{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T06:31:04Z","timestamp":1786516264040,"version":"build-2736575974"},"reference-count":90,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Recurrent urinary tract infections (UTIs) are frequently associated with persistent uropathogenic\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    (UPEC) lineages that combine antimicrobial resistance with virulence traits, contributing to treatment failure. Whole-genome sequencing was performed on 199 UPEC isolates recovered from patients with recurrent or difficult-to-treat UTIs for whom autovaccine therapy was recommended. Assemblies were analysed using AMRFinderPlus, VFDB, MOB-suite, mobile genetic element detection, serotyping, and clonotype assignment tools, MLST, cgMLST and SNP-based phylogenetic analyses. Recurrent urinary tract infections (UTIs) were associated with multiple pandemic UPEC lineages, including ST131, ST69, ST10 and the emerging ST1193. Genomic analyses identified acquired antimicrobial resistance genes in nearly 80% of isolates, including extended-spectrum\n                    <jats:italic>\u03b2<\/jats:italic>\n                    -lactamase (ESBL) genes such as\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>CTX-M-15<\/jats:sub>\n                    and\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>CTX-M-27<\/jats:sub>\n                    , alongside chromosomal resistance-associated mutations linked to fluoroquinolone resistance. All ST131 and ST1193 isolates fulfilled the molecular UPEC criteria, while all but one isolate was classified as extraintestinal pathogenic\n                    <jats:italic>E. coli<\/jats:italic>\n                    (ExPEC). MOB-suite plasmid prediction analysis showed that IncF replicons were the most common and frequently associated with ESBL genes. Almost half of the plasmids were predicted to be mobilizable or conjugative, and one third indicated multireplicon structures. Phylogenetic analyses identified the predominant ST131 O25: H4\/CH40-30 and O16: H5\/CH40-41 lineages, while most ST1193 isolates belonged to the O75: H5\/CH14-64 lineage. Mobile genetic element profiling identified lineage-associated insertion sequence repertoires, class 1 integrons and distinct\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>CTX-M<\/jats:sub>\n                    -associated genetic environments. The results indicate that recurrent UTIs in Romania are largely driven by globally disseminated ExPEC clones that combine ESBL production, fluoroquinolone resistance-associated mutations and virulence-associated traits. The detection of closely related isolates recovered in different collection years is consistent with the circulation of successful UPEC lineages within the studied population.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1891649","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T05:56:38Z","timestamp":1786514198000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Whole-genome characterisation of high-risk ST131 and the emerging ST1193 UPEC lineages in Romanian patients with recurrent urinary tract infections"],"prefix":"10.3389","volume":"17","author":[{"given":"Laura-Ioana","family":"Popa","sequence":"first","affiliation":[{"name":"Genomics, Transcriptomics, and Bioinformatics Platform, Cantacuzino National Military Medical Institute for Research and Development","place":["Bucharest, Romania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sorin","family":"Dinu","sequence":"additional","affiliation":[{"name":"Molecular Epidemiology for Communicable Diseases Laboratory, Cantacuzino National Military Medical Institute for Research and Development","place":["Bucharest, Romania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Cristea","sequence":"additional","affiliation":[{"name":"Enteric Bacterial Infections Laboratory - Cantacuzino National Military Medical Institute for Research and Development","place":["Bucharest, Romania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreea","family":"Ghi\u021b\u0103","sequence":"additional","affiliation":[{"name":"Enteric Bacterial Infections Laboratory - Cantacuzino National Military Medical Institute for Research and Development","place":["Bucharest, Romania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriel","family":"Ionescu","sequence":"additional","affiliation":[{"name":"Medical Laboratory - Cantacuzino National Military Medical Institute for Research and Development","place":["Bucharest, Romania"]},{"name":"Department II, \u201cCantacuzino\u201d Microbiology Discipline, Carol Davila University of Medicine and Pharmacy Bucharest","place":["Bucharest, Romania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mihaela","family":"Oprea","sequence":"additional","affiliation":[{"name":"Molecular Epidemiology for Communicable Diseases Laboratory, Cantacuzino National Military Medical Institute for Research and Development","place":["Bucharest, Romania"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,12]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1097\/JU.0000000000000296","article-title":"Recurrent uncomplicated urinary tract infections in women: AUA\/CUA\/SUFU guideline","volume":"202","author":"Anger","year":"2019","journal-title":"J. Urol."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1093\/jac\/dkw574","article-title":"Role of uhpT, glpT, cyaA, and ptsI genes in fosfomycin resistance in Escherichia coli","volume":"72","author":"Ballestero-T\u00e9llez","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1002\/emmm.201303133","article-title":"Heteropathogenic virulence and phylogeny reveal phased pathogenic metamorphosis in Escherichia coli O2:H6","volume":"6","author":"Bielaszewska","year":"2014","journal-title":"EMBO Mol. Med."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"e00607-21","DOI":"10.1128\/MRA.00607-21","article-title":"Complete genome sequence of Escherichia coli sequence type 1193 isolate AVS0096 recovered from river water in Switzerland","volume":"10","author":"Biggel","year":"2021","journal-title":"Microbiol. Resour. Announc."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1038\/s42003-022-03660-x","article-title":"Convergence of virulence and antimicrobial resistance in increasingly prevalent Escherichia coli ST131 papGII+ sublineages","volume":"5","author":"Biggel","year":"2022","journal-title":"Commun. Biol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"885","DOI":"10.3201\/eid2305.161865","article-title":"CTX-M-27-producing Escherichia coli of sequence type 131 and clade C1-M27, France","volume":"23","author":"Birgy","year":"2017","journal-title":"Emerg. Infect. Dis."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1626422","DOI":"10.3389\/fimmu.2025.1626422","article-title":"Autovaccine immunoprophylaxis in patients with neurogenic bladder experiencing recurrent urinary tract infections","volume":"16","author":"Bonillo-Garc\u00eda","year":"2025","journal-title":"Front. Immunol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"e00532","DOI":"10.1128\/spectrum.00532-24","article-title":"PmrB Y358N, E123D amino acid substitutions are not associated with colistin resistance but with phylogeny in Escherichia coli","volume":"12","author":"Butters","year":"2024","journal-title":"Microbiol. Spectrum"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: hierarchical and refined dataset for big data analysis\u201410 years on","volume":"44","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"848","DOI":"10.3390\/microorganisms8060848","article-title":"A clinical perspective on the antimicrobial resistance spectrum of uropathogens in a Romanian male population","volume":"8","author":"Chibelean","year":"2020","journal-title":"Microorganisms"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1111\/1758-2229.12019","article-title":"The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups","volume":"5","author":"Clermont","year":"2013","journal-title":"Environ. Microbiol. Rep."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"5712371","DOI":"10.1155\/2019\/5712371","article-title":"Snapshot of phylogenetic groups, virulence, and resistance markers in Escherichia coli uropathogenic strains isolated from outpatients with urinary tract infections in Bucharest, Romania","volume":"2019","author":"Cristea","year":"2019","journal-title":"Biomed. Res. Int."},{"key":"ref13","first-page":"73","article-title":"Mechanisms of resistance to ciprofloxacin and genetic diversity of Escherichia coli strains originating from urine cultures performed for Romanian adults","volume":"74","author":"Cristea","year":"2015","journal-title":"Roum. Arch. Microbiol. Immunol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1016\/j.jgar.2020.10.020","article-title":"Resistance among urinary tract pathogens collected in Europe during 2018","volume":"23","author":"Critchley","year":"2020","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref9001","doi-asserted-by":"publisher","first-page":"4539","DOI":"10.1093\/nar\/gkw319","article-title":"Identification and analysis of integrons and cassette arrays in bacterial genomes","volume":"44","author":"Cury","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"4368","DOI":"10.1016\/j.jmb.2019.04.008","article-title":"Direct detection of tissue-resident bacteria and chronic inflammation in the bladder wall of postmenopausal women with recurrent urinary tract infection","volume":"431","author":"De Nisco","year":"2019","journal-title":"J. Mol. Biol."},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1099\/acmi.0.000179","article-title":"Plasmids shape the diverse accessory resistomes of Escherichia coli ST131","volume":"3","author":"Decano","year":"2020","journal-title":"Access Microbiol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1128\/CMR.00068-15","article-title":"Fosfomycin","volume":"29","author":"Falagas","year":"2016","journal-title":"Clin. Microbiol. Rev."},{"key":"ref18","year":"2018"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"e00483","DOI":"10.1128\/AAC.00483-19","article-title":"Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates","volume":"63","author":"Feldgarden","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"125","DOI":"10.3389\/fcimb.2020.00125","article-title":"High prevalence of ST131 subclades C2-H30Rx and C1-M27 among extended-spectrum \u03b2-lactamase-producing Escherichia coli causing human extraintestinal infections in patients from two hospitals of Spain and France during 2015","volume":"10","author":"Flament-Simon","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1038\/nrmicro3432","article-title":"Urinary tract infections: epidemiology, mechanisms of infection and treatment options","volume":"13","author":"Flores-Mireles","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"e104400","DOI":"10.1371\/journal.pone.0104400","article-title":"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","volume":"9","author":"Forde","year":"2014","journal-title":"PLoS One"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"3643","DOI":"10.1038\/s41467-019-11571-5","article-title":"Population dynamics of an Escherichia coli ST131 lineage during recurrent urinary tract infection","volume":"10","author":"Forde","year":"2019","journal-title":"Nat. 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Commun."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"151533","DOI":"10.1016\/j.ijmm.2021.151533","article-title":"Comparative phenotypic characterization of hybrid Shiga toxin-producing\/uropathogenic Escherichia coli, canonical uropathogenic and Shiga toxin-producing Escherichia coli","volume":"311","author":"Gati","year":"2021","journal-title":"Int. J. Med. Microbiol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1707","DOI":"10.1093\/jac\/dkaf130","article-title":"A comparative study of the molecular characteristics of human uropathogenic Escherichia coli collected from two hospitals in Norway and France in 2019","volume":"80","author":"Handal","year":"2025","journal-title":"J. Antimicrob. Chemother."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"1329","DOI":"10.2147\/IDR.S355010","article-title":"Genomic and phenotypic characterization of a colistin-resistant Escherichia coli isolate co-harboring blaNDM-5, blaOXA-1, and blaCTX-M-55 isolated from urine","volume":"15","author":"Hao","year":"2022","journal-title":"Infect. Drug Resist."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"4702","DOI":"10.1038\/s41598-025-89240-5","article-title":"Epidemiological trends and predictions of urinary tract infections in the global burden of disease study 2021","volume":"15","author":"He","year":"2025","journal-title":"Sci. Rep."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"2252","DOI":"10.4102\/ajlm.v13i1.2252","article-title":"Fosfomycin susceptibility testing and resistance mechanisms in Enterobacterales in South Africa","volume":"13","author":"Hurwitz","year":"2024","journal-title":"Afr. J. Lab. Med"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1186\/s12879-025-10524-2","article-title":"Evaluating the use of Uromune\u00ae autovaccine in recurrent urinary tract infections: a pilot unicenter retrospective study in Reus","volume":"25","author":"Iftimie","year":"2025","journal-title":"Spain. BMC Infect. Dis."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"2410","DOI":"10.1128\/JCM.00008-15","article-title":"Rapid and easy in silico serotyping of Escherichia coli using whole genome sequencing (WGS) data","volume":"53","author":"Joensen","year":"2015","journal-title":"J.Clin.Microbiol."},{"key":"ref9002","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1093\/jac\/dkaa390","article-title":"Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder","volume":"76","author":"Johansson","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1186\/s12866-015-0574-6","article-title":"Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India","volume":"15","author":"Johnning","year":"2015","journal-title":"BMC Microbiol."},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00121-16","article-title":"Separate F-type plasmids have shaped the evolution of the H30 subclone of Escherichia coli sequence type 131","volume":"1","author":"Johnson","year":"2016","journal-title":"mSphere"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"2161","DOI":"10.1128\/AAC.47.7.2161-2168.2003","article-title":"Isolation and molecular characterization of nalidixic acid-resistant extraintestinal pathogenic Escherichia coli from retail chicken products","volume":"47","author":"Johnson","year":"2003","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1038\/nbt.2522","article-title":"Updating benchtop sequencing performance comparison","volume":"31","author":"J\u00fcnemann","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"2077","DOI":"10.3390\/life12122077","article-title":"Emergence and dissemination of extraintestinal pathogenic high-risk international clones of Escherichia coli","volume":"12","author":"Kocsis","year":"2022","journal-title":"Life"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"2400727","DOI":"10.2807\/1560-7917.ES.2024.29.47.2400727","article-title":"Emergence of Escherichia coli ST131 carrying carbapenemase genes, European Union\/European economic area, august 2012 to may 2024","volume":"29","author":"Kohlenberg","year":"2024","journal-title":"Euro Surveill."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1038\/s41598-019-56763-7","article-title":"Meta-analysis of pandemic Escherichia coli ST131 plasmidome proves restricted plasmid-clade associations","volume":"10","author":"Kondratyeva","year":"2020","journal-title":"Sci. Rep."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"403","DOI":"10.33073\/pjm-2019-048","article-title":"Antibiotic resistance among uropathogenic Escherichia coli","volume":"68","author":"Kot","year":"2019","journal-title":"Pol. J. Microbiol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/j.eururo.2024.03.035","article-title":"European association of urology guidelines on urological infections: summary of the 2024 guidelines","volume":"86","author":"Kranz","year":"2024","journal-title":"Eur. Urol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"7656752","DOI":"10.1155\/2018\/7656752","article-title":"Community-acquired urinary tract infection by Escherichia coli in the era of antibiotic resistance","volume":"2018","author":"Lee","year":"2018","journal-title":"Biomed. Res. Int."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref9003","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.3389\/fmicb.2019.01530","article-title":"Sequence types, clonotypes, serotypes, and virotypes of extended-spectrum \u03b2-lactamase-producing Escherichia coli causing bacteraemia in a Spanish hospital over a 12-year period (2000 to 2011)","volume":"10","author":"Mamani","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1854","DOI":"10.3390\/microorganisms13081854","article-title":"Genomic epidemiology of ESBL- and carbapenemase-producing Enterobacterales in a Spanish hospital: exploring the clinical-environmental interface","volume":"13","author":"Mart\u00ednez-\u00c1lvarez","year":"2025","journal-title":"Microorganisms"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1900","DOI":"10.3201\/eid2211.160519","article-title":"Global Escherichia coli sequence type 131 clade with blaCTX-M-27 gene","volume":"22","author":"Matsumura","year":"2016","journal-title":"Emerg. Infect. Dis."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e00179","DOI":"10.1128\/AAC.00179-17","article-title":"Rapid identification of different Escherichia coli sequence type 131 clades","volume":"61","author":"Matsumura","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref47","first-page":"4900","article-title":"Genetic analysis of virulence and pathogenicity features of uropathogenic Escherichia coli isolated from patients with neurogenic bladder","volume":"14","author":"Mladin","year":"2009","journal-title":"Rom. Biotechnol. Lett."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1186\/1471-2180-13-147","article-title":"Molecular epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli in Tunisia and characterization of their virulence factors and plasmid addiction systems","volume":"13","author":"Mnif","year":"2013","journal-title":"BMC Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"e0240978","DOI":"10.1371\/journal.pone.0240978","article-title":"Class 1 integron-borne cassettes harboring blaCARB-2 gene in multidrug-resistant and virulent Salmonella Typhimurium ST19 strains recovered from clinical human stool samples, United States","volume":"15","author":"Monte","year":"2020","journal-title":"PLoS One"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"000733","DOI":"10.1099\/mgen.0.000733","article-title":"Genomic insights into the circulation of pandemic fluoroquinolone-resistant extra-intestinal pathogenic Escherichia coli ST1193 in Vietnam","volume":"7","author":"Nguyen","year":"2021","journal-title":"Microb. Genom."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1128\/CMR.00125-13","article-title":"Escherichia coli ST131, an intriguing clonal group","volume":"27","author":"Nicolas-Chanoine","year":"2014","journal-title":"Clin. Microbiol. Rev."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1093\/jac\/dkm464","article-title":"Intercontinental emergence of Escherichia coli clone O25:H4-ST131 producing CTX-M-15","volume":"61","author":"Nicolas-Chanoine","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref53","volume-title":"Country Health Profile 2025: Romania","year":"2025"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"331","DOI":"10.2478\/rrlm-2020-0023","article-title":"Characterization of antibiotic resistance integrons harbored by Romanian Escherichia coli uropathogenic strains","volume":"28","author":"Oprea","year":"2020","journal-title":"Rev. Rom. Med. Lab."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"855","DOI":"10.3390\/antibiotics14090855","article-title":"Escherichia coli urinary tract infections from a Romanian pediatric hospital: antimicrobial resistance trends, ESBL prevalence, and empirical treatment implications","volume":"14","author":"P\u0103curar","year":"2025","journal-title":"Antibiotics"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"1613","DOI":"10.3390\/microorganisms9081613","article-title":"Recovering Escherichia coli plasmids in the absence of long-read sequencing data","volume":"9","author":"Paganini","year":"2021","journal-title":"Microorganisms"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"e00088","DOI":"10.1128\/cmr.00088-17","article-title":"Mobile genetic elements associated with antimicrobial resistance","volume":"31","author":"Partridge","year":"2018","journal-title":"Clin. Microbiol. Rev."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"e0122369","DOI":"10.1371\/journal.pone.0122369","article-title":"Molecular characterization of a multidrug resistance IncF plasmid from the globally disseminated Escherichia coli ST131 clone","volume":"10","author":"Phan","year":"2015","journal-title":"PLoS One"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"9","DOI":"10.3389\/fmicb.2012.00009","article-title":"Extraintestinal pathogenic Escherichia coli: a combination of virulence with antibiotic resistance","volume":"3","author":"Pitout","year":"2012","journal-title":"Front. Microbiol."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"195","DOI":"10.12688\/f1000research.10609.1","article-title":"Escherichia coli ST131: a multidrug-resistant clone primed for global domination","volume":"6","author":"Pitout","year":"2017","journal-title":"F1000Res."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"104265","DOI":"10.1016\/j.meegid.2020.104265","article-title":"The evolutionary puzzle of Escherichia coli ST131","volume":"81","author":"Pitout","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"e0051122","DOI":"10.1128\/aac.00511-22","article-title":"Escherichia coli ST1193: following in the footsteps of E. coli ST131","volume":"66","author":"Pitout","year":"2022","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1128\/AAC.49.1.447-450.2005","article-title":"ISEcp1B-mediated transposition of blaCTX-M in Escherichia coli","volume":"49","author":"Poirel","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref64","first-page":"13572","article-title":"Genotypic characterization of virulence and resistance markers in ESBL positive Escherichia coli strains isolated from ambulatory urinary tract infections","volume":"23","author":"Porumbel","year":"2018","journal-title":"Rom. Biotechnol. Lett."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2014approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"ref9004","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1016\/j.tim.2014.04.007","article-title":"Fluoroquinolone resistance: mechanisms, impact on bacteria, and role in evolutionary success","volume":"22","author":"Redgrave","year":"2014","journal-title":"Trends Microbiol."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1111\/1469-0691.12646","article-title":"Pandemic lineages of extraintestinal pathogenic Escherichia coli","volume":"20","author":"Riley","year":"2014","journal-title":"Clin. Microbiol. Infect."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"e000206","DOI":"10.1099\/mgen.0.000206","article-title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"Robertson","year":"2018","journal-title":"Microb. Genom."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"e00063","DOI":"10.1128\/JCM.00063-18","article-title":"CHTyper, a web tool for subtyping of extraintestinal pathogenic Escherichia coli based on the fumC and fimH alleles","volume":"56","author":"Roer","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"2680","DOI":"10.1128\/AAC.02897-15","article-title":"Antibiotic resistance among urinary isolates from female outpatients in the United States in 2003 and 2012","volume":"60","author":"Sanchez","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref70","author":"Seemann","year":"2015"},{"key":"ref71","author":"Seemann","year":"2016"},{"key":"ref72","doi-asserted-by":"publisher","first-page":"D36","DOI":"10.1093\/nar\/gkx1125","article-title":"The European nucleotide archive in 2017","volume":"46","author":"Silvester","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.3390\/pathogens10111355","article-title":"Extraintestinal pathogenic Escherichia coli: virulence factors and antibiotic resistance","volume":"10","author":"Sora","year":"2021","journal-title":"Pathogens"},{"key":"ref74","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s13059-018-1540-z","article-title":"SKESA: strategic k-mer extension for scrupulous assemblies","volume":"19","author":"Souvorov","year":"2018","journal-title":"Genome Biol."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"4115","DOI":"10.1128\/IAI.00752-12","article-title":"Escherichia coli isolates that carry vat, fyuA, chuA, and yfcV efficiently colonize the urinary tract","volume":"80","author":"Spurbeck","year":"2012","journal-title":"Infect. Immun."},{"key":"ref76","doi-asserted-by":"publisher","first-page":"14740","DOI":"10.1073\/pnas.1903002116","article-title":"Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci","volume":"116","author":"Tchesnokova","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref77","doi-asserted-by":"publisher","first-page":"1566","DOI":"10.3389\/fmicb.2017.01566","article-title":"Uropathogenic Escherichia coli (UPEC) infections: virulence factors, bladder responses, antibiotic, and non-antibiotic antimicrobial strategies","volume":"8","author":"Terlizzi","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref78","first-page":"5","article-title":"Escherichia coli ST131 causing invasive infections in Romanian patients\u2014a threat we can no longer ignoreRoum","volume":"73","author":"Usein","year":"2014","journal-title":"Arch. Microbiol. Immunol"},{"key":"ref79","first-page":"35","article-title":"Phylogenetic background and extraintestinal virulence genotypes of Escherichia coli vaginal strains isolated from adult women","volume":"19","author":"Usein","year":"2011","journal-title":"Rev. Rom. Med. Lab."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"acmi000143","DOI":"10.1099\/acmi.0.000143","article-title":"Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool","volume":"2","author":"Waters","year":"2020","journal-title":"Access Microbiol."},{"key":"ref81","volume-title":"Surveillance of Antimicrobial Resistance in Europe, 2024 data: Executive Summary","year":"2025"},{"key":"ref82","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1111\/j.1365-2958.2006.05172.x","article-title":"Sex and virulence in Escherichia coli: an evolutionary perspective","volume":"60","author":"Wirth","year":"2006","journal-title":"Mol. Microbiol."},{"key":"ref83","doi-asserted-by":"publisher","first-page":"e01834-17","DOI":"10.1128\/JCM.01834-17","article-title":"Persistent pandemic lineages of uropathogenic Escherichia coli in a college community from 1999 to 2017","volume":"56","author":"Yamaji","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"1732","DOI":"10.1186\/s12879-025-12044-5","article-title":"Comparative genomic and phenotypic analysis of Escherichia coli ST1193 and ST131 from urinary and bloodstream infections: insights into resistance, virulence, and divergent strategies","volume":"25","author":"Zeng","year":"2025","journal-title":"BMC Infect. 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