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;213(1):6–13.

Article  CAS  PubMed  Google Scholar 

Rogers BA, Sidjabat HE, Paterson DL. Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain. J Antimicrob Chemother. 2011;66(1):1–14.

Article  CAS  PubMed  Google Scholar 

Sarowska J, Futoma-Koloch B, Jama-Kmiecik A, Frej-Madrzak M, Ksiazczyk M, Bugla-Ploskonska G, Choroszy-Krol I. Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports. Gut pathogens. 2019;11:10.

Article  PubMed  PubMed Central  Google Scholar 

Rouzé A, Jaillette E, Nseir S. Relationship between microaspiration of gastric contents and ventilator-associated pneumonia. Ann Transl Med. 2018;6(21):428.

Article  PubMed  PubMed Central  Google Scholar 

La Combe B, Clermont O, Messika J, Eveillard M, Kouatchet A, Lasocki S, Corvec S, Lakhal K, Billard-Pomares T, Fernandes R, et al. Pneumonia-specific Escherichia coli with Distinct phylogenetic and virulence profiles, France, 2012–2014. Emerg Infect Dis. 2019;25(4):710–8.

Article  PubMed  PubMed Central  Google Scholar 

Okimoto N, Hayashi T, Ishiga M, Nanba F, Kishimoto M, Yagi S, Kurihara T, Asaoka N, Tamada S. Clinical features of Escherichia coli pneumonia. J Infect Chemother. 2010;16(3):216–8.

Article  PubMed  Google Scholar 

Kózka M, Sega A, Wojnar-Gruszka K, Tarnawska A, Gniadek A. Risk factors of pneumonia associated with mechanical ventilation. Int J Environ Res Public Health. 2020;17(2):656.

Article  PubMed  PubMed Central  Google Scholar 

Birgy A, Levy C, Bidet P, Thollot F, Derkx V, Béchet S, Mariani-Kurkdjian P, Cohen R, Bonacorsi S. ESBL-producing Escherichia coli ST131 versus non-ST131: evolution and risk factors of carriage among French children in the community between 2010 and 2015. J Antimicrob Chemother. 2016;71(10):2949–56.

Article  CAS  PubMed  Google Scholar 

Cha MK, Kang CI, Kim SH, Cho SY, Ha YE, Wi YM, Chung DR, Peck KR, Song JH. Comparison of the microbiological characteristics and virulence factors of ST131 and non-ST131 clones among extended-spectrum β-lactamase-producing Escherichia coli causing bacteremia. Diagn Microbiol Infect Dis. 2016;84(2):102–4.

Article  CAS  PubMed  Google Scholar 

Luna-Pineda VM, Ochoa SA, Cruz-Córdova A, Cázares-Domínguez V, Reyes-Grajeda JP, Flores-Oropeza MA, Arellano-Galindo J, Hernández-Castro R, Flores-Encarnación M, Ramírez-Vargas A, et al. Features of urinary Escherichia coli isolated from children with complicated and uncomplicated urinary tract infections in Mexico. PLoS ONE. 2018;13(10):e0204934.

Article  PubMed  PubMed Central  Google Scholar 

Peirano G, Pitout JDD. Extended-Spectrum β-Lactamase-Producing enterobacteriaceae: update on molecular epidemiology and treatment options. Drugs. 2019;79(14):1529–41.

Article  CAS  PubMed  Google Scholar 

CLSI. Performance standards for antimicrobial susceptibility testing. Wayne, PA: Clinical and Laboratory Standards Institute; 2019.

Google Scholar 

Breakpoint tables for interpretation of MICs and zone diameters. Versions 4.0 to 9.0. https://www.eucast.org/clinical_breakpoints/ Accessed 29 Nov 2022

Guidelines for detection of resistance mechanisms and specific resistances of clinical and/or epidemiological importance. Version 2.0. pp. 1–43. http://www.eucast.org/resistance_mechanisms/ Accessed 29 Nov 2022

Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG, Harbarth S, Hindler JF, Kahlmeter G, Olsson-Liljequist B, 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  PubMed  Google Scholar 

Wolfensberger A, Kuster SP, Marchesi M, Zbinden R, Hombach M. The effect of varying multidrug-resistence (MDR) definitions on rates of MDR gram-negative rods. Antimicrob Resist Infect Control. 2019;8(1):193.

Article  PubMed  PubMed Central  Google Scholar 

Le Bouguenec C, Archambaud M, Labigne A. Rapid and specific detection of the pap, afa, and sfa adhesin-encoding operons in uropathogenic Escherichia coli strains by polymerase chain reaction. J Clin Microbiol. 1992;30(5):1189–93.

Article  PubMed  PubMed Central  Google Scholar 

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  PubMed  Google Scholar 

Dallenne C, Da Costa A, Decré D, Favier C, Arlet G. Development of a set of multiplex PCR assays for the detection of genes encoding important beta-lactamases in Enterobacteriaceae. J Antimicrob Chemother. 2010;65(3):490–5.

Article  CAS  PubMed  Google Scholar 

Woodford N, Fagan EJ, Ellington MJ. Multiplex PCR for rapid detection of genes encoding CTX-M extended-spectrum (beta)-lactamases. J Antimicrob Chemother. 2006;57(1):154–5.

Article  CAS  PubMed  Google Scholar 

Cattoir V, Poirel L, Nordmann P. Plasmid-mediated quinolone resistance pump QepA2 in an Escherichia coli isolate from France. Antimicrob Agents Chemother. 2008;52(10):3801–4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cattoir V, Poirel L, Rotimi V, Soussy CJ, Nordmann P. Multiplex PCR for detection of plasmid-mediated quinolone resistance qnr genes in ESBL-producing enterobacterial isolates. J Antimicrob Chemother. 2007;60(2):394–7.

Article  CAS  PubMed  Google Scholar 

Cattoir V, Weill FX, Poirel L, Fabre L, Soussy CJ, Nordmann P. Prevalence of qnr genes in Salmonella in France. J Antimicrob Chemother. 2007;59(4):751–4.

Article  CAS  PubMed  Google Scholar 

Hansen LH, Sørensen SJ, Jørgensen HS, Jensen LB. The prevalence of the OqxAB multidrug efflux pump amongst olaquindox-resistant Escherichia coli in pigs. Microb Drug Resist. 2005;11(4):378–82.

Article  CAS  PubMed  Google Scholar 

Kraychete GB, Botelho LA, Campana EH, Picão RC, Bonelli RR. Updated multiplex PCR for detection of all six plasmid-mediated qnr Gene families. Antimicrob Agents Chemother. 2016;60(12):7524–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ni Q, Tian Y, Zhang L, Jiang C, Dong D, Li Z, Mao E, Peng Y. Prevalence and quinolone resistance of fecal carriage of extended-spectrum β-lactamase-producing Escherichia coli in 6 communities and 2 physical examination center populations in Shanghai. China Diagn Microbiol Infect Dis. 2016;86(4):428–33.

Article  CAS  PubMed  Google Scholar 

Ambrozic Avgustin J, Keber R, Zerjavic K, Orazem T, Grabnar M. Emergence of the quinolone resistance-mediating gene aac(6’)-Ib-cr in extended-spectrum-beta-lactamase-producing Klebsiella isolates collected in Slovenia between 2000 and 2005. Antimicrob Agents Chemother. 2007;51(11):4171–3.

Article  PubMed  PubMed Central  Google Scholar 

Clermont O, Bonacorsi S, Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol. 2000;66(10):4555–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doumith M, Day M, Ciesielczuk H, Hope R, Underwood A, Reynolds R, Wain J, Livermore DM, Woodford N. Rapid identification of major Escherichia coli sequence types causing urinary tract and bloodstream infections. J Clin Microbiol. 2015;53(1):160–6.

Article  CAS  PubMed  Google Scholar 

Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, Karch H, Reeves PR, Maiden MC, Ochman H, et al. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol. 2006;60(5):1136–51.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Clermont O, Dhanji H, Upton M, Gibreel T, Fox A, Boyd D, Mulvey MR, Nordmann P, Ruppé E, Sarthou JL, et al. Rapid detection of the O25b-ST131 clone of Escherichia coli encompassing the CTX-M-15-producing strains. J Antimicrob Chemother. 2009;64(2):274–7.

Article  CAS  PubMed  Google Scholar 

Johnson JR, Russo TA, Tarr PI, Carlino U, Bilge SS, Vary JC Jr, Stell AL. Molecular epidemiological and phylogenetic associations of two novel putative virulence genes, iha and iroN (E. coli), among Escherichia coli isolates from patients with urosepsis. Infect Immun. 2000;68(5):304–7.

Article  Google Scholar 

Johnson JR, Stapleton AE, Russo TA, Scheutz F, Brown JJ, Maslow JN. Characteristics and prevalence within serogroup O4 of a J96-like clonal group of uropathogenic Escherichia coli O4:H5 containing the class I and class III alleles of papG. Infect Immun. 1997;65(6):2153–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Johnson JR, Stell AL. Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise. J Infect Dis. 2000;181(1):261–72.

Article  CAS  PubMed  Google Scholar 

Johnson TJ, Wannemuehler Y, Doetkott C, Johnson SJ, Rosenberger SC, Nolan LK. Identification of minimal predictors of avian pathogenic Escherichia coli virulence for use as a rapid diagnostic tool. J Clin Microbiol. 2008;46(12):3987–96.

Article  CAS  PubMed  PubMed Central  Google Scho