{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T15:18:33Z","timestamp":1772119113087,"version":"3.50.1"},"reference-count":94,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T00:00:00Z","timestamp":1771977600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100017503","name":"Recovery and Resilience Facility","doi-asserted-by":"publisher","award":["RRF-2.3.1-21-2022-00001"],"award-info":[{"award-number":["RRF-2.3.1-21-2022-00001"]}],"id":[{"id":"10.13039\/501100017503","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Background: Extended-spectrum \u03b2-lactamase (ESBL)-producing E. coli are a major One Health concern because they compromise critically important cephalosporins and may spread via mobile genetic elements, including plasmids and transposon-associated modules, within food-animal production systems. Objectives: The aim of this study was to characterize cefotaxime (CTX)\/clavulanic acid (CLA) inhibitor-positive phenotype profiles in pig-associated multidrug-resistant (MDR) E. coli and resolve their genetic basis using whole-genome sequencing, with emphasis on ESBL determinants and their predicted mobility context. Methods: MDR E. coli isolates (n = 203) from four large-scale pig farms in Hungary were tested by broth microdilution minimum inhibitory concentration (MIC) determination and Clinical and Laboratory Standards Institute (CLSI) inhibitor-based ESBL confirmation using cefotaxime with\/without clavulanic acid. CTX\/CLA inhibitor-positive isolates (inhibitor-positive phenotype) were subjected to whole-genome sequencing (WGS; n = 116) and resistome profiling; antimicrobial resistance genes (ARGs) were called against the Comprehensive Antibiotic Resistance Database (CARD) and mobility context was inferred using plasmid-origin and MGE-proximity prediction. Results: Overall, 127\/203 isolates (62.6%) showed a CTX\/CLA inhibitor-positive phenotype with a pronounced inhibitory effect (median cefotaxime\/cefotaxime\u2013clavulanate ratio: 33.3). In the sequenced subset (n = 116), 5427 ARG hits were identified (82 unique ARGs in the export), including frequent acquired determinants affecting tetracyclines, sulfonamides\/trimethoprim, aminoglycosides, and phenicols; plasmid-mediated quinolone resistance (qnrB5) and mobilizable colistin resistance (mcr-1) were detected at low frequency. Classical \u03b2-lactamase genes were detected, including CTX-M (ESBL genes) and TEM alleles. CTX-M and\/or TEM were detected in 47\/116 genomes (40.5%), dominated by CTX-M-32 (11.2%) and TEM-1 (23.3%); detected ESBL determinants were predominantly predicted to be located on contigs predicted to be of plasmid origin, with a subset showing signatures consistent with transposition-associated mobilization. Conclusion: The high burden of inhibitor-positive phenotype, together with an inferred plasmid-\/MGE-associated context for a subset of ESBL genes, and substantial phenotype\u2013genotype heterogeneity, supports integrated phenotypic\u2013genomic surveillance to refine AMR risk assessment and guide targeted stewardship and biosecurity interventions in pig production.<\/jats:p>","DOI":"10.3390\/ani16050722","type":"journal-article","created":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T13:58:03Z","timestamp":1772114283000},"page":"722","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated Phenotypic and Genomic Characterization of Cefotaxime\/Clavulanic Acid Inhibitor-Positive Multidrug-Resistant Escherichia coli from Large-Scale Pig Farms in Hungary"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7837-2459","authenticated-orcid":false,"given":"\u00c1d\u00e1m","family":"Kerek","sequence":"first","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine, Istv\u00e1n utca 2, H-1078 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, Istv\u00e1n utca 2, H-1078 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, Istv\u00e1n utca 2, H-1078 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, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5750-1872","authenticated-orcid":false,"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, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"One Health Institute, University of Debrecen, Nagyerdei Krt. 98, H-4032 Debrecen, Hungary"},{"name":"Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"Department of Bioinformatics, University of Debrecen, Nagyerdei Krt. 98, H-4032 Debrecen, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7778-9116","authenticated-orcid":false,"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, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"One Health Institute, University of Debrecen, Nagyerdei Krt. 98, H-4032 Debrecen, Hungary"},{"name":"Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"Department of Bioinformatics, University of Debrecen, Nagyerdei Krt. 98, H-4032 Debrecen, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0236-4117","authenticated-orcid":false,"given":"Patrik","family":"Mag","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3380-0827","authenticated-orcid":false,"given":"\u00c1kos","family":"Jerzsele","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Toxicology, University of Veterinary Medicine, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine, Istv\u00e1n utca 2, H-1078 Budapest, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Mancuso, G., Midiri, A., Gerace, E., and Biondo, C. 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