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. 2015 Apr 9;3(2):e00272-15. doi: 10.1128/genomeA.00272-15

Complete Genome Sequence of a Carbapenem-Resistant Extraintestinal Pathogenic Escherichia coli Strain Belonging to the Sequence Type 131 H30R Subclade

Timothy J Johnson a,✉, Melissa Hargreaves b, Kristin Shaw b, Paula Snippes b, Ruth Lynfield b, Maliha Aziz c,d, Lance B Price c,d
PMCID: PMC4392156  PMID: 25858844

Abstract

Here, we report the completed genome sequence of a carbapenem-resistant extraintestinal pathogenic Escherichia coli sequence type 131 (ST131) isolate, MNCRE44. The isolate was obtained in 2012 in Minnesota, USA, from a sputum sample from a hospitalized patient with multiple comorbidities, and it belongs to the H30R sublineage.

GENOME ANNOUNCEMENT

Extraintestinal pathogenic Escherichia coli, or ExPEC, poses a significant burden on health care systems worldwide (1). Recently, ExPEC sequence type 131 (ST131) has emerged worldwide as the predominant ExPEC subtype isolated from human clinical cases (2). Within ST131, a subclade known as H30R is particularly concerning because of its reduced susceptibility to fluoroquinolones, and some of these isolates (H30Rx) also display reduced susceptibility toward third-generation cephalosporins (3). Recent reports of ExPEC ST131 isolates that are also resistant to carbapenems are rare, yet concerning (4–8).

ExPEC strain MNCRE44 was isolated in 2012 from the sputum sample from a patient with multiple comorbidities in Minnesota, and it was initially characterized as PCR positive for the Klebsiella pneumoniae carbapenemase (KPC)-encoding gene blaKPC and displayed reduced susceptibilities to cefotaxime, ceftazidime, ciprofloxacin, ertapenem, and gentamicin. MNCRE44 was sequenced using a combination of PacBio (100× coverage, P5-C3 chemistry) and Illumina MiSeq (125× coverage, TruSeq chemistry) sequencing. The PacBio sequences were assembled using HGAP version 3 in the PacBio SMRT Portal, which resulted in closed circular plasmids and a circular chromosome. The PacBio sequence reads were manually error corrected using a MiSeq assembly from CLC Genomics Workbench version 7. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline, followed by manual curation of the plasmid sequences. Antimicrobial resistance genes were identified using the CARD database (9). Plasmid replicons were identified using PlasmidFinder (10).

The complete genome of MNCRE44 contains a 5,010,884-bp chromosome, a G+C content of 50.8%, 5,407 coding sequences, 86 tRNAs, and 22 rRNA features. Six plasmids are present in MNCRE44 (pMNCRE44_1 to pMNCRE44_6) of sizes 1.5, 4.0, 5.1, 30, 116, and 122 kb, respectively. In addition to its chromosomally encoded fluoroquinolone resistance phenotype, MNCRE44 also possesses a 116-kb hybrid IncX3/IncFIA(HI1) plasmid (pMNCRE44_5) containing sul2, aph(3′)-Ib, aph(6)-Id, blaTEM-1, blaOXA-9, aadA1, aacA4, two copies of blaKPC-3, and blaSHV-12. Additionally, MNCRE44 possesses an IncFII(pRSB107)/FIA/FIB(AP001918) plasmid (pMNCRE44_6) containing a copy of blaTEM-1. MNCRE44 contains an IncX4 plasmid (pMNCRE44_4) that does not carry genes encoding resistance-associated elements. A phylogenetic comparison of the single nucleotide polymorphisms in the core genome of MNCRE44 compared to those in a known collection of ST131 isolates placed it in the H30R sublineage.

MNCRE44 is the first complete genome sequence for an H30R ST131 isolate that includes all plasmids. This is also the first completed sequence of a carbapenem-resistant ST131 ExPEC isolate. The genome sequence provides the genetic context related to the emergence of carbapenem resistance in ST131 ExPEC isolates.

Nucleotide sequence accession numbers.

The complete sequences of the chromosome of E. coli MNCRE44 and its six plasmids, pMNCRE44_1 through pMNCRE44_6, have been deposited in GenBank (accession numbers CP010876, CP010877, CP010878, CP010879, CP010880, CP010881, and CP010882, respectively).

ACKNOWLEDGMENTS

This work was supported by University of Minnesota College of Veterinary Medicine funding.

Computing resources were provided by the University of Minnesota Supercomputing Institute.

We thank Kevin Silverstein, University of Minnesota Supercomputing Institute, for assistance with the PacBio assemblies.

Footnotes

Citation Johnson TJ, Hargreaves M, Shaw K, Snippes P, Lynfield R, Aziz M, Price LB. 2015. Complete genome sequence of a carbapenem-resistant extraintestinal pathogenic Escherichia coli strain belonging to the sequence type 131 H30R subclade. Genome Announc 3(2):e00272-15. doi:10.1128/genomeA.00272-15.

REFERENCES

  • 1.Johnson JR, Russo TA. 2002. Extraintestinal pathogenic Escherichia coli: “the other bad E. coli.” J Lab Clin Med 139:155–162. doi: 10.1067/mlc.2002.121550. [DOI] [PubMed] [Google Scholar]
  • 2.Nicolas-Chanoine MH, Bertrand X, Madec JY. 2014. Escherichia coli ST131, an intriguing clonal group. Clin Microbiol Rev 27:543–574. doi: 10.1128/CMR.00125-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Price LB, Johnson JR, Aziz M, Clabots C, Johnston B, Tchesnokova V, Nordstrom L, Billig M, Chattopadhyay S, Stegger M, Andersen PS, Pearson T, Riddell K, Rogers P, Scholes D, Kahl B, Keim P, Sokurenko EV. 2013. The epidemic of extended-spectrum-β-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx. mBio 4(6):e00377-13. doi: 10.1128/mBio.00377-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Netikul T, Sidjabat HE, Paterson DL, Kamolvit W, Tantisiriwat W, Steen JA, Kiratisin P. 2014. Characterization of an IncN2-type blaNDM-1-carrying plasmid in Escherichia coli ST131 and Klebsiella pneumoniae ST11 and ST15 isolates in Thailand. J Antimicrob Chemother 69:3161–3163 doi: 10.1093/jac/dku275. [DOI] [PubMed] [Google Scholar]
  • 5.Kutumbaka KK, Han S, Mategko J, Nadala C, Buser GL, Cassidy MP, Beldavs ZG, Weissman SJ, Morey KE, Vega R, Samadpour M. 2014. Draft genome sequence of blaNDM-1-positive Escherichia coli O25b–ST131 clone isolated from an environmental sample. Genome Announc 2(3):e00462-14. doi: 10.1128/genomeA.00462-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Cai JC, Zhang R, Hu YY, Zhou HW, Chen GX. 2014. Emergence of Escherichia coli sequence type 131 isolates producing KPC-2 carbapenemase in China. Antimicrob Agents Chemother 58:1146–1152. doi: 10.1128/AAC.00912-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Chen L, Hu H, Chavda KD, Zhao S, Liu R, Liang H, Zhang W, Wang X, Jacobs MR, Bonomo RA, Kreiswirth BN. 2014. Complete sequence of a KPC-producing IncN multidrug-resistant plasmid from an epidemic Escherichia coli sequence type 131 strain in China. Antimicrob Agents Chemother 58:2422–2425 doi: 10.1128/AAC.02587-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Accogli M, Giani T, Monaco M, Giufrè M, García-Fernández A, Conte V, D’Ancona F, Pantosti A, Rossolini GM, Cerquetti M. 2014. Emergence of Escherichia coli ST131 sub-clone H30 producing VIM-1 and KPC-3 carbapenemases, Italy. J Antimicrob Chemother 69:2293–2296. doi: 10.1093/jac/dku132. [DOI] [PubMed] [Google Scholar]
  • 9.McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O’Brien JS, Pawlowski AC, Piddock LJ, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD. 2013. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57:3348–3357. doi: 10.1128/AAC.00419-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H. 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895–3903. doi: 10.1128/AAC.02412-14. [DOI] [PMC free article] [PubMed] [Google Scholar]

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