Investigation of Chlamydia pecorum in yaks from Qinghai reveals high genetic diversity among the strains.

Chlamydia pecorum (C. pecorum), an obligate intracellular, gram-negative bacterium, causes endemic infections in livestock. However, data on the strain diversity of C. pecorum infecting yaks in Qinghai, China, remain limited. In this study, we aimed to assess the genetic diversity of C. pecorum in yaks from Qinghai. A total of 1564 rectal swabs were collected from yaks, and C. pecorum DNA was detected using quantitative polymerase chain reaction (qPCR). Positive samples were further analyzed by ompA sequence, and multilocus sequence typing (MLST) targeting seven housekeeping genes (gatA, oppA, hftX, gidA, enoA, hemN, and fumC). The results showed an overall prevalence of C. pecorum of 11.4 % (178/1564) in the sampled yaks. The ompA sequence of C. pecorum obtained demonstrated substantial genetic diversity. Four novel sequence types (STs) ST381, ST385, ST386, and ST376, were identified, with ST381, ST385, and ST386 reported for the first time. The strains formed three primary clonal complexes centered around ST63, ST69, and ST376, along with minor branches and independent lineages. This study confirms the widespread prevalence and high genetic diversity of C. pecorum among yaks in Qinghai. These findings provide critical molecular insights for regional pathogen surveillance and control strategies, and expand the global genomic database of C. pecorum.