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In Japan, several hundred cases of Japanese spotted fever, caused by<jats:italic>Rickettsia japonica<\/jats:italic>, are reported annually. Other<jats:italic>Rickettsia<\/jats:italic>species are also known to exist in ixodid ticks; however, their phylogenetic position and pathogenic potential are poorly understood. We conducted a nationwide cross-sectional survey on questing ticks to understand the overall diversity of SFG rickettsiae in Japan. Out of 2,189 individuals (19 tick species in 4 genera), 373 (17.0%) samples were positive for<jats:italic>Rickettsia<\/jats:italic>spp. as ascertained by real-time PCR amplification of the citrate synthase gene (<jats:italic>gltA<\/jats:italic>). Conventional PCR and sequencing analyses of<jats:italic>gltA<\/jats:italic>indicated the presence of 15 different genotypes of SFG rickettsiae. Based on the analysis of five additional genes, we characterised five<jats:italic>Rickettsia<\/jats:italic>species;<jats:italic>R<\/jats:italic>.<jats:italic>asiatica<\/jats:italic>,<jats:italic>R<\/jats:italic>.<jats:italic>helvetica<\/jats:italic>,<jats:italic>R<\/jats:italic>.<jats:italic>monacensis<\/jats:italic>(formerly reported as<jats:italic>Rickettsia<\/jats:italic>sp. In56 in Japan),<jats:italic>R<\/jats:italic>.<jats:italic>tamurae<\/jats:italic>, and<jats:italic>Candidatus<\/jats:italic>R. tarasevichiae and several unclassified SFG rickettsiae. We also found a strong association between rickettsial genotypes and their host tick species, while there was little association between rickettsial genotypes and their geographical origins. These observations suggested that most of the SFG rickettsiae have a limited host range and are maintained in certain tick species in the natural environment.<\/jats:p>","DOI":"10.1038\/s41598-018-37836-5","type":"journal-article","created":{"date-parts":[[2019,2,6]],"date-time":"2019-02-06T11:04:47Z","timestamp":1549451087000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":65,"title":["Diversity of spotted fever group rickettsiae and their association with host ticks in Japan"],"prefix":"10.1038","volume":"9","author":[{"given":"May June","family":"Thu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongjin","family":"Qiu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4205-6526","authenticated-orcid":false,"given":"Keita","family":"Matsuno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masahiro","family":"Kajihara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akina","family":"Mori-Kajihara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryosuke","family":"Omori","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naota","family":"Monma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuki","family":"Chiba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junji","family":"Seto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mutsuyo","family":"Gokuden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masako","family":"Andoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hideo","family":"Oosako","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ken","family":"Katakura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayato","family":"Takada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chihiro","family":"Sugimoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norikazu","family":"Isoda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryo","family":"Nakao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,2,6]]},"reference":[{"key":"37836_CR1","doi-asserted-by":"publisher","first-page":"694","DOI":"10.1128\/CMR.10.4.694","volume":"10","author":"D Raoult","year":"1997","unstructured":"Raoult, D. & Roux, R. 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