| Summary: | Q fever is a neglected zoonosis in South Africa, causing significant losses in livestock and game animals through reproductive disorders. However, there are limited studies on the extent of <i>Coxiella burnetii</i> infections in livestock in South Africa. Further, there is also lack of knowledge about the types of <i>C. burnetii</i> strains that are currently circulating in the country. Therefore, a cross-sectional, abattoir-based study was conducted to determine the seroprevalence of <i>C. burnetii</i> and associated risk factors, and to characterize <i>C. burnetii</i> strains from slaughter livestock at red meat abattoirs in Gauteng, South Africa. Of the 507 animals tested, 6.9% (95% CI: 4.9–9.5%) were positive for antibodies against <i>C. burnetii</i>. The seroprevalence was 9.4% (31/331) in cattle, 4.3% (3/69) in sheep, and 0.9% (1/107) in pigs. Out of the 63 tissue samples from 35 seropositive animals including material from two sheep aborted fetuses from Mangaung district (Free State province), 12.7% (8/63) tested positive by IS<i>1111</i> PCR. Genotyping of the eight PCR-positive tissues from eight animals by MLVA revealed two novel genotypes, not available in <i>Coxiella</i> MLVA databases. It is concluded that slaughter animals pose a risk of exposing abattoir and farm workers to <i>C. burnetii</i> in South Africa.
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