{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T18:19:16Z","timestamp":1783621156085,"version":"3.55.0"},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T00:00:00Z","timestamp":1783555200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003653","name":"Korea National Institute of Health","doi-asserted-by":"crossref","award":["2024-ER2103-01"],"award-info":[{"award-number":["2024-ER2103-01"]}],"id":[{"id":"10.13039\/501100003653","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003653","name":"Korea National Institute of Health","doi-asserted-by":"crossref","award":["2025-NI-025-00"],"award-info":[{"award-number":["2025-NI-025-00"]}],"id":[{"id":"10.13039\/501100003653","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    <jats:italic>Orientia tsutsugamushi<\/jats:italic>\n                    strain Ikeda is a scrub typhus reference strain originally described in Japan, and Ikeda\n                    <jats:italic>56-kDa<\/jats:italic>\n                    type-specific antigen sequence types have also been reported in South Korea. However, complete genome resources for South Korean Ikeda-genotype isolates remain limited. Here, we generated complete genomes for two archived clinical\n                    <jats:italic>O. tsutsugamushi<\/jats:italic>\n                    isolates from northern South Korea, CH219 and K4-135, using a PacBio HiFi and Illumina hybrid assembly approach and compared them with the Japanese reference strain Ikeda and the South Korean reference strain Boryong. Both genomes were assembled as single circular chromosomes and contained a substantial fraction of duplicated identical coding sequences, consistent with the highly repetitive nature of\n                    <jats:italic>O. tsutsugamushi<\/jats:italic>\n                    genomes. Strains CH219 and K4-135 had identical\n                    <jats:italic>56-kDa<\/jats:italic>\n                    TSA sequences and MLST profiles to those of the Ikeda reference strain and clustered within the Ikeda-associated clade in recombination-filtered core-genome phylogeny and ANI analyses. Within this comparison, the two South Korean isolates showed more closely related to each other than to the Japanese Ikeda reference genome. Whole-genome dot plots further indicated structural variation among the Ikeda-associated genomes. Insertion sequence (IS) profiling showed differences in IS-related CDS copy number patterns between the Boryong reference genome and the Ikeda-associated genomes, with strain Boryong showing a higher observed number of ISOt6-related CDS hits and fewer high-identity ISOt3-related hits under the applied thresholds. Together, these genomes provide new resources for Ikeda-like\n                    <jats:italic>O. tsutsugamushi<\/jats:italic>\n                    strains detected in South Korea and support the need for expanded complete and well-supported whole-genome data to better understand genome diversity in scrub typhus agents.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0351070","type":"journal-article","created":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T17:43:01Z","timestamp":1783618981000},"page":"e0351070","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Complete genomes of two Ikeda-genotype Orientia tsutsugamushi isolates from South Korea reveal within-lineage divergence and contrast with the Boryong reference strain"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2868-6748","authenticated-orcid":true,"given":"Hyungsuk","family":"Kang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeon-Joo","family":"Choi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyeonghye","family":"Guk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Misoon","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kwangjun","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2866-4370","authenticated-orcid":true,"given":"Won-Jong","family":"Jang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,7,9]]},"reference":[{"key":"pone.0351070.ref001","article-title":"Scrub 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Choi","year":"2018","journal-title":"Microbiol Immunol"},{"issue":"9","key":"pone.0351070.ref008","first-page":"1201","article-title":"Human co-infection with Rickettsia spp., Borrelia garinii, and Orientia tsutsugamushi in South Korea","volume":"29","author":"W Oh","year":"2024","journal-title":"Syst Appl Acarol"},{"issue":"8","key":"pone.0351070.ref009","article-title":"Differences in clinical features according to Boryoung and Karp genotypes of Orientia tsutsugamushi","volume":"6","author":"D-M Kim","year":"2011","journal-title":"PLoS One"},{"key":"pone.0351070.ref010","volume-title":"Comparative virulence analysis of seven diverse strains of Orientia tsutsugamushi reveals a multifaceted and complex interplay of virulence factors responsible for disease","author":"C Panjaporn","year":"2025"},{"issue":"4","key":"pone.0351070.ref011","doi-asserted-by":"crossref","first-page":"930","DOI":"10.4269\/ajtmh.2010.09-0791","article-title":"Antigenic drift of Orientia tsutsugamushi in South 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