Bacterial and fungal causes of abortion in domestic ruminants

This study investigated detection methods for and significance of bacteria and fungi as agents of abortion in domestic ruminants in South Africa. Retrospective data was collected by searches of case reports (2006-2016) of participating pathology and bacteriology laboratories. During the prospective study (2017-2019), samples were analysed by a combination of conventional bacteriology methods. Quantitative real-time PCR assays for detection of the Chlamydiales, Chlamydia abortus, Chlamydia pecorum, Parachlamydia acanthamoeba and Waddlia chondrophila were created by combining primers and probes selected from literature. These assays were optimized and employed to analyse samples from 25 cases, with placentitis and/or pneumonia lesions, selected from the prospective study. The retrospective study reported 288 cases from six provinces. Diagnostic rate was 35.1%. The prospective study reported 135 cases from six provinces. Diagnostic rate was 42.2%. Brucella species were most commonly isolated in both the retrospective and prospective studies at 7.3% and 7.4% of cases, respectively. The qPCR assays detected Chlamydiales in 60% of cases with placentitis and/or pneumonia. Chlamydia 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).