{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T03:29:23Z","timestamp":1787801363479,"version":"build-2784847793"},"reference-count":51,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T00:00:00Z","timestamp":1771372800000},"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                      Extended-spectrum\n                      <jats:italic>\u03b2<\/jats:italic>\n                      -lactamase (ESBL)\u2013producing\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                      threatens humans and animals.\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>CTX-M-14<\/jats:sub>\n                      , which is prevalent in Asia, is mainly disseminated via incompatibility group I1 (IncI1) plasmids, as they can efficiently transfer across Enterobacterales. However, direct evidence linking livestock and farmers at the genomic level is limited, and our study addresses this concern.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Fecal samples were collected in 2013 from one parent cattle, three calves, and a farmer on a cattle farm in southern Kyushu, Japan. ESBL-producing\n                      <jats:italic>E. coli<\/jats:italic>\n                      were identified and characterized using hybrid Illumina\u2013Nanopore assemblies, resistance gene profiling, and plasmid replicon typing. Clonal relatedness was assessed using core-genome multilocus sequence typing and core single-nucleotide polymorphism (SNP) analysis. Conjugation assays were used to evaluate plasmid transferability.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Seven\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>CTX-M-14<\/jats:sub>\n                      -positive\n                      <jats:italic>E. coli<\/jats:italic>\n                      isolates representing five sequence types (STs) were recovered. Two ST533 isolates from parent cattle and calf 1 were identical by core-genome ST and differed by only one core SNP, indicating recent clonal transmission. Additionally, ST1148, ST1261, and ST1431 were isolated from other calves, while ST448 isolates from the farmer and calf 3 exhibited a large genetic distance (3,891 core SNPs) and distinct cgSTs. All\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>CTX-M-14<\/jats:sub>\n                      genes were located on conserved IncI1 plasmids of approximately 114\u202fkb, showing &amp;gt;99.9% sequence identity, including the IncI1 plasmid. Conjugation frequencies ranged from 10\n                      <jats:sup>\u22122<\/jats:sup>\n                      to 10\n                      <jats:sup>\u22123<\/jats:sup>\n                      . Other resistance genes, including\n                      <jats:italic>tet(A)<\/jats:italic>\n                      and\n                      <jats:italic>mcr-3.1<\/jats:italic>\n                      , were encoded on separate plasmids.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>These findings underscore the possible role of IncI1 plasmids in bridging resistance gene flow across host boundaries and emphasize the benefit of integrated One Health genomic surveillance to monitor and mitigate antimicrobial resistance transmission.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1772995","type":"journal-article","created":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T06:54:41Z","timestamp":1771397681000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Clonal and plasmid-mediated dissemination of CTX-M-14\u2013producing Escherichia coli within a single cattle farm in Japan"],"prefix":"10.3389","volume":"17","author":[{"given":"Ryuichi","family":"Nakano","sequence":"first","affiliation":[{"name":"Department of Microbiology and Infectious Diseases, Nara Medical University","place":["Nara, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuki","family":"Suzuki","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infectious Diseases, Nara Medical University","place":["Nara, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akiyo","family":"Nakano","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infectious Diseases, Nara Medical University","place":["Nara, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Koichi","family":"Yamaguchi","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infectious Diseases, Nara Medical University","place":["Nara, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saori","family":"Horiuchi","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infectious Diseases, Nara Medical University","place":["Nara, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasuo","family":"Ono","sequence":"additional","affiliation":[{"name":"Faculty of Health and Medical Science, Teikyo Heisei University","place":["Tokyo, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hisakazu","family":"Yano","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infectious Diseases, Nara Medical University","place":["Nara, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,2,18]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"109453","DOI":"10.1016\/j.vetmic.2022.109453","article-title":"Clonal and plasmid-mediated flow of ESBL\/AmpC genes in Escherichia coli in a commercial laying hen farm","volume":"270","author":"Aldea","year":"2022","journal-title":"Vet. Microbiol."},{"key":"ref001","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"9929","DOI":"10.1038\/s41598-024-60461-4","article-title":"Colostrum as a source of ESBL-Escherichia coli in feces of newborn calves","volume":"14","author":"Bachmann","year":"2024","journal-title":"Sci. Rep."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"2145","DOI":"10.1093\/jac\/dkx146","article-title":"Global epidemiology of CTX-M \u03b2-lactamases: temporal and geographical shifts in genotype","volume":"72","author":"Bevan","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"1471","DOI":"10.3390\/microorganisms9071471","article-title":"Successful dissemination of plasmid-mediated extended-spectrum \u03b2-lactamases in Enterobacterales over humans to wild fauna","volume":"9","author":"Beyrouthy","year":"2021","journal-title":"Microorganisms."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1128\/AEM.02616-13","article-title":"Detection of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli on flies at poultry farms","volume":"80","author":"Blaak","year":"2014","journal-title":"Appl. Environ. Microbiol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/AAC.48.1.1-14.2004","article-title":"Growing group of extended-spectrum beta-lactamases: the CTX-M enzymes","volume":"48","author":"Bonnet","year":"2004","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"e00047","DOI":"10.1128\/CMR.00047-19","article-title":"Epidemiology of \u03b2-lactamase-producing pathogens","volume":"33","author":"Bush","year":"2020","journal-title":"Clin. Microbiol. Rev."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"110","DOI":"10.3389\/fmicb.2012.00110","article-title":"CTX-M enzymes: origin and diffusion","volume":"3","author":"Cant\u00f3n","year":"2012","journal-title":"Front. Microbiol."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"2227","DOI":"10.1128\/AAC.01707-08","article-title":"Resistance plasmid families in Enterobacteriaceae","volume":"53","author":"Carattoli","year":"2009","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"dlab092","DOI":"10.1093\/jacamr\/dlab092","article-title":"Extended-spectrum \u03b2-lactamases: an update on their characteristics, epidemiology and detection","volume":"3","author":"Castanheira","year":"2021","journal-title":"JAC Antimicrob Resist."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"110072","DOI":"10.1016\/j.vetmic.2024.110072","article-title":"Epidemiological characteristics of human- and chicken-derived CTX-M-type extended-spectrum \u03b2-lactamase-producing Escherichia coli from China","volume":"293","author":"Chen","year":"2024","journal-title":"Vet. Microbiol."},{"key":"ref13","volume-title":"Performance Standards for Antimicrobial Susceptibility Testing, 35th ed; CLSI Supplement M100","year":"2025"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"645","DOI":"10.3201\/eid1704.101009","article-title":"Complete sequence and molecular epidemiology of IncK epidemic plasmid encoding blaCTX-M-14","volume":"17","author":"Cottell","year":"2011","journal-title":"Emerg. Infect. Dis."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"e0143326","DOI":"10.1371\/journal.pone.0143326","article-title":"Occurrence of ESBL-producing Escherichia coli in livestock and farm workers in Mecklenburg-Western Pomerania, Germany","volume":"10","author":"Dahms","year":"2015","journal-title":"PLOS One."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1093\/jac\/dkp498","article-title":"Development of a set of multiplex PCR assays for the detection of genes encoding important beta-lactamases in Enterobacteriaceae","volume":"65","author":"Dallenne","year":"2010","journal-title":"J. Antimicrob. Chemother."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1093\/cid\/civ318","article-title":"Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157","volume":"61","author":"Dallman","year":"2015","journal-title":"Clin. Infect. Dis."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"e1004776","DOI":"10.1371\/journal.pgen.1004776","article-title":"Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages","volume":"10","author":"de Been","year":"2014","journal-title":"PLoS Genet."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.plasmid.2019.02.001","article-title":"Characterization of the first blaCTX-M-14\/ermB-carrying IncI1 plasmid from Latin America","volume":"102","author":"Di Pilato","year":"2019","journal-title":"Plasmid"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/j.ijfoodmicro.2018.08.003","article-title":"High prevalence of blaCTX-M-14 among genetically diverse Escherichia coli recovered from retail raw chicken meat portions in Japan","volume":"284","author":"Hayashi","year":"2018","journal-title":"Int. J. Food Microbiol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"992","DOI":"10.1016\/j.vetmic.2012.10.029","article-title":"ESBL-producing uropathogenic Escherichia coli isolated from dogs and cats in Switzerland","volume":"162","author":"Huber","year":"2013","journal-title":"Vet. Microbiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.jhin.2024.06.002","article-title":"Protracted transmission and persistence of ST80 vancomycin-resistant Enterococcus faecium clonal complex types CT2933, CT2932 and CT1916 in a large Irish hospital: a 39-month whole-genome sequencing study","volume":"151","author":"Kavanagh","year":"2024","journal-title":"J. Hosp. Infect."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"e0202276","DOI":"10.1371\/journal.pone.0202276","article-title":"Molecular epidemiology and clinical features of extended-spectrum beta-lactamase- or carbapenemase-producing Escherichia coli bacteremia in Japan","volume":"13","author":"Komatsu","year":"2018","journal-title":"PLoS One"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1016\/j.jiac.2019.11.003","article-title":"Multicenter surveillance of the epidemiology of gram-negative bacteremia in Japan","volume":"26","author":"Kosai","year":"2020","journal-title":"J. Infect. Chemother."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.3389\/fmicb.2015.01136","article-title":"Characterization of CTX-M-14-producing Escherichia coli from food-producing animals","volume":"6","author":"Liao","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/S1473-3099(15)00424-7","article-title":"Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study","volume":"16","author":"Liu","year":"2016","journal-title":"Lancet Infect. Dis."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1186\/s12866-018-1270-0","article-title":"Molecular characteristics of extended-spectrum \u03b2-lactamase-producing Escherichia coli isolated from the rivers and lakes in Northwest China","volume":"18","author":"Liu","year":"2018","journal-title":"BMC Microbiol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"e472","DOI":"10.1016\/S2666-5247(21)00117-8","article-title":"Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study","volume":"2","author":"Ludden","year":"2021","journal-title":"Lancet Microbe."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1089\/mdr.2021.0062","article-title":"Predominance of CTX-M-9 group among ESBL-producing Escherichia coli isolated from healthy individuals in Japan","volume":"28","author":"Masui","year":"2022","journal-title":"Microb. Drug Resist."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"100524","DOI":"10.1016\/j.onehlt.2023.100524","article-title":"Genetic relatedness of third-generation cephalosporin-resistant Escherichia coli among livestock, farmers, and patients in Japan","volume":"16","author":"Nakano","year":"2023","journal-title":"One Health."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"3117","DOI":"10.1128\/JCM.00920-13","article-title":"Genetic characteristics of CTX-M-type extended-spectrum-\u03b2-lactamase (ESBL)-producing enterobacteriaceae involved in mastitis cases on Japanese dairy farms, 2007 to 2011","volume":"51","author":"Ohnishi","year":"2013","journal-title":"J. Clin. Microbiol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"e1010018","DOI":"10.1371\/journal.pcbi.1010018","article-title":"Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming","volume":"18","author":"Peng","year":"2022","journal-title":"PLoS Comput. Biol."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1186\/s12864-018-4976-3","article-title":"Whole genome analyses of CMY-2-producing Escherichia coli isolates from humans, animals and food in Germany","volume":"19","author":"Pietsch","year":"2018","journal-title":"BMC Genomics"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"65","DOI":"10.3390\/pathogens9010065","article-title":"High prevalence of CTX-M type extended-spectrum beta-lactamase genes and detection of NDM-1 carbapenemase gene in extraintestinal pathogenic Escherichia coli in Cuba","volume":"9","author":"Qui\u00f1ones","year":"2020","journal-title":"Pathogens."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the genomic gold standard for the prokaryotic species definition","volume":"106","author":"Richter","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1093\/jac\/dkx488","article-title":"Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae","volume":"73","author":"Rozwandowicz","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"2541","DOI":"10.1038\/s41598-024-84754-w","article-title":"Prevalence and genomic insights of carbapenem resistant and ESBL producing multidrug resistant Escherichia coli in urinary tract infections","volume":"15","author":"Sivarajan","year":"2025","journal-title":"Sci. Rep."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1016\/S1473-3099(17)30753-3","article-title":"Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis","volume":"18","author":"Tacconelli","year":"2018","journal-title":"Lancet Infect. Dis."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"eaaw1944","DOI":"10.1126\/science.aaw1944","article-title":"Global trends in antimicrobial resistance in animals in low- and middle-income countries","volume":"365","author":"Van Boeckel","year":"2019","journal-title":"Science"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1007\/978-1-4939-9877-7_22","article-title":"Plasmid typing and classification","volume":"2075","author":"Villa","year":"2020","journal-title":"Methods Mol. Biol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"1179","DOI":"10.1038\/s41467-018-03205-z","article-title":"The global distribution and spread of the mobilized colistin resistance gene mcr-1","volume":"9","author":"Wang","year":"2018","journal-title":"Nat. Commun."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"e1005595","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"ref43","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":"ref44","doi-asserted-by":"publisher","first-page":"982","DOI":"10.1128\/AAC.02746-15","article-title":"IncI1 plasmids carrying various blaCTX-M genes contribute to ceftriaxone resistance in Salmonella enterica serovar Enteritidis in China","volume":"60","author":"Wong","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"101973","DOI":"10.1016\/j.cimid.2023.101973","article-title":"Genomes-based MLST, cgMLST, wgMLST and SNP analysis of Salmonella Typhimurium from animals and humans","volume":"96","author":"Yan","year":"2023","journal-title":"Comp. Immunol. Microbiol. Infect. Dis."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e64359","DOI":"10.1371\/journal.pone.0064359","article-title":"Molecular characteristics of extended-spectrum \u03b2-lactamases in clinical isolates from Escherichia coli at a Japanese tertiary hospital","volume":"8","author":"Yano","year":"2013","journal-title":"PLoS One"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"e00543","DOI":"10.1128\/mBio.00543-17","article-title":"Novel plasmid-mediated colistin resistance gene mcr-3 in Escherichia coli","volume":"8","author":"Yin","year":"2017","journal-title":"MBio"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"101036","DOI":"10.1016\/j.drup.2023.101036","article-title":"Global spread characteristics of CTX-M-type extended-spectrum \u03b2-lactamases: a genomic epidemiology analysis","volume":"73","author":"Yu","year":"2024","journal-title":"Drug Resist. Updat."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1093\/jac\/dky446","article-title":"Detection and characterization of ESBL-producing Escherichia coli expressing mcr-1 from dairy cows in China","volume":"74","author":"Zheng","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"1395","DOI":"10.1101\/gr.232397.117","article-title":"GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens","volume":"28","author":"Zhou","year":"2018","journal-title":"Genome Res."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"3645","DOI":"10.1093\/bioinformatics\/btab234","article-title":"HierCC: a multi-level clustering scheme for population assignments based on core genome MLST","volume":"37","author":"Zhou","year":"2021","journal-title":"Bioinformatics"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1772995\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T06:54:42Z","timestamp":1771397682000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1772995\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,18]]},"references-count":51,"alternative-id":["10.3389\/fmicb.2026.1772995"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1772995","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,18]]},"article-number":"1772995"}}