Objective To investigate the epidemiological characteristics of scrub typhus in Chuxiong Yi autonomous prefecture (Chuxiong prefecture), Yunnan province, China, and to analyze the genotypes of the pathogen Orientia tsutsugamushi (Ot). Methods The data of scrub typhus cases were collected for epidemiological analysis. Blood samples from the patients were obtained to detect the nucleic acids of Ot by PCR and sequence the Tsa56 gene. Homology and phylogenetic analyses were performed using bioinformatics software. Results A total of 2 507 cases of scrub typhus were reported in Chuxiong prefecture from 2015 to 2018, with a mean annual incidence of 22.79/100 000. Scrub typhus occurred in all 10 counties/cities of the prefecture, and 96.01% (2 407/2 507) of the total cases were distributed in Chuxiong, Dayao, Yongren, Nanhua, and Shuangbai counties/cities. The cases occurring during July to October accounted for 88.35% (2 215/2 507) of the total number. The male-to-female ratio was 1:1.34. The majority of the patients were aged from 30 to 69 years (78.42%, 1 966/2 507), and most cases were farmers (84.92%, 2 129/2 507). PCR detected 4 samples (CX1601, CX1602, CX1603, and CX1604) positive for Ot nucleic acids from 6 blood samples of scrub typhus patients. The Tsa56 gene was obtained for sequencing, and the homology and phylogenetic analyses showed that CX1601 and CX1604 shared high homology and close genetic relationship with the Kato strains of Ot, while CX1602 and CX1603 were highly homologous and closely related to Gilliam strains, but relatively low homology and large genetic distances with other strains. Conclusion Scrub typhus in Chuxiong prefecture belongs to Kato or Gilliam type. In recent years, there was a high incidence and an increasing trend year by year. It is necessary to strengthen the surveillance and control of the host and vector.
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