{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T06:18:21Z","timestamp":1790662701983,"version":"4.1.0"},"reference-count":74,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T00:00:00Z","timestamp":1775088000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012550","name":"National Recovery Fund budget estimate, RRF-2.3.1-21 funding scheme","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\/501100012550","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: Multidrug-resistant (MDR) Escherichia coli in intensive pig production represents a persistent animal health and One Health concern. Here, we integrated quantitative phenotypic susceptibility data with whole-genome sequencing (WGS) to characterize the resistome and its inferred genomic context (chromosomal vs. plasmid-predicted contigs and mobile genetic element (MGE)-proximal regions) in swine-associated MDR E. coli from Hungary. Methods: A total of 203 E. coli isolates from large-scale pig farms were tested by broth microdilution. Based on resistance-oriented screening from an extended-spectrum \u03b2-lactamase (ESBL)-screen-positive pool, 116 isolates were subjected to whole-genome sequencing (WGS) as a resistance-enriched subset. Resistance determinants were annotated using the Comprehensive Antibiotic Resistance Database (CARD). Results: Resistance-oriented screening indicated frequent \u03b2-lactamase activity and ESBL screening positivity (110\/203 and 127\/203 isolates, respectively), consistent with strong antimicrobial selection pressure in the source population. Across the full phenotypic panel, 78\/203 isolates (38.4%) met the MDR definition (non-susceptible to \u22653 antimicrobial classes), with marked between-farm variation (p &lt; 0.001) but no age-group effect (p = 0.75). Non-\u03b2-lactam minimum inhibitory concentration (MIC) distributions showed pronounced, site-dependent high-MIC \u201ctails\u201d, most notably for tetracyclines, trimethoprim\u2013sulfamethoxazole, fluoroquinolones, and colistin. In the WGS cohort (n = 116), we detected 82 distinct resistance determinants (5433 total occurrences), featuring a conserved chromosomal backbone enriched for intrinsic multidrug resistance components and lipid A modification pathways, alongside common plasmid- and MGE-associated acquired ARG modules involving tetracycline (tetA\/tetB), sulfonamide\/trimethoprim (sul\/dfrA), aminoglycoside-modifying enzymes, and phenicol determinants (floR\/cat). High-priority mobile determinants were rare but present, including mcr-1 (3\/116; plasmid-associated) and plasmid-mediated quinolone resistance qnrB5 (2\/116). Conclusions: Importantly, mobility\/context inferences are restricted to this ESBL-screen-enriched WGS subset. Swine-associated E. coli from Hungarian large-scale farms harbors complex resistance architectures shaped by co-selection of mobile ARG modules on top of a pervasive chromosomal resistance backbone. Mobility-aware surveillance and stewardship are warranted to mitigate dissemination risks at the animal\u2013environment\u2013human interface.<\/jats:p>","DOI":"10.3390\/antibiotics15040367","type":"journal-article","created":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T14:09:54Z","timestamp":1775138994000},"page":"367","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Inferred Mobility-Resolved Resistome Architecture Suggests Recurrent Co-Resistance Modules on a Conserved Chromosomal Backbone in Multidrug-Resistant Escherichia coli from Intensive Swine Production in Hungary"],"prefix":"10.3390","volume":"15","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, H-1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"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":[{"vocabulary":"crossref","role":"author"}]},{"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"},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine, H-1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"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"},{"name":"National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine, H-1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00e1t\u00e9","family":"Hety\u00e9sy","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, H-1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"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, 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 u 2, H-1078 Budapest, Hungary"},{"name":"Department of Bioinformatics, University of Debrecen, Nagyerdei Krt. 98, H-4032 Debrecen, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"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, 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 u 2, H-1078 Budapest, Hungary"},{"name":"Department of Bioinformatics, University of Debrecen, Nagyerdei Krt. 98, H-4032 Debrecen, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"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, H-1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"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, H-1078 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2198","DOI":"10.1021\/acs.jcim.0c01441","article-title":"AMPGAN v2: Machine Learning Guided Design of Antimicrobial Peptides","volume":"61","author":"Ferrell","year":"2021","journal-title":"J. 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