Optimization and Application of Real-Time qPCR Assays in Detection and Identification of Chlamydiales in Products of Domestic Ruminant Abortion

Domestic ruminant abortions due to infectious agents represent an important cause of economic losses in the agricultural industry. This study aimed to optimise and apply qPCR assays for detection of Chlamydiales in domestic ruminant abortion cases. Primers and probes for detection of the order Chlamydiales, Chlamydia abortus, Chlamydia pecorum, Parachlamydia acanthamoeba and Waddlia chondrophila were taken from the literature to create one singleplex and two duplex assays and the assays were optimised. Placentitis and pneumonia are pathological lesions associated with Chlamydiales infection. In a previous study, twenty-five clinical cases had pathological lesions of placentitis or pneumonia. These cases were investigated further by application of the qPCR assays in this study. Chlamydiales were detected in 16 cases. C. abortus, P. acanthamoeba and W. chondrophila were detected in bovine; and C. pecorum and W. chondrophila in ovine and caprine cases. Chlamydiales were detected in three previously inconclusive cases. Identification was improved from genus to species level (C. pecorum). Four cases remained inconclusive. In conclusion, detection of Chlamydiales and differentiation to species level was improved. This study reports the first detection of P. acanthamoeba and W. chondrophila in abortion cases in South Africa, indicating a potentially significant role in abortions in this country.