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In 2018, a multistate outbreak of <jats:italic>S. enterica<\/jats:italic> subsp. <jats:italic>enterica<\/jats:italic> serovar Thompson infection associated with contaminated chocolate cakes in schools was reported in South Korea. In this study, we sequenced the 37 <jats:italic>S.<\/jats:italic> Thompson strains isolated from chocolate cakes, egg whites, preserves, and cookware associated with the outbreak. In addition, we analyze the genomic sequences of 61 <jats:italic>S<\/jats:italic>. Thompson strains (37 chocolate cake-related outbreak strains, 4 strains isolated from outbreaks in South Korea and 20 strains available in the National Center for Biotechnology Information) to assess the genomic characteristics of outbreak-related strains by comparative genomics and phylogenetic analysis. The results showed that identically classified clusters divided strains into two clusters, sub-clusters A &amp; I (with strains from 2018 in South Korea) and sub-clusters B &amp; II (with strains from 2014 to 2015 in South Korea). <jats:italic>S.<\/jats:italic> Thompson isolated from South Korea were accurately distinguished from publicly-available strains. Unlike other <jats:italic>S<\/jats:italic>. Thompson genomes, those of chocolate cake outbreak-related strains had three <jats:italic>Salmonella<\/jats:italic> phages (SEN8, vB SosS Oslo, and SI7) integrated into their chromosome. Comparative genomics revealed several genes responsible for the specific genomic features of chocolate cake outbreak-related strains and three bacteriophages that may contribute to the pathogenicity of other <jats:italic>S<\/jats:italic>. Thompson strains.<\/jats:p>","DOI":"10.1038\/s41598-022-22168-2","type":"journal-article","created":{"date-parts":[[2022,11,29]],"date-time":"2022-11-29T11:03:12Z","timestamp":1669719792000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Genomic characteristics and comparative genomics analysis of Salmonella enterica subsp. enterica serovar Thompson isolated from an outbreak in South Korea"],"prefix":"10.1038","volume":"12","author":[{"given":"Woojung","family":"Lee","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eiseul","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyunwoo","family":"Zin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soohyun","family":"Sung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jungha","family":"Woo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min Jung","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seung-Min","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seung Hwan","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soon Han","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hae-Yeong","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,11,29]]},"reference":[{"key":"22168_CR1","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1016\/j.micres.2017.09.010","volume":"206","author":"A Lamas","year":"2018","unstructured":"Lamas, A. et al. 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