Nasopharyngeal Swabs for Orientia tsutsugamushi Detection in Doxycycline Treatment: A Prospective Cohort Study in Hainan, China

Scrub typhus, caused by <i>Orientia tsutsugamushi</i>, remains a neglected cause of acute febrile illness. Molecular testing of blood supports early diagnosis, yet once doxycycline is started, blood qPCR positivity can drop rapidly, complicating short-term follow-up and relapse surveillance. We compared detection across multiple clinical specimens and evaluated nasopharyngeal swabs (NPSs) as noninvasive supplementary specimens during treatment initiation. In a prospective single-center cohort from Hainan, China, we enrolled 20 patients with scrub typhus. Blood, NPS, urine, and stool were collected before doxycycline administration 24 h after the first dose and on day 5. qPCR was performed for the analysis of <i>Orientia tsutsugamushi</i>. qPCR-positive specimens were subjected to nested PCR targeting TSA56, and nested PCR-positive amplicons were Sanger sequenced for genotyping. Before treatment, <i>O. tsutsugamushi</i> DNA was detected in 15/20 blood samples (75.00%) and 5/20 NPS samples (25.00%), but 0/20 urine samples (0%) and 0/20 stool samples (0%). At 24 h after treatment, detection in blood was 0/20 (0%) while NPS samples were positive in 3/20 (15.00%). All specimens were negative by day 5 after treatment. Across sequenced NPS positives (<i>n</i> = 3), <i>Karp</i> 2/3 (66.77%) and <i>Gilliam</i> 1/3 (33.33%) predominated. In paired blood-NPS positives, inter-specimen homology was high (percentage nucleotide identity 100% for <i>Karp</i> and 100% for <i>Gilliam</i>). NPS is not sensitive enough for primary diagnosis; however, within the first 24 h after doxycycline it offers a practical, noninvasive supplementary specimen to support short-term follow-up and community-based sampling when venipuncture or transport are constrained. Larger, multi-center studies are warranted to refine sampling windows and diagnostic performance.