection against host innate immune factors. Among the different K capsule types, the K1 serotype is strongly associated with UPEC strains that cause UTI, bloodstream infections and meningitis. In this study, we employed a combination of a lytic K1 capsule-specific phage, saturated Tn5 transposon mutagenesis, and high-throughput transposon directed insertion-site sequencing (TraDIS) to identify genes associated with K1 capsule production in the clinical urosepsis isolate PA45B.",2017-09-05T00:00:00Z,,,2017-09-28T21:52:15.495Z,2017-09-28T21:52:15.495Z,,,50.52,"CP021288,CP021289",5221926,Escherichia coli strain PA45B,Complete,Escherichia,Australia: Brisbane,,,,,,Homo sapiens,,Australia,,,,,,,562,,,,,,,5243,,1,,,4883,,2,University of Queensland,120.0x,PacBio,,O2:K1:H7,,PA45B,,,"Included in the study, passed QC/QA"
1290,562.19192,collected_by:Asa Sjoling,,,,GCA_002302315.1,HGAP3 v. 3,,PRJNA398221,SAMN07503734,,,,,1,22-Mar-2006,"Genomic comparison of Enterotoxigenic E. coli collected from diarrheal stool in Dhaka, Bangladesh 2006.",2017-09-14T00:00:00Z,,,2017-09-28T23:33:27.926Z,2017-09-28T23:33:27.926Z,,,50.64,"CP023346,CP023347,CP023348",5319464,Escherichia coli strain ETEC-2265,Complete,Escherichia,Bangladesh: Dhaka,,,,,Secretory diarrhea,Homo sapiens,,Bangladesh,,Diarrheal stool,,,,,562,,,,,,,5631,,2,,,5512,,3,Karolinska Institutet,596x,PacBio,,,,ETEC-2265,,,"Included in the study, passed QC/QA"
1291,562.19193,collected_by:Asa Sjoling,,,,GCA_002302335.1,HGAP3 v. 3,,PRJNA398221,SAMN07503733,,,,,1,21-Mar-2006,"Genomic comparison of Enterotoxigenic E. coli collected from diarrheal stool in Dhaka, Bangladesh 2006.",2017-09-14T00:00:00Z,,,2017-09-28T23:33:17.395Z,2017-09-28T23:33:17.395Z,,,50.69,"CP023349,CP023350,CP023351,CP023352",5207995,Escherichia coli strain ETEC-2264,Complete,Escherichia,Bangladesh: Dhaka,,,,,Secretory diarrhea,Homo sapiens,,Bangladesh,,Diarrheal stool,,,,,562,,,,,,,5464,,3,,,5356,,4,Karolinska Institutet,894x,PacBio,,,,ETEC-2264,,,"Included in the study, passed QC/QA"
1292,562.19202,sample_type:whole organism,,,,GCA_002310555.1,De-novo v. Celera Assembler 8.8,,PRJNA402083,SAMN07618127,,,,,1,2002,"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.",2017-09-18T00:00:00Z,,,2017-09-29T00:34:20.858Z,2017-09-29T00:34:20.858Z,,,50.75,"CP023359,CP023360,CP023361,CP023362",5000721,Escherichia coli strain 1943,Complete,Escherichia,"United Kingdom: Scotland, Edinburgh",,,,,,canine,isolated from urinary tract infections in dogs,United Kingdom,,urinary tract infections,,,,,562,,,,,,,5148,,3,,,5046,,4,The Roslin Institute,20x,PacBio,,,,1943,,,"Included in the study, passed QC/QA"
1293,562.19203,sample_type:whole organism,,,,GCA_002310575.1,De-novo v. Celera Assembler 8.9,,PRJNA402083,SAMN07618128,,,,,1,2002,"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.",2017-09-18T00:00:00Z,,,2017-09-29T00:34:36.876Z,2017-09-29T00:34:36.876Z,,,50.54,"CP023357,CP023358",5135913,Escherichia coli strain 317,Complete,Escherichia,"United Kingdom: Scotland, Edinburgh",,,,,,canine,isolated from urinary tract infections in dogs,United Kingdom,,urinary tract infections,,,,,562,,,,,,,5255,,1,,,5129,,2,The Roslin Institute,20x,PacBio,,,,317,,,"Included in the study, passed QC/QA"
1294,562.19204,sample_type:whole organism,,,,GCA_002310595.1,De-novo v. Celera Assembler 8.7,,PRJNA402083,SAMN07618126,,,,,1,2002,"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.",2017-09-18T00:00:00Z,,,2017-09-29T00:35:00.861Z,2017-09-29T00:35:00.861Z,,,50.56,"CP023364,CP023363,CP023365",5361252,Escherichia coli strain 144,Complete,Escherichia,"United Kingdom: Scotland, Edinburgh",,,,,,canine,isolated from urinary tract infections in dogs,United Kingdom,,urinary tract infections,,,,,562,,,,,,,5494,,2,,,5356,,3,The Roslin Institute,20x,PacBio,,,,144,,,"Included in the study, passed QC/QA"
1295,562.19205,sample_type:whole organism,,,,GCA_002310615.1,De-novo v. Celera Assembler 8.2,,PRJNA402083,SAMN07618121,,,,,1,2002,"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.",2017-09-18T00:00:00Z,,,2017-09-29T00:34:49.764Z,2017-09-29T00:34:49.764Z,,,50.83,"CP023386,CP023387",4987038,Escherichia coli strain 1190,Complete,Escherichia,"United Kingdom: Scotland, Edinburgh",,,,,,canine,isolated from urinary tract infections in dogs,United Kingdom,,urinary tract infections,,,,,562,,,,,,,5043,,1,,,4994,,2,The Roslin Institute,20x,PacBio,,,,1190,,,"Included in the study, passed QC/QA"
1296,562.19206,sample_type:whole organism,,,,GCA_002310635.1,De-novo v. Celera Assembler 8.1,,PRJNA402083,SAMN07618120,,,,,1,2002,"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.",2017-09-18T00:00:00Z,,,2017-09-29T00:34:54.712Z,2017-09-29T00:34:54.712Z,,,50.51,"CP023388,CP023389",5133746,Escherichia coli strain 1105,Complete,Escherichia,"United Kingdom: Scotland, Edinburgh",,,,,,canine,isolated from urinary tract infections in dogs,United Kingdom,,urinary tract infections,,,,,562,,,,,,,5291,,1,,,5164,,2,The Roslin Institute,20x,PacBio,,,,1105,,,"Included in the study, passed QC/QA"
1297,562.19207,sample_type:whole organism,,,,GCA_002310655.1,De-novo v. Celera Assembler 8.10,,PRJNA402083,SAMN07618129,,,,,1,2002,"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.",2017-09-18T00:00:00Z,,,2017-09-29T00:35:38.107Z,2017-09-29T00:35:38.107Z,,,50.69,"CP023353,CP023354,CP023355,CP023356",5319278,Escherichia coli strain 746,Complete,Escherichia,"United Kingdom: Scotland, Edinburgh",,,,,,canine,isolated from urinary tract infections in dogs,United Kingdom,,urinary tract infections,,,,,562,,,,,,,5538,,3,,,5388,,4,The Roslin Institute,20x,PacBio,,,,746,,,"Included in the study, passed QC/QA"
1298,562.19208,sample_type:whole organism,,,,GCA_002310675.1,De-novo v. Celera Assembler 8.4,,PRJNA402083,SAMN07618123,,,,,1,2002,"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.",2017-09-18T00:00:00Z,,,2017-09-29T00:35:42.030Z,2017-09-29T00:35:42.030Z,,,50.64,"CP023377,CP023378,CP023379,CP023380,CP023381,CP023382",5091284,Escherichia coli strain 127,Complete,Escherichia,"United Kingdom: Scotland, Edinburgh",,,,,,canine,isolated from urinary tract infections in dogs,United Kingdom,,urinary tract infections,,,,,562,,,,,,,5540,,5,,,5402,,6,The Roslin Institute,20x,PacBio,,,,127,,,"Included in the study, passed QC/QA"
1299,562.19209,sample_type:whole organism,,,,GCA_002310695.1,De-novo v. Celera Assembler 8.6,,PRJNA402083,SAMN07618125,,,,,1,2002,"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.",2017-09-18T00:00:00Z,,,2017-09-29T00:35:33.120Z,2017-09-29T00:35:33.120Z,,,50.51,"CP023366,CP023367,CP023368,CP023369,CP023370",5309743,Escherichia coli strain 1428,Complete,Escherichia,"United Kingdom: Scotland, Edinburgh",,,,,,canine,isolated from urinary tract infections in dogs,United Kingdom,,urinary tract infections,,,,,562,,,,,,,5513,,4,,,5399,,5,The Roslin Institute,20x,PacBio,,,,1428,,,"Included in the study, passed QC/QA"
1300,562.1921,sample_type:whole organism,,,,GCA_002310715.1,De-novo v. Celera Assembler 8.3,,PRJNA402083,SAMN07618122,,,,,1,2002,"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.",2017-09-18T00:00:00Z,,,2017-09-29T00:35:10.364Z,2017-09-29T00:35:10.364Z,,,50.63,"CP023383,CP023384,CP023385",4951571,Escherichia coli strain 1223,Complete,Escherichia,"United Kingdom: Scotland, Edinburgh",,,,,,canine,isolated from urinary tract infections in dogs,United Kingdom,,urinary tract infections,,,,,562,,,,,,,5159,,2,,,5057,,3,The Roslin Institute,20x,PacBio,,,,1223,,,"Included in the study, passed QC/QA"
1301,562.19211,sample_type:whole organism,,,,GCA_002310735.1,De-novo v. Celera Assembler 8.5,,PRJNA402083,SAMN07618124,,,,,1,2002,"Objectives: To determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs.Single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible.Results: This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases.Conclusions: This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements pathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.",2017-09-18T00:00:00Z,,,2017-09-29T00:35:16.434Z,2017-09-29T00:35:16.434Z,,,50.75,"CP023371,CP023372,CP023374,CP023373,CP023375,CP023376",4920052,Escherichia coli strain 1283,Complete,Escherichia,"United Kingdom: Scotland, Edinburgh",,,,,,canine,isolated from urinary tract infections in dogs,United Kingdom,,urinary tract infections,,,,,562,,,,,,,5103,,5,,,5032,,6,The Roslin Institute,20x,PacBio,,,,1283,,,"Included in the study, passed QC/QA"
1302,562.1932,,,,,GCA_900186905.1,,,PRJEB6403,SAMEA4364219,,,,,1,1884/1920,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,2017-08-15T00:00:00Z,,NCTC:122,2017-09-29T14:27:25.613Z,2017-09-29T14:27:25.613Z,,,50.96,LT906474,4625968,Escherichia coli strain NCTC122,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4447,,,,,4165,,1,SC,,,,,,NCTC122,,,"Included in the study, passed QC/QA"
1303,562.19574,"collected_by:Ministry of Food and Drug Safety, Republic of Korea",,,,GCA_002220265.1,PacBio SMRT Analysis v. 2.3.0,,PRJNA330605,SAMN05417814,,,,,1,2015-03-09,Complete genome sequence of Escherichia coli FORC_044,2017-07-17T00:00:00Z,,,2017-09-29T15:34:51.371Z,2017-09-29T15:34:51.371Z,,,50.5,"CP016755,CP018625,CP018626",5703173,Escherichia coli strain FORC_044,Complete,Escherichia,South Korea: Seoul,,,,,,Homo sapiens,,South Korea,,Stool,,,,,562,,,,,,,6094,,2,,,5892,,3,"Food-borne Pathogen Omics Research Center, FORC",111.79,PacBio,,O157:H7,,FORC_044,,,"Included in the study, passed QC/QA"
1304,562.19575,sample_type:not applicable,,,,GCA_002220215.1,SPAdes v. 3.7.1,,PRJNA389489,SAMN07251590,,,,,1,2015,Genetic status of the D-Serine Utilization Locus dsdCXA and Biofilm Adhesin Genes pgaABCD Defines Survival fitness and Resistance Formation Potential of Gut Microbiome Strains,2017-07-17T00:00:00Z,,,2017-09-29T15:34:35.419Z,2017-09-29T15:34:35.419Z,,,50.74,CP022393,4914770,Escherichia coli strain E62,Complete,Escherichia,China,,,,,,rat,,,,feces,,,,,562,,,,,,,4998,,,,,4908,,1,Polyu,50x,PacBio,,,,E62,,,"Included in the study, passed QC/QA"
1305,562.19631,,,Susceptible;Resistant;Not defined,AMR Panel,GCA_002180215.1,canu v. 1.3,,PRJNA292902,SAMN04014992,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-08T00:00:00Z,,,2017-09-29T16:41:50.184Z,2017-09-29T16:41:50.184Z,,,50.77,"CP021691,CP021692,CP021693",4959341,Escherichia coli strain AR_0151,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,5104,,2,,,4991,,3,Centers for Disease Control and Prevention,228x,PacBio RSII,,,,AR_0151,,,"Included in the study, passed QC/QA"
1306,562.19632,,,Susceptible;Resistant;Not defined;Intermediate,AMR Panel,GCA_002180195.1,canu v. 1.3,,PRJNA292904,SAMN04014899,,,,,1,,Collection of bacterial pathogens that are assembled to challenge assays that detect carbapenemase production representing a range of gram-negative bacteria,2017-06-08T00:00:00Z,,,2017-09-29T16:41:56.896Z,2017-09-29T16:41:56.896Z,,,50.83,"CP021689,CP021690",5103486,Escherichia coli strain AR_0058,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,5334,,1,,,5231,,2,Centers for Disease Control and Prevention,178x,PacBio RSII,,,,AR_0058,,,"Included in the study, passed QC/QA"
1307,562.19633,,,Resistant;Not defined;Susceptible,AMR Panel,GCA_002180095.1,HGAP v. 2.3,,PRJNA292902,SAMN04014960,,,,,1,,Collection of bacterial pathogens that consist of carbapenemase-producing Enterobacteriaceae representing a diversity of species,2017-06-08T00:00:00Z,,,2017-09-29T16:42:06.844Z,2017-09-29T16:42:06.844Z,,,50.58,"CP021535,CP021536,CP021537,CP021538",5435963,Escherichia coli strain AR_0149,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,5784,,3,,,5655,,4,Centers for Disease Control and Prevention,215x,PacBio RSII,,,,AR_0119,,,"Included in the study, passed QC/QA"
1308,562.19635,sample_type:not collected,,,,GCA_002237305.1,SMRT Portal HGAP assembly v. 3,,PRJNA292046,SAMN03963238,,,,,1,,Escherichia coli PAR complete genome sequencing and assembly,2017-07-31T00:00:00Z,,,2017-09-29T20:49:22.643Z,2017-09-29T20:49:22.643Z,,,50.4,CP012379,4859743,Escherichia coli strain PAR,Complete,Escherichia,China,,,,,,,,,,cockatoo feces,,,,,562,C,,,,,,4729,,,,,4686,,1,Nankai University,117x,Illumina GAIIx; PacBio,,,,PAR,,,"Included in the study, passed QC/QA"
1309,562.19636,sample_type:not collected,,,,GCA_002237325.1,SMRT Portal HGAP assembly v. 3,,PRJNA292047,SAMN03963241,,,,,1,,Escherichia coli WAT complete genome,2017-07-31T00:00:00Z,,,2017-09-29T20:49:19.380Z,2017-09-29T20:49:19.380Z,,,50.84,CP012380,4847481,Escherichia coli strain WAT,Complete,Escherichia,China,,,,,,,,,,park pond water,,,,,562,C,,,,,,4748,,,,,4669,,1,Nankai University,130x,Illumina GAIIx; PacBio,,,,WAT,,,"Included in the study, passed QC/QA"
1310,562.19642,sample_type:not collected,,,,GCA_002237325.1,SMRT Portal HGAP assembly v. 3,,PRJNA292047,SAMN03963241,,,,,1,,Escherichia coli WAT complete genome,2017-07-31T00:00:00Z,,,2017-09-29T21:33:02.280Z,2017-09-29T21:33:02.280Z,,,50.84,CP012380,4847481,Escherichia coli strain WAT,Complete,Escherichia,China,,,,,,,,,,park pond water,,,,,562,C,,,,,,4748,,,,,4669,,1,Nankai University,130x,Illumina GAIIx; PacBio,,,,WAT,,,"Included in the study, passed QC/QA"
1311,562.19643,sample_type:not collected,,,,GCA_002237305.1,SMRT Portal HGAP assembly v. 3,,PRJNA292046,SAMN03963238,,,,,1,,Escherichia coli PAR complete genome sequencing and assembly,2017-07-31T00:00:00Z,,,2017-09-29T21:33:12.409Z,2017-09-29T21:33:12.409Z,,,50.4,CP012379,4859743,Escherichia coli strain PAR,Complete,Escherichia,China,,,,,,,,,,cockatoo feces,,,,,562,C,,,,,,4729,,,,,4686,,1,Nankai University,117x,Illumina GAIIx; PacBio,,,,PAR,,,"Included in the study, passed QC/QA"
1312,562.574,,,,,GCA_000784925.1,SMRT Portal v. 2.0,,PRJNA242851,SAMN02709589,,,,,1,2013,Whole genome sequencing of Escherichia coli,2014-11-17T00:00:00Z,4,,2015-03-12T14:00:38.693Z,2015-03-16T03:17:09.594Z,,,50.41,"CP009859.1,CP009860.1,CP009862.1,CP009861.1",5559642,Escherichia coli ECONIH1,Complete,Escherichia,USA,,,,,,"Human, Homo sapiens",,United States,,perirectal swab,,,,,562,,,,,,,5434,,3,25232178,"NZ_CP009859.1,NZ_CP009861.1,NZ_CP009862.1,NZ_CP009860.1",5322,,4,NIH,,PacBio RSII,,,,ECONIH1,,,"Included in the study, passed QC/QA"
1313,562.5741,,,,,GCA_000801165.1,CLC Genomics Workbench v. 7.0,,PRJNA253935,SAMN03264844,,,,,1,2009,Complete Genome Sequence and Comparison of Two Shiga Toxin-Producing Escherichia coli O104 Strains,2014-12-15T00:00:00Z,2,,2015-03-12T14:00:39.009Z,2015-03-16T03:17:09.594Z,,,50.71,"CP009104.1,CP009105.1",4995948,Escherichia coli RM9387,Complete,Escherichia,USA: California,,,,,,,,United States,,Cow feces,,,,,562,,,,,,,4838,,1,-,"NZ_CP009104.1,NZ_CP009105.1",4544,,2,USDA-ARS,>30x,Sequence generated by Ion Torrent and,,,,RM9387,,,"Included in the study, passed QC/QA"
1314,562.5742,,,,,GCA_000801185.1,CLC Genomics Workbench v. 7.0; Celera,,PRJNA253936,SAMN03262652,,,,,1,1994,Complete Genome Sequence and Comparison of Two Shiga Toxin-Producing Escherichia coli O104 Strains,2014-12-15T00:00:00Z,2,,2015-03-12T14:00:39.334Z,2015-03-16T03:17:09.594Z,,,50.66,"CP009106.1,CP009107.1",5064032,Escherichia coli 94-3024,Complete,Escherichia,USA: Montana,,,,,,,,United States,,Montana milk 1994 outbreak strain fromCDC,,,,,562,,,,,,,4880,,1,-,"NZ_CP009106.1,NZ_CP009107.1",4557,,2,USDA-ARS,>30x,Sequence generated by Ion Torrent and,,,,94-3024,,,"Included in the study, passed QC/QA"
1315,562.5744,,,,,GCA_000819645.1,Newbler (Roche) v. 04,,PRJNA262513,SAMN03083542,,,,,1,,"Avian colisepticemia is a severe systemic disease of birds causing high morbidity and mortality and resulting in severe economic losses. Genomic and genetic analysis of Escherichia coli strains of serotype O78, the major cause of the disease, have been performed to identify potential virulence factors conserved in all colisepticemic strains examined.",2015-01-16T00:00:00Z,4,,2015-03-12T14:00:40.687Z,2015-03-16T03:17:09.594Z,,,50.78,"CP010315.1,CP010318.1,CP010317.1,CP010316.1",5273074,Escherichia coli 789,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,5135,,3,25587010,"NZ_CP010315.1,NZ_CP010317.1,NZ_CP010318.1,NZ_CP010316.1",5011,,4,Georg-August University of Goettingen,12.0x,454,,serovar O78,,789,,,"Included in the study, passed QC/QA"
1316,562.5745,,,,,GCA_000830035.1,Newbler v. 2009,,PRJNA273434,SAMN03292179,,,,,1,2009,"The Escherichia coli strain C41(DE3) was derived from BL21(DE3) for its improved ability to produce recombinant proteins (see: J Mol Biol. 1996 Jul 19;260(3):289-98). This study aims at identifying and understanding the genetic adaptations that have occurred during the isolation of C41(DE3). Such knowledge may provide leads for future studies aimed at the isolation of improved protein production mutants, and help to facilitate recombinant protein production in Escherichia coli.",2015-01-29T00:00:00Z,1,,2015-03-12T14:00:41.414Z,2015-03-16T03:17:09.594Z,,,50.83,CP010585.1,4557511,Escherichia coli C41(DE3),Complete,Escherichia,Sweden,,,,,,,derived from BL21(DE3) for its improved ability to produce recombinant proteins (see: J Mol Biol,Sweden,,BL21(DE3) for its improved ability to produce recombinant proteins (see: J Mol Biol,,,,,562,,,,,,,4342,,,-,NZ_CP010585.1,4299,,1,Stockholm University,43x (454),454; Sanger,,,,C41(DE3),,,"Included in the study, passed QC/QA"
1317,562.5746,,,,,GCA_000833145.1,CLC Genomics Workbench v. 6.5.1,,PRJNA272570,SAMN03301757,,,,,1,,To identify genomic differences among laboratory E. coli strains,2015-02-05T00:00:00Z,1,,2015-03-12T14:00:42.345Z,2015-03-16T03:17:09.594Z,,,50.8,CP010816.1,4528118,Escherichia coli BL21 (TaKaRa),Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4308,,,-,NZ_CP010816.1,4260,,1,KRIBB,850.0x,Illumina HiSeq,,,,BL21 (TaKaRa),,,"Included in the study, passed QC/QA"
1318,562.6958,,,,,GCF_000597845.1,SMRT PORTAL HGAP v. 2.O,,PRJNA238952,SAMN02647163,,,,Bacilli,1,,To study Nitrofurantoin resistant mechanism,2014-04-16T00:00:00Z,,,2016-01-17T15:34:35.422Z,2016-01-17T15:34:35.422Z,,,51.11,CP007265,4758629,Escherichia coli strain ST540,Complete,Escherichia,Belgium,Negative,,,,,"Human, Homo sapiens",,Belgium,,gut,,,,Yes,562,,,,,,,4835,,,24723707,NZ_CP007265.1,4526,,1,University of Antwerpen,28x,PacBio,,,,ST540,,,"Included in the study, passed QC/QA"
1319,562.6959,,,,,GCF_000599625.1,"HGAP, SMRT Analysis Portal v. 2.0.1",,PRJNA238952,SAMN02666434,,,,Bacilli,1,2012-04-12,To study Nitrofurantoin resistant mechanism,2014-04-16T00:00:00Z,,,2016-01-17T15:34:36.786Z,2016-01-17T15:34:36.786Z,,,51.04,CP007390,4807977,Escherichia coli strain ST540,Complete,Escherichia,Belgium,Negative,,,,,,,Belgium,,water,,,,Yes,562,,,,,,,4901,,,24723707,NZ_CP007390.1,4562,,1,University of Antwerpen,25x,PacBio,,,,ST540,,,"Included in the study, passed QC/QA"
1320,562.696,,,,,GCF_000599645.1,"HGAP, SMRT Analysis Portal v. 2.0.1",,PRJNA238952,SAMN02666695,,,,Bacilli,1,2012-03-12,To study Nitrofurantoin resistant mechanism,2014-04-16T00:00:00Z,,,2016-01-17T15:34:37.171Z,2016-01-17T15:34:37.171Z,,,51.02,CP007391,4875682,Escherichia coli strain ST540,Complete,Escherichia,Belgium,Negative,,,,,,,Belgium,,water,,,,Yes,562,,,,,,,5032,,,24723707,NZ_CP007391.1,4607,,1,University of Antwerpen,25x,PacBio,,,,ST540,,,"Included in the study, passed QC/QA"
1321,562.6961,,,,,GCF_000599665.1,"HGAP, SMRT Analysis Portal v. 2.0.1",,PRJNA238952,SAMN02666696,,,,Bacilli,1,2012-09-11,To study Nitrofurantoin resistant mechanism,2014-04-16T00:00:00Z,,,2016-01-17T15:34:37.531Z,2016-01-17T15:34:37.531Z,,,50.65,CP007392,5054509,Escherichia coli strain ST2747,Complete,Escherichia,Belgium,Negative,,,,,,,Belgium,,water,,,,Yes,562,,,,,,,4982,,,24723707,NZ_CP007392.1,4631,,1,University of Antwerpen,25x,PacBio,,,,ST2747,,,"Included in the study, passed QC/QA"
1322,562.6962,,,,,GCF_000599685.1,"HGAP, SMRT Analysis Portal v. 2.0.1",,PRJNA238952,SAMN02666697,,,,Bacilli,1,2012-07-22,To study Nitrofurantoin resistant mechanism,2014-04-16T00:00:00Z,,,2016-01-17T15:34:37.920Z,2016-01-17T15:34:37.920Z,,,50.65,CP007393,4998910,Escherichia coli strain ST2747,Complete,Escherichia,Belgium,Negative,,,,,,,Belgium,,water,,,,Yes,562,,,,,,,4918,,,24723707,NZ_CP007393.1,4560,,1,University of Antwerpen,25x,PacBio,,,,ST2747,,,"Included in the study, passed QC/QA"
1323,562.6963,,,,,GCF_000599705.1,"HGAP, SMRT Analysis Portal v. 2.0.1",,PRJNA238952,SAMN02666698,,,,Bacilli,1,2012-04-18,To study Nitrofurantoin resistant mechanism,2014-04-16T00:00:00Z,,,2016-01-17T15:34:38.250Z,2016-01-17T15:34:38.250Z,,,50.78,CP007394,5090442,Escherichia coli strain ST2747,Complete,Escherichia,Belgium,Negative,,,,,,,Belgium,,water,,,,Yes,562,,,,,,,5136,,,24723707,NZ_CP007394.1,4572,,1,University of Antwerpen,25x,PacBio,,,,ST2747,,,"Included in the study, passed QC/QA"
1324,562.7071,collected_by:Health care provider,,,,GCF_000931565.1,CLC Genomics Workbench v. 7; HGAP v. 3,,PRJNA272863,SAMN03287565,,,,,1,Apr-2012,Sequencing of multiple CRE isolates from Minnesota for genomic comparisons,2015-04-15T00:00:00Z,,,2016-01-17T15:44:36.051Z,2016-01-17T15:44:36.051Z,,,50.75,"CP010876,CP010877,CP010878,CP010879,CP010880,CP010881,CP010882",5292269,Escherichia coli strain MNCRE44,Complete,Escherichia,USA: Minnesota,,,,,sepsis,"Human, Homo sapiens",,United States,,sputum,,,,,562,,,,,,,5509,UPEC,6,25858844,"NZ_CP010876.1,NZ_CP010877.1,NZ_CP010878.1,NZ_CP010879.1,NZ_CP010880.1,NZ_CP010881.1,NZ_CP010882.1",5134,,7,University of Minnesota,125x; 100x,Illumina MiSeq 2x300; PacBio,,,,MNCRE44,,,"Included in the study, passed QC/QA"
1325,562.7214,,,,,GCF_000952955.1,,,PRJEB6354,SAMEA2547783,,,,,1,,"Escherichia coli str. K-12 substr. RV308 (ATCC 31608), complete genome",2014-10-01T00:00:00Z,,ATCC:31608,2016-01-17T15:48:56.520Z,2016-01-17T15:48:56.520Z,,,50.79,LM995446,4585620,Escherichia coli strain K-12 substr. RV308,Complete,Escherichia,,,,,,,,,,,,,,,,562,,,,,,,4532,,,,NZ_LM995446.1,4247,,1,Austrian Centre of Industrial Biotechnology,,,,,,K-12 substr. RV308,,,"Included in the study, passed QC/QA"
1326,562.7228,,,,,GCF_000967155.1,,,PRJEA76335,,,,,,1,,-,2015-01-07T00:00:00Z,,,2016-01-17T15:52:24.313Z,2016-01-17T15:52:24.313Z,,,50.65,"HF572917,HE610900,HE610901,HE610902",5443340,Escherichia coli strain HUSEC2011,Complete,Escherichia,Germany:Frankfurt am Main,,,,,,"Human, Homo sapiens",,Germany,,,,,,,562,,,,,,,5581,,3,,"NZ_HF572917.1,NC_022742.1,NC_022743.1,NC_022741.1",5494,,4,Justus-Liebig-University Giessen,,,,,,HUSEC2011,,,"Included in the study, passed QC/QA"
1327,562.7235,sample_type:Bacterial isolate,,,,GCF_000971615.1,,,PRJNA277394,SAMN03390066,,,,,1,,Sequencing of E. coli CI5,2015-06-10T00:00:00Z,,,2016-01-17T15:53:31.370Z,2016-01-17T15:53:31.370Z,,,50.66,"CP011018,CP011019",5092643,Escherichia coli strain CI5,Complete,Escherichia,,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,5163,,1,26021932,"NZ_CP011018.1,NZ_CP011019.1",4879,,2,National University of Singapore and Genome Institute of Singapore,,,,,,CI5,,,"Included in the study, passed QC/QA"
1328,562.7244,,,,,GCF_000987875.1,de novo v. 4.11,,PRJNA244370,SAMN03576594,,,,,1,,This is a strain isolated from diarrhea piglet.,2015-05-04T00:00:00Z,,,2016-01-17T15:56:51.615Z,2016-01-17T15:56:51.615Z,,,50.76,CP007594,5153435,Escherichia coli strain SEC470,Complete,Escherichia,,,,,,,"Pig, Sus scrofa",isolated from diarrhea piglet,,,diarrhea piglet,,,,,562,,,,,,,5307,,,,NZ_CP007594.1,4941,,1,"Institute of Subtropical Agriculture, Chinese Academy of Sciences",50x,Illumina,,,,SEC470,,,"Included in the study, passed QC/QA"
1329,562.7245,sample_type:single cell,,,,GCF_000988355.1,CLCBio Genomics Workbench v. 7.0.4,,PRJNA241498,SAMN03276545,,,,,1,2008,Genomic sequence of a ribosomal deletion construct of E. coli MG1655,2015-05-06T00:00:00Z,,,2016-01-17T15:56:59.454Z,2016-01-17T15:56:59.454Z,,,50.79,CP011320,4633461,Escherichia coli strain SQ37,Complete,Escherichia,USA,Negative,,,,,,,United States,,not applicable,,,,,562,,,,,,,4589,,,,NZ_CP011320.1,4314,,1,AstraZeneca,66x,Illumina,,,,SQ37,,,"Included in the study, passed QC/QA"
1330,562.7246,sample_type:single cell,,,,GCF_000988385.1,CLCBio Genomics Workbench v. 7.0.4,,PRJNA241498,SAMN03276546,,,,,1,2008,Genomic sequence of a ribosomal deletion construct of E. coli MG1655,2015-05-06T00:00:00Z,,,2016-01-17T15:56:59.770Z,2016-01-17T15:56:59.770Z,,,50.78,CP011321,4610881,Escherichia coli strain SQ88,Complete,Escherichia,USA,Negative,,,,,,,United States,,not applicable,,,,,562,,,,,,,4588,,,,NZ_CP011321.1,4313,,1,AstraZeneca,63x,Illumina,,,,SQ88,,,"Included in the study, passed QC/QA"
1331,562.7247,sample_type:single cell,,,,GCA_000988425.1,CLCBio Genomics Workbench v. 7.0.4,,PRJNA241498,SAMN03276543,,,,,1,2008,Genomic sequence of a ribosomal deletion construct of E. coli MG1655,2015-05-06T00:00:00Z,,,2016-01-17T15:57:00.551Z,2016-01-17T15:57:00.551Z,,,50.78,CP011322,4605135,Escherichia coli strain SQ110,Complete,Escherichia,USA,Negative,,,,,,,United States,,not applicable,,,,,562,,,,,,,4584,,,,,4313,,1,AstraZeneca,103x,Illumina,,,,SQ110,,,"Included in the study, passed QC/QA"
1332,562.7248,sample_type:single cell,,,,GCA_000988445.1,CLCBio Genomics Workbench v. 7.0.4,,PRJNA241498,SAMN03276544,,,,,1,2008,Genomic sequence of a ribosomal deletion construct of E. coli MG1655,2015-05-06T00:00:00Z,,,2016-01-17T15:57:00.934Z,2016-01-17T15:57:00.934Z,,,50.78,CP011323,4599702,Escherichia coli strain SQ171,Complete,Escherichia,USA,Negative,,,,,,,United States,,not applicable,,,,,562,,,,,,,4586,,,,,4314,,1,AstraZeneca,45x,Illumina,,,,SQ171,,,"Included in the study, passed QC/QA"
1333,562.7249,sample_type:single cell,,,,GCF_000988465.1,CLCBio Genomics Workbench v. 7.0.4,,PRJNA241498,SAMN03276542,,,,,1,2008,Genomic sequence of a ribosomal deletion construct of E. coli MG1655,2015-05-06T00:00:00Z,,,2016-01-17T15:57:01.246Z,2016-01-17T15:57:01.246Z,,,50.78,CP011324,4605301,Escherichia coli strain SQ2203,Complete,Escherichia,USA,Negative,,,,,,,United States,,not applicable,,,,,562,,,,,,,4587,,,,NZ_CP011324.1,4313,,1,AstraZeneca,50x,Illumina,,,,SQ2203,,,"Included in the study, passed QC/QA"
1334,562.7257,,,,,GCF_001007915.1,SMRT Portal HGAP v. 2.3.0,,PRJNA243331,SAMN03612246,,,,,1,2012-04-15,Draft and complete genome sequences of foodborne bacterial pathogens collected for research purposes at the FDA's Center for Food Safety and Applied Nutrition.,2015-05-15T00:00:00Z,,,2016-01-17T16:02:30.567Z,2016-01-17T16:02:30.567Z,,,50.53,"CP011416,CP011417,CP011418",5288947,Escherichia coli strain CFSAN029787,Complete,Escherichia,Italy:Milan,,,,,none,"Human, Homo sapiens",,Italy,,Stool sample,,,,,562,,,,,,,5537,,2,,"NZ_CP011416.1,NZ_CP011417.1,NZ_CP011418.1",5103,,3,FDA/CFSAN,350X,PacBio RS,,O96:H19,,CFSAN029787,,,"Included in the study, passed QC/QA"
1335,562.7299,sample_type:cell culture,,,,GCF_001039415.1,CLC NGS Cell v. 5.5.1,,PRJNA275043,SAMN03761398,,,,,1,2009,E. coli C43(DE3) is a derivative of E. coli C41(DE3) with improved production of some membrane proteins,2015-06-25T00:00:00Z,,,2016-01-17T16:10:27.851Z,2016-01-17T16:10:27.851Z,,,50.81,CP011938,4501450,Escherichia coli strain C43(DE3),Complete,Escherichia,South Korea,,,,,,,,South Korea,,,,,,,562,,,,,,,4517,,,,NZ_CP011938.1,4264,,1,Yonsei University,972.0x,Illumina GAII; 454,,,,C43(DE3),,,"Included in the study, passed QC/QA"
1336,562.73,isolate:K-12;sample_type:whole organism,,,,GCF_001043215.1,SPAdes v. 3.1.0,,PRJNA284094,SAMN03659038,,,,,1,24-May-2014,"The widely-used E. coli strain MG1655 has several metabolic deficits whose origins do not readily map to loci or operons nominally controlling the related genotype. NCM3722 is a prototrophic K-12 isolate used as a wild-type K-12 strain in the laboratory of Sydney Kustu, Terrance Hwa, Suckjoon Jun, and others.",2015-09-02T00:00:00Z,,,2016-01-17T16:10:51.710Z,2016-01-17T16:10:51.710Z,,,50.76,"CP011495,CP011496",4745591,Escherichia coli strain NCM3722,Complete,Escherichia,USA: California,,,,,,"Human, Homo sapiens",,United States,,,,,,,562,C,,,,,,4800,,1,26251500,"NZ_CP011495.1,NZ_CP011496.1",4539,,2,University of California - San Diego,68.0x,PacBio; Illumina HiSeq,,,,NCM3722,,,"Included in the study, passed QC/QA"
1337,562.7382,,,,,GCA_001182745.1,,,PRJEB6403,SAMEA2517362,,,,,1,1952,http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/,2015-05-09T00:00:00Z,,,2016-01-17T16:40:22.719Z,2016-01-17T16:40:22.719Z,,,50.68,"LN831040,LN831041,LN831042,LN831046,LN831047",1822639,Escherichia coli strain NCTC9001,Complete,Escherichia,Denmark: Copenhagen,,,,,,"Human, Homo sapiens",,Denmark,,urine,,,,,562,,,host_health_state:disease: cystitis,,,,1836,,4,,,1719,,5,SC,,,,o1:k1(l1):h7,,NCTC9001,,,"Excluded from the study, failed QC/QA."
1338,562.7386,sample_type:cell culture,,,,GCF_001183645.1,Geneious v. 8.1.2,,PRJNA290012,SAMN03861948,,,,,1,01-Dec-2013,Whole genome sequencing to detect off-target changes (if any) after CRISPR-Cas9 editings,2015-07-21T00:00:00Z,,,2016-01-17T16:40:37.644Z,2016-01-17T16:40:37.644Z,,,50.83,CP012125,4614223,Escherichia coli strain DH1Ec095,Complete,Escherichia,USA: Walnut Creek,,,,,,,,United States,,,,,,,562,C,,,,,,4607,,,,NZ_CP012125.1,4352,,1,Joint Genome Institute,>200x,Illumina,,,,DH1Ec095,,,"Included in the study, passed QC/QA"
1339,562.7387,sample_type:cell culture,,,,GCF_001183665.1,Geneious v. 8.1.2,,PRJNA290012,SAMN03863255,,,,,1,01-Jun-2014,Whole genome sequencing to detect off-target changes (if any) after CRISPR-Cas9 editings,2015-07-21T00:00:00Z,,,2016-01-17T16:40:37.959Z,2016-01-17T16:40:37.959Z,,,50.83,CP012126,4612363,Escherichia coli strain DH1Ec104,Complete,Escherichia,USA: Walnut Creek,,,,,,,,United States,,,,,,,562,C,,,,,,4606,,,,NZ_CP012126.1,4350,,1,Joint Genome Institute,>200x,Illumina,,,,DH1Ec104,,,"Included in the study, passed QC/QA"
1340,562.7388,sample_type:cell culture,,,,GCF_001183685.1,Geneious v. 8.1.2,,PRJNA290012,SAMN03863378,,,,,1,01-Jul-2014,Whole genome sequencing to detect off-target changes (if any) after CRISPR-Cas9 editings,2015-07-21T00:00:00Z,,,2016-01-17T16:40:38.331Z,2016-01-17T16:40:38.331Z,,,50.82,CP012127,4609522,Escherichia coli strain DH1Ec169,Complete,Escherichia,USA: Walnut Creek,,,,,,,,United States,,,,,,,562,C,,,,,,4602,,,,NZ_CP012127.1,4348,,1,Joint Genome Institute,>200x,Illumina,,,,DH1Ec169,,,"Included in the study, passed QC/QA"
1341,562.7564,sample_type:cell culture,,,,GCF_001276585.1,CLC Genomics Workbench v. 6.5,,PRJNA272568,SAMN03384316,,,,,1,,To trace genetic makeup of a common laboratory strain; comparative genomic research purpose,2015-08-31T00:00:00Z,,KCTC:2134,2016-01-17T17:04:53.790Z,2016-01-17T17:04:53.790Z,,,50.82,CP011113,4587291,Escherichia coli strain RR1,Complete,Escherichia,,,,,,,"Human, Homo sapiens",,,,,,,,,562,,,,,,,4585,,,,,4344,,1,KRIBB,1000.0x,Illumina HiSeq,,,,RR1,,,"Included in the study, passed QC/QA"
1342,562.7585,collected_by:SFGH,,,,GCA_001280325.1,HGAP v. 3,,PRJNA294467,SAMN04026225,,,,,1,06-Sep-2007,Genomic analysis of E. coli ST95 strains isolated from bloodstream infections.,2015-11-24T00:00:00Z,,,2016-01-17T17:05:53.651Z,2016-01-17T17:05:53.651Z,,Bloodstream infection,50.66,"CP012635,CP012636,CP012637,CP012638",5206997,Escherichia coli strain SF-088,Complete,Escherichia,USA: San Francisco,,,,,bloodstream infection,"Human, Homo sapiens",isolated from bloodstream infections,United States,,patient blood,,,,,562,C,,,,,,5357,,3,26543109,"NZ_CP012635.1,NZ_CP012636.1,NZ_CP012637.1,NZ_CP012638.1",5028,,4,Santa Clara University,90X,PacBio,,,,SF-088,,,"Included in the study, passed QC/QA"
1343,562.7586,collected_by:SFGH,,,,GCA_001280345.1,HGAP v. 3,,PRJNA294467,SAMN04026228,,,,,1,05-Apr-2010,Genomic analysis of E. coli ST95 strains isolated from bloodstream infections.,2015-11-24T00:00:00Z,,,2016-01-17T17:05:53.966Z,2016-01-17T17:05:53.966Z,,Bloodstream infection,50.65,"CP012625,CP012626,CP012627,CP012628,CP012629,CP012630",5358643,Escherichia coli strain SF-468,Complete,Escherichia,USA: San Francisco,,,,,bloodstream infection,"Human, Homo sapiens",isolated from bloodstream infections,United States,,patient blood,,,,,562,C,,,,,,5564,,5,26543109,"NZ_CP012625.1,NZ_CP012626.1,NZ_CP012627.1,NZ_CP012628.1,NZ_CP012629.1,NZ_CP012630.1",5231,,6,Santa Clara University,90X,PacBio,,,,SF-468,,,"Included in the study, passed QC/QA"
1344,562.7587,collected_by:SFGH,,,,GCA_001280385.1,HGAP v. 3,,PRJNA294467,SAMN04026226,,,,,1,25-Jun-2008,Genomic analysis of E. coli ST95 strains isolated from bloodstream infections.,2015-11-24T00:00:00Z,,,2016-01-17T17:05:54.752Z,2016-01-17T17:05:54.752Z,,Bloodstream infection,50.62,"CP012633,CP012634",5025183,Escherichia coli strain SF-166,Complete,Escherichia,USA: San Francisco,,,,,bloodstream infection,"Human, Homo sapiens",isolated from bloodstream infections,United States,,patient blood,,,,,562,C,,,,,,5046,,1,26543109,"NZ_CP012633.1,NZ_CP012634.1",4785,,2,Santa Clara University,90X,PacBio,,,,SF-166,,,"Included in the study, passed QC/QA"
1345,562.7588,collected_by:SFGH,,,,GCF_001280405.1,HGAP v. 3,,PRJNA294467,SAMN04026227,,,,,1,27-May-2008,Genomic analysis of E. coli ST95 strains isolated from bloodstream infections.,2015-11-24T00:00:00Z,,,2016-01-17T17:05:55.131Z,2016-01-17T17:05:55.131Z,,Bloodstream infection,50.67,"CP012631,CP012632",5152806,Escherichia coli strain SF-173,Complete,Escherichia,USA: San Francisco,,,,,bloodstream infection,"Human, Homo sapiens",isolated from bloodstream infections,United States,,patient blood,,,,,562,C,,,,,,5205,,1,26543109,"NZ_CP012631.1,NZ_CP012632.1",4943,,2,Santa Clara University,90X,PacBio,,,,SF-173,,,"Included in the study, passed QC/QA"
1346,562.7622,,,,,GCA_001283245.1,,,PRJEB2827,SAMEA1531060,,,,,,2008,"http://www.sanger.ac.uk/resources/downloads/bacteria/escherichia-coli.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2015-08-22T00:00:00Z,1,,2016-01-17T17:06:41.453Z,2016-01-17T17:06:41.453Z,,,51.27,CYEJ01000000,567150,Escherichia coli strain 300073,Complete,Escherichia,Mozambique,,,,,,"Human, Homo sapiens",,Mozambique,,faeces,,,,,562,,,host_health_state:Not known,,,,524,,,,,503,,1,SC,,,,Not known,,300073,,,"Excluded from the study, failed QC/QA."
1347,562.7692,,,,,GCA_001284645.1,,,PRJEB2827,SAMEA1531007,,,,,,2009,"http://www.sanger.ac.uk/resources/downloads/bacteria/escherichia-coli.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2015-08-22T00:00:00Z,1,,2016-01-17T17:07:06.911Z,2016-01-17T17:07:06.911Z,,,51.26,CYEP01000000,391326,Escherichia coli strain 401907,Complete,Escherichia,Kenya,,,,,,"Human, Homo sapiens",,Kenya,,faeces,,,,,562,,,host_health_state:Not known,,,,383,,,,,358,,1,SC,,,,Not known,,401907,,,"Excluded from the study, failed QC/QA."
1348,562.7736,,,,,GCA_001285545.1,,,PRJEB2827,SAMEA1531058,,,,,,2010,"http://www.sanger.ac.uk/resources/downloads/bacteria/escherichia-coli.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/",2015-08-22T00:00:00Z,1,,2016-01-17T17:07:22.190Z,2016-01-17T17:07:22.190Z,,,49.68,CYEI01000000,455856,Escherichia coli strain 703273,Complete,Escherichia,Pakistan,,,,,,"Human, Homo sapiens",,Pakistan,,faeces,,,,,562,,,host_health_state:Not known,,,,462,,,,,434,,1,SC,,,,Not known,,703273,,,"Excluded from the study, failed QC/QA."
1349,562.7808,sample_type:monoisolate,,,,GCF_001308125.1,bowtie v. 2-2.2.3,,PRJNA268139,SAMN03203488,,,,,1,28-Feb-2014,The E. coli wildtype(strain MG1655) was subjected to lab evolution experiments to study the development of resistance to trimethoprim and the associated genome wide changes,2015-10-08T00:00:00Z,,,2016-01-17T17:13:43.762Z,2016-01-17T17:13:43.762Z,,,50.79,CP012869,4641684,Escherichia coli strain K-12 substrain MG1655_TMP32XR1,Complete,Escherichia,India:Bangalore,,,,,,,,India,,culture,,,,,562,,,,,,,4645,,,,NZ_CP012869.1,4424,,1,Indian Institute of Science,100x,Illumina,,,,K-12,,,"Included in the study, passed QC/QA"
1350,562.7809,sample_type:monoisolate,,,,GCF_001308165.1,bowtie v. 2-2.2.3,,PRJNA268139,SAMN03203489,,,,,1,28-Feb-2014,The E. coli wildtype(strain MG1655) was subjected to lab evolution experiments to study the development of resistance to trimethoprim and the associated genome wide changes,2015-10-08T00:00:00Z,,,2016-01-17T17:13:44.450Z,2016-01-17T17:13:44.450Z,,,50.79,CP012870,4641689,Escherichia coli strain K-12 substrain MG1655_TMP32XR2,Complete,Escherichia,India:Bangalore,,,,,,,,India,,culture,,,,,562,,,,,,,4644,,,,NZ_CP012870.1,4425,,1,Indian Institute of Science,100x,Illumina,,,,K-12,,,"Included in the study, passed QC/QA"
1351,562.7845,isolate:MC1061,,,,GCA_001405275.1,,,PRJEB9491,SAMEA3432775,,,,,1,,"Here we use RNASeq to identify gene expression patterns controlled by, or derived from, Stx prophage carriage and determine their influence on the biology of the Shigatoxigenic E. coli lysogen.",2015-10-01T00:00:00Z,,,2016-01-17T17:37:39.235Z,2016-01-17T17:37:39.235Z,,,47.4,LN877770,5027063,Escherichia coli strain MC1061,Complete,Escherichia,,,,,,,,"derived from, Stx prophage carriage and determine their influence on the biology of the Shigatoxigenic E. coli lysogen",,,", Stx prophage carriage and determine their influence on the biology of the Shigatoxigenic E",,,,,562,,,,,,,4937,,,,,4609,,1,CGR,,,,,,MC1061,,,"Excluded from the study, failed QC/QA."
1352,562.7943,sample_type:urine,,,,GCF_001442495.1,HGAP v. 2.1,,PRJNA300553,SAMN04227566,,,,,1,2012-08-20,to characterize an UTI Escherichia coli isolate producing fosA6,2015-11-10T00:00:00Z,,,2016-01-17T17:47:51.965Z,2016-01-17T17:47:51.965Z,,,50.56,CP013112,4863501,Escherichia coli strain YD786,Complete,Escherichia,USA,,,,,,"Human, Homo sapiens",,United States,,urine,,,,,562,C,,,,,,4891,,,,NZ_CP013112.1,4645,,1,"Huashan Hospital, Fudan University",124.0x,PacBio,,,,YD786,,,"Included in the study, passed QC/QA"
1353,562.7955,collected_by:CDC,,,,GCA_001420955.1,HGAP v. v3,,PRJNA218110,SAMN02991226,,,,,1,Mar-2008,PulseNet STEC genome reference library,2015-10-30T00:00:00Z,,,2016-01-17T17:41:59.070Z,2016-01-17T17:41:59.070Z,,,50.79,"CP013025,CP013024,CP013026,CP013027",5514343,Escherichia coli strain 2009C-3133,Complete,Escherichia,USA,,,0-4,,,"Human, Homo sapiens",,United States,,Stool,,,,,562,,,,,,,5747,,3,,"NZ_CP013025.1,NZ_CP013024.1,NZ_CP013026.1,NZ_CP013027.1",5368,,4,CDC,158,Pacific Biosciences,,E. coli O119:H4,,2009C-3133,,,"Included in the study, passed QC/QA"
1354,562.7956,collected_by:CDC,,,,GCA_001420935.1,HGAP v. v3,,PRJNA218110,SAMN03952643,,,,,1,2012,PulseNet STEC genome reference library,2015-10-30T00:00:00Z,,,2016-01-17T17:41:58.767Z,2016-01-17T17:41:58.767Z,,,50.58,"CP013029,CP013028,CP013030",5375210,Escherichia coli strain 2012C-4227,Complete,Escherichia,USA,,,,,,"Human, Homo sapiens",,United States,,,,,,,562,,,,,,,5839,,2,,"NZ_CP013029.1,NZ_CP013028.1,NZ_CP013030.1",5224,,3,CDC,157,Pacific Biosciences,,O165:H25,,2012C-4227,,,"Included in the study, passed QC/QA"
1355,562.8472,sample_type:whole organism,,,,GCF_001455385.1,Newbler v. 2.9,,PRJNA303642,SAMN04288058,,,,,1,15-Sep-2007,The goal of this study is to reveal the bacteria resistant mechanisms.,2015-12-02T00:00:00Z,,,2016-01-30T11:00:34.310Z,2016-01-30T11:00:34.310Z,,,50.77,CP013253,4579074,Escherichia coli strain CQSW20,Complete,Escherichia,China: Chongqing,,,,,,"Human, Homo sapiens",,China,,,,,"MLST.Escherichia_coli_2.262,MLST.Escherichia_coli_1.1060",,562,C,,,,,,4723,,,,NZ_CP013253.1,4176,,1,Third Military Medical University,30,IonTorrent,,,,CQSW20,,,"Included in the study, passed QC/QA"
1356,562.8473,collected_by:unknown,,,,GCF_001455405.1,SPAdes v. 3.0.0,,PRJNA286320,SAMN03768475,,,,,,,Comparison between avian and human strains in order to predict zoonotic potential.,2015-12-02T00:00:00Z,1,,2016-01-30T11:00:26.209Z,2016-01-30T11:00:26.209Z,,,50.66,CP013048,4689408,Escherichia coli strain RS76,Complete,Escherichia,,,,,,colibacillosis,"Chicken, Gallus gallus",,,,cellulitis,,,"MLST.Escherichia_coli_1.93,MLST.Escherichia_coli_2.83",,562,C,,,,,,4682,,,,,4447,,1,Universidade Estadual de Campinas,100x,Sanger; Illumina,,O7:HNT,,RS76,,,"Included in the study, passed QC/QA"
1357,562.8489,collected_by:MMM,,,,GCF_001469815.1,HGAP v. 27-Jun-2014,,PRJNA297860,SAMN04159541,,,,,,2005-01-01,"ST131 is one of the most common E. coli lineages found in clinical specimens globally. It is frequently associated with antimicrobial resistance to several drug classes, including to fluoroquinolones, aminoglycosides and extended-spectrum cephalosporins. Resistance to extended-spectrum cephalosporins is often attributable to the presence of CTX-M genes encoding extended spectrum beta-lactamases. This study used whole genome sequencing to characterize the evolutionary history of the lineage as it has emerged and spread worldwide, and to explain the genetic context of the CTX-M genes. In order to do this, several DH10B E. coli isolates were transformed with extracted CTX-M plasmids, then sequenced, enabling an approximate reconstruction of the plasmid sequences by bioinformatically removing DH10B-associated reads and undertaking de novo assembly of the residual data.",2015-12-18T00:00:00Z,1,,2016-01-31T09:05:39.835Z,2016-01-31T09:05:39.835Z,,,50.83,"CP013658,CP013657",5250410,Escherichia coli strain uk_P46212,Complete,Escherichia,United Kingdom,,,,,Escherichia coli [E. coli] as the cause of diseases classified elsewhere,"Human, Homo sapiens",,United Kingdom,,urine,,,MLST.Escherichia_coli_1.131,,562,C,,,,,,5376,,1,,"NZ_CP013658.1,NZ_CP013657.1",5072,,2,University of Oxford,,PacBio,,,,uk_P46212,,,"Included in the study, passed QC/QA"
1358,562.8507,isolate:Pleural Effusion of Patients with Empyema Thoracis;collected_by:Dezhi Li,,,,GCF_001485455.1,Newbler v. 2.3; Consed,,PRJNA248607,SAMN02800875,,,,,1,2009-05-24,Complete Genome Sequence of Multiple Antibiotic Resistant Escherichia coli Isolated from Pleural Effusion of Patients with Empyema Thoracis,2016-01-05T00:00:00Z,,,2016-02-01T02:10:03.376Z,2016-02-01T02:10:03.376Z,,,50.57,"CP008697,CP008715,CP008716,CP008717,CP008718,CP008719,CP008720,CP008721",5195832,Escherichia coli strain ST648,Complete,Escherichia,China:Beijing,,,,,Empyema Thoracis,"Human, Homo sapiens",,China,,Pleural Effusion,,,MLST.Escherichia_coli_1.648,,562,,,,,,,5219,,7,,"NZ_CP008697.1,NZ_CP008715.1,NZ_CP008716.1,NZ_CP008717.1,NZ_CP008718.1,NZ_CP008719.1,NZ_CP008720.1,NZ_CP008721.1",4578,,8,Peking University People's hospital,40x; 350x,Roche 454 GS FLX; Illumina Hiseq 2000;,,,,ST648,,,"Included in the study, passed QC/QA"
1359,562.8516,collected_by:unknown,,,,GCF_001513615.1,HGAP 3 (PacBio) v. SEPT-2015,,PRJNA307507,SAMN04381845,,,,,1,2002,Comparative sequencing of ExPEC ST131,2016-01-12T00:00:00Z,,,2016-02-02T21:00:39.556Z,2016-02-02T21:00:39.556Z,,,50.87,"CP013831,CP013832",5219043,Escherichia coli strain CD306,Complete,Escherichia,USA: New York,,,,,unknown,Cat,,United States,,unknown,,,MLST.Escherichia_coli_1.131,,562,C,,,,,,5371,,1,,"NZ_CP013831.1,NZ_CP013832.1",5057,,2,University of Minnesota,100.0x,PacBio,,,,CD306,,,"Included in the study, passed QC/QA"
1360,562.8517,collected_by:unknown,,,,GCF_001513635.1,HGAP 3 (PacBio) v. SEPT-2015,,PRJNA307507,SAMN04381854,,,,,1,2008,Comparative sequencing of ExPEC ST131,2016-01-12T00:00:00Z,,,2016-02-02T21:00:43.782Z,2016-02-02T21:00:43.782Z,,,50.82,"CP013835,CP013833,CP013834",5317099,Escherichia coli strain JJ2434,Complete,Escherichia,USA: Minneapolis,,,,,unknown,"Human, Homo sapiens",,United States,,unknown,,,MLST.Escherichia_coli_1.131,,562,C,,,,,,5484,,2,,"NZ_CP013835.1,NZ_CP013833.1,NZ_CP013834.1",5145,,3,University of Minnesota,100.0x,PacBio,,,,JJ2434,,,"Included in the study, passed QC/QA"
1361,562.8518,collected_by:unknown,,,,GCA_001513655.1,HGAP 3 (PacBio) v. SEPT-2015,,PRJNA307507,SAMN04381850,,,,,1,2004,Comparative sequencing of ExPEC ST131,2016-01-12T00:00:00Z,,,2016-02-02T21:00:54.784Z,2016-02-02T21:00:54.784Z,,,50.78,"CP013837,CP013836",5315043,Escherichia coli strain JJ1897,Complete,Escherichia,USA: Minneapolis,,,,,unknown,"Human, Homo sapiens",,United States,,unknown,,,MLST.Escherichia_coli_1.131,,562,C,,,,,,5799,,1,,,4739,,2,University of Minnesota,100.0x,PacBio,,,,JJ1897,,,"Included in the study, passed QC/QA"
1362,562.8522,,,,,GCF_001515725.1,Newbler v. Newbler version 2.3,,PRJNA239653,SAMN04385793,,,,,1,,To find out the virulence factors and reveals the pathogenic mechanism,2016-01-15T00:00:00Z,,,2016-02-02T21:05:33.431Z,2016-02-02T21:05:33.431Z,,,50.69,CP007491,4879931,Escherichia coli strain ACN002,Complete,Escherichia,,,,,,,,,,,,,,"MLST.Escherichia_coli_2.708,MLST.Escherichia_coli_1.23",,562,,,,,,,4811,,,,NZ_CP007491.1,4677,,1,Huazhong Agricultural University,35.8,454,,,,ACN002,,,"Included in the study, passed QC/QA"
1363,562.8526,sample_type:single isolate,,,,GCA_001518955.1,GS De Novo Assembler v. 2.04,,PRJNA244370,SAMN04395036,,,,,,2010-01-01,This is a strain isolated from diarrhea piglet.,2016-01-20T00:00:00Z,1,,2016-02-02T21:12:40.131Z,2016-02-02T21:12:40.131Z,,,50.26,CP013962,5610558,Escherichia coli strain SEC470,Complete,Escherichia,China,,,,,,"Pig, Sus scrofa",isolated from diarrhea piglet,China,,intestinal tract,,,"MLST.Escherichia_coli_2.66,MLST.Escherichia_coli_1.88",,562,,,,,,,5954,,,,,5621,,1,"Institute of Subtropical Agriculture, Chinese Academy of Sciences",100.0x,Illumina,,,,SEC470,,,"Included in the study, passed QC/QA"
1364,562.9018,,,,,GCF_000953515.1,,,PRJEB6353,SAMEA2547782,,,,,1,,"Escherichia coli str. K-12 substr. HMS174 (ATCC 47011), complete genome",2014-10-01T00:00:00Z,,ATCC:47011,2016-02-29T18:08:52.523Z,2016-02-29T18:08:52.523Z,,,50.82,LM993812,4584860,Escherichia coli strain K-12 substr. HMS174,Complete,Escherichia,,,,,,,,,,,,,,"MLST.Escherichia_coli_1.1060,MLST.Escherichia_coli_2.2",,562,,,,,,,4530,,,,NZ_LM993812.1,4243,,1,Austrian Centre of Industrial Biotechnology,,,,,,K-12 substr. HMS174,,,"Included in the study, passed QC/QA"
1365,562.9021,collected_by:Huazhong Agricultural University,,,,GCF_001542545.1,SOAPdenovo v. 1.05,,PRJNA308786,SAMN04017854,,,,,1,2006,Extraintestinal pathogenic Escherichia coli strain PPECC42 genome sequencing and assembly,2016-02-02T00:00:00Z,,,2016-02-29T20:45:08.577Z,2016-02-29T20:45:08.577Z,,,50.69,CM003707,5019692,Escherichia coli strain PPECC42,Complete,Escherichia,China: Hunan,,Terrestrial,,not collected,resipiratory disease,"Pig, Sus scrofa",,China,,lung,,,"MLST.Escherichia_coli_1.5147,MLST.Escherichia_coli_2.597",,562,C,,host_disease_outcome:acute disease;host_disease_stage:dying stage;host_health_state:after sampling,,,Aerobic,5026,Extraintestinal pathogennic Eschericia coli,,25243151,,4825,,1,Huazhong Agricultural University,100.0x,Illumina HiSeq,,O11,,PPECC42,Thermophilic,,"Included in the study, passed QC/QA"
1366,562.9022,sample_type:environmental isolate,,,,GCF_001542675.2,HGAP2 v. 2.2.0,,PRJNA308372,SAMN04395032,,,,,1,1950,Escherichia coli MRE600 sequencing and assembly,2016-02-18T00:00:00Z,,ATCC:29417,2016-02-29T21:20:34.886Z,2016-02-29T21:20:34.886Z,,,50.78,"CP014197,CP014198,CP014199,CP014200",4980796,Escherichia coli strain MRE600,Complete,Escherichia,United Kingdom,,Unknown,,,,,,United Kingdom,,environmental,,,,,562,37 C,,,,,Facultative,5428,,3,26802429,"NZ_CP014197.1,NZ_CP014198.2,NZ_CP014199.1,NZ_CP014200.1",5026,,4,Weill Cornell Medical College,184X,Pacific Biosciences,,,,MRE600,Mesophilic,,"Included in the study, passed QC/QA"
1367,562.903,collected_by:FLUFL,,,,GCF_001558995.1,FALCON v. 3/2015,,PRJNA298331,SAMN04191546,,,,,1,13-Aug-2013,Whole genome sequencing of cultured E. coli as part of the US Food and Drug Administration surveillance project for the rapid detection of foodborne contamination events.,2016-02-11T00:00:00Z,,,2016-03-01T19:56:51.824Z,2016-03-01T19:56:51.824Z,,,50.49,CP014314,5478683,Escherichia coli strain JEONG-1266,Complete,Escherichia,USA:FL,,,,,,Bos taurus,,United States,,fecal,,,,,562,C,,,,,,5784,,,,,5481,,1,US Food and Drug Administration,101x,PacBio,,,,JEONG-1266,,,"Included in the study, passed QC/QA"
1368,562.9095,collected_by:FDA CFSAN,,,,GCF_001563715.1,HGAP3 v. Oct 2014,,PRJNA231221,SAMN03996336,,,,,1,,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",2016-02-17T00:00:00Z,,FDA:FDAARGOS_95,2016-03-01T21:26:01.467Z,2016-03-01T21:26:01.467Z,,,50.4,"CP014092,CP014074,CP014075,CP014076,CP014077,CP014078,CP014079,CP014080,CP014081,CP014082,CP014083,CP014084,CP014085,CP014086,CP014087,CP014088,CP014089,CP014090,CP014091",5655051,Escherichia coli strain 268-78-1,Complete,Escherichia,USA,,,not applicable,not applicable,not applicable,,,United States,,,,,,,562,,,,,,,6050,,18,,,5467,,19,US Food and Drug Administration,17.362x,Pacbio,,,,not applicable,,,"Included in the study, passed QC/QA"
1369,562.9096,,,,,GCF_001566615.1,HGAP v. 3,,PRJNA307507,SAMN04381849,,,,,,2007,Comparative sequencing of ExPEC ST131,2016-02-23T00:00:00Z,1,,2016-03-01T22:25:59.452Z,2016-03-01T22:25:59.452Z,,,50.65,"CP014495,CP014496",5176044,Escherichia coli strain SaT040,Complete,Escherichia,USA: Burlington,,,,,,"Human, Homo sapiens",,United States,,,,,MLST.Escherichia_coli_1.131,,562,C,,,,,,5300,,1,,"NZ_CP014495.1,NZ_CP014496.1",5087,,2,University of Minnesota,100x,PacBio,,,,SaT040,,,"Included in the study, passed QC/QA"
1370,562.9097,,,,,GCF_001566635.1,HGAP v. 3,,PRJNA307507,SAMN04381851,,,,,1,2010,Comparative sequencing of ExPEC ST131,2016-02-23T00:00:00Z,,,2016-03-01T22:30:56.714Z,2016-03-01T22:30:56.714Z,,,50.55,"CP014488,CP014489,CP014490,CP014491",5219972,Escherichia coli strain G749,Complete,Escherichia,USA: Seattle,,,,,,"Human, Homo sapiens",,United States,,,,,,,562,C,,,,,,5342,,3,,"NZ_CP014488.1,NZ_CP014489.1,NZ_CP014490.1,NZ_CP014491.1",5107,,4,University of Minnesota,100x,PacBio,,,,G749,,,"Included in the study, passed QC/QA"
1371,562.9098,,,,,GCA_001566655.1,HGAP v. 3,,PRJNA307507,SAMN04381852,,,,,1,2010,Comparative sequencing of ExPEC ST131,2016-02-23T00:00:00Z,,,2016-03-01T22:28:36.828Z,2016-03-01T22:28:36.828Z,,,50.77,"CP014492,CP014493,CP014494",5014243,Escherichia coli strain MVAST0167,Complete,Escherichia,USA: Minneapolis,,,,,,"Human, Homo sapiens",,United States,,,,,,,562,C,,,,,,5260,,2,,"NZ_CP014492.1,NZ_CP014493.1,NZ_CP014494.1",4870,,3,University of Minnesota,100x,PacBio,,,,MVAST0167,,,"Included in the study, passed QC/QA"
1372,562.9099,,,,,GCF_001566675.1,HGAP v. 3,,PRJNA307507,SAMN04381846,,,,,1,2004,Comparative sequencing of ExPEC ST131,2016-02-23T00:00:00Z,,,2016-03-01T22:25:15.584Z,2016-03-01T22:25:15.584Z,,,50.89,"CP014497,CP014498",5256378,Escherichia coli strain ZH193,Complete,Escherichia,,,,,,,"Human, Homo sapiens",,,,,,,,,562,C,,,,,,5442,,1,,"NZ_CP014497.1,NZ_CP014498.1",5182,,2,University of Minnesota,100x,PacBio,,,,ZH193,,,"Included in the study, passed QC/QA"
1373,562.9316,,,,,GCF_001577325.1,HGAP v. 3,,PRJNA307507,SAMN04381853,,,,,1,2002,Comparative sequencing of ExPEC ST131,2016-02-29T00:00:00Z,,,2016-03-18T09:16:10.778Z,2016-03-18T09:16:10.778Z,,,50.73,"CP014522,CP014523,CP014524",5197049,Escherichia coli strain ZH063,Complete,Escherichia,Canada: Winnipeg,,,,,,"Human, Homo sapiens",,Canada,,,,,,,562,C,,,,,,5326,,2,,"NZ_CP014522.1,NZ_CP014523.1,NZ_CP014524.1",5104,,3,University of Minnesota,100x,PacBio,,,,ZH063,,,"Included in the study, passed QC/QA"
1374,562.9857,collected_by:Genevieve A. Barkocy-Gallagher et al.,,,,GCF_001612475.1,SMRT Analysis v. 2.3.0,,PRJNA299666,SAMN04202540,,,,,,Aug-1999,The current BioProject aims to assemble a complete genome sequence of the organism Escherichia coli O157:H7 strain 28RC1. The obtained sequence will use for genomic and transcriptomic comparison between Escherichia coli O157:H7 strains with different levels of acid resistance.,2016-04-06T00:00:00Z,1,,2016-04-28T03:52:08.549Z,2016-04-28T03:52:08.549Z,,,50.55,"CP015020,CP015021",5643099,Escherichia coli strain 28RC1,Complete,Escherichia,USA:midwest,,,,,,,,United States,,Bovine carcass,,,"MLST.Escherichia_coli_2.628,MLST.Escherichia_coli_1.11",,562,C,,,,,,5946,STEC,1,,"NZ_CP015020.1,NZ_CP015021.1",5641,,2,USDA,107.5X,PacBio; IonTorrent,,O157:H7,,28RC1,,,"Included in the study, passed QC/QA"
1375,564.14,collected_by:Children's National Hospital;isolate:not applicable,,,,GCF_001471755.1,HGAP3 v. Oct 2014,,PRJNA231221,SAMN03996315,,,,,,24-Jun-2014,"FDA, in collaboration with the National Center for Biotechnology Information (NCBI), the Department of Defense (DoD) and the Institute for Genome Sciences at the University of Maryland, established a publicly available, well-curated reference database (FDA-ARGOS: dAtabase for Regulatory Grade micrObial Sequences; BioProject 231221) of regulatory-grade-quality sequences from diverse infectious microorganisms. This database, which is still growing, comprises data collected from multiple collaborators. Diagnostic test manufacturers develop sequence-based tests to identify infectious agents and/or to detect resistance or virulence markers; will use this database to advance their development programs and to support the regulatory science review of such tests. This work will facilitate the development of these tests, which are aimed at improving patient outcomes. Continued success of the database and adoption by the community is contingent on populating and curating the database, which in turn will support development of guidance and standards for clinical use of this technology. Discussions held at a relating public workshop on advancing regulatory science for high throughput sequencing devices for microbial identification and detection of antimicrobial resistance markers were essential to establish the safety and effectiveness of these devices.",2015-12-21T00:00:00Z,1,FDA:FDAARGOS_170,2016-01-31T10:44:19.591Z,2016-01-31T10:44:19.591Z,,,50.44,LORS01000000,5236118,Escherichia fergusonii strain FDAARGOS_170,Complete,Escherichia,USA: DC,,,12M,female,Urinary tract infection,"Human, Homo sapiens",,United States,,Urine cathether,,,MLST.Escherichia_coli_1.73,,564,,,,,,,5381,,,,,4955,,1,US Food and Drug Administration,18.602x,Pacbio,,,,FDAARGOS_170,,,"Included in the study, passed QC/QA"
1376,566546.3,,,,,GCF_000258145.1,,,PRJNA62301,SAMN02604169,,,,,1,,"ATCC 9637 (E coli W) is the parent of KO11, a strain engineered to ferment sugars (glucose and xylose) into ethanol.",2014-01-31T00:00:00Z,,ATCC:9637,2016-01-17T15:28:50.003Z,2016-01-17T15:28:50.003Z,,,50.82,"CP002967,CP002968,CP002969",5005347,Escherichia coli W,Complete,Escherichia,,,,,,,,,,,,,,,,566546,,,,,,,4964,,2,22075923,"NC_017664.1,NC_017665.1,NC_017662.1",4731,,3,University of Florida,,,,,,W,,,"Included in the study, passed QC/QA"
1377,566546.4,,,,,GCA_000184185.1,,,PRJNA48011,,,,,Rod,1,1943,Escherichia coli W.This strain is available from the ATCC 9637Escherichia coli W (ATCC 9637) is the only native sucrose utilizing laboratory strain of E. coli. It has been used to study E. coli metabolism and for the production of bulk chemicals.,2010-12-14T00:00:00Z,,ATCC 9637,2014-12-08T22:11:36.457Z,2015-03-16T03:17:09.594Z,,,50.82,"CP002185,CP002186,CP002187",5008864,Escherichia coli W,Complete,Escherichia,,-,Multiple,,,,,"E. coli W (ATCC 9637) was originally isolated from the soil of a cemetery near Rutgers University around 1943 by Selman  A. Waksman, around the same time he and Alan Schatz discovered streptomycin (Eliora Ron, personal communication). Waksman coined the term 'antibiotic', and his discovery of streptomycin (and many other antibiotics) led to him being awarded the Nobel Prize in Physiology or Medicine in 1952. The strain was termed 'Waksman's strain' or 'W strain' because it showed the highest sensitivity to streptomycin compared to other isolated E. coli strains in Waksman's collection (Archer et al., 2011 PMID: 21208457)",,,,,,"MLST.Escherichia_coli_1.1079,MLST.Escherichia_coli_2.360",Yes,566546,-,Escherichia coli W,,,,Facultative,4825,,2,21208457,"NC_017635.1,NC_017637.1,NC_017636.1",4700,,3,"AIBN/KRIBB|Australian Institute for Bioengineering & Nanotechnology|Australian Institute for Bioengineering and Nanotechnology, Australia, Brisbane|Korea Research Institute of Bioscience & Biotechnology",,,complete,,No,W,Mesophilic,,"Included in the study, passed QC/QA"
1378,569579.3,"collected_by:Scott J. Hultgren, William R. Schwan, Anthony J. Schaeffer, James L. Duncan",,,,GCF_002024865.1,HGAP3 v. 3,,PRJNA373796,SAMN06314223,,,,,1,1986,Sequencing of uropathogenic E. coli strain NU14,2017-03-10T00:00:00Z,,,2017-03-20T09:03:42.395Z,2017-03-20T09:03:42.395Z,,,50.59,CP019777,5076615,Escherichia coli NU14 strain NU14,Complete,Escherichia,USA,,,,female,Urinary tract infection,"Human, Homo sapiens",,,,Urine,,,"MLST.Escherichia_coli_2.1,MLST.Escherichia_coli_1.95",,569579,,,,,,,5206,,,,NZ_CP019777.1,5102,,1,National University of Singapore and Genome Institute of Singapore,300.0x,PacBio,,,,NU14,,,"Included in the study, passed QC/QA"
1379,573235.3,,,,,GCA_000091005.1,,,PRJNA32509,,,,,Rod,1,,"Escherichia coli O26:H11 str. 11368. Escherichia coli O26:H11 str. 11368 is a human enterohemorrhagic E. coli which attaches to and effaces cells in the large intestine. The identifier O26:H11 refers to the serotype of EHEC, and reflects the specific antigenic markers found on the surface of the cell. This strain will be used for comparative analysis with other pathogenic and nonpathogenic E. coli.",2009-09-10T00:00:00Z,,,2014-12-08T22:11:32.851Z,2015-03-16T03:17:09.594Z,,Hemorrhagic colitis,50.6,"AP010953,AP010955,AP010956,AP010954,AP010957",5855531,Escherichia coli O26:H11 str. 11368,Complete,Escherichia,,-,Multiple,,,,,,,,,,,"MLST.Escherichia_coli_1.21,MLST.Escherichia_coli_2.481",Yes,573235,37,Escherichia coli O26:H11 str. 11368,,,,Facultative,5986,EHEC,4,,"NC_013361,NC_013363,NC_013369,NC_013362,NC_014543",5519,,5,"University of Tokyo, Japan",,,complete,,No,11368,Mesophilic,,"Included in the study, passed QC/QA"
1380,574521.7,,,,,GCA_000026545.1,,,PRJNA32571,SAMEA1705959,,,,Rod,1,1969,"Escherichia coli O127:H6 E2348/69. Enteropathogenic Escherichia coli (EPEC) is an important cause of fatal infant diarrhea. EPEC induces diarrhea by attaching and effacing to host cells in the small intestine, inducing cytoskeletal rearrangements that result in pedastel formation, and then by introducing toxins into the host cell. Important virulence functions such as the type III secretion system are encoded by the locus of enterocyte effacement. Escherichia coli 0127:H6 E2348/69 is an enteropathogenic E. coli strain to be used for comparative studies with related Escherichia and Shigella species. ",2008-11-26T00:00:00Z,,,2014-12-08T22:11:32.187Z,2015-03-16T03:17:09.594Z,,,50.5,"FM180568,FM180569,FM180570",5069678,Escherichia coli O127:H6 str. E2348/69,Complete,Escherichia,United Kingdom: Taunton,-,Host-associated,,,,"Human, Homo sapiens","isolated in Taunton, United Kingdom, in 1969 during an outbreak of infantile diarrhea",United Kingdom,,outbreak,,,"MLST.Escherichia_coli_1.15,MLST.Escherichia_coli_2.491",Yes,574521,37,Escherichia coli O127:H6 str. E2348/69,,,,Facultative,4903,EHEC,2,,"NC_011601,NC_011603,NC_011602",4653,,3,Wellcome Trust Sanger Institute,,,complete,,No,E2348/69,Mesophilic,,"Included in the study, passed QC/QA"
1381,585034.5,,,,,GCA_000026265.1,,,PRJNA33373,SAMEA3138230,,,,Rod,1,,Escherichia coli IAI1. Escherichia coli IAI1 is a serogroup O8 strain and will be used for comparative analysis.,2008-12-18T00:00:00Z,,,2014-12-08T22:11:27.352Z,2015-03-16T03:17:09.594Z,,,50.8,CU928160,4700560,Escherichia coli IAI1,Complete,Escherichia,,-,Multiple,,,,,,,,,,,"MLST.Escherichia_coli_1.1128,MLST.Escherichia_coli_2.294",Yes,585034,-,Escherichia coli IAI1,,,,Facultative,4493,Nonpathogenic,,19165319,NC_011741,4353,,1,Genoscope,,,complete,,No,IAI1,Mesophilic,,"Included in the study, passed QC/QA"
1382,585035.6,,,,,GCA_000026285.1,,,PRJNA33375,SAMEA3138231,,,,Rod,1,,Escherichia coli S88. Escherichia coli S88 is a serotype O45:K1 strain isolated from a case of neonatal meningitis and will be used for comparative analysis.,2008-12-18T00:00:00Z,,,2014-12-08T22:11:34.479Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,50.6,"CU928161,CU928146",5166121,Escherichia coli S88,Complete,Escherichia,,-,Multiple,,,,,isolated from a case of neonatal meningitis and will be used for comparative analysis,,,case of neonatal meningitis,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",Yes,585035,-,Escherichia coli S88,,,,Facultative,5120,ExPEC,1,"19165319,19307211","NC_011742,NC_011747",4832,,2,Genoscope,,,complete,serovar O45,No,S88,Mesophilic,,"Included in the study, passed QC/QA"
1383,585054.5,,,,,GCA_000026225.1,,,PRJNA33369,SAMEA3138228,,,,Rod,1,,Escherichia fergusonii ATCC 35469. Escherichia fergusonii ATCC 35469 was isolated from human feces and will be used for comparative analysis with other Escherichia species.,2008-12-18T00:00:00Z,,ATCC 35469,2014-12-08T22:11:36.843Z,2015-03-16T03:17:09.594Z,,Urinary tract infection (UTI);Bacteremia,49.9,"CU928158,CU928144",4643861,Escherichia fergusonii ATCC 35469,Complete,Escherichia,,-,Multiple,,,,"Human, Homo sapiens",isolated from human feces and will be used for comparative analysis with other Escherichia species,,,human feces,,,,Yes,585054,-,Escherichia fergusonii ATCC 35469,,,,Facultative,4373,,1,19165319,"NC_011740,NC_011743",4321,,2,Genoscope,,,complete,,No,ATCC 35469,Mesophilic,,"Included in the study, passed QC/QA"
1384,585055.8,,,,,GCA_000026245.1,,,PRJNA33413,SAMEA3138229,,,,Rod,1,,Escherichia coli 55989. Escherichia coli 55989 is a clinical enteroaggregative isolate. Enteroaggregative E. coli strains adhere to mucosal cells and are an emerging cause of gastroenteritis.,2008-12-18T00:00:00Z,,,2014-12-08T22:11:20.430Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,50.7,CU928145,5227344,Escherichia coli 55989,Complete,Escherichia,,-,Multiple,,,,,,,,clinical enteroaggregative isolate,,,"MLST.Escherichia_coli_1.678,MLST.Escherichia_coli_2.290",Yes,585055,-,Escherichia coli 55989,,,,Facultative,5178,EAEC,1,19165319,NC_011748,4866,,2,Genoscope,,,complete,,No,55989,Mesophilic,,"Included in the study, passed QC/QA"
1385,585056.7,,,,,GCA_000026325.1,,,PRJNA33415,SAMEA3138233,,,,Rod,1,,Escherichia coli UMN026. Escherichia coli UMN026 is a serotype O7:K1 clinical isolate. This strain is drug resistant and will be used for comparative analysis.,2008-12-18T00:00:00Z,,,2014-12-08T22:11:36.190Z,2015-03-16T03:17:09.594Z,,Urinary tract infection,50.7,"CU928163,CU928148,CU928149",5358200,Escherichia coli UMN026,Complete,Escherichia,,-,Multiple,,,,,,,,,,,"MLST.Escherichia_coli_1.597,MLST.Escherichia_coli_2.3",Yes,585056,-,Escherichia coli UMN026,,,,Facultative,5198,UPEC,2,19165319,"NC_011751,NC_011749,NC_011739",5017,,3,Genoscope,,,complete,serovar O7,No,UMN026,Mesophilic,,"Included in the study, passed QC/QA"
1386,585057.6,,,,,GCA_000026345.1,,,PRJNA33411,SAMEA3138234,,,,Rod,1,,Escherichia coli IAI39. Escherichia coli IAI39 is a serotype O7:K1 strain from a urinary tract infection and will be used for comparative analysis.,2008-12-18T00:00:00Z,,,2014-12-08T22:11:27.371Z,2015-03-16T03:17:09.594Z,,Urinary tract infection,50.6,CU928164,5132068,Escherichia coli IAI39,Complete,Escherichia,,-,Multiple,,,,,,,,,,,"MLST.Escherichia_coli_1.62,MLST.Escherichia_coli_2.254",Yes,585057,-,Escherichia coli IAI39,,,,Facultative,5094,UPEC,,19165319,NC_011750,4732,,1,Genoscope,,,complete,serovar O7,No,IAI39,Mesophilic,,"Included in the study, passed QC/QA"
1387,585395.4,,,,,GCA_000010745.1,,,PRJNA32511,,,,,Rod,1,,Escherichia coli O103:H2 str. 12009.An enterohemorrhagic E. coli (EHEC) strain.This strain will be used for comparative genome analysis.,2009-09-10T00:00:00Z,,,2014-12-08T22:11:31.324Z,2015-03-16T03:17:09.594Z,,,50.6,"AP010958,AP010959",5524860,Escherichia coli O103:H2 str. 12009,Complete,Escherichia,,-,,,,,,,,,,,,MLST.Escherichia_coli_2.135,,585395,-,Escherichia coli O103:H2 str. 12009,,,,Facultative,5604,EHEC,1,,"NC_013353,NC_013354",5121,,2,"University of Tokyo, Japan",,,complete,,,12009,Mesophilic,,"Included in the study, passed QC/QA"
1388,585396.4,,,,,GCA_000010765.1,,,PRJNA32513,,,,,Rod,1,,Escherichia coli O111:H- str. 11128.An enterohemorrhagic E. coli (EHEC) strain.This strain will be used for comparative genome analysis.,2009-09-10T00:00:00Z,,,2014-12-08T22:11:32.031Z,2015-03-16T03:17:09.594Z,,,50.4,"AP010960,AP010963,AP010964,AP010965,AP010962,AP010961",5766081,Escherichia coli O111:H- str. 11128,Complete,Escherichia,,-,,,,,,,,,,,,"MLST.Escherichia_coli_1.16,MLST.Escherichia_coli_2.480",,585396,-,Escherichia coli O111:H- str. 11128,,,,Facultative,5903,EHEC,5,,"NC_013364,NC_013366,NC_013367,NC_013368,NC_013370,NC_013365",5407,,6,"University of Tokyo, Japan",,,complete,,,11128,Mesophilic,,"Included in the study, passed QC/QA"
1389,585397.9,,,,,GCA_000026305.1,,,PRJNA33409,SAMEA3138232,,,,Rod,1,,Escherichia coli ED1a. Escherichia coli ED1a is an avirulent serogroup O81 strain and will be used for comparative analysis.,2008-12-18T00:00:00Z,,,2014-12-08T22:11:25.001Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,50.7,CU928162,5329142,Escherichia coli ED1a,Complete,Escherichia,,-,Multiple,,,,,,,,,,,"MLST.Escherichia_coli_1.452,MLST.Escherichia_coli_2.149",Yes,585397,-,Escherichia coli ED1a,,,,Facultative,5388,Nonpathogenic,1,19165319,NC_011745,5053,,2,Genoscope,,,complete,,No,ED1a,Mesophilic,,"Included in the study, passed QC/QA"
1390,591946.4,,,,,GCA_000284495.1,,,PRJNA33825,SAMEA3138414,,,,Rod,1,,Escherichia coli LF82. Escherichia coli LF82 is an adherent-invasive E. coli (AIEC) strain isolated from a patient with Crohn's disease. AIEC strains adhere and colonize the intestinal mucosa and are able to invade and replicate in intestinal epithelial cells. This strain will be used for comparative analysis with other E. coli strains.,2009-01-27T00:00:00Z,,,2014-12-08T22:11:30.332Z,2015-03-16T03:17:09.594Z,,Enterocolitis,50.7,CU651637,4773108,Escherichia coli LF82,Complete,Escherichia,,-,Multiple,,,Crohn's disease,"Human, Homo sapiens",isolated from a patient with Crohn's disease,,,patient with Crohn's disease,,,"MLST.Escherichia_coli_1.135,MLST.Escherichia_coli_2.64",Yes,591946,-,Escherichia coli LF82,,,,Facultative,4555,AIEC,,,NC_011993.1,4376,,1,Genoscope,,,complete,,No,LF82,Mesophilic,,"Included in the study, passed QC/QA"
1391,595495.17,,,,,GCF_000258025.1,,,PRJNA62299,SAMN02604168,,,,,1,,KO11 is a widely used E coli strain engineered to ferment sugars (glucose and xylose) into ethanol.,2014-01-31T00:00:00Z,,,2016-01-17T15:28:49.582Z,2016-01-17T15:28:49.582Z,,,50.78,"CP002970,CP002971",5027172,Escherichia coli KO11FL,Complete,Escherichia,,,,,,,,,,,,,,,,595495,,,,,,,4910,,1,22075923,"NC_017660.1,NC_017661.1",4709,,2,University of Florida,,,,,,KO11,,,"Included in the study, passed QC/QA"
1392,595495.5,,,,,GCA_000147855.3,,,PRJNA33875,,,,,,1,,Escherichia coli KO11.This strain will be used for comparative genome analysis.,2010-09-13T00:00:00Z,,,2014-12-08T22:11:27.619Z,2015-03-16T03:17:09.594Z,,,50.81,"CP002516,CP002517,CP002518",5029323,Escherichia coli KO11FL,Complete,Escherichia,,,,,,,,,,,,,,"MLST.Escherichia_coli_1.1079,MLST.Escherichia_coli_2.360",,595495,-,Escherichia coli KO11,,,,,4845,,2,,"NC_016902.1,NC_016904.1,NC_016903.1",4653,,3,US DOE Joint Genome Institute (JGI-PGF)|JGI|JGI-PGF,,,complete,,,KO11,,,"Included in the study, passed QC/QA"
1393,595496.3,,,,,GCA_000022345.1,,,PRJNA33775,SAMN02603900,,,,Rod,1,,Escherichia coli BW2952. Escherichia coli BW2952 is a strain MC4100 derivative containing a malG-lacZ fusion and will be used for comparative analysis with other E. coli strains.,2009-06-04T00:00:00Z,,,2014-12-08T22:11:22.651Z,2015-03-16T03:17:09.594Z,,,50.8,CP001396,4578159,Escherichia coli BW2952,Complete,Escherichia,,-,Multiple,,,,,,,,,,,"MLST.Escherichia_coli_1.10,MLST.Escherichia_coli_2.2",Yes,595496,-,Escherichia coli BW2952,,,,Facultative,4494,,,19376874,NC_012759,4084,,1,"TEDA School of Biological Sciences and Biotechnology, Nankai University",,,complete,,No,BW2952,Mesophilic,,"Included in the study, passed QC/QA"
1394,655817.3,,,,,GCA_000148365.1,,,PRJNA38725,SAMN02603258,,,,Rod,1,,Escherichia coli ABU 83972. Escherichia coli ABU 83972 causes an asymptomatic bacteriuria.,2010-09-22T00:00:00Z,,,2014-12-08T22:11:21.725Z,2015-03-16T03:17:09.594Z,,Asymptomatic bacteriuria,50.58,"CP001671,CP001833",5132961,Escherichia coli ABU 83972,Complete,Escherichia,,-,Multiple,,,,,,,,,,,"MLST.Escherichia_coli_1.73,MLST.Escherichia_coli_2.4",Yes,655817,-,Escherichia coli ABU 83972,,,,Facultative,5212,UPEC,1,,"NC_017631.1,NC_017629.1",4796,,2,Georg-August-University Goettingen|Goettingen Genomics Laboratory,,,complete,,No,ABU 83972,Mesophilic,,"Included in the study, passed QC/QA"
1395,679895.18,,,,,GCA_000750555.1,Newbler v. 2.6,,PRJNA257976,SAMN03013572,,,,,1,2000,Parent strain of Keio Collection single gene knockouts mutants. Whole genome sequencing for genome assembly and comparative genomics.,2014-09-09T00:00:00Z,1,,2014-12-08T23:19:06.013Z,2015-03-16T03:17:09.594Z,,,50.8,CP009273.1,4631470,Escherichia coli BW25113,Complete,Escherichia,USA: Indiana,,,,,,,,United States,,,,,,,679895,,,,,,,4436,,,25323716,NZ_CP009273.1,4313,,1,Universite de Sherbrooke,100x,Illumina HiSeq; Sanger,,,,BW25113,,,"Included in the study, passed QC/QA"
1396,685038.3,,,,,GCA_000183345.1,,,PRJNA41221,SAMN02603727,,,,Rod,1,,Escherichia coli O83:H1 str. NRG 857C. This strain is associated with Crohn's disease.,2010-11-30T00:00:00Z,,,2014-12-08T22:11:33.054Z,2015-03-16T03:17:09.594Z,,,50.69,"CP001855,CP001856",4894879,Escherichia coli O83:H1 str. NRG 857C,Complete,Escherichia,,-,Multiple,,,,,,,,,,,"MLST.Escherichia_coli_1.135,MLST.Escherichia_coli_2.64",Yes,685038,35,Escherichia coli O83:H1 str. NRG 857C,,,,Facultative,4686,AIEC,1,"17900983,18312396,21108814","NC_017634.1,NC_017659.1",4582,,2,Public Health Agency of Canada Laboratory for Foodborne Zoonoses,,,complete,,No,NRG 857C,Mesophilic,,"Included in the study, passed QC/QA"
1397,696406.3,,,,,GCA_000212715.2,,,PRJNA42137,SAMN02604221,,,,Rod,1,,Escherichia coli UMNK88. Post-weaning diarrhea in pigs continues to be a major problem for the commercial swine industry.  E. coli K88 strains are one of the most common causes of this disease.  E. coli strain UMNK88 is being sequenced in an effort to better understand the virulence mechanisms employed by K88 strains and to identify novel vaccine candidates.  This strain also contains at least 5 large plasmids.,2011-05-09T00:00:00Z,,,2014-12-08T22:11:36.243Z,2015-03-16T03:17:09.594Z,,Diarrhea,50.71,"CP002729,CP002730,CP002731,CP002732,CP002733",5506191,Escherichia coli UMNK88,Complete,Escherichia,USA: Minnesota,-,Multiple,,,,"Pig, Sus scrofa",,United States,,,,,MLST.Escherichia_coli_1.100,Yes,696406,-,Escherichia coli UMNK88,,,,Facultative,5607,ETEC,4,21858108,"NC_017641.1,NC_017645.1,NC_017642.1,NC_017640.1,NC_017643.1,NC_017639.1",5435,,5,University of Minnesota,,,complete,,No,UMNK88,Mesophilic,,"Included in the study, passed QC/QA"
1398,701177.3,,,,,GCA_000025165.1,,,PRJNA42729,SAMN02603636,,,,Rod,1,2003,Escherichia coli O55:H7 str. CB9615. Escherichia coli O55:H7 str. CB9615 was isolated from an infant with diarrhea in Germany in 2003 and confirmed to belong to the same multilocus sequence type (ST11) as the O157:H7 clone. The O55:H7 and O157:H7 E. coli clones have been shown to be closely related and will be useful for the analysis of recombination events and mutational events. ,2010-03-08T00:00:00Z,,,2014-12-08T22:11:32.950Z,2015-03-16T03:17:09.594Z,,Gastroenteritis,50.5,"CP001846,CP001847",5452353,Escherichia coli O55:H7 str. CB9615,Complete,Escherichia,Germany,-,Multiple,infant,,,"Human, Homo sapiens",isolated from an infant with diarrhea in Germany in 2003 and confirmed to belong to the same multilocus sequence type (ST11) as the O157:H7 clone,Germany,,infant with diarrhea,,,"MLST.Escherichia_coli_1.335,MLST.Escherichia_coli_2.553",Yes,701177,-,Escherichia coli O55:H7 str. CB9615,,,,Facultative,5362,EHEC,1,20090843,"NC_013941,NC_013942",5121,,2,Nankai University|Tianjin Biochip,,,complete,,No,CB9615,Mesophilic,,"Included in the study, passed QC/QA"
1399,714962.3,,,,,GCA_000025745.1,,,PRJNA43693,SAMN02603334,,,,Rod,1,1976,"Escherichia coli IHE3034. Escherichia coli IHE3034(O18:K1:H7, ST95) is a neonatal meningitis-associated strain isolated in Finland in 1976. The IHE3034 strain sequenced in this work has lost its plasmids during laboratory passages and is more virulent than the ancestor strain in the sepsis mouse model.",2010-04-12T00:00:00Z,,,2014-12-08T22:11:27.380Z,2015-03-16T03:17:09.594Z,,Meningitis,50.7,CP001969,5108383,Escherichia coli IHE3034,Complete,Escherichia,Finland,-,Host-associated,,,,,neonatal meningitis-associated strain isolated in Finland in 1976,Finland,,,,,"MLST.Escherichia_coli_1.95,MLST.Escherichia_coli_2.1",Yes,714962,-,Escherichia coli IHE3034,,,,Facultative,4995,ExPEC,,,NC_017628.1,4757,,1,IGS|JCVI,,,complete,,No,IHE3034,Mesophilic,,"Included in the study, passed QC/QA"
1400,741093.3,,,,,GCA_000262125.1,,,PRJNA45823,SAMN02603645,,,,Bacilli,1,1999,-,2011-04-08T00:00:00Z,,,2014-12-08T22:11:36.565Z,2015-03-16T03:17:09.594Z,,Hemolytic uremic syndrome (HUS),50.3828,"CP001925.1,CP001927.1,CP001926.1",5516736,Escherichia coli Xuzhou21,Complete,Escherichia,China,Negative,Multiple,,,,"Human, Homo sapiens",,China,,,,,MLST.Escherichia_coli_1.11,No,741093,,Escherichia coli Xuzhou21,,,,Facultative,5540,,2,22558360,"NC_017906.1,NC_017903.1,NC_017907.1",5183,,3,"National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention",,,complete,,,Xuzhou21,Mesophilic,,"Included in the study, passed QC/QA"
1401,745156.3,,,,,GCA_000829985.1,Newbler v. 2.0.00.20; MIRA v. 3.4.0.1,,PRJNA46529,SAMN02949643,,,,Bacilli,1,, Escherichia coli 1303. This strain will be used for comparative genome analysis.,2015-01-29T00:00:00Z,4,,2015-03-12T14:02:14.928Z,2015-03-16T03:17:09.594Z,,,50.61,"CP009166.1,CP009167.1,CP009169.1,CP009168.1",5156928,Escherichia coli 1303,Complete,Escherichia,,Negative,,,,,Bos taurus,,,,udder acute mastitis,,,,,745156,,,,,,Facultative,4925,,3,-,"NZ_CP009166.1,NZ_CP009167.1,NZ_CP009169.1,NZ_CP009168.1",4734,,4,Georg-August-University Goettingen,95x,Sanger dideoxy sequencing; 454; Illumina,,,,1303,Mesophilic,,"Included in the study, passed QC/QA"
1402,758831.4,,,,,GCF_000831565.1,Newbler v. 2.3; MIRA v. 3.4.0.1,,PRJNA257276,SAMN02949644,,,,,1,,This strain will be used for comparative genome analysis.,2015-04-08T00:00:00Z,,,2016-01-17T15:43:17.860Z,2016-01-17T15:43:17.860Z,,,50.73,"CP010344,CP010345",4903812,Escherichia coli ECC-1470,Complete,Escherichia,USA: New York State,,,,,,Bos taurus,,United States,,udder,,,,,758831,,,,,,,4845,,1,25814601,"NZ_CP010344.1,NZ_CP010345.1",4506,,2,"Georg-August-University Goettingen, Genomic and Applied Microbiology, Goettingen Genomics Laboratory",88x,Sanger; 454; Illumina,,Ont:Hnt,,ECC-1470,,,"Included in the study, passed QC/QA"
1403,83333.103,identified_by:Anthony Kingston;sample_type:Cell Culture,,,,GCF_000974405.1,SMRT Analysis v. 2.3,,PRJNA271807,SAMN03277616,,,,,1,Jun-14,"Provides the genomic sequences of a donor, recipient, and six recombinants from a mating system designed to identify novel horizontal gene transfer mechanisms.",2015-04-21T00:00:00Z,,,2016-01-17T15:54:13.642Z,2016-01-17T15:54:13.642Z,,,50.79,CP010438,4619729,Escherichia coli K-12 strain ER3454,Complete,Escherichia,,,,,,,,,,,not applicable,,,,,83333,,,,,genotype:fhuA2::IS2 _(lacZ)4826 glnX44 trpE31 _(hisG)1 gyrA96 recA::cat(FRT)(CmR)  recD1014 rpsL104(StrR) xyl-7 mtlA2(Fs) metB1(FS) mrr::tetAR serB28,,4638,,,,NZ_CP010438.1,4379,,1,New England Biolabs,50-200,PacBio,,,,K-12 MG1655,,,"Included in the study, passed QC/QA"
1404,83333.104,identified_by:Anthony Kingston;sample_type:Cell Culture,,,,GCF_000974465.1,SMRT Analysis v. 2.3,,PRJNA271807,SAMN03277613,,,,,1,Jun-14,"Provides the genomic sequences of a donor, recipient, and six recombinants from a mating system designed to identify novel horizontal gene transfer mechanisms.",2015-04-21T00:00:00Z,,,2016-01-17T15:54:15.031Z,2016-01-17T15:54:15.031Z,,,50.81,CP010439,4604543,Escherichia coli K-12 strain ER3440,Complete,Escherichia,,,,,,,,,,,not applicable,,,,,83333,,,,,genotype:fhuA2::IS2 _(lacZ)4826 glnX44 trpE31 _(hisG)1 gyrA96 recA::cat(FRT)(CmR) recD1014 rpsL104(StrR) xyl-7 mtlA2(Fs) metB1(FS) _(yjiT-mrr)::npt(KnR) serB28,,4630,,,,NZ_CP010439.1,4369,,1,New England Biolabs,50-200,PacBio,,,,K-12 MG1655,,,"Included in the study, passed QC/QA"
1405,83333.105,identified_by:Anthony Kingston;sample_type:Cell Culture,,,,GCF_000974505.1,SMRT Analysis v. 2.3,,PRJNA271807,SAMN03277619,,,,,1,Jun-14,"Provides the genomic sequences of a donor, recipient, and six recombinants from a mating system designed to identify novel horizontal gene transfer mechanisms.",2015-04-21T00:00:00Z,,,2016-01-17T15:54:15.662Z,2016-01-17T15:54:15.662Z,,,50.79,CP010440,4621164,Escherichia coli K-12 strain ER3476,Complete,Escherichia,,,,,,,,,,,not applicable,,,,,83333,,,,,genotype:fhuA2::IS2 _(lacZ)4826 glnX44 trpE31 _(hisG)1 gyrA96 recA::cat(FRT) recD1014 rpsL104(StrR) xyl-7 mtlA2(Fs) metB1(FS) mrr::tetAR,,4664,,,,NZ_CP010440.1,4358,,1,New England Biolabs,50-200,PacBio,,,,K-12 MG1655,,,"Included in the study, passed QC/QA"
1406,83333.106,identified_by:Anthony Kingston;sample_type:Cell Culture,,,,GCF_000974535.1,SMRT Analysis v. 2.3,,PRJNA271807,SAMN03277614,,,,,1,Jun-14,"Provides the genomic sequences of a donor, recipient, and six recombinants from a mating system designed to identify novel horizontal gene transfer mechanisms.",2015-04-21T00:00:00Z,,,2016-01-17T15:54:16.351Z,2016-01-17T15:54:16.351Z,,,50.81,CP010441,4607634,Escherichia coli K-12 strain ER3445,Complete,Escherichia,,,,,,,,,,,not applicable,,,,,83333,,,,,genotype:supQ80? _(hisG)1 e14- (McrA-) gyrA96 recA::cat(FRT)(CmR) recD1014 rpsL104(StrR) xyl-7 mtlA2(Fs) metB1(FS) mrr::tetAR,,4616,,,,NZ_CP010441.1,4363,,1,New England Biolabs,50-200,PacBio,,,,K-12 MG1655,,,"Included in the study, passed QC/QA"
1407,83333.107,identified_by:Anthony Kingston;sample_type:Cell Culture,,,,GCF_000974575.1,SMRT Analysis v. 2.3,,PRJNA271807,SAMN03277617,,,,,1,Jun-14,"Provides the genomic sequences of a donor, recipient, and six recombinants from a mating system designed to identify novel horizontal gene transfer mechanisms.",2015-04-21T00:00:00Z,,,2016-01-17T15:54:16.981Z,2016-01-17T15:54:16.981Z,,,50.78,CP010442,4660432,Escherichia coli K-12 strain ER3466,Complete,Escherichia,,,,,,,,,,,not applicable,,,,,83333,,,,,genotype:supQ80 _(hisG)1 gyrA96 e14- (McrA-) rpsL104(StrR) recA::cat(FRT) recD1014 xyl-7 mtlA2(Fs) thiE1 mrr::tetAR,,4687,,,,NZ_CP010442.1,4419,,1,New England Biolabs,50-200,PacBio,,,,K-12 MG1655,,,"Included in the study, passed QC/QA"
1408,83333.108,identified_by:Anthony Kingston;sample_type:Cell Culture,,,,GCF_000974825.1,SMRT Analysis v. 2.3,,PRJNA271807,SAMN03277615,,,,,1,Jun-14,"Provides the genomic sequences of a donor, recipient, and six recombinants from a mating system designed to identify novel horizontal gene transfer mechanisms.",2015-04-21T00:00:00Z,,,2016-01-17T15:54:21.121Z,2016-01-17T15:54:21.121Z,,,50.81,CP010443,4606859,Escherichia coli K-12 strain ER3446,Complete,Escherichia,,,,,,,,,,,not applicable,,,,,83333,,,,,genotype:supQ80? _(hisG)1 e14- (McrA-) gyrA96 recA::cat(FRT)(CmR)  recD1014 rpsL104(StrR) xyl-7 mtlA2(Fs) metB1(FS) mrr::tetAR,,4612,,,,NZ_CP010443.1,4361,,1,New England Biolabs,50-200,PacBio,,,,K-12 MG1655,,,"Included in the study, passed QC/QA"
1409,83333.109,identified_by:Anthony Kingston;sample_type:Cell Culture,,,,GCF_000974865.1,SMRT Analysis v. 2.3,,PRJNA271807,SAMN03277618,,,,,1,Jun-14,"Provides the genomic sequences of a donor, recipient, and six recombinants from a mating system designed to identify novel horizontal gene transfer mechanisms.",2015-04-21T00:00:00Z,,,2016-01-17T15:54:21.899Z,2016-01-17T15:54:21.899Z,,,50.8,CP010444,4609629,Escherichia coli K-12 strain ER3475,Complete,Escherichia,,,,,,,,,,,not applicable,,,,,83333,,,,,genotype:supQ80 _(hisG)1 e14- (McrA-) gyrA96 recA::cat(FRT) recD1014 rpsL104(StrR) xyl-7 mtlA2(Fs) metB1(FS) mrr::tetAR,,4619,,,,NZ_CP010444.1,4362,,1,New England Biolabs,50-200,PacBio,,,,K-12 MG1655,,,"Included in the study, passed QC/QA"
1410,83333.11,identified_by:Anthony Kingston;sample_type:Cell Culture,,,,GCF_000974885.1,SMRT Analysis v. 2.3,,PRJNA271807,SAMN03277612,,,,,1,Jun-14,"Provides the genomic sequences of a donor, recipient, and six recombinants from a mating system designed to identify novel horizontal gene transfer mechanisms.",2015-04-21T00:00:00Z,,,2016-01-17T15:54:22.284Z,2016-01-17T15:54:22.284Z,,,50.77,CP010445,4682086,Escherichia coli K-12 strain ER3435,Complete,Escherichia,,,,,,,,,,,not applicable,,,,,83333,,,,,genotype:supQ80 thiE1 e14- (McrA-) ÆrecA::FRT relA1 spoT1 mrr::tetAR,,4686,,,,NZ_CP010445.1,4447,,1,New England Biolabs,50-200,PacBio,,,,K-12 MG1655,,,"Included in the study, passed QC/QA"
1411,83333.111,,,,,GCF_000981485.1,,,PRJEB7832,SAMEA3143339,,,,,1,,"Escherichia coli K12 (AG100) was targeted with two antibiotics, erythromycin (a macrolide, ERY) and doxycycline (a tetracycline, DOX) that bind to different ribosomal RNA subunits, thereby inhibiting translation. Two treatment of 8 seasons of 12 hours at dosages corresponding to the IC50 of each drug were sequenced; IC50 denotes the antibiotic concentration that reduces bacterial density by a factor of 50% relative to that produced without antibiotic in one season. We studied one 50-50 combination using a half-dose of both drug for each season, and the EDEDEDED treatment, writing 'E' for a season of ERY and D for DOX. Library preparation method: DNA was fragmented by sonication using a Biorupter for 30s on, 90s off, using low power for 10 minutes on ice. Libraries were prepared using SPRIworks cartridges for Illumina (Beckman Coulter) and Nextflex indexed adapters, with 300-600 bp size selection, amplified with 8 cycles PCR using Kapa HiFi DNA polymerase and purified using GeneRead kit (Qiagen). Concentrations were determined using a Bioanalyser 7500 DNA chip. Libraries were pooled in equimolar amounts, denatured, diluted to 6.5 pMol and clustered on a flowcell using a cBot (Illumina). 100 paired end sequencing with a custom barcode read was completed on a HiSeq 2500 using Truseq SBS v3 reagents Illumina).",2015-04-02T00:00:00Z,,,2016-01-17T15:55:26.002Z,2016-01-17T15:55:26.002Z,,,50.83,LN832404,4638126,Escherichia coli K-12,Complete,Escherichia,,,,,,,,,,,,,,,,83333,,,,,,,4581,,,,NZ_LN832404.1,4165,,1,UNIVERSITY OF EXETER,,,,,,K-12,,,"Included in the study, passed QC/QA"
1412,83333.113,isolate:Lac-,,,,GCF_001021005.2,ALLPATHS-LG v. 42411,,PRJNA224131,SAMN02404590,,,,,1,,Escherichia coli K-12 GM4792 Lac-,2015-10-21T00:00:00Z,,,2016-01-17T16:05:27.932Z,2016-01-17T16:05:27.932Z,,,50.8,CP011343,4621656,Escherichia coli K-12,Complete,Escherichia,,,,,,,,,,,,,,,,83333,,,,,,,4548,,,,NZ_CP011343.2,4043,,1,"College of Life Sciences, Beijing Normal University",330x,Illumina HiSeq,,,,K12,,,"Included in the study, passed QC/QA"
1413,83333.117,sample_type:cell culture,,,,GCF_001559655.1,HGAP.3/Quiver v. 2.3.0,,PRJNA309536,SAMN04435497,,,,,1,,"Complete genome sequences of SHuffle K-12, SHuffle B, and their parental strains DHB4 and C2566, respectively.",2016-02-11T00:00:00Z,,,2016-03-01T20:06:52.396Z,2016-03-01T20:06:52.396Z,,,50.73,"CP014270,CP014271",4779803,Escherichia coli K-12 strain K-12 DHB4,Complete,Escherichia,USA,,,,,,,,United States,,laboratory,,,,,83333,C,,,,,,4842,,1,,"NZ_CP014270.1,NZ_CP014271.1",4628,,2,New England Biolabs,200x,PacBio,,,,K-12 DHB4,,,"Included in the study, passed QC/QA"
1414,83333.118,sample_type:cell culture,,,,GCF_001559675.1,HGAP.3/Quiver v. 2.3.0,,PRJNA309537,SAMN04435499,,,,,1,,"Complete genome sequences of E. coli SHuffle-K-12 and SHuffle-B and their parental strains, DHB4 and C2566, respectively.",2016-02-11T00:00:00Z,,,2016-03-01T20:07:45.085Z,2016-03-01T20:07:45.085Z,,,50.76,"CP014272,CP014273",4959179,Escherichia coli K-12 strain K-12 C3026,Complete,Escherichia,USA,,,,,,,,United States,,laboratory,,,MLST.Escherichia_coli_1.10,,83333,C,,,,,,5086,,1,,"NZ_CP014272.1,NZ_CP014273.1",4851,,2,New England Biolabs,250x,PacBio,,,,K-12 C3026,,,"Excluded from the study, failed QC/QA."
1415,83333.84,,,,,GCA_000800765.1,,,PRJNA263793,SAMN03107000,,,,,1,,"Complete Genome Sequence of ER3413, a DNA Methyltransferase-Deficient Laboratory Strain of Escherichia coli",2014-12-11T00:00:00Z,1,,2015-03-12T14:02:27.756Z,2015-03-16T03:17:09.594Z,,,50.8,CP009789.1,4558660,Escherichia coli K-12 ER3413,Complete,Escherichia,USA,,,,,,,,United States,,,,,,,83333,,,,,,,4357,,,-,NZ_CP009789.1,4083,,1,New England Biolabs,,,,,,K-12,,,"Included in the study, passed QC/QA"
1416,83334.178,sample_type:culture collection specimen;biomaterial_provider:Collection de l'Institute Pasteur;passage_history:CDC => CIP => WS,,,,GCA_001307215.1,PacBio HGAP v. May-2104,,PRJNA296759,SAMN04103124,,,,,1,2003,"Escherichia coli O157:H7 EDL933 isolated 1982 in the USA was the first EHEC sequenced. Unfortunately, European labs can not receive the original strain anymore. We checked three European EDL933 derivatives and found major genetic deviations (deletions, inversions) in two strains. All EDL933 strains contain the cryptic EHEC-plasmid, not reported before. This is strain WS4202.",2015-10-06T00:00:00Z,,,2016-01-17T17:13:30.931Z,2016-01-17T17:13:30.931Z,,,50.48,"CP012802,CP012803,CP012804",5428108,Escherichia coli O157:H7 strain WS4202,Complete,Escherichia,France: Paris,,,,,,,isolated 1982 in the USA was the first EHEC sequenced,France,,"derived from CIP 106327 (Collection de l'Institute Pasteur, Paris, France)",,,,,83334,C,,,,,,5676,,2,,"NZ_CP012802.1,NZ_CP012803.1,NZ_CP012804.1",5326,,3,Technische Universitaet Muenchen,100.0x,PacBio,,O157:H7,,WS4202,,,"Included in the study, passed QC/QA"
1417,83334.19,collected_by:FLUFL,,,,GCF_001651925.1,HGAP v. 3,,PRJNA322195,SAMN04191551,,,,,1,20-Jul-11,Comparative genomics using PacBio sequencing,2016-05-25T00:00:00Z,,,2016-07-05T12:48:43.682Z,2016-07-05T12:48:43.682Z,,,50.51,"CP015846,CP015847",5740824,Escherichia coli O157:H7 strain FRIK2069,Complete,Escherichia,USA: FL,,,,,,Bos taurus,,United States,,feces,,,"MLST.Escherichia_coli_2.628,MLST.Escherichia_coli_1.11",,83334,,,,,,,6101,,1,,,5784,,2,University of Florida,25x,PacBio,,,,FRIK2069,,,"Included in the study, passed QC/QA"
1418,83334.191,collected_by:FLUFL,,,,GCF_001651945.1,HGAP v. 3,,PRJNA322195,SAMN04191553,,,,,1,20-Jul-11,Comparative genomics using PacBio sequencing,2016-05-25T00:00:00Z,,,2016-07-05T12:48:47.691Z,2016-07-05T12:48:47.691Z,,,50.55,CP015842,5645219,Escherichia coli O157:H7 strain FRIK2533,Complete,Escherichia,USA: FL,,,,,,Bos taurus,,United States,,feces,,,"MLST.Escherichia_coli_2.628,MLST.Escherichia_coli_1.11",,83334,,,,,,,5984,,,,NZ_CP015842.1,5678,,1,University of Florida,25x,PacBio,,,,FRIK2533,,,"Included in the study, passed QC/QA"
1419,83334.192,collected_by:FLUFL,,,,GCF_001651965.1,HGAP v. 3,,PRJNA322195,SAMN04531998,,,,,1,20-Jul-11,Comparative genomics using PacBio sequencing,2016-05-25T00:00:00Z,,,2016-07-05T12:49:07.259Z,2016-07-05T12:49:07.259Z,,,50.44,"CP015843,CP015845,CP015844",5718414,Escherichia coli O157:H7 strain FRIK2455,Complete,Escherichia,USA: FL,,,,,,Bos taurus,,United States,,feces from steer,,,"MLST.Escherichia_coli_2.628,MLST.Escherichia_coli_1.11",,83334,,,,,,,6086,,2,,,5766,,3,University of Florida,25x,PacBio,,,,FRIK2455,,,"Included in the study, passed QC/QA"
1420,83334.194,collected_by:FLUFL,,,,GCF_001695515.1,HGAP v. 3,,PRJNA322195,SAMN04510563,,,,,1,16-Sep-2014,Comparative genomics using PacBio sequencing,2016-07-27T00:00:00Z,,,2016-09-11T17:11:34.875Z,2016-09-11T17:11:34.875Z,,,50.55,"CP016625,CP016626",5866200,Escherichia coli O157:H7 strain FRIK944,Complete,Escherichia,USA: FL,,,,,,Bos taurus,,United States,,calf feces,,,,,83334,,,,,,,6321,,1,,"NZ_CP016625.1,NZ_CP016626.1",5941,,2,University of Florida,25x,PacBio,,,,FRIK944,,,"Included in the study, passed QC/QA"
1421,83334.197,collected_by:T. M. Arthur,,,,GCF_001753445.1,RS_HGAP_Assembly v. 3,,PRJNA291880,SAMN04447635,,,,,1,2003-06,Whole genome sequencing of STEC O157:H7 strains.,2016-10-06T00:00:00Z,,,2016-11-17T00:14:18.717Z,2016-11-17T00:14:18.717Z,,,50.47,"CP017434,CP017435",5509007,Escherichia coli O157:H7 strain 1130,Complete,Escherichia,USA:Kansas,,Multiple,,,,,,United States,,Cattle Hide,,,,,83334,37 C,,,,,Facultative,5798,EHEC,1,,"NZ_CP017434.1,NZ_CP017435.1",5489,,2,United State Department of Agriculture,350X,PacBio,,O157:H7,,1130,Mesophilic,,"Included in the study, passed QC/QA"
1422,83334.198,collected_by:T. M. Arthur,,,,GCF_001753465.1,RS_HGAP_Assembly v. 3,,PRJNA291880,SAMN04447629,,,,,1,2003-06,Whole genome sequencing of STEC O157:H7 strains.,2016-10-06T00:00:00Z,,,2016-11-16T23:22:12.022Z,2016-11-16T23:22:12.022Z,,,50.47,"CP017436,CP017437",5500773,Escherichia coli O157:H7 strain 2149,Complete,Escherichia,USA:Nebraska,,Multiple,,,,,,United States,,Cattle Hide,,,,,83334,37 C,,,,,Facultative,5779,EHEC,1,,"NZ_CP017436.1,NZ_CP017437.1",5481,,2,United State Department of Agriculture,346X,PacBio,,O157:H7,,2149,Mesophilic,,"Included in the study, passed QC/QA"
1423,83334.199,collected_by:T. M. Arthur,,,,GCF_001753485.1,RS_HGAP_Assembly v. 3,,PRJNA291880,SAMN04447624,,,,,1,2003-09,Whole genome sequencing of STEC O157:H7 strains.,2016-10-06T00:00:00Z,,,2016-11-16T23:21:56.022Z,2016-11-16T23:21:56.022Z,,,50.47,"CP017444,CP017445",5530258,Escherichia coli O157:H7 strain 8368,Complete,Escherichia,Canada: Alberta,,Multiple,,,,,,Canada,,Cattle Hide,,,,,83334,37 C,,,,,Facultative,5813,EHEC,1,,"NZ_CP017444.1,NZ_CP017445.1",5519,,2,United State Department of Agriculture,296X,PacBio,,O157:H7,,8368,Mesophilic,,"Included in the study, passed QC/QA"
1424,83334.2,collected_by:T. M. Arthur,,,,GCF_001753505.1,RS_HGAP_Assembly v. 3,,PRJNA291880,SAMN04447630,,,,,1,2003-06,Whole genome sequencing of STEC O157:H7 strains.,2016-10-06T00:00:00Z,,,2016-11-16T23:25:31.644Z,2016-11-16T23:25:31.644Z,,,50.47,"CP017438,CP017439",5509229,Escherichia coli O157:H7 strain 2159,Complete,Escherichia,USA:Nebraska,,Multiple,,,,,,United States,,Cattle Hide,,,,,83334,37 C,,,,,Facultative,5798,EHEC,1,,"NZ_CP017438.1,NZ_CP017439.1",5494,,2,United State Department of Agriculture,171X,PacBio,,O157:H7,,2159,Mesophilic,,"Included in the study, passed QC/QA"
1425,83334.201,collected_by:T. M. Arthur,,,,GCF_001753525.1,RS_HGAP_Assembly v. 3,,PRJNA291880,SAMN04447632,,,,,1,2003-10,Whole genome sequencing of STEC O157:H7 strains.,2016-10-06T00:00:00Z,,,2016-11-16T23:29:56.803Z,2016-11-16T23:29:56.803Z,,,50.47,"CP017446,CP017447",5503176,Escherichia coli O157:H7 strain 9234,Complete,Escherichia,USA:Texas,,Multiple,,,,,,United States,,Cattle Hide,,,,,83334,37 C,,,,,Facultative,5785,EHEC,1,,"NZ_CP017446.1,NZ_CP017447.1",5486,,2,United State Department of Agriculture,244X,PacBio,,O157:H7,,9234,Mesophilic,,"Included in the study, passed QC/QA"
1426,83334.202,collected_by:T. M. Arthur,,,,GCF_001753545.1,RS_HGAP_Assembly v. 3,,PRJNA291880,SAMN04447623,,,,,1,2003-07,Whole genome sequencing of STEC O157:H7 strains.,2016-10-06T00:00:00Z,,,2016-11-16T23:29:28.209Z,2016-11-16T23:29:28.209Z,,,50.47,"CP017440,CP017441",5531320,Escherichia coli O157:H7 strain 3384,Complete,Escherichia,USA:Kansas,,Multiple,,,,,,United States,,Cattle Hide,,,,,83334,37 C,,,,,Facultative,5805,EHEC,1,,"NZ_CP017440.1,NZ_CP017441.1",5521,,2,United State Department of Agriculture,274X,PacBio,,O157:H7,,3384,Mesophilic,,"Included in the study, passed QC/QA"
1427,83334.203,collected_by:T. M. Arthur,,,,GCF_001753565.1,RS_HGAP_Assembly v. 3,,PRJNA291880,SAMN04447636,,,,,1,2003-08,Whole genome sequencing of STEC O157:H7 strains.,2016-10-06T00:00:00Z,,,2016-11-16T23:33:51.995Z,2016-11-16T23:33:51.995Z,,,50.47,"CP017442,CP017443",5497141,Escherichia coli O157:H7 strain 4276,Complete,Escherichia,USA:Idaho,,Multiple,,,,,,United States,,Cattle Hide,,,,,83334,37 C,,,,,Facultative,5770,EHEC,1,,"NZ_CP017442.1,NZ_CP017443.1",5474,,2,United State Department of Agriculture,323X,PacBio,,O157:H7,,4276,Mesophilic,,"Included in the study, passed QC/QA"
1428,83334.221,,,,,GCA_002259555.1,Celera Assembler v. March-2016,,PRJNA395316,SAMN07369154,,,,,3,,"Escherichia coli serotype O157:H7 strain B6-914 is a human fecal isolate that was submitted to the Centers for Disease Control and Prevention and later deposited with the American Type Culture Collection (ATCC) as strain ATCC 43888. Its virulence is attenuated due to the lack of stx1, stx2, or stx variants, which resulted in its widespread use in applied microbiology studies for safety reasons. A B6-914 isolate in one USDA culture collection (designated B6-914ARS) has been shown to have unique properties with regard to biofilm formation and persistence on processing surfaces that likely stem from variations in genomic regions that carry bacteriophage insertions. Therefore, it would be valuable to determine the entire genomic sequence of strain B6-914 for use in comparative studies with sequences of deposited serotype O157:H7 strains.",2017-08-18T00:00:00Z,,,2017-09-28T20:44:43.157Z,2017-09-28T20:44:43.157Z,,,50.28,NOKN00000000,5652987,Escherichia coli O157:H7,Complete,Escherichia,USA: Washington (state),,,,,,Homo sapiens,,USA,,fecal sample,,,,,83334,,,,,,,6192,,1,,,5952,,4,U.S. Department of Agriculture,20.0x,PacBio,,O157:H7,,B6-914ARS,,,"Included in the study, passed QC/QA"
1429,869729.3,,,,,GCA_000148605.1,,,PRJNA50883,SAMN00017915,,,,,1,,"The MBRI has completed the genome sequence of the Adherent invasive Escherichia coli strain UM146, a highly invasive strain associated with ileal Crohn's disease.",2010-09-24T00:00:00Z,,,2014-12-08T22:11:35.073Z,2015-03-16T03:17:09.594Z,,,50.59,"CP002167,CP002168",5107563,Escherichia coli UM146,Complete,Escherichia,,,,,,,,,,,,,,"MLST.Escherichia_coli_1.643,MLST.Escherichia_coli_2.1",,869729,-,Escherichia coli UM146,,,,,5231,AIEC,1,21075930,"NC_017632.1,NC_017630.1",4783,,2,MBRI,,,complete,,,UM146,,,"Included in the study, passed QC/QA"
1430,885275.3,,,,,GCA_000233895.1,,,PRJNA52023,SAMN02603903,,,,,1,,-,2011-11-03T00:00:00Z,,,2014-12-08T22:11:36.744Z,2015-03-16T03:17:09.594Z,,,50.56,CP002212,5038386,Escherichia coli str. 'clone D i14',Complete,Escherichia,,,,,,,,,,,,,,"MLST.Escherichia_coli_1.73,MLST.Escherichia_coli_2.4",,885275,-,Escherichia coli str. 'clone D i14',,,,,4804,,,22046404,NC_017652.1,4919,,1,"TEDA School of Biological Sciences and Biotechnology, Nankai University|Tianjin Biochip Corporation",,,unfinished,,,clone D i14,,,"Included in the study, passed QC/QA"
1431,885276.3,,,,,GCA_000233875.1,,,PRJNA52021,SAMN02603902,,,,,1,,-,2011-11-03T00:00:00Z,,,2014-12-08T22:11:36.753Z,2015-03-16T03:17:09.594Z,,,50.56,CP002211,5038386,Escherichia coli str. 'clone D i2',Complete,Escherichia,,,,,,,,,,,,,,"MLST.Escherichia_coli_1.73,MLST.Escherichia_coli_2.4",,885276,-,Escherichia coli str. 'clone D i2',,,,,4809,,,22046404,NC_017651.1,4919,,1,"TEDA School of Biological Sciences and Biotechnology, Nankai University|Tianjin Biochip Corporation",,,unfinished,,,'clone D i2',,,"Included in the study, passed QC/QA"
1432,910348.4,,,,,GCA_000257275.1,,,PRJNA59455,SAMN02603904,,,,,1,,-,2012-04-02T00:00:00Z,, ,2014-12-08T22:11:34.148Z,2015-03-16T03:17:09.594Z,,,50.9,CP002291.1,4935294,Escherichia coli P12b,Complete,Escherichia,,,,,,,,,,,,,,MLST.Escherichia_coli_1.10,,910348,,Escherichia coli P12b,,,,,4926,,,,NC_017663.1,4393,,1,"TEDA School of Biological Sciences and Biotechnology, Nankai University",,,complete,,,P12b,,,"Included in the study, passed QC/QA"
1433,930406.3,,,,,GCA_000827105.1,SOAPdenovo v. 2.4,,PRJNA240262,SAMN02673556,,,,,1,2011-08-03,Presence and isolation of a special pathogenic EHEC O157 in clinical healthy adult laying duck,2015-01-21T00:00:00Z,1,,2015-03-12T14:02:40.030Z,2015-03-16T03:17:09.594Z,,,50.6,CP007592.1,5104557,Escherichia coli O157:H16 Santai,Complete,Escherichia,"China: Santai, mianyang city, sichuan province",,,,,,Duck,,China,,rectum of clinical healthy adult layingduck,,,,,930406,,,,,,,4843,,,-,NZ_CP007592.1,,,1,BGI,275.0x,Illumina HiSeq,,,,Santai,,,"Included in the study, passed QC/QA"
1434,941323.4,sample_type:Bacterial culture,,,,GCF_000968515.1,SMRTanalysis v. 2.0.0,,PRJEA61445,SAMN03371467,,,,,1,,Escherichia coli VR50 is an asymptomatic bacteruria isolate.,2015-04-02T00:00:00Z,,,2016-01-17T15:52:45.340Z,2016-01-17T15:52:45.340Z,,,50.8,"CP011134,CP011135,CP011136,CP011137,CP011138,CP011139,CP011140,CP011141,CP011142,CP011143",5196066,Escherichia coli VR50,Complete,Escherichia,,,,,,,"Human, Homo sapiens",,,,urine,,,,,941323,,,,,,,5282,,9,25667270,"NZ_CP011134.1,NZ_CP011135.1,NZ_CP011136.1,NZ_CP011137.1,NZ_CP011138.1,NZ_CP011139.1,NZ_CP011140.1,NZ_CP011141.1,NZ_CP011142.1,NZ_CP011143.1",4788,,10,The University of Queensland,65x,Pacific Biosciences SMRT sequencing,,OR:K1:H-,,VR50,,,"Included in the study, passed QC/QA"