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Articles

Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex

, , , , , , , & ORCID Icon show all
Pages 1780-1792 | Received 12 Apr 2020, Accepted 14 Jul 2020, Published online: 07 Aug 2020

References

  • Pitout JD. Extraintestinal pathogenic Escherichia coli: a combination of virulence with antibiotic resistance. Front Microbiol. 2012;3:9.
  • Pitout JD, DeVinney R. Escherichia coli ST131: a multidrug-resistant clone primed for global domination. 2017;6:F1000 Faculty Rev-195.
  • Cho S, Gupta SK, McMillan EA, et al. Genomic analysis of multidrug-resistant Escherichia coli from surface water in Northeast Georgia, United States: presence of an ST131 epidemic strain containing blaCTX-M-15 on a phage-like plasmid. Microb Drug Resist. 2019 Nov 14;26(5):447–455.
  • Cho S, Nguyen HAT, McDonald JM, et al. Genetic characterization of antimicrobial-resistant Escherichia coli isolated from a mixed-use watershed in Northeast Georgia, USA. Int J Environ Res Public Health. 2019 Oct 7;16(19):3761.
  • Melo LC, Haenni M, Saras E, et al. Emergence of the C1-M27 cluster in ST131 Escherichia coli from companion animals in France. J Antimicrob Chemother. 2019 Oct 1;74(10):3111–3113.
  • Reid CJ, McKinnon J, Djordjevic SP. Clonal ST131-H22 Escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids. Microb Genom. 2019 Sep;5(9):e000295.
  • Seenama C, Thamlikitkul V, Ratthawongjirakul P. Multilocus sequence typing and bla ESBL characterization of extended-spectrum beta-lactamase-producing Escherichia coli isolated from healthy humans and swine in Northern Thailand. Infect Drug Resist. 2019;12:2201–2214.
  • Banerjee R, Johnson JR. A new clone sweeps clean: the enigmatic emergence of Escherichia coli sequence type 131. Antimicrob Agents Chemother. 2014 Sep;58(9):4997–5004.
  • Burgess MJ, Johnson JR, Porter SB, et al. Long-term care facilities are reservoirs for antimicrobial-resistant sequence type 131 Escherichia coli. Open Forum Infect Dis. 2015 Jan;2(1): ofv011.
  • Diekema DJ, Hsueh PR, Mendes RE, et al. The microbiology of bloodstream Infection: 20-year trends from the SENTRY antimicrobial surveillance program. Antimicrob Agents Chemother. 2019 Jul;63(7):e00355–19.
  • Mineau S, Kozak R, Kissoon M, et al. Emerging antimicrobial resistance among Escherichia coli strains in bloodstream infections in Toronto, 2006-2016: a retrospective cohort study. CMAJ Open. 2018 Oct-Dec;6(4):E580–E586.
  • Poolman JT, Wacker M. Extraintestinal pathogenic Escherichia coli, a common human pathogen: challenges for vaccine development and progress in the field. J Infect Dis. 2016 Jan 1;213(1):6–13.
  • Ben Zakour NL, Alsheikh-Hussain AS, Ashcroft MM, et al. Sequential acquisition of virulence and fluoroquinolone resistance has shaped the evolution of Escherichia coli ST131. mBio. 2016 Apr 26;7(2):e00347–16.
  • Decano AG, Downing T. An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates. Sci Rep. 2019 Nov 22;9(1):17394.
  • Petty NK, Ben Zakour NL, Stanton-Cook M, et al. Global dissemination of a multidrug resistant Escherichia coli clone. Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):5694–5699.
  • Price LB, Johnson JR, Aziz M, et al. The epidemic of extended-spectrum-beta-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx. MBio. 2013 Dec 17;4(6):e00377–13.
  • Stoesser N, Sheppard AE, Pankhurst L, et al. Evolutionary history of the global emergence of the Escherichia coli epidemic Clone ST131. mBio. 2016 Mar 22;7(2):e02162.
  • Mathers AJ, Peirano G, Pitout JD. Escherichia coli ST131: the quintessential example of an international multiresistant high-risk clone. Adv Appl Microbiol. 2015;90:109–154.
  • Johnson TJ, Danzeisen JL, Youmans B, et al. Separate F-type plasmids have shaped the evolution of the H30 Subclone of Escherichia coli sequence type 131. mSphere. 2016 Jul-Aug;1(4):e00121–16.
  • Feil EJ, Li BC, Aanensen DM, et al. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol. 2004 Mar;186(5):1518–1530.
  • Rasko DA, Rosovitz MJ, Myers GS, et al. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol. 2008 Oct;190(20):6881–6893.
  • Dahbi G, Mora A, Lopez C, et al. Emergence of new variants of ST131 clonal group among extraintestinal pathogenic Escherichia coli producing extended-spectrum beta-lactamases. Int J Antimicrob Agents. 2013 Oct;42(4):347–351.
  • Hastak P, Cummins ML, Gottlieb T, et al. Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital. Microb Genom. 2020 May 6;6(5):e000371.
  • Magiorakos AP, Srinivasan A, Carey RB, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect. 2012 Mar;18(3):268–281.
  • Bell JM, Turnidge JD, Coombs GW, et al. Australian Group on antimicrobial resistance Australian Enterobacteriaceae Sepsis Outcome Programme, Annual Report 2014. In: Curran M, editor. Communicable diseases intelligence. June 2016 ed. Australia: The Department of Health; 2016. p. 229–235.
  • Darling AE, McKinnon J, Worden P, et al. A draft genome of Escherichia coli sequence type 127 strain 2009-46. Gut Pathog. 2014;6:32.
  • Wick RR, Judd LM, Gorrie CL, et al. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017 Jun;13(6):e1005595.
  • Brettin T, Davis JJ, Disz T, et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015 Feb 10;5:8365.
  • Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402.
  • Gertz EM, Yu YK, Agarwala R, et al. Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol. 2006 Dec 7:41.
  • Schaffer AA, Aravind L, Madden TL, et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 2001 Jul 15;29(14):2994–3005.
  • Alikhan NF, Petty NK, Ben Zakour NL, et al. BLAST ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011 Aug 8;12:402.
  • Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011 Apr 1;27(7):1009–1010.
  • Page AJ, Cummins CA, Hunt M, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015 Nov 15;31(22):3691–3693.
  • R Core Team. R: a language and environment for stastical computing. R Foundation for Statistical computing. Vienna: European Environmental Agency; 2019.
  • Treangen TJ, Ondov BD, Koren S, et al. The harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 2014;15(11):524.
  • Forde BM, Ben Zakour NL, Stanton-Cook M, et al. The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. PLoS One. 2014;9(8):e104400.
  • Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014 May 1;30(9):1312–1313.
  • Ronquist F, Teslenko M, van der Mark P, et al. Mrbayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012 May;61(3):539–542.
  • Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016 Jul 8;44(W1):W242–W245.
  • McNally A, Oren Y, Kelly D, et al. Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations. PLoS Genet. 2016 Sep;12(9):e1006280.
  • Rambaut A, Lam TT, Max Carvalho L, et al. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016 Jan;2(1): vew007.
  • Waack S, Keller O, Asper R, et al. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics. 2006 Mar 16;7(142).
  • Holden N, Totsika M, Dixon L, et al. Regulation of P-fimbrial phase variation frequencies in Escherichia coli CFT073. Infect Immun. 2007 Jul;75(7):3325–3334.
  • Harmer CJ, Hall RM. IS26-mediated precise excision of the IS26-aphA1a translocatable unit. MBio. 2015 Dec 8;6(6):e01866–15.
  • Harmer CJ, Moran RA, Hall RM. Movement of IS26-associated antibiotic resistance genes occurs via a translocatable unit that includes a single IS26 and preferentially inserts adjacent to another IS26. MBio. 2014 Oct 7;5(5):e01801–14.
  • Forde BM, Roberts LW, Phan MD, et al. Population dynamics of an Escherichia coli ST131 lineage during recurrent urinary tract infection. Nat Commun. 2019 Aug 13;10(1):3643.
  • Hawkey J, Edwards DJ, Dimovski K, et al. Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm. BMC Genomics. 2013 Nov 19;14:800.
  • Brooks L, Kaze M, Sistrom M. A curated, comprehensive database of plasmid sequences. Microbiol Resour Announc. 2019 Jan;8(1):e01325–18.
  • Yang H, Chen H, Yang Q, et al. High prevalence of plasmid-mediated quinolone resistance genes qnr and aac(6’)-Ib-cr in clinical isolates of Enterobacteriaceae from nine teaching hospitals in China. Antimicrob Agents Chemother. 2008 Dec;52(12):4268–4273.
  • Yang L, Yang L, Lu DH, et al. Co-prevalance of PMQR and 16S rRNA methylase genes in clinical Escherichia coli isolates with high diversity of CTX-M from diseased farmed pigeons. Vet Microbiol. 2015 Aug 5;178(3-4):238–245.
  • Bonnet R. Growing group of extended-spectrum beta-lactamases: the CTX-M enzymes. Antimicrob Agents Chemother. 2004 Jan;48(1):1–14.
  • Bevan ER, Jones AM, Hawkey PM. Global epidemiology of CTX-M beta-lactamases: temporal and geographical shifts in genotype. J Antimicrob Chemother. 2017 Aug 1;72(8):2145–2155.
  • Poirel L, Bonnin RA, Nordmann P. Genetic support and diversity of acquired extended-spectrum beta-lactamases in Gram-negative rods. Infect Genet Evol. 2012 Jul;12(5):883–893.
  • Robicsek A, Strahilevitz J, Sahm DF, et al. qnr prevalence in ceftazidime-resistant Enterobacteriaceae isolates from the United States. Antimicrob Agents Chemother. 2006 Aug;50(8):2872–2874.
  • Verdet C, Benzerara Y, Gautier V, et al. Emergence of DHA-1-producing Klebsiella spp. in the Parisian region: genetic organization of the ampC and ampR genes originating from Morganella morganii. Antimicrob Agents Chemother. 2006 Feb;50(2):607–617.
  • Poirel L, Gniadkowski M, Nordmann P. Biochemical analysis of the ceftazidime-hydrolysing extended-spectrum beta-lactamase CTX-M-15 and of its structurally related beta-lactamase CTX-M-3. J Antimicrob Chemother. 2002 Dec;50(6):1031–1034.