{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T01:14:14Z","timestamp":1791854054126,"version":"4.3.4"},"reference-count":122,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,1,24]],"date-time":"2024-01-24T00:00:00Z","timestamp":1706054400000},"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:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      Recurrent urinary tract infections (RUTIs) caused by uropathogenic\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                      are costly public health problems impacting patients\u2019 quality of life.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Aim<\/jats:title>\n                    <jats:p>In this work, a comparative genomics analysis of three clinical RUTI strains isolated from bladder biopsy specimens was performed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Materials and methods<\/jats:title>\n                    <jats:p>\n                      One hundred seventy-two whole genomes of urinary tract\n                      <jats:italic>E. coli<\/jats:italic>\n                      strains were selected from the NCBI database. The search for virulence factors, fitness genes, regions of interest, and genetic elements associated with resistance was manually carried out. The phenotypic characterization of antibiotic resistance, haemolysis, motility, and biofilm formation was performed. Moreover, adherence and invasion assays with human bladder HTB-5 cells, and transmission electron microscopy (TEM) were performed.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The UTI-1_774U and UTI-3_455U\/ST1193 strains were associated with the extraintestinal pathotypes, and the UTI-2_245U\/ST295 strain was associated with the intestinal pathotype, according to a phylogenetic analysis of 172\n                      <jats:italic>E. coli<\/jats:italic>\n                      urinary strains. The three RUTI strains were of clinical, epidemiological, and zoonotic relevance. Several resistance genes were found within the plasmids of these strains, and a multidrug resistance phenotype was revealed. Other virulence genes associated with CFT073 were not identified in the three RUTI strains (genes for type 1 and P fimbriae, haemolysin\n                      <jats:italic>hlyA,<\/jats:italic>\n                      and\n                      <jats:italic>sat<\/jats:italic>\n                      toxin). Quantitative adherence analysis showed that UTI-1_774U was significantly (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009&amp;lt;\u20090.0001) more adherent to human bladder HTB-5 cells. Quantitative invasion analysis showed that UTI-2_245U was significantly more invasive than the control strains. No haemolysis or biofilm activity was detected in the three RUTI strains. The TEM micrographs showed the presence of short and thin fimbriae only in the UTI-2_245U strain.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The high variability and genetic diversity of the RUTI strains indicate that are a mosaic of virulence, resistance, and fitness genes that could promote recurrence in susceptible patients.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2023.1340427","type":"journal-article","created":{"date-parts":[[2024,1,24]],"date-time":"2024-01-24T05:46:00Z","timestamp":1706075160000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":15,"title":["Comparative genomic analysis of uropathogenic Escherichia coli strains from women with recurrent urinary tract infection"],"prefix":"10.3389","volume":"14","author":[{"given":"Marco A.","family":"Flores-Oropeza","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara A.","family":"Ochoa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ariadnna","family":"Cruz-C\u00f3rdova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rolando","family":"Chavez-Tepecano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eva","family":"Mart\u00ednez-Pe\u00f1afiel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Rembao-Boj\u00f3rquez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergio","family":"Zavala-Vega","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rigoberto","family":"Hern\u00e1ndez-Castro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcos","family":"Flores-Encarnacion","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9","family":"Arellano-Galindo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"V\u00e9lez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Xicohtencatl-Cortes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,1,24]]},"reference":[{"key":"ref1","first-page":"411","article-title":"Associated epidemiologic factors with recurring infection of the lower urinary tract in pregnant women","volume":"4","author":"Acu\u00f1a-Ru\u00edz","year":"2022","journal-title":"Rev. Med. Inst. Mex. Seguro Soc."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"861","DOI":"10.3390\/healthcare11060861","article-title":"Prevalence and associated risk factors of urinary tract infection among diabetic patients: a cross-sectional study","volume":"11","author":"Ahmed","year":"2023","journal-title":"Healthcare"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"412","DOI":"10.21149\/spm.v57i5.7621","article-title":"Risk factors for extended-spectrum b-lactamases-producing Escherichia coli urinary tract infections in a tertiary hospital","volume":"57","author":"Alc\u00e1ntar-Curiel","year":"2015","journal-title":"Salud P\u00fablica M\u00e9x."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1099\/0022-1317-50-9-780","article-title":"Distribution and structural variation of the she pathogenicity island in enteric bacterial pathogens","volume":"50","author":"Al-Hasani","year":"2001","journal-title":"J. Med. Microbiol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"575","DOI":"10.3855\/jidc.6661","article-title":"Distribution of ESBLs among Escherichia coli isolates from outpatients with recurrent UTIs and their antimicrobial resistance","volume":"10","author":"Al-Mayahie","year":"2016","journal-title":"J. Infect. Dev. Ctries."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1093\/genetics\/iyac022","article-title":"Harmonizing model organism data in the Alliance of genome resources","volume":"220","author":"Anagnostopoulos","year":"2022","journal-title":"Genetics"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1097\/JU.0000000000000296","article-title":"Recurrent Untcomplicated urinary tract infections in women: AUA\/CUA\/SUFU guideline","volume":"202","author":"Anger","year":"2019","journal-title":"J. Urol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: a better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"345","DOI":"10.5604\/17322693.1145173","article-title":"Well-known and new variants of pathogenic Escherichia coli as a consequence of the plastic genome","volume":"69","author":"Baldy-Chudzik","year":"2015","journal-title":"Postepy Hig. Med. Dosw."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"2381","DOI":"10.3390\/microorganisms9112381","article-title":"Morphotypes as important trait for Uropathogenic E. coli diagnostic; a virulence-phenotype-phylogeny study","volume":"9","author":"Ballesteros-Monrreal","year":"2021","journal-title":"Microorganisms."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"e000192","DOI":"10.1099\/mgen.0.000192","article-title":"ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping","volume":"4","author":"Beghain","year":"2018","journal-title":"Microb. Genom."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1007\/s12223-019-00719-x","article-title":"Classical chaperone-usher (CU) adhesive fimbriome: uropathogenic Escherichia coli (UPEC) and urinary tract infections (UTIs)","volume":"65","author":"Behzadi","year":"2020","journal-title":"Folia Microbiol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1183236","DOI":"10.3389\/fmicb.2023.1183236","article-title":"Editorial: Uropathogens, urinary tract infections, the host-pathogen interactions and treatment","volume":"14","author":"Behzadi","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"W30","DOI":"10.1093\/nar\/gkx343","article-title":"IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets","volume":"45","author":"Bertelli","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"5968","DOI":"10.1038\/s41467-020-19714-9","article-title":"Horizontally acquired papGII-containing pathogenicity islands underlie the emergence of invasive uropathogenic Escherichia coli lineages","volume":"11","author":"Biggel","year":"2020","journal-title":"Nat. Commun."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"6550","DOI":"10.1128\/aac.03183-14","article-title":"Characterization of a P1-like bacteriophage carrying an SHV-2 extended-spectrum \u03b2-lactamase from an Escherichia coli strain","volume":"58","author":"Billard-Pomares","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"1298","DOI":"10.3390\/microorganisms11051298","article-title":"Whole-genome sequencing of Shiga toxin-producing Escherichia coli for characterization and outbreak investigation","volume":"11","author":"Blankenship","year":"2023","journal-title":"Microorganisms"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1007\/s00192-022-05132-6","article-title":"Incidence of urosepsis or pyelonephritis after uncomplicated urinary tract infection in older women","volume":"33","author":"Bradley","year":"2022","journal-title":"Int. Urogynecol. J."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1038\/nature17042","article-title":"Antibacterial drug discovery in the resistance era","volume":"529","author":"Brown","year":"2016","journal-title":"Nature"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"1479","DOI":"10.1002\/nau.24707","article-title":"Recurrent urinary tract infection: association of clinical profiles with urobiome composition in women","volume":"40","author":"Burnett","year":"2021","journal-title":"Neurourol. Urodyn."},{"key":"ref9001","first-page":"15","article-title":"Blood agar plates and hemolysis protocols","volume-title":"American Society for Microbiology","author":"Buxton","year":"2005"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"14572","DOI":"10.1096\/fj.202000760r","article-title":"Restriction of chronic Escherichia coli urinary tract infection depends upon T cell-derived interleukin-17, a deficiency of which predisposes to flagella-driven bacterial persistence","volume":"34","author":"Chamoun","year":"2020","journal-title":"FASEB J."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"3107","DOI":"10.1111\/1462-2920.14713","article-title":"Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential","volume":"21","author":"Clermont","year":"2019","journal-title":"Environ. Microbiol."},{"key":"ref23","volume-title":"Performance standards for antimicrobial susceptibility testing; twenty-six informational, supplement. M100-S26","year":"2022"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1016\/j.chom.2016.08.013","article-title":"Inflammation-induced adhesin-receptor interaction provides a fitness advantage to uropathogenic E. coli during chronic infection","volume":"20","author":"Conover","year":"2016","journal-title":"Cell Host Microbe"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"2299","DOI":"10.3390\/microorganisms9112299","article-title":"Molecular epidemiology of multidrug-resistant uropathogenic Escherichia coli O25b strains associated with complicated urinary tract infection in children","volume":"9","author":"Contreras-Alvarado","year":"2021","journal-title":"Microorganisms"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"E3101","DOI":"10.1073\/pnas.1520255113","article-title":"Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation","volume":"113","author":"Das","year":"2016","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1184081","DOI":"10.3389\/fcimb.2023.1184081","article-title":"Hospital and community wastewater as a source of multidrug-resistant ESBL-producing Escherichia coli","volume":"13","author":"Davidova-Gerzova","year":"2023","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref28","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":"ref29","doi-asserted-by":"publisher","first-page":"2065","DOI":"10.3389\/fmicb.2020.02065","article-title":"Pathogenicity factors of genomic islands in intestinal and extraintestinal Escherichia coli","volume":"11","author":"Desvaux","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1016\/j.chom.2011.12.003","article-title":"The UPEC pore-forming toxin \u03b1-hemolysin triggers proteolysis of host proteins to disrupt cell adhesion, inflammatory, and survival pathways","volume":"11","author":"Dhakal","year":"2012","journal-title":"Cell Host Microbe"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"e100","DOI":"10.1371\/journal.ppat.0030100","article-title":"Integrin-mediated host cell invasion by type 1\u2013piliated uropathogenic Escherichia coli","volume":"3","author":"Eto","year":"2007","journal-title":"PLoS Pathog."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"e1004649","DOI":"10.1371\/journal.pgen.1004649","article-title":"Comprehensive mapping of the Escherichia coli flagellar regulatory network","volume":"10","author":"Fitzgerald","year":"2014","journal-title":"PLoS Genet."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"1712","DOI":"10.3390\/microorganisms8111712","article-title":"Molecular characteristics of extraintestinal pathogenic E. coli (ExPEC), uropathogenic E. coli (UPEC), and multidrug resistant E. coli isolated from healthy dogs in Spain. Whole genome sequencing of canine ST372 isolates and comparison with human isolates causing extraintestinal infections","volume":"8","author":"Flament-Simon","year":"2020","journal-title":"Microorganisms"},{"key":"ref35","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":"ref36","author":"Flores-Oropeza","year":"2017"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1038\/nrurol.2010.190","article-title":"The epidemiology of urinary tract infection","volume":"7","author":"Foxman","year":"2010","journal-title":"Nat. Rev. Urol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"162564","DOI":"10.1016\/j.scitotenv.2023.162564","article-title":"Genomic evidences of gulls as reservoirs of critical priority CTX-M-producing Escherichia coli in Corcovado gulf, Patagonia","volume":"874","author":"Fuentes-Castillo","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"114859","DOI":"10.1016\/j.biopha.2023.114859","article-title":"Ferritinophagy-mediated iron competition in RUTIs: tug-of-war between UPEC and host","volume":"163","author":"Gao","year":"2023","journal-title":"Biomed. Pharmacother."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"e0004122","DOI":"10.1128\/spectrum.00041-22","article-title":"Occurrence and genomic characterization of clone ST1193 Clonotype 14-64 in uncomplicated urinary tract infections caused by Escherichia coli in Spain","volume":"10","author":"Garc\u00eda-Meni\u00f1o","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref41","first-page":"97","article-title":"Biofilm score: is it a differential element within gram negative bacilli?","volume":"26","author":"Gomez","year":"2013","journal-title":"Rev. Esp. Quimioter."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"1745","DOI":"10.4314\/tjpr.v15i8.21","article-title":"Antibiotic resistance properties of uropathogenic Escherichia coli isolated from pregnant women with history of recurrent urinary tract infections","volume":"15","author":"Habibi","year":"2016","journal-title":"Trop. J. Pharm. Res."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1007\/s00192-019-04079-5","article-title":"Latin American consensus on uncomplicated recurrent urinary tract infection\u20142018","volume":"31","author":"Haddad","year":"2020","journal-title":"Int. Urogynecol. J."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1638","DOI":"10.3390\/antibiotics11111638","article-title":"Recurrent E. coli urinary tract infections in nursing homes: insight in sequence types and antibiotic resistance patterns","volume":"11","author":"Hidad","year":"2022","journal-title":"Antibiotics"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1007\/s13353-020-00542-y","article-title":"Clinical cases, drug resistance, and virulence genes profiling in Uropathogenic Escherichia coli","volume":"61","author":"Hozzari","year":"2020","journal-title":"J. Appl. Genet."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e00023","DOI":"10.1128\/mbio.00023-13","article-title":"RpoS contributes to phagocyte oxidase-mediated stress resistance during urinary tract infection by Escherichia coli CFT073","volume":"4","author":"Hryckowian","year":"2013","journal-title":"MBio"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"3999","DOI":"10.1128\/iai.73.7.3999-4006.2005","article-title":"Suppression of bladder epithelial cytokine responses by uropathogenic Escherichia coli","volume":"73","author":"Hunstad","year":"2005","journal-title":"Infect. Immun."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"1409","DOI":"10.2174\/1381612825999190619130216","article-title":"Antimicrobial agents and urinary tract infections","volume":"25","author":"Issakhanian","year":"2019","journal-title":"Curr. Pharm. Des."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"2410","DOI":"10.1128\/JCM.00008-15","article-title":"Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data","volume":"53","author":"Joensen","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1128\/ecosalplus.esp-0004-2017","article-title":"Molecular epidemiology of extraintestinal pathogenic Escherichia coli","volume":"8","author":"Johnson","year":"2018","journal-title":"EcoSal Plus"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1080\/13697137.2018.1551871","article-title":"The etiology and management of recurrent urinary tract infections in postmenopausal women","volume":"22","author":"Jung","year":"2019","journal-title":"Climacteric"},{"key":"ref9003","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1038\/nrmicro818","article-title":"Pathogenic Escherichia coli","volume":"2","author":"Kaper","year":"2004","journal-title":"Nat Rev Microbiol"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"1138","DOI":"10.3390\/microorganisms9061138","article-title":"Identity of Bla CTX-M carrying plasmids in Sequential ESBL-E. coli isolates from patients with recurrent urinary tract infections","volume":"9","author":"Karami","year":"2021","journal-title":"Microorganisms"},{"key":"ref56","first-page":"56","article-title":"Asymptomatic infections of the urinary tract","volume":"69","author":"Kass","year":"1956","journal-title":"Trans. Assoc. Am. Phys."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"3541","DOI":"10.1128\/iai.68.6.3541-3547.2000","article-title":"Receptor structure for F1C fimbriae of uropathogenic Escherichia coli","volume":"68","author":"Khan","year":"2000","journal-title":"Infect. Immun."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"100881","DOI":"10.1016\/j.mgene.2021.100881","article-title":"The prevalence of type 3 fimbriae in Uropathogenic Escherichia coli isolated from clinical urine samples","volume":"28","author":"Khonsari","year":"2021","journal-title":"Meta Gene"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"192","DOI":"10.5213\/inj.2040472.236","article-title":"What is the cause of recurrent urinary tract infection? Contemporary microscopic concepts of pathophysiology","volume":"25","author":"Kim","year":"2021","journal-title":"Int. Neurourol. J."},{"key":"ref9002","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1038\/356252a0","article-title":"P pili in uropathogenic E. coli are composite fibres with distinct fibrillar adhesive tips","volume":"356","author":"Kuehn","year":"1992","journal-title":"Nature"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1111\/bju.15756","article-title":"Guideline of guidelines: management of recurrent urinary tract infections in women","volume":"130","author":"Kwok","year":"2022","journal-title":"BJU Int."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"3532","DOI":"10.1128\/JB.01744-06","article-title":"Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli","volume":"189","author":"Lloyd","year":"2007","journal-title":"J. Bacteriol."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1128\/mmbr.00052-12","article-title":"Role of pore-forming toxins in bacterial infectious diseases","volume":"77","author":"Los","year":"2013","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"2063","DOI":"10.3389\/fmicb.2019.02063","article-title":"Curli of uropathogenic Escherichia coli enhance urinary tract colonization as a fitness factor","volume":"10","author":"Luna-Pineda","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1186\/1471-2164-10-552","article-title":"Genome reannotation of Escherichia coli CFT073 with new insights into virulence","volume":"10","author":"Luo","year":"2009","journal-title":"BMC Genomics"},{"key":"ref66","doi-asserted-by":"publisher","first-page":"4002","DOI":"10.1128\/JCM.02086-12","article-title":"Similarity and divergence of phylogenies, antimicrobial susceptibilities, and virulence factor profiles of Escherichia coli isolates causing recurrent urinary tract infections that persist or result from reinfection","volume":"50","author":"Luo","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1266\/ggs.74.227","article-title":"Complete nucleotide sequence of the prophage VT2-Sakai carrying the verotoxin 2 genes of the enterohemorrhagic Escherichia coli O157:H7 derived from the Sakai outbreak","volume":"74","author":"Makino","year":"1999","journal-title":"Genes Genet. Syst."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/s0923-2508(97)81900-6","article-title":"Human uropathogenic and bovine septicaemic Escherichia coli strains carry an identical F17-related adhesin","volume":"148","author":"Martin","year":"1997","journal-title":"Res. Microbiol."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"2803","DOI":"10.1093\/emboj\/19.12.2803","article-title":"Type 1 pilus-mediated bacterial invasion of bladder epithelial cells","volume":"19","author":"Martinez","year":"2000","journal-title":"EMBO J."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"15364","DOI":"10.1038\/s41598-017-15539-7","article-title":"Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction","volume":"7","author":"Matamoros","year":"2017","journal-title":"Sci. Rep."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"77","DOI":"10.4321\/s0004-06142007000100015","article-title":"Follicular cystitis. Case report and bibliographic review","volume":"60","author":"Mateos Blanco","year":"2007","journal-title":"Arch. Esp. Urol."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1093\/gbe\/evt038","article-title":"The evolutionary path to extraintestinal pathogenic, drug-resistant Escherichia coli is marked by drastic reduction in detectable recombination within the core genome","volume":"5","author":"McNally","year":"2013","journal-title":"Genome Biol. Evol."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1111\/j.1574-695x.2002.tb00567.x","article-title":"Type 1, P and S fimbriae, and afimbrial adhesin I are not essential for uropathogenic Escherichia coli to adhere to and invade bladder epithelial cells","volume":"33","author":"Miyazaki","year":"2002","journal-title":"FEMS Immunol. Med. 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Agents Chemother."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1007\/s10123-021-00221-w","article-title":"Genetic diversity and virulence characteristics of biofilm-producing uropathogenic Escherichia coli","volume":"25","author":"Qasemi","year":"2021","journal-title":"Int. Microbiol."},{"key":"ref85","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1007\/s00284-015-0842-6","article-title":"Analysis of yeh fimbrial gene cluster in Escherichia coli O157: H7 in order to find a genetic marker for this serotype","volume":"71","author":"Ravan","year":"2015","journal-title":"Curr. Microbiol."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"e0140388","DOI":"10.1371\/journal.pone.0140388","article-title":"Congo red interactions with curli-producing E. 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Immun."},{"key":"ref94","doi-asserted-by":"publisher","first-page":"e00700","DOI":"10.1128\/mra.00700-20","article-title":"Complete genome sequences of seven uropathogenic Escherichia coli strains isolated from postmenopausal women with recurrent urinary tract infection","volume":"9","author":"Sharon","year":"2020","journal-title":"Microbiol. Resour. Announc."},{"key":"ref95","doi-asserted-by":"publisher","first-page":"750","DOI":"10.1038\/s41585-018-0106-x","article-title":"Nonantibiotic prevention and management of recurrent urinary tract infection","volume":"15","author":"Sihra","year":"2018","journal-title":"Nat. Rev. Urol."},{"key":"ref96","doi-asserted-by":"publisher","first-page":"4833","DOI":"10.1128\/iai.00630-08","article-title":"PapX, a P fimbrial operon-encoded inhibitor of motility in uropathogenic Escherichia coli","volume":"76","author":"Simms","year":"2008","journal-title":"Infect. Immun."},{"key":"ref97","doi-asserted-by":"publisher","first-page":"434","DOI":"10.1128\/mmbr.00020-10","article-title":"Mobility of plasmids","volume":"74","author":"Smillie","year":"2010","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref98","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1016\/j.juro.2006.08.081","article-title":"Biofilm formation in uropathogenic escherichia coli strains: relationship with prostatitis, urovirulence factors and antimicrobial resistance","volume":"177","author":"Soto","year":"2007","journal-title":"J. Urol."},{"key":"ref99","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1038\/nature22972","article-title":"Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist","volume":"546","author":"Spaulding","year":"2017","journal-title":"Nature"},{"key":"ref100","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":"ref101","doi-asserted-by":"publisher","first-page":"e86565","DOI":"10.1371\/journal.pone.0086565","article-title":"Evaluation of the prevalence and production of escherichia coli common pilus among avian pathogenic E. 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Med."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1111\/j.1600-0463.2007.apm_630.x","article-title":"Quantification of biofilm in microtiter plates: overview of testing conditions and practical recommendations for assessment of biofilm production by staphylococci","volume":"115","author":"Stepanovi\u0107","year":"2007","journal-title":"APMIS"},{"key":"ref104","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1111\/jsap.12225","article-title":"Comparison of urine and bladder or urethral mucosal biopsy culture obtained by transurethral cystoscopy in dogs with chronic lower urinary tract disease: 41 cases (2002 to 2011)","volume":"55","author":"Sycamore","year":"2014","journal-title":"J. Small Anim. Pract."},{"key":"ref105","doi-asserted-by":"publisher","first-page":"2233","DOI":"10.1128\/jcm.33.9.2233-2239.1995","article-title":"Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing","volume":"33","author":"Tenover","year":"1995","journal-title":"J. Clin. Microbiol."},{"key":"ref106","doi-asserted-by":"publisher","first-page":"e01977","DOI":"10.1128\/mBio.01977-19","article-title":"Comparative genomics of antibiotic-resistant uropathogens implicates three routes for recurrence of urinary tract infections","volume":"10","author":"Thanert","year":"2019","journal-title":"MBio"},{"key":"ref107","doi-asserted-by":"publisher","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the universal protein knowledgebase in 2023","volume":"51","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref108","doi-asserted-by":"publisher","first-page":"184","DOI":"10.2527\/jas2016.94supplement4184x","article-title":"P8008 the NCBI eukaryotic genome annotation pipeline","volume":"94","author":"Thibaud-Nissen","year":"2016","journal-title":"J. Anim. Sci."},{"key":"ref109","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1097\/00005392-199501000-00085","article-title":"Culture of bladder epithelium from cystoscopic biopsies of patients with interstitial cystitis","volume":"153","author":"Trifillis","year":"1995","journal-title":"J. Urol."},{"key":"ref110","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1515\/pjvs-2016-0004","article-title":"The irp2 and fyuA genes in high Pathogenicity Islands are involved in the pathogenesis of infections caused by avian pathogenic Escherichia coli (APEC)","volume":"19","author":"Tu","year":"2016","journal-title":"Pol. J. Vet. Sci."},{"key":"ref111","doi-asserted-by":"publisher","first-page":"16256","DOI":"10.1038\/nmicrobiol.2016.256","article-title":"Bacterial pathogenesis: Remodelling recurrent infection","volume":"2","author":"Ulett","year":"2016","journal-title":"Nat. Microbiol."},{"key":"ref112","doi-asserted-by":"publisher","first-page":"492","DOI":"10.3389\/fcimb.2020.00492","article-title":"Genetic and virulence characteristics of a hybrid atypical enteropathogenic and uropathogenic Escherichia coli (aEPEC\/UPEC) strain","volume":"10","author":"Valiatti","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref113","doi-asserted-by":"publisher","first-page":"e0228959","DOI":"10.1371\/journal.pone.0228959","article-title":"Secreted autotransporter toxin (sat) induces cell damage during enteroaggregative Escherichia coli infection","volume":"15","author":"Vieira","year":"2020","journal-title":"PLoS One"},{"key":"ref114","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1373\/clinchem.2008.112789","article-title":"Next-generation sequencing: from basic research to diagnostics","volume":"55","author":"Voelkerding","year":"2009","journal-title":"Clin. Chem."},{"key":"ref115","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1080\/14737167.2017.1359543","article-title":"Social and economic burden of recurrent urinary tract infections and quality of life: a patient web-based study (GESPRIT)","volume":"18","author":"Wagenlehner","year":"2018","journal-title":"Expert Rev. Pharmacoecon. Outcomes Res."},{"key":"ref9004","doi-asserted-by":"crossref","DOI":"10.1038\/s41585-020-0362-4","article-title":"Epidemiology, definition and treatment of complicated urinary tract infections","author":"Wagenlehner","year":"2020","journal-title":"Nat Rev Urol"},{"key":"ref116","doi-asserted-by":"publisher","first-page":"W768","DOI":"10.1093\/nar\/gkac321","article-title":"Vrprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens","volume":"50","author":"Wang","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref117","doi-asserted-by":"publisher","first-page":"13139","DOI":"10.1111\/jcmm.15920","article-title":"Depletion of multidrug-resistant uropathogenic Escherichia coli BC1 by ebselen and silver ion","volume":"24","author":"Wang","year":"2020","journal-title":"J. Cell. Mol. Med."},{"key":"ref118","doi-asserted-by":"publisher","first-page":"1085","DOI":"10.1016\/j.urology.2007.12.091","article-title":"Urinary tract infection and inflammation at onset of interstitial cystitis\/painful bladder syndrome","volume":"71","author":"Warren","year":"2008","journal-title":"Urology"},{"key":"ref119","doi-asserted-by":"publisher","first-page":"17020","DOI":"10.1073\/pnas.252529799","article-title":"Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli","volume":"99","author":"Welch","year":"2002","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref120","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1016\/j.jprot.2015.11.001","article-title":"Comparative proteomics of uropathogenic Escherichia coli during growth in human urine identify UCA-like (UCL) fimbriae as an adherence factor involved in biofilm formation and binding to uroepithelial cells","volume":"131","author":"Wurpel","year":"2016","journal-title":"J. Proteome"},{"key":"ref121","doi-asserted-by":"publisher","first-page":"979","DOI":"10.3390\/ijms17070979","article-title":"Subinhibitory concentrations of allicin decrease uropathogenic Escherichia coli (UPEC) biofilm formation, adhesion ability, and swimming motility","volume":"17","author":"Yang","year":"2016","journal-title":"Int. J. Mol. Sci."},{"key":"ref122","doi-asserted-by":"publisher","first-page":"W347","DOI":"10.1093\/nar\/gkr485","article-title":"PHAST: a fast phage search tool","volume":"39","author":"Zhou","year":"2011","journal-title":"Nucleic Acids Res."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2023.1340427\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,24]],"date-time":"2024-01-24T05:46:08Z","timestamp":1706075168000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2023.1340427\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,24]]},"references-count":122,"alternative-id":["10.3389\/fmicb.2023.1340427"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2023.1340427","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1,24]]},"article-number":"1340427"}}