{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T15:47:34Z","timestamp":1791820054658,"version":"4.3.4"},"reference-count":31,"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":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"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":"publisher","award":["2024-ER2103-02"],"award-info":[{"award-number":["2024-ER2103-02"]}],"id":[{"id":"10.13039\/501100003653","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003653","name":"Korea National Institute of Health","doi-asserted-by":"publisher","award":["2025-NI-025-01"],"award-info":[{"award-number":["2025-NI-025-01"]}],"id":[{"id":"10.13039\/501100003653","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","ijidonline.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["International Journal of Infectious Diseases"],"published-print":{"date-parts":[[2026,10]]},"DOI":"10.1016\/j.ijid.2026.109040","type":"journal-article","created":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T13:18:37Z","timestamp":1786022317000},"page":"109040","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"C","title":["Genomic insights into emerging South Korean uncommon Orientia tsutsugamushi strains and their value as new surveillance resources"],"prefix":"10.1016","volume":"171","author":[{"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":"Sunwoo","family":"Hwang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Misoon","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seon-Do","family":"Hwang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2866-4370","authenticated-orcid":false,"given":"Won-Jong","family":"Jang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"Supplement-3","key":"10.1016\/j.ijid.2026.109040_bib0001","doi-asserted-by":"crossref","first-page":"S203","DOI":"10.1086\/596576","article-title":"Scrub Typhus: the geographic distribution of phenotypic and genotypic variants of Orientia tsutsugamushi","volume":"48","author":"Kelly","year":"2009","journal-title":"Clin Infect Dis"},{"issue":"37","key":"10.1016\/j.ijid.2026.109040_bib0002","doi-asserted-by":"crossref","DOI":"10.3346\/jkms.2025.40.e234","article-title":"Classifying eschar morphologies: Enhancing early diagnosis of scrub typhus","volume":"40","author":"Lee","year":"2025","journal-title":"J Korean Med Sci"},{"issue":"3","key":"10.1016\/j.ijid.2026.109040_bib0003","doi-asserted-by":"crossref","first-page":"368","DOI":"10.4269\/ajtmh.2010.09-0233","article-title":"Diagnosis of scrub typhus","volume":"82","author":"Koh","year":"2010","journal-title":"Am J Trop Med Hyg"},{"issue":"9","key":"10.1016\/j.ijid.2026.109040_bib0004","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1016\/j.tim.2020.02.014","article-title":"Orientia tsutsugamushi","volume":"28","author":"Wongsantichon","year":"2020","journal-title":"Trends Microbiol"},{"issue":"8","key":"10.1016\/j.ijid.2026.109040_bib0005","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0022731","article-title":"Differences in clinical features according to Boryoung and Karp genotypes of Orientia tsutsugamushi","volume":"6","author":"Kim","year":"2011","journal-title":"PLOS ONE"},{"key":"10.1016\/j.ijid.2026.109040_bib0006","series-title":"Comparative virulence analysis of seven diverse strains of Orientia tsutsugamushi reveals a multifaceted and complex interplay of virulence factors responsible for disease","author":"Panjaporn","year":"2025"},{"issue":"6","key":"10.1016\/j.ijid.2026.109040_bib0007","doi-asserted-by":"crossref","first-page":"469","DOI":"10.3947\/ic.2012.44.6.469","article-title":"Severe scrub typhus with enterocolitis by the Ikeda strain of Orientia tsutsugamushi","volume":"44","author":"Kim","year":"2012","journal-title":"Infect Chemother"},{"issue":"9","key":"10.1016\/j.ijid.2026.109040_bib0008","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1111\/j.1348-0421.1996.tb01120.x","article-title":"Demonstration of antigenic and genotypic variation in Orientia tsutsugamushi which were isolated in Japan, and their classification into type and subtype","volume":"40","author":"Ohashi","year":"1996","journal-title":"Microbiol Immunolology"},{"issue":"5","key":"10.1016\/j.ijid.2026.109040_bib0009","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1093\/dnares\/dsq018","article-title":"Genome comparison and phylogenetic analysis of Orientia tsutsugamushi strains","volume":"17","author":"Nakayama","year":"2010","journal-title":"DNA Res"},{"issue":"4","key":"10.1016\/j.ijid.2026.109040_bib0010","doi-asserted-by":"crossref","first-page":"930","DOI":"10.4269\/ajtmh.2010.09-0791","article-title":"Antigenic drift of Orientia tsutsugamushi in South Korea as identified by the sequence analysis of a 56-kDa protein-encoding gene","volume":"83","author":"Park","year":"2010","journal-title":"Am J Trop Med Hyg"},{"issue":"9","key":"10.1016\/j.ijid.2026.109040_bib0011","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1111\/1348-0421.12639","article-title":"Geographical distribution of Orientia tsutsugamushi strains in chiggers from three provinces in Korea","volume":"62","author":"Choi","year":"2018","journal-title":"Microbiol Immunol"},{"issue":"3","key":"10.1016\/j.ijid.2026.109040_bib0012","doi-asserted-by":"crossref","first-page":"263","DOI":"10.3347\/PHD.22148","article-title":"Prevalence of chigger mites and Orientia tsutsugamushi strains in northern regions of Gangwon-do, Korea","volume":"61","author":"Kim","year":"2023","journal-title":"Parasites hosts dis"},{"issue":"2","key":"10.1016\/j.ijid.2026.109040_bib0013","first-page":"65","article-title":"Epidemiological aspects of tsutsugamushi disease (scrub typhus) outbreaks in Republic of Korea and Japan","volume":"32","author":"Lee","year":"2022","journal-title":"KJAsEM"},{"issue":"3","key":"10.1016\/j.ijid.2026.109040_bib0014","doi-asserted-by":"crossref","first-page":"658","DOI":"10.4269\/ajtmh.2010.09-0608","article-title":"Phylogenetic analysis of 56-kDa type-specific antigen gene of Orientia tsutsugamushi isolates in Taiwan","volume":"83","author":"Lu","year":"2010","journal-title":"Am J Trop Med Hyg"},{"issue":"9","key":"10.1016\/j.ijid.2026.109040_bib0015","first-page":"1201","article-title":"Human co-infection with Rickettsia spp., Borrelia garinii, and Orientia tsutsugamushi in South Korea","volume":"29","author":"Oh","year":"2024","journal-title":"Syst Appl Acarol"},{"issue":"2","key":"10.1016\/j.ijid.2026.109040_bib0016","doi-asserted-by":"crossref","first-page":"215","DOI":"10.3390\/genes15020215","article-title":"Exploring the impact of primer\u2013template mismatches on PCR performance of DNA polymerases varying in proofreading activity","volume":"15","author":"Huang","year":"2024","journal-title":"Genes"},{"issue":"1","key":"10.1016\/j.ijid.2026.109040_bib0017","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-025-98444-8","article-title":"Using machine learning models to predict the impact of template mismatches on polymerase chain reaction assay performance","volume":"15","author":"Knight","year":"2025","journal-title":"Sci Rep"},{"issue":"19","key":"10.1016\/j.ijid.2026.109040_bib0018","doi-asserted-by":"crossref","first-page":"7981","DOI":"10.1073\/pnas.0611553104","article-title":"Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes","volume":"104","author":"Cho","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"10.1016\/j.ijid.2026.109040_bib0019","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/dnares\/dsn011","article-title":"The whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution","volume":"15","author":"Nakayama","year":"2008","journal-title":"DNA Res"},{"issue":"6","key":"10.1016\/j.ijid.2026.109040_bib0020","doi-asserted-by":"crossref","first-page":"e00268","DOI":"10.1128\/msphere.00268-23","article-title":"Orientia tsutsugamushi: comprehensive analysis of the mobilome of a highly fragmented and repetitive genome reveals the capacity for ongoing lateral gene transfer in an obligate intracellular bacterium","volume":"8","author":"Giengkam","year":"2023","journal-title":"mSphere"},{"key":"10.1016\/j.ijid.2026.109040_bib0021","doi-asserted-by":"crossref","DOI":"10.1017\/S0950268825100988","article-title":"Phylogeographic diversity of Orientia tsutsugamushi strains from clinical isolates in South Korea","volume":"154","author":"Kang","year":"2026","journal-title":"Epidemiol Infect"},{"issue":"3","key":"10.1016\/j.ijid.2026.109040_bib0022","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"10.1016\/j.ijid.2026.109040_bib0023","doi-asserted-by":"crossref","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.Org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res"},{"key":"10.1016\/j.ijid.2026.109040_bib0024","unstructured":"National Library of Medicine. National Library of Medicine: National Center for Biotechnology Information 2024 [https:\/\/www.ncbi.nlm.nih.gov\/genbank\/]. Accessed October 16, 2025."},{"key":"10.1016\/j.ijid.2026.109040_bib0025","doi-asserted-by":"crossref","unstructured":"Kumar S., Stecher G., Suleski M., Sanderford M., Sharma S., Tamura K. MEGA12: Molecular evolutionary genetic analysis version 12 for adaptive and green computing. Molec Biol Evol 2024;41(12):msae263.","DOI":"10.1093\/molbev\/msae263"},{"key":"10.1016\/j.ijid.2026.109040_bib0026","series-title":"Integrated Development Environment for R","year":"2025"},{"issue":"1","key":"10.1016\/j.ijid.2026.109040_bib0027","doi-asserted-by":"crossref","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat Commun"},{"issue":"6","key":"10.1016\/j.ijid.2026.109040_bib0028","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0006566","article-title":"Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi","volume":"12","author":"Batty","year":"2018","journal-title":"PLOS Negl Trop Dis"},{"issue":"4","key":"10.1016\/j.ijid.2026.109040_bib0029","doi-asserted-by":"crossref","first-page":"299","DOI":"10.3390\/pathogens13040299","article-title":"Concatenated ScaA and TSA56 surface antigen sequences reflect genome-scale phylogeny of Orientia tsutsugamushi: An analysis including two genomes from Taiwan","volume":"13","author":"Minahan","year":"2024","journal-title":"Pathogens"},{"issue":"9","key":"10.1016\/j.ijid.2026.109040_bib0030","article-title":"Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity","volume":"4","author":"Fleshman","year":"2018","journal-title":"Microb Genom"},{"issue":"8","key":"10.1016\/j.ijid.2026.109040_bib0031","first-page":"mgen000855","article-title":"Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia","volume":"8","author":"Udaondo","year":"2022","journal-title":"Microb Genom"}],"container-title":["International Journal of Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1201971226006752?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1201971226006752?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T14:49:58Z","timestamp":1791816598000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1201971226006752"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10]]},"references-count":31,"alternative-id":["S1201971226006752"],"URL":"https:\/\/doi.org\/10.1016\/j.ijid.2026.109040","relation":{},"ISSN":["1201-9712"],"issn-type":[{"value":"1201-9712","type":"print"}],"subject":[],"published":{"date-parts":[[2026,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Genomic insights into emerging South Korean uncommon Orientia tsutsugamushi strains and their value as new surveillance resources","name":"articletitle","label":"Article Title"},{"value":"International Journal of Infectious Diseases","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ijid.2026.109040","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.","name":"copyright","label":"Copyright"}],"article-number":"109040"}}