{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T04:54:23Z","timestamp":1776315263294,"version":"3.50.1"},"reference-count":62,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T00:00:00Z","timestamp":1776297600000},"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. Vet. Sci."],"abstract":"\n Background<\/jats:title>\n \n Swine production can sustain dense reservoirs of multidrug-resistant (MDR)\n Escherichia coli<\/jats:italic>\n in which mobilizable resistance may co-occur with virulence modules relevant to animal health and One Health risk. We profiled the virulome of Hungarian swine-associated MDR\n E. coli<\/jats:italic>\n and assessed whether key virulence signatures co-segregate with selected high-impact resistance flags.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n In late 2023,\n E. coli<\/jats:italic>\n isolates were obtained from four large-scale Hungarian pig farms through routine veterinary diagnostic\/surveillance sampling. Phenotypic antimicrobial susceptibility testing was performed for the full collection (\n n<\/jats:italic>\n \u202f=\u202f203), including extended-spectrum\n \u03b2<\/jats:italic>\n -lactamase (ESBL) confirmation (\n n<\/jats:italic>\n \u202f=\u202f127). A whole-genome sequencing (WGS) subset (\n n<\/jats:italic>\n \u202f=\u202f116) underwent Illumina sequencing and\n de novo<\/jats:italic>\n assembly. Virulence genes were identified in silico using curated virulence databases with harmonized identity\/coverage thresholds and summarized as gene prevalence and functional modules. Marker-based definitions were applied for extraintestinal pathogenic\n E. coli<\/jats:italic>\n (ExPEC)-like and diarrheagenic\n E. coli<\/jats:italic>\n (DEC)-like signatures. Acquired antimicrobial resistance genes were annotated using CARD\/RGI, and focused analyses considered\n CTX-M<\/jats:italic>\n extended-spectrum beta-lactamase (ESBL) genes and rare, high-consequence determinants (\n mcr-1<\/jats:italic>\n ,\n qnrB5<\/jats:italic>\n ). Associations between virulence markers and resistance flags were tested using Fisher\u2019s exact test. Rather than performing a comprehensive resistome analysis, we focused on selected high-impact resistance determinants (\n CTX-M<\/jats:italic>\n ,\n mcr-1<\/jats:italic>\n ,\n qnrB5<\/jats:italic>\n ) and their co-carriage with virulence markers.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n Across 116 genomes, 208 distinct virulence-associated genes were detected; virulence gene load per genome was heterogeneous. Extraintestinal-associated iron acquisition modules were common, including aerobactin (\n iucABCD<\/jats:italic>\n \/\n iutA<\/jats:italic>\n ) in 31\/116 (26.7%), yersiniabactin (\n fyuA\/irp1\/irp2<\/jats:italic>\n ) in 27\/116 (23.3%), and salmochelin (\n iroB\/iroN<\/jats:italic>\n ) in 17\/116 (14.7%). Toxin-associated determinants were frequent, with\n hlyA<\/jats:italic>\n in 33\/116 (28.4%). DEC markers occurred in 33\/116 (28.4%), including\n eae<\/jats:italic>\n in 23\/116 (19.8%),\n stx2<\/jats:italic>\n in 6\/116 (5.2%), predominantly enterohemorrhagic\n E. coli<\/jats:italic>\n (EHEC)-like (\n stx2<\/jats:italic>\n and\n eae<\/jats:italic>\n ) profiles (5\/116; 4.3%) and\n estIa<\/jats:italic>\n in 10\/116 (8.6%);\n astA<\/jats:italic>\n was present in 27\/116 (23.3%). Stringent ExPEC-like criteria were met by 6\/116 (5.2%), while 15\/116 (12.9%) showed convergent profiles co-carrying aerobactin with at least one DEC marker.\n CTX-M<\/jats:italic>\n genes were detected in 24\/116 (20.7%) and were enriched among aerobactin-positive isolates and DEC-marker-positive isolates; all EHEC-like isolates carried\n CTX-M<\/jats:italic>\n . Rare but critical determinants included\n mcr-1<\/jats:italic>\n (3\/116; 2.6%) and\n qnrB5<\/jats:italic>\n (2\/116; 1.7%).\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n \n Hungarian swine-associated MDR\n E. coli<\/jats:italic>\n show virulome heterogeneity with frequent aerobactin\/toxin modules and DEC markers.\n CTX-M<\/jats:italic>\n enrichment in these profiles indicates virulome\u2013resistome convergence, supporting integrated One Health surveillance.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fvets.2026.1813532","type":"journal-article","created":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T04:20:51Z","timestamp":1776313251000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Virulome\u2013resistome convergence in swine-associated multidrug-resistant Escherichia coli from Hungary: virulence marker profiles and zoonotic potential"],"prefix":"10.3389","volume":"13","author":[{"given":"\u00c1d\u00e1m","family":"Kerek","sequence":"first","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine","place":["Budapest, Hungary"]},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine","place":["Budapest, Hungary"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bal\u00e1zs","family":"Nagyh\u00e1zi","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine","place":["Budapest, Hungary"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gergely \u00c1lmos","family":"Tornyos","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine","place":["Budapest, Hungary"]},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine","place":["Budapest, Hungary"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Levente Hunor","family":"Husz","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine","place":["Budapest, Hungary"]},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine","place":["Budapest, Hungary"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M\u00e1t\u00e9","family":"Hety\u00e9sy","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine","place":["Budapest, Hungary"]},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine","place":["Budapest, Hungary"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eszter","family":"Kaszab","sequence":"additional","affiliation":[{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine","place":["Budapest, Hungary"]},{"name":"One Health Institute, University of Debrecen","place":["Debrecen, Hungary"]},{"name":"Department of Microbiology and Infectious Diseases, University of Veterinary Medicine","place":["Budapest, Hungary"]},{"name":"Department of Bioinformatics, University of Debrecen","place":["Debrecen, Hungary"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Enik\u0151","family":"Feh\u00e9r","sequence":"additional","affiliation":[{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine","place":["Budapest, Hungary"]},{"name":"One Health Institute, University of Debrecen","place":["Debrecen, Hungary"]},{"name":"Department of Microbiology and Infectious Diseases, University of Veterinary Medicine","place":["Budapest, Hungary"]},{"name":"Department of Bioinformatics, University of Debrecen","place":["Debrecen, Hungary"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrik","family":"Mag","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine","place":["Budapest, Hungary"]},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine","place":["Budapest, Hungary"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00c1kos","family":"Jerzsele","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine","place":["Budapest, Hungary"]},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine","place":["Budapest, Hungary"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,4,16]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1649","DOI":"10.1016\/j.clinthera.2020.07.004","article-title":"Antibiotic stewardship in food-producing animals: challenges, progress, and opportunities","volume":"42","author":"Patel","year":"2020","journal-title":"Clin Ther"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"e51","DOI":"10.1093\/cid\/ciw118","article-title":"Implementing an antibiotic stewardship program: guidelines by the Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America","volume":"62","author":"Barlam","year":"2016","journal-title":"Clin Infect Dis"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"5649","DOI":"10.1073\/pnas.1503141112","article-title":"Global trends in antimicrobial use in food animals","volume":"112","author":"Van Boeckel","year":"2015","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"469","DOI":"10.56385\/magyallorv.2025.08.469-481","article-title":"Role of microbiota in cattle reproduction: literature review","volume":"147","author":"Varga-Balogh","year":"2025","journal-title":"Magy Allatorv Lapja"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"100058","DOI":"10.1016\/j.vas.2019.100058","article-title":"Patterns of antibiotic use in global pig production: a systematic review","volume":"7","author":"Lekagul","year":"2019","journal-title":"Vet Anim Sci"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1038\/260040a0","article-title":"Spread of antibiotic-resistant plasmids from chicken to chicken and from chicken to man","volume":"260","author":"Levy","year":"1976","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"723","DOI":"10.56385\/magyallorv.2024.12.723-742","article-title":"Biosecurity situation of large-scale poultry farms in Hungary according to the databases of National Food Chain Safety Office Centre for disease control and biosecurity audit system of poultry product Board of Hungary in the period of 2021\u20132022","volume":"146","author":"Farkas","year":"2024","journal-title":"Magy Allatorv Lapja"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"1524","DOI":"10.3389\/fmicb.2020.01524","article-title":"Antimicrobial resistance in wildlife in Guadeloupe (French West Indies): distribution of a single blaCTX\u2013M\u20131\/IncI1\/ST3 plasmid among humans and wild animals","volume":"11","author":"Guyomard-Rabenirina","year":"2020","journal-title":"Front Microbiol"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1002\/jobm.200900066","article-title":"Wild boars as reservoirs of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli of different phylogenetic groups","volume":"49","author":"Poeta","year":"2009","journal-title":"J Basic Microbiol"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"e0210686","DOI":"10.1371\/journal.pone.0210686","article-title":"High prevalence and diversity of extended-spectrum \u03b2-lactamase and emergence of OXA-48 producing Enterobacterales in wildlife in Catalonia","volume":"14","author":"Darwich","year":"2019","journal-title":"PLoS One"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"55","DOI":"10.24272\/j.issn.2095-8137.2017.003","article-title":"The role of wildlife (wild birds) in the global transmission of antimicrobial resistance genes","volume":"38","author":"Wang","year":"2017","journal-title":"Zool Res"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1186\/s40168-017-0369-0","article-title":"Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey","volume":"5","author":"Ma","year":"2017","journal-title":"Microbiome"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"10.1128\/mbio.02227-15","DOI":"10.1128\/mbio.02227-15","article-title":"Antimicrobial resistance in agriculture","volume":"7","author":"Thanner","year":"2016","journal-title":"MBio"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"1481","DOI":"10.1007\/s10068-022-01157-1","article-title":"Emergence and spread of antibiotic-resistant foodborne pathogens from farm to table","volume":"31","author":"Kim","year":"2022","journal-title":"Food Sci Biotechnol"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"91","DOI":"10.56385\/magyallorv.2024.02.91-105","article-title":"The rise of antimicrobial resistance in wild birds: potential AMR sources and wild birds as AMR reservoirs and disseminators: literature review","volume":"146","author":"Benmazouz","year":"2024","journal-title":"Magy Allatorv Lapja"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/s13756-017-0294-9","article-title":"World Health Organization (WHO) guidelines on use of medically important antimicrobials in food-producing animals","volume":"7","author":"Aidara-Kane","year":"2018","journal-title":"Antimicrob Resist Infect Control"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"429","DOI":"10.56385\/magyallorv.2025.7.429-441","article-title":"The relevance of epigenetic research in veterinary sciences: literature review","volume":"147","author":"L\u0151rincz","year":"2025","journal-title":"Magy Allatorv Lapja"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"1753","DOI":"10.1086\/315418","article-title":"Proposal for a new inclusive designation for extraintestinal pathogenic isolates of Escherichia coli: ExPEC","volume":"181","author":"Russo","year":"2000","journal-title":"J Infect Dis"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/s13099-019-0290-0","article-title":"Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports","volume":"11","author":"Sarowska","year":"2019","journal-title":"Gut Pathog"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1128\/CMR.11.1.142","article-title":"Diarrheagenic Escherichia coli","volume":"11","author":"Nataro","year":"1998","journal-title":"Clin Microbiol Rev"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.3390\/antibiotics12061061","article-title":"Antimicrobial resistance and clonal lineages of Escherichia coli from food-producing animals","volume":"12","author":"Silva","year":"2023","journal-title":"Antibiotics"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"642","DOI":"10.1016\/j.ijmm.2011.09.006","article-title":"What defines extraintestinal pathogenic Escherichia coli?","volume":"301","author":"K\u00f6hler","year":"2011","journal-title":"Int J Med Microbiol"},{"key":"ref23","first-page":"429","article-title":"Enteropathogenic Escherichia coli (EPEC): short literature summary","volume":"143","author":"Adorj\u00e1n","year":"2021","journal-title":"Magy Allatorv Lapja"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"4555","DOI":"10.1128\/AEM.66.10.4555-4558.2000","article-title":"Rapid and simple determination of the Escherichia coli phylogenetic group","volume":"66","author":"Clermont","year":"2000","journal-title":"Appl Environ Microbiol"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"603","DOI":"10.3390\/microorganisms10030603","article-title":"Extended-Spectrum \u00df-lactamase-producing Escherichia coli in conventional and organic pig fattening farms","volume":"10","author":"Meissner","year":"2022","journal-title":"Microorganisms"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"001204","DOI":"10.1099\/mic.0.001204","article-title":"Genomic characterization of antimicrobial resistance in mcr-carrying ESBL-producing Escherichia coli from pigs and humans","volume":"168","author":"Pungpian","year":"2022","journal-title":"Microbiology (Reading)"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1128\/CMR.14.4.933-951.2001","article-title":"Extended-Spectrum \u03b2-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat","volume":"14","author":"Bradford","year":"2001","journal-title":"Clin Microbiol Rev"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1128\/AAC.39.6.1211","article-title":"A functional classification scheme for beta-lactamases and its correlation with molecular structure","volume":"39","author":"Bush","year":"1995","journal-title":"Antimicrob Agents Chemother"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"1486","DOI":"10.1016\/j.addr.2005.04.004","article-title":"Bacterial resistance to antibiotics: active efflux and reduced uptake","volume":"57","author":"Kumar","year":"2005","journal-title":"Adv Drug Deliv Rev"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1128\/CMR.19.2.382-402.2006","article-title":"Clinically relevant chromosomally encoded multidrug resistance efflux pumps in bacteria","volume":"19","author":"Piddock","year":"2006","journal-title":"Clin Microbiol Rev"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1016\/j.bbrc.2009.01.081","article-title":"The multidrug resistance efflux complex, EmrAB from Escherichia coli forms a dimer in vitro","volume":"380","author":"Tanabe","year":"2009","journal-title":"Biochem Biophys Res Commun"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2018\/9519718","article-title":"The growing genetic and functional diversity of extended Spectrum Beta-lactamases","volume":"2018","author":"Ur Rahman","year":"2018","journal-title":"Biomed Res Int"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1097\/PAT.0000000000000235","article-title":"Whole genome sequencing in clinical and public health microbiology","volume":"47","author":"Kwong","year":"2015","journal-title":"Pathology"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"1774","DOI":"10.3390\/antibiotics11121774","article-title":"Whole genome sequencing (WGS) analysis of virulence and AMR genes in extended-Spectrum \u03b2-lactamase (ESBL)-producing Escherichia coli from animal and environmental samples in four Italian swine farms","volume":"11","author":"Bonvegna","year":"2022","journal-title":"Antibiotics (Basel)"},{"key":"ref35","first-page":"e05709","article-title":"Technical specifications on harmonised monitoring of antimicrobial resistance in zoonotic and indicator bacteria from food-producing animals and food","volume-title":"EFSA J","author":"Aerts","year":"2019"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"e07867","DOI":"10.2903\/j.efsa.2023.7867","article-title":"The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2020\/2021","volume":"21","year":"2023","journal-title":"EFSA J"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"707","DOI":"10.56385\/magyallorv.2025.12.707-718","article-title":"Possibilities of in vitro modelling of porcine infectious enteropathies: literature review","volume":"147","author":"Somogyi","year":"2025","journal-title":"Magy Allatorv Lapja"},{"key":"ref38","volume-title":"Clinical and Laboratory Standards Institute. CLSI. Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria that Grow Aerobically","year":"2024"},{"key":"ref39","volume-title":"DNA Extraction with Zymo Quick-DNATM Fungal\/Bacterial Miniprep Kit","author":"Shen","year":"2025"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1007\/978-1-60327-411-1_5","article-title":"Next-generation sequencing methods: impact of sequencing accuracy on SNP discovery","volume":"578","author":"Chan","year":"2009","journal-title":"Methods Mol Biol"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"pdb.prot107900","DOI":"10.1101\/pdb.prot107900","article-title":"Small-scale Illumina library preparation using the Illumina Nextera XT DNA library preparation kit","volume":"2023","author":"Zeden","year":"2023","journal-title":"Cold Spring Harb Protoc"},{"key":"ref42","article-title":"FastQC a quality control tool for high throughput sequence data","author":"Andrews","year":"2012"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref44","article-title":"Bloocoo, a memory efficient read corrector","author":"Benoit","year":"2014"},{"key":"ref45","article-title":"Trim Galore","author":"Krueger","year":"2022"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"3262","DOI":"10.1093\/bioinformatics\/btv337","article-title":"Assembling short reads from jumping libraries with large insert sizes","volume":"31","author":"Vasilinetc","year":"2015","journal-title":"Bioinformatics"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"S6","DOI":"10.1186\/1471-2105-14-S7-S6","article-title":"GAM-NGS: genomic assemblies merger for next generation sequencing","volume":"14","author":"Vicedomini","year":"2013","journal-title":"BMC Bioinform"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes","volume":"38","author":"Manni","year":"2021","journal-title":"Mol Biol Evol"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"2202","DOI":"10.1093\/bioinformatics\/btx153","article-title":"GenomeScope: fast reference-free genome profiling from short reads","volume":"33","author":"Vurture","year":"2017","journal-title":"Bioinformatics"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinform"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"D517","DOI":"10.1093\/nar\/gkz935","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1093\/jac\/dkaa390","article-title":"Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder","volume":"76","author":"Johansson","year":"2021","journal-title":"J Antimicrob Chemother"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"e35","DOI":"10.1093\/nar\/gkx1321","article-title":"PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures","volume":"46","author":"Krawczyk","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1186\/s13073-018-0587-5","article-title":"Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae","volume":"10","author":"Lam","year":"2018","journal-title":"Genome Med"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1016\/S0378-1097(01)00060-X","article-title":"The Yersinia high-pathogenicity island is highly predominant in virulence-associated phylogenetic groups of Escherichia coli","volume":"196","author":"Clermont","year":"2001","journal-title":"FEMS Microbiol Lett"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1186\/s12917-024-04317-z","article-title":"Isolation and evaluation of the pathogenicity of a hybrid Shiga toxin-producing and Enterotoxigenic Escherichia coli in pigs","volume":"20","author":"Nammuang","year":"2024","journal-title":"BMC Vet Res"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/s0378-1135(02)00262-6","article-title":"Detection of the enteroaggregative Escherichia coli heat-stable enterotoxin 1 (EAST1) gene and its relationship with fimbrial and enterotoxin markers in E. coli isolates from pigs with diarrhoea","volume":"91","author":"Osek","year":"2003","journal-title":"Vet Microbiol"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"1704407","DOI":"10.3389\/fcimb.2025.1704407","article-title":"Impact of virulence genes and pathotypes of intestinal pathogenic Escherichia coli on gastrointestinal lesions in pre- and post-weaning piglets","volume":"15","author":"Sukali\u0107","year":"2026","journal-title":"Front Cell Infect Microbiol"}],"container-title":["Frontiers in Veterinary Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fvets.2026.1813532\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T04:20:53Z","timestamp":1776313253000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fvets.2026.1813532\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,16]]},"references-count":62,"alternative-id":["10.3389\/fvets.2026.1813532"],"URL":"https:\/\/doi.org\/10.3389\/fvets.2026.1813532","relation":{},"ISSN":["2297-1769"],"issn-type":[{"value":"2297-1769","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,16]]},"article-number":"1813532"}}