Here, we announce the draft genome sequence of Enterobacter hormaechei 2B-MC1, isolated from a shrimp sample collected from a farmer’s market in Atlanta, Georgia. The assembled genome sequence observed was 4,661,561 bp long with a G+C content of 55.3%. The isolate harbored sul1, sul2, qnrA1, oqxB, dfrA23, blaACT, floR, fosA, tet(A), aph(6)-Id, and aph(3″)-Ib antibiotic resistance genes.
ABSTRACT
Here, we announce the draft genome sequence of Enterobacter hormaechei 2B-MC1, isolated from a shrimp sample collected from a farmer’s market in Atlanta, Georgia. The assembled genome sequence observed was 4,661,561 bp long with a G+C content of 55.3%. The isolate harbored sul1, sul2, qnrA1, oqxB, dfrA23, blaACT, floR, fosA, tet(A), aph(6)-Id, and aph(3″)-Ib antibiotic resistance genes.
ANNOUNCEMENT
We isolated and characterized a multidrug-resistant (MDR) Enterobacter hormaechei 2B-MC1 strain from raw farm-raised shrimp from Ecuador which was collected from a farmer’s market in Atlanta, Georgia, on 30 March 2019. Thirty-one shrimp samples were screened for the presence of extended-spectrum β-lactam strains as previously described (1). The 110 isolates obtained were purified by streaking onto nutrient agar. The genus and species of isolates were identified after 16S rRNA gene sequencing using 27F and 511R primers (2). Isolates were screened for MDR strains using the disk diffusion assay (3). E. hormaechei 2B-MC1 was found to be resistant to multiple classes of antimicrobials and was selected for whole-genome sequencing. A pure culture of the strain was grown in tryptic soy broth, and DNA from the overnight culture was extracted using the DNeasy PowerFood microbial kit (Qiagen). The quality and quantity of the DNA were measured using a NanoDrop One spectrophotometer (Thermo Fisher). Libraries from the DNA sample were prepared and sequenced at a Florida State University (Florida, USA) molecular cloning facility. Libraries were sequenced using a MiSeq 2 microkit (Illumina) at 9 pM with 5% PhiX. Default parameters for all software were used during analyses unless otherwise specified. The raw Illumina sequences were quality filtered using Trimmomatic (v0.36) (4). The high-quality reads were de novo assembled with Velvet (1.2.10) (5) with a k-mer size of 51. We only considered contigs longer than 200 bp in computing. CheckM (v1.0.7) with “lineage_wf” workflow (6) was used to estimate the completeness of the draft genome. The most closely related complete genomes of E. hormaechei 2B-MC1 were identified using Microbial Genomes Atlas MiGA online tool (7) with the NCBI prokaryotic genome database. The assemblies were annotated with the Prokka (v1.11) (8) annotation pipeline. Antimicrobial-resistant gene sequences were identified with NCBI AMRFinder (9). The analysis of harbored plasmid(s) within the draft genome were detected using the PLSDB database (10) with Mash software (11). The identified plasmids were further confirmed with BLAST alignment.
A total of 4,397,799 paired-end reads were sequenced. These raw sequences were trimmed and then quality filtered (about 8% of the reads were eliminated), resulting in approximately 363,705 reads. These high-quality reads were assembled into contigs. CheckM estimated the completeness of this genome as 99.8%. This assembly produced 160 contigs and an N50 value of 82,480 bp. This draft genome was 4,661,561 bp long with a G+C content of 55.3%. Genome annotation with Prokka identified 4,336 open reading frames and 36 RNAs (1 rRNA, 34 tRNAs, and 1 transfer-messenger RNA [tmRNA]). A total of 1,567 genes were associated with KEGG pathways. The closest relatives of E. hormaechei 2B-MC1 found by MiGA in the database were Enterobacter sp. strain CRENT-193 (GenBank accession number NZ_CP024812.1) and E. hormaechei (NZ_CP030076) with an average nucleotide identity of 99.19%. AMRFinder identified genes and mutations that confer resistance to sulfonamides (sul1 and sul2), quinolones (qnrA1), phenicol/quinolones (oqxB), trimethoprim (dfrA23), beta-lactamases (blaACT), phenicols (floR), fosfomycin (fosA), tetracycline [tet(A)], and aminoglycosides [aph(6)-Id and aph(3″)-Ib]. The following six putative plasmids were present in the draft genome: pESBL176 (MT230180.1), pESBL31 (MT230288.1, MT230289.1, MT230292.1, and MT230305.1), pESBL87 (MT230381.1), pESBL96 (MT230424.1 and MT230426.1), unnamed4 plasmid (NZ_CP020513.1), and pKP2442_7c331 (NZ_KX434882.1).
Data availability.
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JACVEK000000000. The version described in this paper is the first version, JACVEK010000000. Raw Illumina data have been deposited in the NCBI Sequence Read Archive with the accession number SRR12586817 under the BioProject accession number PRJNA661375.
ACKNOWLEDGMENT
This study was funded by Florida State University startup funds.
REFERENCES
- 1.Hutchinson H, Finney S, Muñoz-Vargas L, Feicht S, Masterson M, Habing G. 2017. Prevalence and transmission of antimicrobial resistance in a vertically integrated veal calf production system. Foodborne Pathog Dis 14:711–718. doi: 10.1089/fpd.2017.2310. [DOI] [PubMed] [Google Scholar]
- 2.Liu A-C, Chou C-Y, Chen L-L, Kuo C-H. 2015. Bacterial community dynamics in a swine wastewater anaerobic reactor revealed by 16S rDNA sequence analysis. J Biotechnol 194:124–131. doi: 10.1016/j.jbiotec.2014.11.026. [DOI] [PubMed] [Google Scholar]
- 3.Clinical and Laboratory Standards Institute. 2015. Performance standards for antimicrobial disk susceptibility tests; approved standard—12th edition Clinical and Laboratory Standards Institute, Wayne, PA. [Google Scholar]
- 4.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. doi: 10.1101/gr.074492.107. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. doi: 10.1101/gr.186072.114. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM, Cole JR, Konstantinidis KT. 2018. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Res 46:W282–W288. doi: 10.1093/nar/gky467. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
- 9.Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu C-H, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W. 2019. Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob Agents Chemother 63:e00483-19. doi: 10.1128/AAC.00483-19. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Galata V, Fehlmann T, Backes C, Keller A. 2019. PLSDB: a resource of complete bacterial plasmids. Nucleic Acids Res 47:D195–D202. doi: 10.1093/nar/gky1050. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. 2016. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17:132. doi: 10.1186/s13059-016-0997-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JACVEK000000000. The version described in this paper is the first version, JACVEK010000000. Raw Illumina data have been deposited in the NCBI Sequence Read Archive with the accession number SRR12586817 under the BioProject accession number PRJNA661375.