Genome Announcements

Genome Announc. 4(5): e00863-16

Genome Sequence of Avian Escherichia coli Strain IHIT25637, an Extraintestinal Pathogenic E. coli Strain of ST131 Encoding Colistin Resistance Determinant MCR-1

http://orcid.org/0000-0001-6167-1340Christa Ewersa, Stephan Göttigb, Maria Bültea, Sophie Fiedlera, Manuela Tietgenb, Ursula Leidnera, Carsten Heydela, Rolf Bauerfeinda, Torsten Semmlerc

a. Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University, Giessen, Germany

b. Institute of Medical Microbiology and Infection Control, Hospital of the Johann Wolfgang von Goethe-University, Frankfurt am Main, Germany

c. Robert Koch Institute, Berlin, Germany

Address correspondence to Christa Ewers, christa.ewers@vetmed.uni-giessen.de.

Copyright © 2016 Ewers et al.

DOI: 10.1128/genomeA.00863-16

Published online: 1 September 2016

Abstract

Sequence type 131 (ST131) is one of the predominant Escherichia coli lineages among extraintestinal pathogenic E. coli (ExPEC) that causes a variety of diseases in humans and animals and frequently shows multidrug resistance. Here, we report the first genome sequence of an ST131-ExPEC strain from poultry carrying the plasmid-encoded colistin resistance gene mcr-1.

GENOME ANNOUNCEMENT

Extraintestinal pathogenic Escherichia coli (ExPEC) strains are a versatile group of bacteria revealing a complex phylogeny and considerable genomic plasticity. ExPEC strains cause a variety of disease syndromes, ranging from uncomplicated urinary tract infections to life-threatening bloodstream infections in humans and septicemia, peritonitis, and yolk sac infections in poultry (1, 2). Certain subpopulations of avian ExPEC have been suggested to be zoonotic agents (3, 4), which is of great concern, because they also have been associated with multidrug resistant clonal lineages, such as sequence type 131 (ST131) (2, 5).

We report the genome sequence of colistin-resistant avian ExPEC strain IHIT25637 carrying the plasmid-mediated mcr-1 gene, which was described first in human and food animal samples in China in 2015 (6). IHIT25637 was isolated in Germany in October 2010 from the liver of a broiler chicken that had died of septicemia. Whole-genome sequencing was performed on a MiSeq sequencer using a MiSeq reagent kit v3 (Illumina, USA) resulting in 300 bp paired-end reads and an average coverage of 100×. Filtered 1.75 M clean reads were de novo assembled after quality trimming using SPAdes v3.7.1 (7) into scaffolds, and corresponding 90-fold coverage of the genome was generated. The draft genome sequence of E. coli IHIT25637 was 5,692,160 bp in size and had a G+C content of 50.4% in 183 contigs (maximum length, 402,413 bp; minimum length, 200 bp; N₅₀ contig size 234,455 bp; mean coverage 90). The genome was annotated using the Rapid Annotation using Subsystem Technology (RAST) server (8). Annotation of this assembly identified 5,614 coding sequences (CDSs), 85 tRNAs, and 19 rRNAs.

The sequence type of IHIT25637 was identified as ST131 (https://cge.cbs.dtu.dk/services/), and its serotype was O25:H4 as determined by slide agglutination testing. Several virulence-related genes known to be associated with the ExPEC pathotype, like adhesin genes csgA, fim, iha, tsh, and focA, iron-acquisition related gene chuA, iroN, eitA, etsB/C, fyuA, irp2, iucD, and iutA, and invasion, serum resistance and capsule synthesis genes ibeA, iss, kpsMTII, and neuC, were present in strain IHIT25637. The allele type of the type I fimbrial adhesin gene was determined as fimH22, which has been associated with a fluoroquinolone-susceptible ST131-subgroup (9). Genome data revealed the presence of colistin resistance gene mcr-1 which most likely conferred phenotypic resistance to the “last resort” antibiotics colistin and polymyxin B (MIC: 8 mg/L). Mcr-1 was located on an IncHI2 plasmid (>200 kbp) of plasmid sequence type ST4 (10), which are major carriers of mcr-1 in E. coli isolates from livestock and food and also from humans (11–13). In addition to mcr-1, the genome of IHIT25637 carried several resistance genes, such as aph(3′)-Ic, aac(3)-IIa, aadA1, aadA2, strA and strB, blaTEM-1, cmlA1, catA1 sul1/2/3, dfrA1, and tet(A), but lacked genes for known extended-spectrum β-lactamases and carbapenemases. Only two ST131 E. coli strains carrying mcr-1 have yet been described, namely, from chicken meat of European origin imported to Denmark in 2012 and from the urine of a human patient in Taiwan in 2014 (14, 15). However, the appearance of mcr-1-harboring, colistin resistant ExPEC belonging to the epidemiological successful clonal lineage ST131 poses a serious public health threat.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number MAIV00000000. The version described in this paper is version MAIV00000000.1.

Footnotes

Citation Ewers C, Göttig S, Bülte M, Fiedler S, Tietgen M, Leidner U, Heydel C, Bauerfeind R, Semmler T. 2016. Genome sequence of avian Escherichia coli strain IHIT25637, an extraintestinal pathogenic E. coli strain of ST131 encoding colistin resistance determinant MCR-1. Genome Announc 4(5):e00863-16. doi:10.1128/genomeA.00863-16.

ACKNOWLEDGMENTS

We thank Petra Krienke, Inga Eichhorn, and Bettina Hopf for excellent technical assistance.

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)

PMC Copyright Notice

The articles available from the PMC site are protected by copyright, even though access is free. Copyright is held by the respective authors or publishers who provide these articles to PMC. Users of PMC are responsible for complying with the terms and conditions defined by the copyright holder.

Users should assume that standard copyright protection applies to articles in PMC, unless an article contains an explicit license statement that gives a user additional reuse or redistribution rights. PMC does not allow automated/bulk downloading of articles that have standard copyright protection.

See the copyright notice on the PMC site, https://www.ncbi.nlm.nih.gov/pmc/about/copyright/, for further details and specific exceptions.

REFERENCES

C EwersG LiH WilkingS KiesslingK AltEM AntáoC LaturnusI DiehlS GloddeT HomeierU BöhnkeH SteinrückHC PhilippLH Wieler 2007 Avian pathogenic, uropathogenic, and newborn meningitis-causing Escherichia coli: how closely related are they? Int J Med Microbiol 297:163–176. doi:10.1016/j.ijmm.2007.01.003.17374506

AP DaleN Woodford 2015 Extra-intestinal pathogenic Escherichia coli (ExPEC): disease, carriage and clones. J Infect 71:615–626. doi:10.1016/j.jinf.2015.09.009.26409905

M Mellata 2013 Human and avian extraintestinal pathogenic Escherichia coli: infections, zoonotic risks, and antibiotic resistance trends. Foodborne Pathog Dis 10:916–932. doi:10.1089/fpd.2013.1533.23962019

N NandanwarT JanssenM KühlN AhmedC EwersLH Wieler 2014 Extraintestinal pathogenic Escherichia coli (ExPEC) of human and avian origin belonging to sequence type complex 95 (STC95) portray indistinguishable virulence features. Int J Med Microbiol 304:835–842. doi:10.1016/j.ijmm.2014.06.009.25037925

C EwersA BetheT SemmlerS GuentherLH Wieler 2012 Extended-spectrum beta-lactamase-producing and AmpC-producing Escherichia coli from livestock and companion animals, and their putative impact on public health: a global perspective. Clin Microbiol Infect 18:646–655. doi:10.1111/j.1469-0691.2012.03850.x.22519858

YY LiuY WangTR WalshLX YiR ZhangJ SpencerY DoiG TianB DongX HuangLF YuD GuH RenX ChenL LvD HeH ZhouZ LiangJH LiuJ Shen 2016 Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis 16:161–168. doi:10.1016/S1473-3099(15)00424-7.26603172

A BankevichS NurkD AntipovAA GurevichM DvorkinAS KulikovVM LesinSI NikolenkoS PhamAD PrjibelskiAV PyshkinAV SirotkinN VyahhiG TeslerMA AlekseyevPA Pevzner 2012 SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:10.1089/cmb.2012.0021.22506599

RK AzizD BartelsAA BestM DeJonghT DiszRA EdwardsK FormsmaS GerdesEM GlassM KubalF MeyerGJ OlsenR OlsonAL OstermanRA OverbeekLK McNeilD PaarmannT PaczianB ParrelloGD PuschC ReichR StevensO VassievaV VonsteinA WilkeO Zagnitko 2008 The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi:10.1186/1471-2164-9-75.18261238

R BanerjeeJR Johnson 2014 A new clone sweeps clean: the enigmatic emergence of Escherichia coli sequence type 131. Antimicrob Agents Chemother 58:4997–5004. doi:10.1128/AAC.02824-14.24867985

A García-FernándezA Carattoli 2010 Plasmid double locus sequence typing for IncHI2 plasmids, a subtyping scheme for the characterization of IncHI2 plasmids carrying extended-spectrum beta-lactamase and quinolone resistance genes. J Antimicrob Chemother 65:1155–1161. doi:10.1093/jac/dkq101.20356905

K VeldmanA van Essen-ZandbergenM RapalliniB WitR HeymansW van PeltD Mevius 2016 Location of colistin resistance gene mcr-1 in Enterobacteriaceae from livestock and meat. J Antimicrob Chemother 71:2340–2342. doi:10.1093/jac/dkw181.27246233

M HaenniL PoirelN KiefferP ChâtreE SarasV MétayerR DumoulinP NordmannJ Madec 2016 Co-occurrence of extended spectrum beta lactamase and MCR-1 encoding genes on plasmids. Lancet Infect Dis 16:281–282. doi:10.1016/S1473-3099(16)00007-4.26774244

L FalgenhauerSE WaezsadaY YaoC ImirzaliogluA KasbohrerU RoeslerGB MichaelS SchwarzG WernerL KreienbrockT Chakraborty 2016 Colistin resistance gene mcr-1 in extended-spectrum β-lactamase-producing and carbapenemase-producing Gram-negative bacteria in Germany. Lancet Infect Dis 16:282–283. doi:10.1016/S1473-3099(16)00009-8.26774242

H HasmanAM HammerumF HansenRS HendriksenB OlesenY AgersøE ZankariP LeekitcharoenphonM SteggerRS KaasLM CavacoDS HansenFM AarestrupRL Skov 2015 Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015. Euro Surveill 20:49. doi:10.2807/1560-7917.ES.2015.20.49.30085.

SC KuoWC HuangHY WangYR ShiauMF ChengTL Lauderdale 2016 Colistin resistance gene mcr-1 in Escherichia coli isolates from humans and retail meats, Taiwan. J Antimicrob Chemother 71:1922–1932. doi:10.1093/jac/dkw122.27098012