Vihta KD, Stoesser N, Llewelyn MJ, Quan TP, Davies T, Fawcett NJ, et al. Trends over time in Escherichia coli bloodstream infections, urinary tract infections, and antibiotic susceptibilities in Oxfordshire, UK, 1998–2016: a study of electronic health records. Lancet Infect Dis. 2018;18(10):1138–49.
Article
Google Scholar
Flores-Mireles AL, Walker JN, Caparon M, Hultgren SJ. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol. 2015;13(5):269–84.
Article
CAS
Google Scholar
Critchley IA, Cotroneo N, Pucci MJ, Mendes R. The burden of antimicrobial resistance among urinary tract isolates of Escherichia coli in the United States in 2017. PLoS One. 2019;14(12):e0220265.
Article
CAS
Google Scholar
Zhen X, Lundborg CS, Sun X, Hu X, Dong H. Economic burden of antibiotic resistance in ESKAPE organisms: a systematic review. Antimicrob Resist Infect Control. 2019;8:137.
Article
Google Scholar
Naylor NR, Pouwels KB, Hope R, Green N, Henderson KL, Knight GM, et al. The health and cost burden of antibiotic resistant and susceptible Escherichia coli bacteraemia in the English hospital setting: a national retrospective cohort study. PLoS One. 2019;14(9):e0221944.
Article
CAS
Google Scholar
Sader HS, Castanheira M, Flamm RK, Jones RN. Antimicrobial activities of ceftazidime-avibactam and comparator agents against Gram-negative organisms isolated from patients with urinary tract infections in U.S. medical centers, 2012 to 2014. Antimicrob Agents Chemother. 2016;60(7):4355–60.
Article
CAS
Google Scholar
Karlowsky JA, Kelly LJ, Thornsberry C, Jones ME, Sahm DF. Trends in antimicrobial resistance among urinary tract infection isolates of Escherichia coli from female outpatients in the United States. Antimicrob Agents Chemother. 2002;46(8):2540–5.
Article
CAS
Google Scholar
Sawatwong P, Sapchookul P, Whistler T, Gregory CJ, Sangwichian O, Makprasert S, et al. High burden of extended-spectrum β-lactamase–producing Escherichia coli and Klebsiella pneumoniae bacteremia in older adults: a seven-year study in two rural Thai provinces. Am J Trop Med Hyg. 2019;100(4):943–51.
Article
CAS
Google Scholar
Ludden C, Coll F, Gouliouris T, Restif O, Blane B, Blackwell GA, et al. Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study. Lancet. Microbe. 2021;0(0). 2021;2(9):e472-80.
Raphael E, Glymour MM, Chambers HF. Trends in prevalence of extended-spectrum beta-lactamase-producing Escherichia coli isolated from patients with community- and healthcare-associated bacteriuria: results from 2014 to 2020 in an urban safety-net healthcare system. Antimicrob Resist Infect Control. 2021;10(1):118.
Centers for Disease Control and Prevention (U.S.). Antibiotic resistance threats in the United States, 2019 [Internet]. Centers for Disease Control and Prevention (U.S.); 2019. Available from: https://stacks.cdc.gov/view/cdc/82532. [Cited 2021 May 24].
Denamur E, Clermont O, Bonacorsi S, Gordon D. The population genetics of pathogenic Escherichia coli. Nat Rev Microbiol. 2021;19(1):37-45.
Biggel M, Xavier BB, Johnson JR, Nielsen KL, Frimodt-Møller N, Matheeussen V, et al. Horizontally acquired papGII-containing pathogenicity islands underlie the emergence of invasive uropathogenic Escherichia coli lineages. Nat Commun. 2020;11(1):5968.
Article
CAS
Google Scholar
Kaper JB, Nataro JP, Mobley HLT. Pathogenic Escherichia coli. Nat Rev Microbiol. 2004;2(2):123–40.
Article
CAS
Google Scholar
Pitout JDD, DeVinney R. Escherichia coli ST131: a multidrug-resistant clone primed for global domination. F1000Research. 2017;6:F1000 Faculty Rev-195.
Article
Google Scholar
Price LB, Johnson JR, Aziz M, Clabots C, Johnston B, Tchesnokova V, et al. The epidemic of extended-spectrum-β-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx. mBio. 2013;4(6): e00377-13.
Johnson JR, Tchesnokova V, Johnston B, Clabots C, Roberts PL, Billig M, et al. Abrupt emergence of a single dominant multidrug-resistant strain of Escherichia coli. J Infect Dis. 2013;207(6):919–28.
Article
CAS
Google Scholar
Fibke CD, Croxen MA, Geum HM, Glass M, Wong E, Avery BP, et al. Genomic epidemiology of major extraintestinal pathogenic Escherichia coli lineages causing urinary tract infections in young women across Canada. Open Forum. Infect Dis Ther. 2019;6(11):ofz431.
Google Scholar
Yamaji R, Rubin J, Thys E, Friedman CR, Riley LW. Persistent pandemic lineages of uropathogenic Escherichia coli in a college community from 1999 to 2017. Diekema DJ, editor. J Clin Microbiol. 2018;56(4):e01834–17.
Article
CAS
Google Scholar
Kallonen T, Brodrick HJ, Harris SR, Corander J, Brown NM, Martin V, et al. Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131. Genome Res. 2017;27(8):1437–49.
Article
CAS
Google Scholar
Duval A, Obadia T, Boëlle PY, Fleury E, Herrmann JL, Guillemot D, et al. Close proximity interactions support transmission of ESBL-K. pneumoniae but not ESBL-E. coli in healthcare settings. PLoS Comput Biol. 2019;15(5):e1006496.
Article
CAS
Google Scholar
CLSI. Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically. 11th ed. CLSI standard M07. Wayne, PA: Clinical and Laboratory Standards Institute; 2018.
Galac MR, Snesrud E, Lebreton F, Stam J, Julius M, Ong AC, et al. A diverse panel of clinical Acinetobacter baumannii for research and development. Antimicrob Agents Chemother. 2020;64(10):e00840–20 /aac/64/10/AAC.00840-20.atom.
Article
CAS
Google Scholar
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–9.
Article
CAS
Google Scholar
Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019;20(1):257.
Article
CAS
Google Scholar
Waters NR, Abram F, Brennan F, Holmes A, Pritchard L. Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool. Access Microbiol. 2020;2(9):acmi000143.
Clermont O, Christenson JK, Denamur E, Gordon DM. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep. 2013;5(1):58–65.
Article
CAS
Google Scholar
Seeman T. mlst - scan contig files against traditional PubMLST typing schemes. Available from: https://github.com/tseemann/mlst. [Accessed 2020 Jan 4].
Jolley KA, Bray J, Maiden MC. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;(3):124 https://pubmlst.org/. Accessed 4 January 2020.
Zhou Z, Alikhan NF, Mohamed K, Fan Y, the Agama Study Group, Achtman M. The EnteroBase user’s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res. 2020;30(1):138–52.
Article
CAS
Google Scholar
Quijada NM, Rodríguez-Lázaro D, Eiros JM, Hernández M. TORMES: an automated pipeline for whole bacterial genome analysis. Bioinformatics. 2019;35(21):4207–12.
Article
CAS
Google Scholar
Joensen KG, Tetzschner AMM, Iguchi A, Aarestrup FM, Scheutz F. Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data. J Clin Microbiol. 2015;53(8):2410–26.
Article
CAS
Google Scholar
Roer L, Tchesnokova V, Allesøe R, Muradova M, Chattopadhyay S, Ahrenfeldt J, et al. Development of a web tool for Escherichia coli subtyping based on fimH alleles. J Clin Microbiol. 2017;55(8):2538–43.
Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, et al. Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob Agents Chemother. 2019;63(11):e00483–19.
Article
CAS
Google Scholar
Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb. Genomics. 2017;3(10):e000131.
Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(7):3895–903.
Article
Google Scholar
Chen L, Zheng D, Liu B, Yang J, Jin Q. VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on. Nucleic Acids Res. 2016;44(D1):D694–7.
Article
CAS
Google Scholar
Biggel, M. EcVGDB. Zenodo [Internet]. 2020; Available from: https://doi.org/10.5281/zenodo.4079473.
Seemann T. ABRicate - mass screening of contigs for antimicrobial resistance or virulence genes. Available from: https://github.com/tseemann/abricate. [Accessed 2022 Feb 23].
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31(22):3691–3.
Article
CAS
Google Scholar
Seeman T. snippy - rapid haploid variant calling and core genome alignment. Available from: https://github.com/tseemann/abricate. [Accessed 2019 Sep 25].
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9(11):e112963.
Article
Google Scholar
Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 2015;43(3):e15.
Article
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3.
Article
CAS
Google Scholar
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W256–9.
Article
CAS
Google Scholar
Stoesser N, Sheppard AE, Pankhurst L, De Maio N, Moore CE, Sebra R, et al. Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131. mBio. 2016;7(2):e02162.
Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, et al. Updating benchtop sequencing performance comparison. Nat Biotechnol. 2013;31(4):294–6.
Article
Google Scholar
Muloi DM, Wee BA, McClean DMH, Ward MJ, Pankhurst L, Phan H, et al. Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape. Nat Microbiol. 2022;7(4):581–9.
Article
CAS
Google Scholar
Johnson JR, Johnston BD, Porter SB, Clabots C, Bender TL, Thuras P, et al. Rapid emergence, subsidence, and molecular detection of Escherichia coli sequence type 1193-fimH64, a new disseminated multidrug-resistant commensal and extraintestinal pathogen. J Clin Microbiol. 2019;57(5):e01664–18.
Article
CAS
Google Scholar
Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG, 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;18(3):268–81.
Article
CAS
Google Scholar
Mshana SE, Falgenhauer L, Mirambo MM, Mushi MF, Moremi N, Julius R, et al. Predictors of blaCTX-M-15 in varieties of Escherichia coli genotypes from humans in community settings in Mwanza, Tanzania. BMC Infect Dis. 2016;16(1):187.
Article
Google Scholar
Day MJ, Hopkins KL, Wareham DW, Toleman MA, Elviss N, Randall L, et al. Extended-spectrum β-lactamase-producing Escherichia coli in human-derived and foodchain-derived samples from England, Wales, and Scotland: an epidemiological surveillance and typing study. Lancet Infect Dis. 2019;19(12):1325–35.
Article
CAS
Google Scholar
Guenther S, Semmler T, Stubbe A, Stubbe M, Wieler LH, Schaufler K. Chromosomally encoded ESBL genes in Escherichia coli of ST38 from Mongolian wild birds. J Antimicrob Chemother. 2017;72(5):1310–3.
Article
CAS
Google Scholar
Kondratyeva K, Salmon-Divon M, Navon-Venezia S. Meta-analysis of pandemic Escherichia coli ST131 plasmidome proves restricted plasmid-clade associations. Sci Rep. 2020;10(1):36.
Article
CAS
Google Scholar
Xia L, Liu Y, Xia S, Kudinha T, Xiao SN, Zhong NS, et al. Prevalence of ST1193 clone and IncI1/ST16 plasmid in E-coli isolates carrying blaCTX-M-55 gene from urinary tract infections patients in China. Sci Rep. 2017;7(1):44866.
Article
CAS
Google Scholar
Ruiz J. Mechanisms of resistance to quinolones: target alterations, decreased accumulation and DNA gyrase protection. J Antimicrob Chemother. 2003;51(5):1109–17.
Article
CAS
Google Scholar
Sarowska J, Futoma-Koloch B, Jama-Kmiecik A, Frej-Madrzak M, Ksiazczyk M, Bugla-Ploskonska G, et al. Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports. Gut Pathog. 2019;11(1):10.
Article
Google Scholar
Ben Zakour NL, Alsheikh-Hussain AS, Ashcroft MM, Khanh Nhu NT, Roberts LW, Stanton-Cook M, et al. Sequential acquisition of virulence and fluoroquinolone resistance has shaped the evolution of Escherichia coli ST131. mBio. 2016;7(2):e00347–16.
Article
CAS
Google Scholar
Jahandeh N, Ranjbar R, Behzadi P, Behzadi E. Uropathogenic Escherichia coli virulence genes: invaluable approaches for designing DNA microarray probes. Cent Eur. J Urol. 2015;68(4):452-458.
Brodrick HJ, Raven KE, Kallonen T, Jamrozy D, Blane B, Brown NM, et al. Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom. Genome Med. 2017;9(1):70.
Article
Google Scholar
Lipworth S, Vihta KD, Chau KK, Kavanagh J, Davies T, George S, et al. Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections. Clin Infect Dis. 2021;73(12):2276–82.
Article
CAS
Google Scholar
Gladstone RA, McNally A, Pöntinen AK, Tonkin-Hill G, Lees JA, Skytén K, et al. Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study. Lancet Microbe. 2021;2(7):e331–41.
Article
CAS
Google Scholar
Mahazu S, Sato W, Ayibieke A, Prah I, Hayashi T, Suzuki T, et al. Insights and genetic features of extended-spectrum beta-lactamase producing Escherichia coli isolates from two hospitals in Ghana. Sci Rep. 2022;12(1):1843.
Article
CAS
Google Scholar
Kallen AJ, Welch HG, Sirovich BE. Current antibiotic therapy for isolated urinary tract infections in women. Arch Intern Med. 2006;166(6):635.
Article
Google Scholar
Johnson TJ, Elnekave E, Miller EA, Munoz-Aguayo J, Flores Figueroa C, Johnston B, et al. Phylogenomic analysis of extraintestinal pathogenic Escherichia coli sequence type 1193, an emerging multidrug-resistant clonal group. Antimicrob Agents Chemother. 2019;63(1):e01913–8.
Article
CAS
Google Scholar
Valenza G, Werner M, Eisenberger D, Nickel S, Lehner-Reindl V, Höller C, et al. First report of the new emerging global clone ST1193 among clinical isolates of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli from Germany. J Glob Antimicrob Resist. 2019;17:305–8.
Article
Google Scholar
Tchesnokova VL, Rechkina E, Larson L, Ferrier K, Weaver JL, Schroeder DW, et al. Rapid and extensive expansion in the United States of a new multidrug-resistant Escherichia coli clonal group, sequence type 1193. Clin Infect Dis. 2019;68(2):334–7.
Article
CAS
Google Scholar
Wu J, Lan F, Lu Y, He Q, Li B. Molecular characteristics of ST1193 clone among phylogenetic group B2 non-ST131 fluoroquinolone-resistant Escherichia coli. Front Microbiol. 2017;8:2294.
Article
Google Scholar
Nguyen Q, Nguyen TTN, Pham P, Chau V, Nguyen LPH, Nguyen TD, et al. Genomic insights into the circulation of pandemic fluoroquinolone-resistant extra-intestinal pathogenic Escherichia coli ST1193 in Vietnam. Microb. Genomics. 2021;7(12):000733.
Tchesnokova V, Radey M, Chattopadhyay S, Larson L, Weaver JL, Kisiela D, et al. Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci. Proc Natl Acad Sci. 2019;116(29):14740–8.
Article
CAS
Google Scholar
Kaye KS, Gupta V, Mulgirigama A, Joshi AV, Scangarella-Oman NE, Yu K, et al. Antimicrobial resistance trends in urine Escherichia coli isolates from adult and adolescent females in the United States from 2011 to 2019: rising ESBL strains and impact on patient management. Clin Infect Dis. 2021;73(11):1992–9.
Article
CAS
Google Scholar
Kourtis AP, Sheriff EA, Weiner-Lastinger LM, Elmore K, Preston LE, Dudeck M, et al. Antibiotic multidrug resistance of Escherichia coli causing device- and procedure-related infections in the United States reported to the National Healthcare Safety Network, 2013–2017. Clin Infect Dis. 2021;73(11):e4552-59.
Murray CJ, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 2022;399(10325):629–55.
Article
CAS
Google Scholar
Roberts LW, Hoi LT, Khokhar FA, Hoa NT, Giang TV, Bui C, et al. Genomic characterisation of multidrug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two intensive care units in Hanoi, Viet Nam: a prospective observational cohort study. Lancet Microbe. 2022;3(11):e857-e866.
Bevan ER, Jones AM, Hawkey PM. Global epidemiology of CTX-M β-lactamases: temporal and geographical shifts in genotype. J Antimicrob Chemother. 2017;72(8):2145–55.
Article
CAS
Google Scholar
Birgy A, Bidet P, Levy C, Sobral E, Cohen R, Bonacorsi S. CTX-M-27-producing Escherichia coli of sequence type 131 and clade C1-M27, France. Emerg. Infect Dis. 2017; 23(5):885.
Matsumura Y, Pitout JDD, Gomi R, Matsuda T, Noguchi T, Yamamoto M, et al. Global Escherichia coli sequence type 131 clade with blaCTX-M-27 gene. Emerg Infect Dis. 2016;22(11):1900–7.
Article
CAS
Google Scholar
Ghosh H, Doijad S, Falgenhauer L, Fritzenwanker M, Imirzalioglu C, Chakraborty T. blaCTX-M-27 –encoding Escherichia coli sequence type 131 lineage C1-M27 clone in clinical isolates. Germany Emerg Infect Dis. 2017;23(10):1754–6.
Article
CAS
Google Scholar
Mills EG, Martin MJ, et al. A one-year genomic investigation of Escherichia coli epidemiology and nosocomial spread at a large U.S. healthcare network. Natl Cent Biotechnol Inf. 2022; Available from: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA809394.