{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T20:40:45Z","timestamp":1792615245643,"version":"4.5.0"},"reference-count":34,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000},"content-version":"vor","delay-in-days":14,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003478","name":"Government of Japan Ministry of Health Labour and Welfare","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003478","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Food Protection"],"published-print":{"date-parts":[[2026,10]]},"DOI":"10.1016\/j.jfp.2026.100948","type":"journal-article","created":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T15:25:08Z","timestamp":1792509908000},"page":"100948","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic epidemiology of Salmonella from retail chicken meat in Japan: decline in pESI-like plasmid-harboring S. Infantis ST32 and predominance of S. Schwarzengrund ST241"],"prefix":"10.1016","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5881-6078","authenticated-orcid":false,"given":"Kanako","family":"Ishihara","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-4127-3113","authenticated-orcid":false,"given":"Christine Dale","family":"Ajero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6704-4601","authenticated-orcid":false,"given":"Hayato","family":"Harima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9897-3905","authenticated-orcid":false,"given":"Yo","family":"Sugawara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4289-1115","authenticated-orcid":false,"given":"Koji","family":"Yahara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norikazu","family":"Kitamura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katsuhiko","family":"Hayashi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2307-9503","authenticated-orcid":false,"given":"Takahiro","family":"Ohnishi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Motoyuki","family":"Sugai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yukiko","family":"Hara-Kudo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8867-3618","authenticated-orcid":false,"given":"Kenji","family":"Ohya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jfp.2026.100948_b0005","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1007261","article-title":"A genomic overview of the population structure of Salmonella","volume":"14","author":"Alikhan","year":"2018","journal-title":"PLoS Genet"},{"key":"10.1016\/j.jfp.2026.100948_b0010","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijfoodmicro.2023.110297","article-title":"A review of the global emergence of multidrug-resistant Salmonella enterica subsp. enterica serovar Infantis","volume":"403","author":"Alvarez","year":"2023","journal-title":"Int J Food Microbiol"},{"key":"10.1016\/j.jfp.2026.100948_b0015","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1111\/j.1348-0421.2007.tb03881.x","article-title":"Long-term prevalence of antimicrobial-resistant Salmonella enterica subspecies enterica serovar Infantis in the broiler chicken industry in Japan","volume":"51","author":"Asai","year":"2007","journal-title":"Microbiol Immunol"},{"key":"10.1016\/j.jfp.2026.100948_b0020","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1111\/1462-2920.12351","article-title":"A unique megaplasmid contributes to stress tolerance and pathogenicity of an emergent Salmonella enterica serovar Infantis strain","volume":"16","author":"Aviv","year":"2014","journal-title":"Environ Microbiol"},{"key":"10.1016\/j.jfp.2026.100948_b0025","doi-asserted-by":"crossref","first-page":"292","DOI":"10.3390\/microorganisms10020292","article-title":"Correlation between phenotypic and in silico detection of antimicrobial resistance in Salmonella enterica in Canada using Staramr","volume":"10","author":"Bharat","year":"2022","journal-title":"Microorganisms"},{"key":"10.1016\/j.jfp.2026.100948_b0030","doi-asserted-by":"crossref","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":"10.1016\/j.jfp.2026.100948_b0035","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1186\/s12859-018-2336-6","article-title":"Rapid and precise alignment of raw reads against redundant databases with KMA","volume":"19","author":"Clausen","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.jfp.2026.100948_b0040","unstructured":"Clinical and Laboratory Standards Institute, 2019. Performance Standards for Antimicrobial Susceptibility Testing, 29th ed. CLSI supplement M100-29. Clinical and Laboratory Standards Institute, Wayne, PA."},{"key":"10.1016\/j.jfp.2026.100948_b0045","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1637\/8516-110908-Reg.1","article-title":"Efficacy of a novel trivalent inactivated vaccine against the shedding of Salmonella in a chicken challenge model","volume":"53","author":"Deguchi","year":"2009","journal-title":"Avian Dis"},{"key":"10.1016\/j.jfp.2026.100948_b0050","doi-asserted-by":"crossref","unstructured":"Dos Santos, A.M.P., Panzenhagen, P., Ferrari, R.G., Conte-Junior, C.A., 2022. Large-scale genomic analysis reveals the pESI-like megaplasmid presence in Salmonella Agona, Muenchen, Schwarzengrund, and Senftenberg. Food Microbiol. 108, 104112. https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0740002022001368","DOI":"10.1016\/j.fm.2022.104112"},{"key":"10.1016\/j.jfp.2026.100948_b0055","doi-asserted-by":"crossref","first-page":"239","DOI":"10.7883\/yoken.JJID.2016.164","article-title":"Prevalence and characteristics of Salmonella and Campylobacter in retail poultry meat in Japan","volume":"70","author":"Furukawa","year":"2017","journal-title":"Jpn J Infect Dis"},{"key":"10.1016\/j.jfp.2026.100948_b0060","doi-asserted-by":"crossref","DOI":"10.1128\/ecosalplus.esp-0001-2023","article-title":"Infection biology of Salmonella enterica","volume":"12","author":"Han","year":"2024","journal-title":"EcoSal Plus"},{"key":"10.1016\/j.jfp.2026.100948_b0065","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1292\/jvms.19-0677","article-title":"Effects of climatic elements on Salmonella contamination in broiler chicken meat in Japan","volume":"82","author":"Ishihara","year":"2020","journal-title":"J Vet Med Sci"},{"key":"10.1016\/j.jfp.2026.100948_b0070","doi-asserted-by":"crossref","first-page":"288","DOI":"10.3390\/antibiotics14030288","article-title":"Determination of antimicrobial resistance megaplasmid-like pESI structures contributing to the spread of Salmonella Schwarzengrund in Japan","volume":"14","author":"Ishihara","year":"2025","journal-title":"Antibiotics"},{"key":"10.1016\/j.jfp.2026.100948_b0075","doi-asserted-by":"crossref","first-page":"270","DOI":"10.4315\/0362-028X.JFP-10-215","article-title":"Prevalence of Salmonella isolates and antimicrobial resistance patterns in chicken meat throughout Japan","volume":"74","author":"Iwabuchi","year":"2011","journal-title":"J Food Prot"},{"key":"10.1016\/j.jfp.2026.100948_b0080","unstructured":"Infectious Agents Surveillance Report, 2022. Salmonella serovars from human sources, 2018\u20132022. https:\/\/www.niid.go.jp\/niid\/ja\/typhi-m\/iasr-reference\/510-graphs\/1524-iasrgb.html (accessed 31 January 2025)"},{"key":"10.1016\/j.jfp.2026.100948_b0085","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: Improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"10.1016\/j.jfp.2026.100948_b0090","doi-asserted-by":"crossref","first-page":"8046","DOI":"10.1038\/s41467-023-43516-4","article-title":"National genomic surveillance integrating standardized quantitative susceptibility testing clarifies antimicrobial resistance in Enterobacterales","volume":"14","author":"Kayama","year":"2023","journal-title":"Nat Commun"},{"key":"10.1016\/j.jfp.2026.100948_b0095","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","article-title":"Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation","volume":"23","author":"Letunic","year":"2007","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jfp.2026.100948_b0100","doi-asserted-by":"crossref","first-page":"1336","DOI":"10.3390\/antibiotics10111336","article-title":"Molecular characteristics and antimicrobial resistance of Salmonella enterica serovar Schwarzengrund from chicken meat in Japan","volume":"10","author":"Matsui","year":"2021","journal-title":"Antibiotics"},{"key":"10.1016\/j.jfp.2026.100948_b0105","doi-asserted-by":"crossref","first-page":"126","DOI":"10.14252\/foodsafetyfscj.2017019","article-title":"Prevalence and antimicrobial resistance of Salmonella serotypes isolated from poultry meat in Japan","volume":"6","author":"Mori","year":"2018","journal-title":"Food Saf"},{"key":"10.1016\/j.jfp.2026.100948_b0110","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1017\/S0950268801005283","article-title":"Environmental survey of Salmonella and comparison of genotypic character with human isolates in Western Japan","volume":"126","author":"Murakami","year":"2001","journal-title":"Epidemiol Infect"},{"key":"10.1016\/j.jfp.2026.100948_b0115","doi-asserted-by":"crossref","first-page":"167","DOI":"10.3390\/foods7100167","article-title":"Antibiotic-resistant Salmonella in the food supply and the potential role of antibiotic alternatives for control","volume":"7","author":"Nair","year":"2018","journal-title":"Foods"},{"key":"10.1016\/j.jfp.2026.100948_b0120","unstructured":"National Veterinary Assay Laboratory, 2025. JVARM. https:\/\/www.maff.go.jp\/nval\/yakuzai\/yakuzai_p3_6.html (accessed 16 September 2025)"},{"key":"10.1016\/j.jfp.2026.100948_b0125","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1186\/s12917-025-05031-0","article-title":"Increased kanamycin-resistant Salmonella Schwarzengrund, serovar changing and antimicrobial susceptibility of Salmonella enterica from broiler chickens in Kagoshima, Japan between 2019 and 2023","volume":"21","author":"Sanga","year":"2025","journal-title":"BMC Vet Res"},{"key":"10.1016\/j.jfp.2026.100948_b0130","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/j.jgar.2025.07.007","article-title":"Salmonella Minnesota sequence type 548 harbouring a type 2 IncC megaplasmid of antimicrobial resistance and virulence (pESM) infecting a companion animal","volume":"44","author":"Sartori","year":"2025","journal-title":"J Glob Antimicrob Resist"},{"key":"10.1016\/j.jfp.2026.100948_b0135","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1292\/jvms.24-0279","article-title":"Geographical variation in antimicrobial resistant Salmonella Schwarzengrund from chicken meat in Japan","volume":"87","author":"Sasaki","year":"2025","journal-title":"J Vet Med Sci"},{"key":"10.1016\/j.jfp.2026.100948_b0140","doi-asserted-by":"crossref","first-page":"2074","DOI":"10.1017\/S0950268812000039","article-title":"Prevalence and antimicrobial susceptibility of Salmonella in Japanese broiler flocks","volume":"140","author":"Sasaki","year":"2012","journal-title":"Epidemiol Infect"},{"key":"10.1016\/j.jfp.2026.100948_b0145","doi-asserted-by":"crossref","first-page":"1541","DOI":"10.3390\/antibiotics10121541","article-title":"Antimicrobial resistance in Salmonella isolated from food workers and chicken products in Japan","volume":"10","author":"Sasaki","year":"2021","journal-title":"Antibiotics"},{"key":"10.1016\/j.jfp.2026.100948_b0150","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1017\/S0950268810002153","article-title":"Salmonella prevalence in commercial raw shell eggs in Japan: A survey","volume":"139","author":"Sasaki","year":"2011","journal-title":"Epidemiol Infect"},{"key":"10.1016\/j.jfp.2026.100948_b0155","unstructured":"Seemann, T., 2017. Shovill: Faster SPAdes assembly of Illumina reads. Available at: https:\/\/github.com\/tseemann\/shovill"},{"key":"10.1016\/j.jfp.2026.100948_b0160","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1038\/s41467-022-35713-4","article-title":"An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance","volume":"14","author":"Sherry","year":"2023","journal-title":"Nat Commun"},{"key":"10.1016\/j.jfp.2026.100948_b0165","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1128\/CMR.00016-09","article-title":"Plasmid-mediated quinolone resistance: A multifaceted threat","volume":"22","author":"Strahilevitz","year":"2009","journal-title":"Clin Microbiol Rev"},{"key":"10.1016\/j.jfp.2026.100948_b0170","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1101\/gr.232397.117","article-title":"GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens","volume":"28","author":"Zhou","year":"2018","journal-title":"Genome Res"}],"container-title":["Journal of Food Protection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0362028X2600253X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0362028X2600253X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T19:49:30Z","timestamp":1792612170000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0362028X2600253X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10]]},"references-count":34,"alternative-id":["S0362028X2600253X"],"URL":"https:\/\/doi.org\/10.1016\/j.jfp.2026.100948","relation":{},"ISSN":["0362-028X"],"issn-type":[{"value":"0362-028X","type":"print"}],"subject":[],"published":{"date-parts":[[2026,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Genomic epidemiology of Salmonella from retail chicken meat in Japan: decline in pESI-like plasmid-harboring S. Infantis ST32 and predominance of S. Schwarzengrund ST241","name":"articletitle","label":"Article Title"},{"value":"Journal of Food Protection","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jfp.2026.100948","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc. on behalf of International Association for Food Protection.","name":"copyright","label":"Copyright"}],"article-number":"100948"}}