{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T18:27:19Z","timestamp":1786645639125,"version":"build-2736575974"},"reference-count":47,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005076","name":"Agricultural Research Development Agency","doi-asserted-by":"publisher","award":["CRP660503068"],"award-info":[{"award-number":["CRP660503068"]}],"id":[{"id":"10.13039\/501100005076","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Center of Excellence of Innovative Diagnosis of Antimicrobial Resistance"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    The global dissemination of antimicrobial-resistant (AMR) bacteria along the pork supply chain is a critical concern, as pigs are significant reservoirs for multidrug-resistant (MDR)\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    , a WHO-listed priority pathogen. This study investigated the genomic characteristics of extended-spectrum \u03b2-lactamase (ESBL)-producing\n                    <jats:italic>E. coli<\/jats:italic>\n                    across the pork production chain in Central Thailand, specifically focusing on the emergence of the last-resort tigecycline resistance gene,\n                    <jats:italic>tet<\/jats:italic>\n                    (X4). ESBL-producing\n                    <jats:italic>E. coli<\/jats:italic>\n                    isolates from a slaughterhouse pig cecum (n\u2009=\u200914) and retail market pork (n\u2009=\u200926) in central Thailand were collected. Whole-genome sequencing (WGS) was employed to analyze the resistome, virulome, and phylogenomic relationships. Analysis included non-metric multidimensional scaling (NMDS) of resistance and virulence gene determinants, single-nucleotide polymorphism (SNP) phylogeny, and core genome MLST (cgMLST). Resistome, virulome, and NMDS analysis demonstrated a shared clustering of antimicrobial resistance genes (ARGs) and virulence factors (VF) genes between cecum and pork isolates. Most isolates possessed extraintestinal pathogenic\n                    <jats:italic>E. coli<\/jats:italic>\n                    (ExPEC)-associated VF genes, underscoring the widespread pathogenic risk.\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) was predominantly found in the dominant ST48 clone and these\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) adjacent to IS\n                    <jats:italic>CR2<\/jats:italic>\n                    , providing evidence of horizontal gene transfer (HGT). cgMLST further demonstrated that these\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) isolates are genetically related to global human, animal, and environmental strains. This study provides the first genomic evidence of\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) circulation in ESBL-producing\n                    <jats:italic>E. coli<\/jats:italic>\n                    population across the slaughterhouse-to-retail continuum in central Thailand. Our findings suggest that the dissemination of\n                    <jats:italic>tet<\/jats:italic>\n                    (X4) in the pork supply chain is primarily via HGT. The implementation of firm food safety policies and enhanced hygiene practices is urgently required to inhibit the transmission of these high-risk strains to consumers.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0355459","type":"journal-article","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T17:28:46Z","timestamp":1786642126000},"page":"e0355459","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Identification of high-risk extended-spectrum \u03b2-lactamase-producing Escherichia coli clones harboring tet(X4) along the pork supply chain in central Thailand"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9426-5568","authenticated-orcid":true,"given":"Variya","family":"Nemidkanam","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramzan","family":"Ahmed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0717-5466","authenticated-orcid":true,"given":"Nuntaree","family":"Chaichanawongsaroj","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,8,13]]},"reference":[{"issue":"11","key":"pone.0355459.ref001","doi-asserted-by":"crossref","first-page":"1496","DOI":"10.4315\/JFP-22-038","article-title":"Codex Alimentarius Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance Are Incompatible with Available Surveillance Data","volume":"85","author":"DD Taylor","year":"2022","journal-title":"J Food Prot"},{"key":"pone.0355459.ref002","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/bs.afnr.2018.04.004","article-title":"Antimicrobial Resistance in the Food Chain in the European Union","volume":"86","author":"D Florez-Cuadrado","year":"2018","journal-title":"Adv Food Nutr Res"},{"key":"pone.0355459.ref003","article-title":"Food balances","author":"FAOSTAT","year":"2025"},{"key":"pone.0355459.ref004","doi-asserted-by":"crossref","first-page":"689015","DOI":"10.3389\/fmicb.2021.689015","article-title":"Reducing the Risk of Transmission of Critical Antimicrobial Resistance Determinants From Contaminated Pork Products to Humans in South-East Asia","volume":"12","author":"W Sirichokchatchawan","year":"2021","journal-title":"Front Microbiol"},{"issue":"5","key":"pone.0355459.ref005","doi-asserted-by":"crossref","first-page":"057004","DOI":"10.1289\/EHP7327","article-title":"Contamination of retail meat samples with multidrug-resistant organisms in relation to organic and conventional production and processing: a cross-sectional analysis of data from the United States National Antimicrobial Resistance Monitoring System, 2012\u20132017","volume":"129","author":"GK Innes","year":"2021","journal-title":"Environmental Health Perspectives"},{"key":"pone.0355459.ref006","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1007\/s10123-023-00445-y","article-title":"Traditional marketed meats as a reservoir of multidrug-resistant Escherichia coli","volume":"28","author":"F Guibert","year":"2025","journal-title":"Int Microbiol"},{"issue":"3","key":"pone.0355459.ref007","doi-asserted-by":"crossref","first-page":"244","DOI":"10.3390\/antibiotics10030244","article-title":"High Risk Clone: A Proposal of Criteria Adapted to the One Health Context with Application to Enterotoxigenic Escherichia coli in the Pig Population","volume":"10","author":"M de Lagarde","year":"2021","journal-title":"Antibiotics (Basel)"},{"issue":"12","key":"pone.0355459.ref008","first-page":"2077","article-title":"Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli","volume":"12","author":"B Kocsis","year":"2022","journal-title":"Life (Basel)"},{"issue":"9","key":"pone.0355459.ref009","doi-asserted-by":"crossref","first-page":"1450","DOI":"10.1038\/s41564-019-0445-2","article-title":"Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans","volume":"4","author":"T He","year":"2019","journal-title":"Nat Microbiol"},{"issue":"8","key":"pone.0355459.ref010","doi-asserted-by":"crossref","DOI":"10.3390\/ijms22083905","article-title":"Acquisition and spread of antimicrobial resistance: A tet(X) case study","volume":"22","author":"R Aminov","year":"2021","journal-title":"Int J Mol Sci"},{"key":"pone.0355459.ref011","doi-asserted-by":"crossref","first-page":"110145","DOI":"10.1016\/j.ijfoodmicro.2023.110145","article-title":"First detection of tet(X4)-positive Enterobacterales in retail vegetables and clonal spread of Escherichia coli ST195 producing Tet(X4) in animals, foods, and humans across China and Thailand","author":"C Yue","year":"2023","journal-title":"Int J Food Microbiol"},{"key":"pone.0355459.ref012","doi-asserted-by":"crossref","first-page":"110574","DOI":"10.1016\/j.ijfoodmicro.2024.110574","article-title":"Emergence of tet(X4)-positive Enterobacterales in retail eggs and the widespread of IncFIA(HI1)-HI1A-HI1B(R27) plasmids carrying tet(X4)","volume":"414","author":"C Yue","year":"2024","journal-title":"Int J Food Microbiol"},{"key":"pone.0355459.ref013","doi-asserted-by":"crossref","first-page":"109692","DOI":"10.1016\/j.ijfoodmicro.2022.109692","article-title":"Characterization of blaNDM-positive Enterobacteriaceae reveals the clonal dissemination of Enterobacter hormaechei coharboring blaNDM and tet(X4) along the pork production chain","volume":"372","author":"R Li","year":"2022","journal-title":"Int J Food Microbiol"},{"issue":"14","key":"pone.0355459.ref014","first-page":"48264","article-title":"Seasonal pollution characteristics of antibiotics on pig farms of different scales","volume":"19","author":"D Du","year":"2022","journal-title":"Int J Environ Res Public Health"},{"key":"pone.0355459.ref015","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.emcon.2021.12.003","article-title":"Occurrence of antibiotics in typical pig farming and its wastewater treatment in Thailand","volume":"8","author":"R Chan","year":"2022","journal-title":"Emerging Contaminants"},{"issue":"5","key":"pone.0355459.ref016","doi-asserted-by":"crossref","first-page":"403","DOI":"10.3390\/antibiotics13050403","article-title":"Antimicrobial Use in Pig Farms in the Midwestern Region of Minas Gerais, Brazil","volume":"13","author":"de Oliveira BC","year":"2024","journal-title":"Antibiotics (Basel)"},{"key":"pone.0355459.ref017","doi-asserted-by":"crossref","first-page":"969769","DOI":"10.3389\/fmicb.2022.969769","article-title":"Dissemination and prevalence of plasmid-mediated high-level tigecycline resistance gene tet (X4)","volume":"13","author":"S Zhang","year":"2022","journal-title":"Front Microbiol"},{"issue":"3","key":"pone.0355459.ref018","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0248536","article-title":"Rapid detection of extended spectrum \u03b2-lactamase producing Escherichia coli isolated from fresh pork meat and pig cecum samples using multiplex recombinase polymerase amplification and lateral flow strip analysis","volume":"16","author":"S Kanokudom","year":"2021","journal-title":"PLoS One"},{"key":"pone.0355459.ref019","volume-title":"Performance standards for antimicrobial susceptibility testing","year":"2019","edition":"29"},{"issue":"9","key":"pone.0355459.ref020","doi-asserted-by":"crossref","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":"NR Waters","year":"2020","journal-title":"Access Microbiol"},{"key":"pone.0355459.ref021","doi-asserted-by":"crossref","DOI":"10.3389\/fbrio.2024.1432292","article-title":"Genomic characterisation of generic Escherichia coli from food-producing animals and products of animal origin in South Africa","volume":"3","author":"R Malesa","year":"2024","journal-title":"Frontiers in Bacteriology"},{"key":"pone.0355459.ref022","doi-asserted-by":"crossref","first-page":"111085","DOI":"10.1016\/j.ijfoodmicro.2025.111085","article-title":"Whole-genome sequence-based comparison of antimicrobial resistant diarrheagenic Escherichia coli in pork and chicken production chains in Korea","volume":"431","author":"H Cho","year":"2025","journal-title":"Int J Food Microbiol"},{"issue":"10","key":"pone.0355459.ref023","doi-asserted-by":"crossref","first-page":"2581","DOI":"10.3390\/microorganisms11102581","article-title":"Antimicrobial Resistance in Bacteria from Meat and Meat Products: A One Health Perspective","volume":"11","author":"S Concei\u00e7\u00e3o","year":"2023","journal-title":"Microorganisms"},{"issue":"6","key":"pone.0355459.ref024","article-title":"Sharing of Antimicrobial Resistance Genes between Humans and Food Animals","volume":"7","author":"H Cao","year":"2022","journal-title":"mSystems"},{"issue":"3","key":"pone.0355459.ref025","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1089\/fpd.2021.0059","article-title":"Occurrence, Antimicrobial Resistance Profile, and Characterization of Extended-Spectrum \u03b2-Lactamase-Producing Escherichia coli Isolates from Minced Meat at Local Markets in Thailand","volume":"19","author":"P Sornsenee","year":"2022","journal-title":"Foodborne Pathog Dis"},{"issue":"4","key":"pone.0355459.ref026","doi-asserted-by":"crossref","first-page":"519","DOI":"10.33073\/pjm-2022-046","article-title":"The emergence of colistin- and imipenem-associated multidrug resistance in Escherichia coli isolates from retail meat","volume":"71","author":"BC Iweriebor","year":"2022","journal-title":"Polish Journal of Microbiology"},{"issue":"14","key":"pone.0355459.ref027","doi-asserted-by":"crossref","first-page":"2010","DOI":"10.3390\/foods11142010","article-title":"International Spread of Tet(X4)-Producing Escherichia coli Isolates","volume":"11","author":"Z Zhang","year":"2022","journal-title":"Foods"},{"issue":"3","key":"pone.0355459.ref028","article-title":"Evolutionary Trajectory of the Tet(X) Family: Critical Residue Changes towards High-Level Tigecycline Resistance","volume":"6","author":"C-Y Cui","year":"2021","journal-title":"mSystems"},{"issue":"12","key":"pone.0355459.ref029","doi-asserted-by":"crossref","first-page":"103142","DOI":"10.1016\/j.psj.2023.103142","article-title":"Decoding the enigma: unveiling the molecular transmission of avian-associated tet(X4)-positive E. coli in Sichuan Province, China","volume":"102","author":"S Zhang","year":"2023","journal-title":"Poult Sci"},{"issue":"10","key":"pone.0355459.ref030","doi-asserted-by":"crossref","first-page":"957","DOI":"10.3390\/antibiotics13100957","article-title":"Phenotypic and Genotypic Characterization of Escherichia coli and Salmonella spp. Isolates from Pigs at Slaughterhouse and from Commercial Pork Meat in Portugal","volume":"13","author":"C Gon\u00e7alves","year":"2024","journal-title":"Antibiotics (Basel)"},{"key":"pone.0355459.ref031","doi-asserted-by":"crossref","first-page":"175705","DOI":"10.1016\/j.scitotenv.2024.175705","article-title":"Epidemiology and antimicrobial resistance profiles of pathogenic Escherichia coli from commercial swine and poultry abattoirs and farms in South Africa: A One Health approach","volume":"951","author":"ST Ogundare","year":"2024","journal-title":"Sci Total Environ"},{"issue":"7","key":"pone.0355459.ref032","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0307544","article-title":"Phylogenetic diversity and virulence gene characteristics of Escherichia coli from pork and patients with urinary tract infections in Thailand","volume":"19","author":"P Ketkhao","year":"2024","journal-title":"PLoS One"},{"issue":"6","key":"pone.0355459.ref033","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1007\/s10096-025-05113-9","article-title":"Large DNA fragment ISEc9-mediated transposition during natural transformation allows interspecies dissemination of antimicrobial resistance genes","volume":"44","author":"S Domingues","year":"2025","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"pone.0355459.ref034","doi-asserted-by":"crossref","first-page":"175475","DOI":"10.1016\/j.scitotenv.2024.175475","article-title":"ESBL-producing Escherichia coli prevalence and sharing across seabirds of central Chile","volume":"951","author":"T Suarez-Yana","year":"2024","journal-title":"Sci Total Environ"},{"issue":"1","key":"pone.0355459.ref035","doi-asserted-by":"crossref","first-page":"79","DOI":"10.3109\/1040841X.2012.691460","article-title":"Epidemiology and genetics of CTX-M extended-spectrum \u03b2-lactamases in Gram-negative bacteria","volume":"39","author":"W-H Zhao","year":"2013","journal-title":"Crit Rev Microbiol"},{"issue":"4","key":"pone.0355459.ref036","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1089\/mdr.2019.0438","article-title":"Presence and Transfer of Antimicrobial Resistance Determinants in Escherichia coli in Pigs, Pork, and Humans in Thailand and Lao PDR Border Provinces","volume":"27","author":"C Pungpian","year":"2021","journal-title":"Microb Drug Resist"},{"issue":"10","key":"pone.0355459.ref037","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.3390\/antibiotics10101236","article-title":"Dissection of Highly Prevalent qnrS1-Carrying IncX Plasmid Types in Commensal Escherichia coli from German Food and Livestock","volume":"10","author":"K Juraschek","year":"2021","journal-title":"Antibiotics (Basel)"},{"issue":"8","key":"pone.0355459.ref038","doi-asserted-by":"crossref","first-page":"700","DOI":"10.3390\/pathogens13080700","article-title":"Phylogenetics and Mobilization of Genomic Traits of Cephalosporin-Resistant Escherichia coli Originated from Retail Meat","volume":"13","author":"E Iwan","year":"2024","journal-title":"Pathogens"},{"issue":"10","key":"pone.0355459.ref039","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1089\/fpd.2021.0011","article-title":"Prevalence and Molecular Characterization of Antimicrobial-Resistant Escherichia coli in Pig Farms, Slaughterhouses, and Terminal Markets in Henan Province of China","volume":"18","author":"Z Hu","year":"2021","journal-title":"Foodborne Pathog Dis"},{"issue":"10","key":"pone.0355459.ref040","first-page":"001549","article-title":"A multi-isolate genomic approach identifies diverse Escherichia coli contamination and antimicrobial resistance carriage on retail foods","volume":"11","author":"G Astorga","year":"2025","journal-title":"Microb Genom"},{"key":"pone.0355459.ref041","doi-asserted-by":"crossref","first-page":"154010","DOI":"10.1016\/j.scitotenv.2022.154010","article-title":"Structural diversity of the ISCR2-mediated rolling-cycle transferable unit carrying tet(X4)","volume":"826","author":"D Liu","year":"2022","journal-title":"Sci Total Environ"},{"key":"pone.0355459.ref042","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/j.jgar.2025.12.006","article-title":"Detection of clinical isolates of tigecycline-resistant Escherichia coli harbouring tet(X4) in Myanmar","volume":"46","author":"M Kirikae","year":"2026","journal-title":"J Glob Antimicrob Resist"},{"issue":"4","key":"pone.0355459.ref043","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.03969-23","article-title":"Comparison of tet(X4)-containing contigs assembled from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects","volume":"12","author":"Y Ding","year":"2024","journal-title":"Microbiol Spectr"},{"key":"pone.0355459.ref044","doi-asserted-by":"crossref","first-page":"1128905","DOI":"10.3389\/fmicb.2023.1128905","article-title":"IncHI1 plasmids mediated the tet(X4) gene spread in Enterobacteriaceae in porcine","volume":"14","author":"J Ma","year":"2023","journal-title":"Front Microbiol"},{"issue":"4","key":"pone.0355459.ref045","article-title":"Large-Scale Studies on Antimicrobial Resistance and Molecular Characterization of Escherichia coli from Food Animals in Developed Areas of Eastern China","volume":"10","author":"J Ma","year":"2022","journal-title":"Microbiol Spectr"},{"issue":"1","key":"pone.0355459.ref046","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1080\/22221751.2019.1653795","article-title":"Emergence of mobile tigecycline resistance mechanism in Escherichia coli strains from migratory birds in China","volume":"8","author":"C Chen","year":"2019","journal-title":"Emerg Microbes Infect"},{"key":"pone.0355459.ref047","doi-asserted-by":"crossref","first-page":"101329","DOI":"10.1016\/j.onehlt.2026.101329","article-title":"Characteristics of Escherichia coli co-harboring blaNDM and mcr-1 genes from market chicken meat","volume":"22","author":"Z Li","year":"2026","journal-title":"One Health"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0355459","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T17:28:53Z","timestamp":1786642133000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0355459"}},"subtitle":[],"editor":[{"given":"Zhi","family":"Ruan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,13]]},"references-count":47,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0355459","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,13]]}}}