{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T08:28:44Z","timestamp":1793262524553,"version":"4.5.0"},"reference-count":69,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,5,10]],"date-time":"2025-05-10T00:00:00Z","timestamp":1746835200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001824","name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["24-12527S"],"award-info":[{"award-number":["24-12527S"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003243","name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["65269705"],"award-info":[{"award-number":["65269705"]}],"id":[{"id":"10.13039\/501100003243","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003243","name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["NU22-09-00645"],"award-info":[{"award-number":["NU22-09-00645"]}],"id":[{"id":"10.13039\/501100003243","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Ecotoxicology and Environmental Safety"],"published-print":{"date-parts":[[2025,7]]},"DOI":"10.1016\/j.ecoenv.2025.118320","type":"journal-article","created":{"date-parts":[[2025,5,26]],"date-time":"2025-05-26T23:44:51Z","timestamp":1748303091000},"page":"118320","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":6,"special_numbering":"C","title":["Comparative genomics of multi-drug resistant Escherichia coli ST131 from human, animal, and environmental sources in the Czech Republic"],"prefix":"10.1016","volume":"299","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0769-1978","authenticated-orcid":false,"given":"Michaela","family":"Ruzickova","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivana","family":"Karola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5668-7014","authenticated-orcid":false,"given":"Tomas","family":"Nohejl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iva","family":"Sukkar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4836-5239","authenticated-orcid":false,"given":"Jana","family":"Palkovicova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0172-4134","authenticated-orcid":false,"given":"Ivo","family":"Papousek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Max L.","family":"Cummins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven P.","family":"Djordjevic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monika","family":"Dolejska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ecoenv.2025.118320_bib1","unstructured":"Bache S. and Wickham H., \u201c_magrittr: A Forward-Pipe Operator for R_. R package version 2.0.3,\u201d 2022."},{"issue":"1","key":"10.1016\/j.ecoenv.2025.118320_bib2","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s12941-018-0295-4","article-title":"Adherent\/invasive Escherichia coli (AIEC) isolates from asymptomatic people: new E. coli ST131 O25:H4\/H30-Rx virotypes","volume":"17","author":"Barrios-Villa","year":"2018","journal-title":"Ann. Clin. Microbiol Antimicrob."},{"issue":"10","key":"10.1016\/j.ecoenv.2025.118320_bib3","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giz119","article-title":"PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria","volume":"8","author":"Bayliss","year":"2019","journal-title":"Gigascience"},{"issue":"2","key":"10.1016\/j.ecoenv.2025.118320_bib4","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00347-16","article-title":"Sequential Acquisition of Virulence and Fluoroquinolone Resistance Has Shaped the Evolution of Escherichia coli ST131","volume":"7","author":"Ben Zakour","year":"2016","journal-title":"mBio"},{"key":"10.1016\/j.ecoenv.2025.118320_bib5","doi-asserted-by":"crossref","DOI":"10.1016\/j.envpol.2023.122476","article-title":"Dissemination of ESBL-producing E. coli ST131 through wastewater and environmental water in Switzerland","volume":"337","author":"Biggel","year":"2023","journal-title":"Environ. Pollut."},{"issue":"10","key":"10.1016\/j.ecoenv.2025.118320_bib6","doi-asserted-by":"crossref","first-page":"3358","DOI":"10.1128\/JCM.01555-13","article-title":"Four Main Virotypes among Extended-Spectrum-\u03b2-Lactamase-Producing Isolates of Escherichia coli O25b:H4-B2-ST131: Bacterial, Epidemiological, and Clinical Characteristics","volume":"51","author":"Blanco","year":"2013","journal-title":"J. Clin. Microbiol"},{"key":"10.1016\/j.ecoenv.2025.118320_bib7","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A Flexible Trimmer for Illumina Sequence Data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"8","key":"10.1016\/j.ecoenv.2025.118320_bib8","doi-asserted-by":"crossref","first-page":"2605","DOI":"10.1128\/JCM.00640-08","article-title":"European Emergence of Ciprofloxacin-Resistant Escherichia coli Clonal Groups O25:H4-ST 131 and O15:K52:H1 Causing Community-Acquired Uncomplicated Cystitis","volume":"46","author":"Cagnacci","year":"2008","journal-title":"J. Clin. Microbiol"},{"issue":"1","key":"10.1016\/j.ecoenv.2025.118320_bib9","doi-asserted-by":"crossref","first-page":"19750","DOI":"10.1038\/s41598-024-70540-1","article-title":"Evolution of extended-spectrum \u03b2-lactamase-producing ST131 Escherichia coli at a single hospital over 15 years","volume":"14","author":"Cho","year":"2024","journal-title":"Sci. Rep."},{"issue":"3","key":"10.1016\/j.ecoenv.2025.118320_bib10","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.ecoenv.2025.118320_bib11","article-title":"The role of potentiating mutations in the evolution of pandemic Escherichia coli clones","author":"Cummins","year":"2021","journal-title":"Springe Sci. Bus. Media Dtschl. GmbH"},{"issue":"6","key":"10.1016\/j.ecoenv.2025.118320_bib12","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.3390\/microorganisms11061513","article-title":"Whole Genome Sequencing of Avian Pathogenic Escherichia coli Causing Bacterial Chondronecrosis and Osteomyelitis in Australian Poultry","volume":"11","author":"Cummins","year":"2023","journal-title":"Microorganisms"},{"issue":"1","key":"10.1016\/j.ecoenv.2025.118320_bib13","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.01212-21","article-title":"F Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses","volume":"7","author":"Cummins","year":"2022","journal-title":"mSystems"},{"issue":"8","key":"10.1016\/j.ecoenv.2025.118320_bib14","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1016\/j.ijmm.2014.10.002","article-title":"Molecular epidemiology and virulence of Escherichia coli O16:H5-ST131: Comparison with H30 and H30-Rx subclones of O25b:H4-ST131","volume":"304","author":"Dahbi","year":"2014","journal-title":"Int. J. Med. Microbiol."},{"key":"10.1016\/j.ecoenv.2025.118320_bib15","doi-asserted-by":"crossref","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"},{"issue":"12","key":"10.1016\/j.ecoenv.2025.118320_bib16","doi-asserted-by":"crossref","first-page":"2784","DOI":"10.1093\/jac\/dkr363","article-title":"CTX-M-15-producing Escherichia coli clone B2-O25b-ST131 and Klebsiella spp. isolates in municipal wastewater treatment plant effluents","volume":"66","author":"Dolejska","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"issue":"3","key":"10.1016\/j.ecoenv.2025.118320_bib17","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.01291-22","article-title":"Genomic and Temporal Trends in Canine ExPEC Reflect Those of Human ExPEC","volume":"10","author":"Elankumaran","year":"2022","journal-title":"Microbiol Spectr."},{"key":"10.1016\/j.ecoenv.2025.118320_bib18","doi-asserted-by":"crossref","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":"10.1016\/j.ecoenv.2025.118320_bib19","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2020.00387","article-title":"Whole Genome Sequencing and Characteristics of mcr-1\u2013Harboring Plasmids of Porcine Escherichia coli Isolates Belonging to the High-Risk Clone O25b:H4-ST131 Clade B","volume":"11","author":"Flament-Simon","year":"2020","journal-title":"Front Microbiol"},{"issue":"11","key":"10.1016\/j.ecoenv.2025.118320_bib20","doi-asserted-by":"crossref","DOI":"10.1093\/ofid\/ofaa410","article-title":"Expansion of a Subset Within the C2 Subclade of Escherichia coli Sequence Type 131 (ST131) Is Driving the Increasing Rates of Aminoglycoside Resistance","volume":"7","author":"Hojabri","year":"2020","journal-title":"Open Forum Infect. Dis."},{"issue":"10","key":"10.1016\/j.ecoenv.2025.118320_bib21","doi-asserted-by":"crossref","first-page":"3353","DOI":"10.1128\/JCM.00901-09","article-title":"\u201cInternational Clones of Klebsiella pneumoniae and Escherichia coli with Extended-Spectrum \u03b2-Lactamases in a Czech Hospital,\u201d","volume":"47","author":"Hrab\u00e1k","year":"2009","journal-title":"J. Clin. Microbiol"},{"key":"10.1016\/j.ecoenv.2025.118320_bib22","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.00519-18","article-title":"Extensive Genetic Commonality among Wildlife, Wastewater, Community, and Nosocomial Isolates of Escherichia coli Sequence Type 131 ( H 30R1 and H 30Rx Subclones) That Carry bla CTX-M-27 or bla CTX-M-15","volume":"62","author":"Jamborova","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"issue":"4","key":"10.1016\/j.ecoenv.2025.118320_bib23","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00121-16","article-title":"Separate F-Type Plasmids Have Shaped the Evolution of the H 30 Subclone of Escherichia coli Sequence Type 131","volume":"1","author":"Johnson","year":"2016","journal-title":"mSphere"},{"issue":"_1","key":"10.1016\/j.ecoenv.2025.118320_bib24","article-title":"Rapid and Specific Detection of Escherichia coli Sequence Type 131 (ST131) and its Key Subclones Using a Novel Single-tube Multiplex PCR Assay","volume":"4","author":"Johnston","year":"2017","journal-title":"Open Forum Infect. Dis."},{"issue":"47","key":"10.1016\/j.ecoenv.2025.118320_bib25","doi-asserted-by":"crossref","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":"Eurosurveillance"},{"key":"10.1016\/j.ecoenv.2025.118320_bib26","unstructured":"Kolde Raivo, \u201c_pheatmap: Pretty Heatmaps_. R package version 1.0.12,\u201d 2019."},{"issue":"1","key":"10.1016\/j.ecoenv.2025.118320_bib27","doi-asserted-by":"crossref","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":"10.1016\/j.ecoenv.2025.118320_bib28","doi-asserted-by":"crossref","DOI":"10.1016\/j.envres.2020.110487","article-title":"Extended-spectrum beta-lactamase-producing Escherichia coli and antimicrobial resistance in municipal and hospital wastewaters in Czech Republic: Culture-based and metagenomic approaches","volume":"193","author":"Kutilova","year":"2021","journal-title":"Environ. Res"},{"key":"10.1016\/j.ecoenv.2025.118320_bib29","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.ecoenv.2025.118320_bib30","article-title":"Genomic comparisons of Escherichia coli ST131 from Australia","volume":"7","author":"Li","year":"2021","journal-title":"Micro Genom."},{"issue":"4","key":"10.1016\/j.ecoenv.2025.118320_bib31","article-title":"Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones","volume":"6","author":"Ludden","year":"2020","journal-title":"Micro Genom."},{"issue":"3","key":"10.1016\/j.ecoenv.2025.118320_bib32","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1128\/CMR.00125-13","article-title":"\u201cEscherichia coli ST131, an Intriguing Clonal Group,\u201d","volume":"27","author":"Marie-H\u00e9l\u00e8ne","year":"2014","journal-title":"Clin. Microbiol Rev."},{"issue":"3","key":"10.1016\/j.ecoenv.2025.118320_bib33","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1128\/CMR.00116-14","article-title":"The Role of Epidemic Resistance Plasmids and International High-Risk Clones in the Spread of Multidrug-Resistant Enterobacteriaceae","volume":"28","author":"Mathers","year":"2015","journal-title":"Clin. Microbiol Rev."},{"issue":"1","key":"10.1016\/j.ecoenv.2025.118320_bib34","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1080\/21505594.2020.1747799","article-title":"Molecularly defined extraintestinal pathogenic Escherichia coli status predicts virulence in a murine sepsis model better than does virotype, individual virulence genes, or clonal subset among E. coli ST131 isolates","volume":"11","author":"Merino","year":"2020","journal-title":"Virulence"},{"issue":"1","key":"10.1016\/j.ecoenv.2025.118320_bib35","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"issue":"1","key":"10.1016\/j.ecoenv.2025.118320_bib36","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/s12866-017-0984-8","article-title":"The ST131 Escherichia coli H22 subclone from human intestinal microbiota: Comparison of genomic and phenotypic traits with those of the globally successful H30 subclone","volume":"17","author":"Nicolas-Chanoine","year":"2017","journal-title":"BMC Microbiol"},{"issue":"7","key":"10.1016\/j.ecoenv.2025.118320_bib37","doi-asserted-by":"crossref","first-page":"3973","DOI":"10.1128\/AAC.00475-12","article-title":"Characterization of Globally Spread Escherichia coli ST131 Isolates (1991 to 2010)","volume":"56","author":"Novais","year":"2012","journal-title":"Antimicrob. Agents Chemother."},{"issue":"4","key":"10.1016\/j.ecoenv.2025.118320_bib38","article-title":"Arrangements of Mobile Genetic Elements among Virotype E Subpopulation of Escherichia coli Sequence Type 131 Strains with High Antimicrobial Resistance and Virulence Gene Content","volume":"6","author":"Omid","year":"2021","journal-title":"mSphere"},{"issue":"1","key":"10.1016\/j.ecoenv.2025.118320_bib39","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1089\/mdr.2014.0070","article-title":"High prevalence of ST131 among CTX-M-producing Escherichia coli from community-acquired infections, in the Czech Republic","volume":"21","author":"Papagiannitsis","year":"2015","journal-title":"Microb. Drug Resist."},{"issue":"3","key":"10.1016\/j.ecoenv.2025.118320_bib40","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","volume":"35","author":"Paradis","year":"2019","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ecoenv.2025.118320_bib41","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1016\/j.watres.2019.05.102","article-title":"Diversity and antibiotic resistance among Escherichia coli populations in hospital and community wastewater compared to wastewater at the receiving urban treatment plant","volume":"161","author":"Paulshus","year":"2019","journal-title":"Water Res"},{"issue":"15","key":"10.1016\/j.ecoenv.2025.118320_bib42","doi-asserted-by":"crossref","first-page":"5694","DOI":"10.1073\/pnas.1322678111","article-title":"Global dissemination of a multidrug resistant Escherichia coli clone","volume":"111","author":"Petty","year":"2014","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"4","key":"10.1016\/j.ecoenv.2025.118320_bib43","doi-asserted-by":"crossref","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"},{"issue":"4","key":"10.1016\/j.ecoenv.2025.118320_bib44","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1007\/s40121-023-00791-4","article-title":"The Significance of Epidemic Plasmids in the Success of Multidrug-Resistant Drug Pandemic Extraintestinal Pathogenic Escherichia coli","volume":"12","author":"Pitout","year":"2023","journal-title":"Infect. Dis. Ther."},{"key":"10.1016\/j.ecoenv.2025.118320_bib45","doi-asserted-by":"crossref","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."},{"issue":"6","key":"10.1016\/j.ecoenv.2025.118320_bib46","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00377-13","article-title":"The Epidemic of Extended-Spectrum-\u03b2-Lactamase-Producing Escherichia coli ST131 Is Driven by a Single Highly Pathogenic Subclone, H30-Rx","volume":"4","author":"Price","year":"2013","journal-title":"mBio"},{"issue":"1","key":"10.1016\/j.ecoenv.2025.118320_bib47","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1038\/s41467-022-28342-4","article-title":"A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58","volume":"13","author":"Reid","year":"2022","journal-title":"Nat. Commun."},{"issue":"9","key":"10.1016\/j.ecoenv.2025.118320_bib48","article-title":"Clonal ST131-H22 Escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids","volume":"5","author":"Reid","year":"2019","journal-title":"Micro Genom."},{"key":"10.1016\/j.ecoenv.2025.118320_bib49","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.16505","article-title":"phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)","volume":"12","author":"Revell","year":"2024","journal-title":"PeerJ"},{"key":"10.1016\/j.ecoenv.2025.118320_bib50","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2016.02147","article-title":"Characteristics of Quinolone Resistance in Escherichia coli Isolates from Humans, Animals, and the Environment in the Czech Republic","volume":"7","author":"R\u00f6derova","year":"2017","journal-title":"Front Microbiol"},{"issue":"1","key":"10.1016\/j.ecoenv.2025.118320_bib51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/jac\/dkq415","article-title":"Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain","volume":"66","author":"Rogers","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.ecoenv.2025.118320_bib52","doi-asserted-by":"crossref","DOI":"10.1016\/j.onehlt.2024.100715","article-title":"Traces of pandemic fluoroquinolone-resistant Escherichia coli clone ST131 transmitted from human society to aquatic environments and wildlife in Japan","volume":"18","author":"Sato","year":"2024","journal-title":"One Health"},{"issue":"4","key":"10.1016\/j.ecoenv.2025.118320_bib53","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1016\/j.cmi.2017.12.016","article-title":"Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene\u2013based approaches","volume":"24","author":"Sch\u00fcrch","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"issue":"14","key":"10.1016\/j.ecoenv.2025.118320_bib54","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"issue":"2","key":"10.1016\/j.ecoenv.2025.118320_bib55","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02162-15","article-title":"Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131","volume":"7","author":"Stoesser","year":"2016","journal-title":"mBio"},{"issue":"5","key":"10.1016\/j.ecoenv.2025.118320_bib56","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1093\/jac\/dks017","article-title":"Escherichia coli with extended-spectrum -lactamase and plasmid-mediated quinolone resistance genes in great cormorants and mallards in Central Europe","volume":"67","author":"Tausova","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"10.1016\/j.ecoenv.2025.118320_bib57","unstructured":"R.Core Team, \u201cR: A language and environment for statistical computing,\u201d R Foundation for Statistical Computing, Vienna, Austria."},{"issue":"11","key":"10.1016\/j.ecoenv.2025.118320_bib58","doi-asserted-by":"crossref","first-page":"5539","DOI":"10.1093\/nar\/gkz361","article-title":"Fast hierarchical Bayesian analysis of population structure","volume":"47","author":"Tonkin-Hill","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"10.1016\/j.ecoenv.2025.118320_bib59","doi-asserted-by":"crossref","first-page":"363","DOI":"10.3390\/antibiotics13040363","article-title":"Genomic Epidemiology of C2\/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary","volume":"13","author":"T\u00f3th","year":"2024","journal-title":"Antibiotics"},{"issue":"10","key":"10.1016\/j.ecoenv.2025.118320_bib60","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0026578","article-title":"Insights into a Multidrug Resistant Escherichia coli Pathogen of the Globally Disseminated ST131 Lineage: Genome Analysis and Virulence Mechanisms","volume":"6","author":"Totsika","year":"2011","journal-title":"PLoS One"},{"issue":"1","key":"10.1016\/j.ecoenv.2025.118320_bib61","doi-asserted-by":"crossref","first-page":"1371","DOI":"10.1038\/s41467-024-45608-1","article-title":"Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales","volume":"15","author":"White","year":"2024","journal-title":"Nat. Commun."},{"issue":"12","key":"10.1016\/j.ecoenv.2025.118320_bib62","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1008162","article-title":"The pandemic Escherichia coli sequence type 131 strain is acquired even in the absence of antibiotic exposure","volume":"15","author":"Whitmer","year":"2019","journal-title":"PLoS Pathog."},{"issue":"43","key":"10.1016\/j.ecoenv.2025.118320_bib63","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the Tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"J. Open Source Softw."},{"key":"10.1016\/j.ecoenv.2025.118320_bib64","unstructured":"Wickham H., Fran\u00e7ois R., Henry L., M\u00fcller K., and Vaughan D., \u201c_dplyr: A Grammar of Data Manipulation_. R package version 2.4.0,\u201d 2023."},{"key":"10.1016\/j.ecoenv.2025.118320_bib65","unstructured":"Wickham H., Hester J., and Bryan J., \u201c_readr: Read Rectangular Text Data_. R package version 2.1.5,\u201d 2024."},{"key":"10.1016\/j.ecoenv.2025.118320_bib66","series-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"issue":"3","key":"10.1016\/j.ecoenv.2025.118320_bib67","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00158-22","article-title":"Urban Wildlife Crisis: Australian Silver Gull Is a Bystander Host to Widespread Clinical Antibiotic Resistance","volume":"7","author":"Wyrsch","year":"2022","journal-title":"mSystems"},{"key":"10.1016\/j.ecoenv.2025.118320_bib68","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2015.00964","article-title":"IncF plasmid diversity in multi-drug resistant Escherichia coli strains from animals in China","volume":"6","author":"Yang","year":"2015","journal-title":"Front Microbiol"},{"issue":"1","key":"10.1016\/j.ecoenv.2025.118320_bib69","article-title":"Using ggtree to Visualize Data on Tree-Like Structures","volume":"69","author":"Yu","year":"2020","journal-title":"Curr. Protoc. Bioinforma."}],"container-title":["Ecotoxicology and Environmental Safety"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0147651325006566?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0147651325006566?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T08:49:38Z","timestamp":1762246178000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0147651325006566"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7]]},"references-count":69,"alternative-id":["S0147651325006566"],"URL":"https:\/\/doi.org\/10.1016\/j.ecoenv.2025.118320","relation":{},"ISSN":["0147-6513"],"issn-type":[{"value":"0147-6513","type":"print"}],"subject":[],"published":{"date-parts":[[2025,7]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Comparative genomics of multi-drug resistant Escherichia coli ST131 from human, animal, and environmental sources in the Czech Republic","name":"articletitle","label":"Article Title"},{"value":"Ecotoxicology and Environmental Safety","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ecoenv.2025.118320","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"118320"}}