{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T10:54:45Z","timestamp":1790506485732,"version":"4.1.0"},"reference-count":47,"publisher":"American Society for Microbiology","issue":"5","license":[{"start":{"date-parts":[[2018,5,1]],"date-time":"2018-05-01T00:00:00Z","timestamp":1525132800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["15fk0108021h0002"],"award-info":[{"award-number":["15fk0108021h0002"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2018,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            <jats:named-content content-type=\"genus-species\">Salmonella enterica<\/jats:named-content>\n            serovar Typhimurium (\n            <jats:named-content content-type=\"genus-species\">Salmonella<\/jats:named-content>\n            Typhimurium) and its monophasic variant (\n            <jats:named-content content-type=\"genus-species\">Salmonella<\/jats:named-content>\n            4,[5],12:i:\u2212) are the major causes of gastroenteritis in both humans and animals. Pulsed-field gel electrophoresis and multilocus variable-number tandem-repeat analysis have been used widely as subtyping methods for these pathogens in molecular epidemiological analyses, but the results do not precisely reflect phylogenetic information. In this study, we performed a phylogenetic analysis of these serovars using whole-genome sequencing data and identified nine distinct genotypic clades. Then, we established an allele-specific PCR-based genotyping method detecting a clade-specific single nucleotide polymorphism to rapidly identify the clade of each isolate. Among a total of 815 isolates obtained from cattle in Japan between 1977 and 2017, clades 1, 7, and 9 contained 77% of isolates. Obvious replacement of the dominant clone was observed five times in this period, and clade 9, which mostly contains\n            <jats:named-content content-type=\"genus-species\">Salmonella<\/jats:named-content>\n            4,[5],12:i:\u2212, is currently dominant. Among 140 isolates obtained from swine in Japan between 1976 and 2017, clades 3 and 9 contained 64% of isolates. Clade 9 is the latest clone as is the case in cattle isolates. Clade 9 is similar to an epidemic clone from Europe, which is characterized by sequence type 34 (ST34), chromosomal\n            <jats:named-content content-type=\"genus-species\">Salmonella<\/jats:named-content>\n            genomic island 3, and a composite transposon containing antimicrobial resistance genes. The increased prevalence of clade 9 among food animals in Japan might be a part of the pandemic of the European\n            <jats:named-content content-type=\"genus-species\">Salmonella<\/jats:named-content>\n            4,[5],12:i:\u2212 clone.\n          <\/jats:p>","DOI":"10.1128\/jcm.01758-17","type":"journal-article","created":{"date-parts":[[2018,3,28]],"date-time":"2018-03-28T16:17:57Z","timestamp":1522253877000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":54,"title":["Phylogenetic Characterization of Salmonella enterica Serovar Typhimurium and Its Monophasic Variant Isolated from Food Animals in Japan Revealed Replacement of Major Epidemic Clones in the Last 4 Decades"],"prefix":"10.1128","volume":"56","author":[{"given":"Nobuo","family":"Arai","sequence":"first","affiliation":[{"name":"Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, 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