Background: Lyme disease, caused by Borrelia burgdorferi sensu lato (BBSL), is commonly found in wild and domestic mammals worldwide. In China, human cases of B. burgdorferi infections have been identified across a wide distribution, but little direct surveillance of potential small mammal reservoirs has been performed in Yunnan Province, a tropical region in southwestern China. Here we report a thorough investigation of BBSL in small mammals collected from 2011 to 2016 from this region.Methods: Small mammals were captured using snap traps in 23 counties located in Yunnan Province. DNA was extracted from spleen tissue using DNA blood and tissue kits. A nested PCR targeting the 5S-23S rRNA intergenic spacer gene of BBSL was used for pathogen detection. Amplicons of 252bp expected sizes were sequenced directly and analyzed using BLAST algorithm. A phylogenetic tree was constructed using MEGA software and statistical analysis were conducted using SPSS version 17.0.Results: Overall, 3659 mammals belonging to 57 species were captured at 159 sample sites located in 23 counties in Yunnan Province. Borrelia burgdorferi s.l. was found in 146 mammals (3.99%), from 30 different species, 20 of which represent the first reported detection in that species. Sequence analysis revealed five genotypes of B. burgdorferi s.l., including B. afzelii, B. burgdorferi sensu stricto, B. japonica, B. garinii and B. valaisiana.Conclusions: Significant differences in prevalence rates of BBSL were observed at varying landscape types and altitudes. Small mammals in forested areas had higher prevalence rates than other landscape types, as did small mammals found at altitudes greater than 2500 meters. The five genotypes of BBSL detected, suggests high genetic diversity within this province.
