{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T12:17:21Z","timestamp":1789733841196,"version":"4.0.1"},"reference-count":47,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,5,20]],"date-time":"2025-05-20T00:00:00Z","timestamp":1747699200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003669","name":"Korea Centers for Disease Control and Prevention","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003669","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002641","name":"Konkuk University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002641","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Vet. Sci."],"abstract":"<jats:p><jats:italic>Salmonella enterica<\/jats:italic> serotype Enteritidis (<jats:italic>S.<\/jats:italic> Enteritidis) is a leading foodborne pathogen associated with poultry products, and the emergence of antimicrobial resistance (AMR) in this serotype poses a growing public health concern, particularly in regions with increasing poultry trade. Between April and June 2024, we collected 114 poultry meat samples (Mongolian domestic and Chinese imported) from retail markets in Mongolia and isolated 45 <jats:italic>S.<\/jats:italic> Enteritidis strains. Antimicrobial susceptibility testing revealed high resistance rates to nalidixic acid (100%), ampicillin (93.3%), and streptomycin (88.9%). Whole-genome sequencing (WGS) identified major resistance genes, including <jats:italic>aac(6\u2032)-Iaa<\/jats:italic>, <jats:italic>aph(3\u2033)-Ib<\/jats:italic>, <jats:italic>bla<\/jats:italic>TEM-1B, and <jats:italic>sul2<\/jats:italic>. Mongolian domestic isolates additionally harbored extended-spectrum <jats:italic>\u03b2<\/jats:italic>-lactamase (ESBL) <jats:italic>bla<\/jats:italic>CTX-M-14 and plasmid-mediated quinolone resistance (PMQR) <jats:italic>qnrS1,<\/jats:italic> both of which are clinically significant. Plasmid replicon typing revealed IncF as the most prevalent type across isolates, while IncI1- <jats:italic>\u03b1<\/jats:italic> was predominantly found in multidrug-resistant (MDR) domestic strains. Phylogenetic analysis using whole-genome SNPs (wgSNPs) demonstrated that domestic and imported isolates clustered separately, indicating that Chinese <jats:italic>S.<\/jats:italic> Enteritidis strains have not yet been introduced into Mongolia\u2019s domestic poultry industry. This study represents the first comprehensive analysis of prevalence and resistance mechanisms of <jats:italic>S.<\/jats:italic> Enteritidis in Mongolia poultry production. The findings underscore the necessity of continuous surveillance and the implementation of effective antibiotic stewardship in the poultry production sector.<\/jats:p>","DOI":"10.3389\/fvets.2025.1595674","type":"journal-article","created":{"date-parts":[[2025,5,20]],"date-time":"2025-05-20T10:04:20Z","timestamp":1747735460000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Whole-genome sequencing analysis of Salmonella enterica serotype Enteritidis isolated from poultry sources in Mongolia"],"prefix":"10.3389","volume":"12","author":[{"given":"Seung-un","family":"Song","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tae-Min","family":"La","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taesoo","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junyoung","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eunkyung","family":"Shin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uyangaa","family":"Temuujin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji-Yeon","family":"Hyeon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong-Hun","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sang-Won","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,5,20]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1756","DOI":"10.3390\/foods12091756","article-title":"Human salmonellosis: a continuous global threat in the farm-to-fork food safety continuum","volume":"12","author":"Teklemariam","year":"2023","journal-title":"Food Secur"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/j.ijid.2021.02.022","article-title":"Outbreaks of foodborne Salmonella enteritidis in the United States between 1990 and 2015: an analysis of epidemiological and spatial-temporal trends","volume":"105","author":"Sher","year":"2021","journal-title":"Int J Infect Dis"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1089\/fpd.2023.0123","article-title":"Epidemiological and whole genome sequencing analysis of restaurant Salmonella Enteritidis outbreak associated with an infected food handler in Jiangxi Province, China, 2023","volume":"21","author":"Peng","year":"2024","journal-title":"Foodborne Pathog Dis"},{"key":"ref4","article-title":"National Surveillance of Bacterial Foodborne Illnesses (Enteric Diseases) | CDC","year":""},{"key":"ref5","doi-asserted-by":"publisher","first-page":"563","DOI":"10.29322\/ijsrp.10.03.2020.p9963","article-title":"The meat processing industry in Mongolia","volume":"10","author":"Munkhdelger","year":"2020","journal-title":"Int J Scientific Res Public"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"e00092-20","DOI":"10.1128\/AAC.00092-20","article-title":"Epidemiological study on prevalence, serovar diversity, multidrug resistance, and CTX-M-type extended-spectrum \u03b2-lactamases of salmonella spp. from patients with diarrhea, food of animal origin, and pets in several provinces of China","volume":"64","author":"Wang","year":"2020","journal-title":"Antimicrob Agents Chemother"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1295769","DOI":"10.3389\/fmicb.2023.1295769","article-title":"Genomic characterization of Salmonella isolated from retail chicken and humans with diarrhea in Qingdao, China","volume":"14","author":"Wang","year":"2023","journal-title":"Front Microbiol"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"e0094423","DOI":"10.1128\/aem.00944-23","article-title":"Poultry production as the main reservoir of ciprofloxacin- and tigecycline-resistant extended-spectrum \u03b2-lactamase (ESBL)producing Salmonella enterica serovar Kentucky ST198.2-2 causing human infections in China","volume":"89","author":"Wang","year":"2023","journal-title":"Appl Environ Microbiol"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"549","DOI":"10.3389\/fmicb.2020.00549","article-title":"Systematic evaluation of whole genome sequence-based predictions of Salmonella serotype and antimicrobial resistance","volume":"11","author":"Cooper","year":"2020","journal-title":"Front Microbiol"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"582","DOI":"10.1089\/fpd.2020.2856","article-title":"Integrated whole-genome sequencing infrastructure for outbreak detection and source tracing of Salmonella enterica serotype Enteritidis","volume":"18","author":"Deng","year":"2021","journal-title":"Foodborne Pathog Dis"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"20887","DOI":"10.1038\/s41598-021-00224-7","article-title":"Whole genome sequencing and protein structure analyses of target genes for the detection of Salmonella","volume":"11","author":"Hu","year":"2021","journal-title":"Sci Rep"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"235","DOI":"10.3844\/ojbsci.2021.235.244","article-title":"Pcr diagnosis for the identification of the virulent gene of salmonella in poultry meat","volume":"21","author":"Zhanabayeva","year":"2021","journal-title":"Online J Biol Sci"},{"key":"ref13","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":"ref14","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J Comput Biol"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"e01746-19","DOI":"10.1128\/AEM.01746-19","article-title":"SeqSero2: rapid and improved salmonella serotype determination using whole-genome sequencing data","volume":"85","author":"Zhang","year":"2019","journal-title":"Appl Environ Microbiol"},{"key":"ref17","year":"2016"},{"key":"ref18","volume-title":"CLSI. Performance standards for antimicrobial susceptibility testing","author":"Limbago","year":"2019"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin Microbiol Infect"},{"key":"ref20","author":"Seemann","year":"2015"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"W443","DOI":"10.1093\/nar\/gkad382","article-title":"PHASTEST: faster than PHASTER, better than PHAST","volume":"51","author":"Wishart","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"e1005944","DOI":"10.1371\/journal.pcbi.1005944","article-title":"MUMmer4: A fast and versatile genome alignment system","volume":"14","author":"Mar\u00e7ais","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"223","DOI":"10.12688\/wellcomeopenres.16291.2","article-title":"Genomic diversity of Salmonella enterica -the UoWUCC 10K genomes project","volume":"5","author":"Achtman","year":"2021","journal-title":"Wellcome Open Res"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1762","DOI":"10.21105\/joss.01762","article-title":"Mashtree: a rapid comparison of whole genome sequence files","volume":"4","author":"Katz","year":"2019","journal-title":"J Open Source Softw"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1186\/s12859-018-2164-8","article-title":"Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity","volume":"19","author":"Menardo","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"5539","DOI":"10.1093\/nar\/gkz361","article-title":"Fast hierarchical Bayesian analysis of population structure","volume":"47","author":"Tonkin-Hill","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J Antimicrob Chemother"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"PlasmidFinder and pMLST: in silico detection and typing of plasmid","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob Agents Chemother"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"2757","DOI":"10.3390\/foods10112757","article-title":"The prevalence and epidemiology of salmonella in retail raw poultry meat in China: a systematic review and meta-analysis","volume":"10","author":"Sun","year":"2021","journal-title":"Food Secur"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"109649","DOI":"10.1016\/j.ijfoodmicro.2022.109649","article-title":"Prevalence and characterization of Salmonella from meat in slaughterhouses in Hangzhou, China","volume":"371","author":"Liu","year":"2022","journal-title":"Int J Food Microbiol"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"136385","DOI":"10.1016\/j.scitotenv.2019.136385","article-title":"Prevalence, abundance, serovars and antimicrobial resistance of Salmonella isolated from retail raw poultry meat in China","volume":"713","author":"Yang","year":"2020","journal-title":"Sci Total Environ"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"29","DOI":"10.3389\/fvets.2020.00029","article-title":"Prevalence of Salmonella isolates and their distribution based on whole-genome sequence in a chicken slaughterhouse in Jiangsu, China","volume":"7","author":"Gu","year":"2020","journal-title":"Front Vet Sci"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1016\/j.bios.2018.09.078","article-title":"Rapid detection of Salmonella enterica in food samples by a novel approach with combination of sample concentration and direct PCR","volume":"129","author":"Vinayaka","year":"2019","journal-title":"Biosens Bioelectron"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"237","DOI":"10.12688\/wellcomeopenres.16305.2","article-title":"Performance of molecular methods for the detection of Salmonella in human stool specimens","volume":"5","author":"Chirambo","year":"2021","journal-title":"Wellcome Open Res"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"835","DOI":"10.1177\/1040638720952359","article-title":"Development of a qPCR for the detection and quantification of Salmonella spp. in sheep feces and tissues","volume":"32","author":"Parker","year":"2020","journal-title":"J Vet Diagn Invest"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"108611","DOI":"10.1016\/j.ijfoodmicro.2020.108611","article-title":"Detection of Salmonella typhimurium and Listeria monocytogenes biofilm cells exposed to different drying and pre-enrichment times using conventional and rapid methods","volume":"324","author":"R\u00edos-Castillo","year":"2020","journal-title":"Int J Food Microbiol"},{"key":"ref40","volume-title":"Isolation and identification of Salmonella from meat, poultry, pasteurized egg, and catfish products and carcass and environmental sponges","author":"Rose","year":"2014"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"e1010174","DOI":"10.1371\/journal.pgen.1010174","article-title":"Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health","volume":"18","author":"Alikhan","year":"2022","journal-title":"PLoS Genet"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"e00729-21","DOI":"10.1128\/msystems.00729-21","article-title":"Horizontal gene transfer is the Main driver of antimicrobial resistance in broiler chicks infected with Salmonella enterica Serovar Heidelberg","volume":"6","author":"Oladeinde","year":"2021","journal-title":"mSystems"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"102392","DOI":"10.1016\/j.plasmid.2018.12.001","article-title":"Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae","volume":"118","author":"Carattoli","year":"2021","journal-title":"Plasmid"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"e00031-20","DOI":"10.1128\/mmbr.00031-20","article-title":"Incompatibility group I1 (IncI1) plasmids: their genetics, biology, and public health relevance","volume":"85","author":"Foley","year":"2021","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1292\/jvms.11-0488","article-title":"Emergence of Salmonella enterica serovar infantis harboring IncI1 plasmid with blaCTX-M-14 in a broiler farm in Japan","volume":"74","author":"Kameyama","year":"2012","journal-title":"J Vet Med Sci"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e00859-17","DOI":"10.1128\/AAC.00859-17","article-title":"Plasmids of diverse Inc groups disseminate the fosfomycin resistance gene fosA3 among Escherichia coli isolates from pigs, chickens, and dairy cows in Northeast China","volume":"61","author":"Wang","year":"2017","journal-title":"Antimicrob Agents Chemother"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1080\/21553769.2015.1051243","article-title":"Salmonella: a review on pathogenesis, epidemiology and antibiotic resistance","volume":"8","author":"Eng","year":"2015","journal-title":"Front Life Sci"}],"container-title":["Frontiers in Veterinary Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fvets.2025.1595674\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,20]],"date-time":"2025-05-20T10:04:32Z","timestamp":1747735472000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fvets.2025.1595674\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,20]]},"references-count":47,"alternative-id":["10.3389\/fvets.2025.1595674"],"URL":"https:\/\/doi.org\/10.3389\/fvets.2025.1595674","relation":{},"ISSN":["2297-1769"],"issn-type":[{"value":"2297-1769","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,20]]},"article-number":"1595674"}}