Molecular epidemiological study of Scrub Typhus in residence, farm and forest habitats from Yunnan Province, China

Abstract

The number of people suffering from scrub typhus, which is not of concern, is increasing year by year, especially in Yunnan Province, China. From June 1, 2021 to August 15, 2022, a total of 505 mammalian samples were collected from farm, forest, and residential habitats with high incidence of scrub typhus in Yunnan, China, for nPCR (nested PCR) and qPCR (quantitative real-time PCR) detection of Orientia tsutsugamushi. A total of 4 orders of murine-like animals, Rodentia (87.52%, n = 442), Insectivora (10.29%, n = 52), Lagomorpha (1.79%, n = 9) and Scandentia (0.40%, n = 2) were trapped. Comparing the qPCR infection rates in the three habitats, it was no significant difference that the infection rate of residential habitat (44.44%) and that of the farm habitat (45.05%, P>0.05), which is much larger than that of the forest habitat (3.08%) (P<0.001). Three genotypes (Karp-like, Kato-like and TA763-like) of O. tsutsugamushi were found from Yunnan, China in this study.

Fig 1. Orientia tsutsugamushi in small mammals, Yunnan Province, China, June 2021-August 2022.

The upper right figure is a map of China, the lower right figure is a sector diagram showing the sampling volume of each habitat, the left figure is a map of Dali city, the brown area represent the sampling area of farm habitat; the blue area represent the sampling area of residential habitat; the green area represent the sampling area of forest habitat. The map was prepared in ArcGIS 10.8 using political boundaries from the National Geomatics Center of China (http://www.ngcc.cn/ngcc) for illustrative purposes only, these data are available free of charge.

Fig 2. Reported cases of scrub typhus.

(A) Cases in Yunnan, China, 2006–2022. (B) Cases in China, 2006–2016.

Fig 3. Phylogenetic trees of partial 56 kDa gene sequences of O. tsutsugamushi at the nucleotide level.