{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:59:52Z","timestamp":1753891192481,"version":"3.41.2"},"reference-count":24,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,4,27]],"date-time":"2022-04-27T00:00:00Z","timestamp":1651017600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Med."],"abstract":"<jats:p>Scrub typhus is a potentially severe rickettsiosis, caused by <jats:italic>Orientia tsutsugamushi<\/jats:italic> in the Asia-Pacific region. Recently, however, two distinct pathogens, \u201c<jats:italic>Candidatus<\/jats:italic> Orientia chuto\u201d and \u201c<jats:italic>Candidatus<\/jats:italic> Orientia chiloensis\u201d, have been discovered in the Middle East and South America, respectively. Since the novel pathogens differ significantly from <jats:italic>O. tsutsugamushi<\/jats:italic>, many established diagnostic methods are unreliable. This work describes the development and validation of a new quantitative real-time PCR (qPCR) assay (Orien16S) for the detection of all known <jats:italic>Orientia<\/jats:italic> species. Based on a 94 bp sequence of the 16S rRNA gene (<jats:italic>rrs<\/jats:italic>), Orien16S recognized DNA samples from <jats:italic>O. tsutsugamushi<\/jats:italic> (<jats:italic>n<\/jats:italic> = 41), <jats:italic>Ca.<\/jats:italic> O. chiloensis (<jats:italic>n<\/jats:italic> = 5), and <jats:italic>Ca.<\/jats:italic> O. chuto (<jats:italic>n<\/jats:italic> = 1), but was negative for DNA preparations from closely related rickettsiae and other members of the order Rickettsiales (<jats:italic>n<\/jats:italic> = 22) as well as unrelated bacterial species (<jats:italic>n<\/jats:italic> = 11). After its implementation in Chile, the assay was verified, correctly identifying all tested eschar and buffy coat samples (<jats:italic>n<\/jats:italic> = 28) of clinical suspected cases. Furthermore, Orien16S detected <jats:italic>Orientia<\/jats:italic> DNA in trombiculid mites collected in endemic regions in southern Chile. The presented novel qPCR assay provides a useful tool for detecting <jats:italic>Orientia<\/jats:italic> and diagnosing scrub typhus from all geographical regions.<\/jats:p>","DOI":"10.3389\/fmed.2022.831045","type":"journal-article","created":{"date-parts":[[2022,4,27]],"date-time":"2022-04-27T10:41:43Z","timestamp":1651056103000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":11,"title":["Development of a New Genus-Specific Quantitative Real-Time PCR Assay for the Diagnosis of Scrub Typhus in South 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