{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T05:01:38Z","timestamp":1787029298822,"version":"build-2736575974"},"reference-count":27,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T00:00:00Z","timestamp":1763683200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Observation and Research Station of Yunnan Province on Important Animal Disease Prevention in Mengla","award":["202505AM340007"],"award-info":[{"award-number":["202505AM340007"]}]},{"name":"Yunnan Joint International R&D Center of Veterinary Public Health","award":["202403AP140033"],"award-info":[{"award-number":["202403AP140033"]}]},{"name":"Yunnan Provincial Innovation Team of Key Technologies for Prevention and Control of Important Livestock and Poultry Diseases","award":["202405AS350004"],"award-info":[{"award-number":["202405AS350004"]}]},{"name":"Yunnan International Joint R&D Center for Veterinary Drugs","award":["202403AP140012"],"award-info":[{"award-number":["202403AP140012"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Background: Mobile antimicrobial resistance genes (ARGs) on plasmids or other elements enable Salmonella Typhimurium to spread resistance across hosts and environments. The emergence of multi-drug resistance (MDR) Salmonella Typhimurium has raised global concern, yet little is reported about these mobile elements from the Thailand pork supply chain, where this risk of transfer to humans remains largely uncharacterized. Methods: Between March 2023 and February 2024, 25 S. Typhimurium isolates were collected from pig carcasses in slaughterhouses and pork swabs from retail markets in northeastern Thailand. Nine representative isolates, sampled across three seasons, were subjected to Illumina whole-genome sequencing. Assemblies were analyzed for sequence types, phylogenetic relationships, antimicrobial resistance (AMR) determinants, plasmid replicons and mobilization features, functional annotation based on COG (Clusters of Orthologous Groups of proteins) classification, and comparative genomics against a reference strain. Results: Genome assemblies ranged from 4.76 to 5.00 Mb with consistent GC (guanine-cytosine) content (52.0\u201352.2%). Phylogenetic analysis revealed three sequence types: ST34 (77.8%), ST19, and ST1543. ST34 isolates displayed the broadest AMR gene repertoires, carrying tetracycline (tetA\/tetB), sulfonamide (sul1\/sul2\/sul3), aminoglycoside (aadA, aph(6)-Id, aph(3\u2033)-Ib), phenicol (floR, catA1), and \u03b2-lactam (bla_TEM-1B) genes, whereas non-ST34 isolates harbored fewer determinants. ARGs frequently co-localized with IncQ1 and Col-type plasmid replicons, MOB_H\/MobA relaxases (enzymes that initiate plasmid transfer), and conjugation modules (type IV secretion and coupling proteins), often alongside virulence loci and metal resistance operons. Functional annotation showed highly conserved metabolic and housekeeping functions, while comparative genomics confirmed &gt;90% core genome conservation, with variability concentrated in genomic islands encoding hypothetical proteins. These genomic patterns were inferred from a limited WGS dataset (nine isolates) and should therefore be considered exploratory and require confirmation in larger collections. Conclusions: Multi-drug resistant ST34 Salmonella Typhimurium predominated in the northeastern Thailand pork supply chain, with diverse resistance genes carried on IncQ1\/Col-type plasmids linked to MOB_H relaxases and conjugation modules. The stability of these mobilizable elements underscores their role in sustaining MDR traits and highlights the risk of foodborne AMR transmission, reinforcing the need for continuous genomic surveillance under a One Health framework.<\/jats:p>","DOI":"10.3390\/pathogens14121190","type":"journal-article","created":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T11:04:31Z","timestamp":1763723071000},"page":"1190","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Genomic Evidence for the Rise of Salmonella Typhimurium ST34 with Increased Plasmid-Mediated Resistance in the Thailand Pork Chain"],"prefix":"10.3390","volume":"14","author":[{"given":"Hongmei","family":"Liu","sequence":"first","affiliation":[{"name":"Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen 40002, Thailand"},{"name":"Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650051, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ning","family":"Wang","sequence":"additional","affiliation":[{"name":"Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650051, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1701-907X","authenticated-orcid":false,"given":"Sunpetch","family":"Angkititrakul","sequence":"additional","affiliation":[{"name":"Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen 40002, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wengui","family":"Li","sequence":"additional","affiliation":[{"name":"Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650051, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongyang","family":"Luo","sequence":"additional","affiliation":[{"name":"Mengla County Animal Husbandry and Veterinary Station, Xishuangbanna Prefecture, Jinghong 666106, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingpeng","family":"Hou","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Xishuangbanna Vocational and Technical College, Menglun 666300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Wu","sequence":"additional","affiliation":[{"name":"Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650051, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yubo","family":"Shi","sequence":"additional","affiliation":[{"name":"Mengla County Animal Husbandry and Veterinary Station, Xishuangbanna Prefecture, Jinghong 666106, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuelin","family":"Wang","sequence":"additional","affiliation":[{"name":"Mengla County Animal Husbandry and Veterinary Station, Xishuangbanna Prefecture, Jinghong 666106, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fengyun","family":"Li","sequence":"additional","affiliation":[{"name":"Mengla County Animal Husbandry and Veterinary Station, Xishuangbanna Prefecture, Jinghong 666106, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5101-8516","authenticated-orcid":false,"given":"Yaowen","family":"Liu","sequence":"additional","affiliation":[{"name":"Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650051, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1549-8764","authenticated-orcid":false,"given":"Xin","family":"Wu","sequence":"additional","affiliation":[{"name":"Yunnan Joint International R&D Center of Veterinary Public Health, College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650051, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7141-9552","authenticated-orcid":false,"given":"Fanan","family":"Suksawat","sequence":"additional","affiliation":[{"name":"Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen 40002, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Cheng, G., Jian, S., Li, W., Yan, L., Chen, T., Cheng, T., Liu, Z., Ye, G., Tang, H., and Zhang, L. 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