Molecular Detection and Surveillance of Zoonotic Abortive Agents in Small Ruminants in Tunisia: Epidemiology and Risk Factors

Abstract Background Abortions in ruminants are a major constraint affecting livestock productivity and pose a significant threat to public health due to their zoonotic nature. In low- and middle-income countries, particularly Tunisia, these diseases remain underdiagnosed due to the lack of systematic molecular syndromic surveillance. We assumed that multiple zoonotic abortive pathogens are actively circulating at high levels in Tunisian small ruminant populations, with frequent co-infections, and that molecular diagnostics would significantly improve their detection and epidemiological characterization. This study aims to establish the first nationwide molecular epidemiological survey of the main pathogens responsible for abortions in small ruminants, to identify associated risk factors, and to assess the relevance of molecular diagnostics for national surveillance. Methods A cross-sectional study was conducted between July 2020 and February 2023 in 24 governorates. A total of 159 samples from abortion cases from 83 farms (sheep and goats) were analyzed by qPCR for the detection of Brucella spp., Coxiella burnetii , and Chlamydia spp. and by PCR to detect Toxoplasma gondii and Salmonella spp. Multivariate logistic regression analysis was conducted to assess the risk factors associated with abortion. Results At the herd level, at least one pathogen was detected in 63.8% of herds. The most common detected pathogens were Brucella spp. and Chlamydia spp. (22.6% each), followed by Toxoplasma gondii (18.8%), Coxiella burnetii (15.7%) and Salmonella spp. (1.3%). Co-infections involving two or more agents were detected in 24.5% of positive herds, which highlights the complex etiology of abortions. Multivariable analysis revealed that the absence of brucellosis vaccination was strongly associated with an increased risk of infectious abortion (OR = 9.11; 95% CI: 3.40–24.39; p  < 0.001), while the presence of abortion on neighboring farms showed a negative association (OR = 0.35; 95% CI: 0.13–0.90; p  = 0.031). Sampling delay significantly influenced the distribution of PCR-positive samples (Spearman’s ρ = −0.86; p  < 0.001), with vaginal swabs maintaining high detection rates beyond 10 days post-abortion. The heterogeneous geographical distribution and seasonality of cases were also characterized: Abortion cases showed a clear seasonal trend, peaking during autumn and winter and decreasing during summer. Most confirmed cases were geographically clustered in the northern and central regions. Conclusion This study revealed a high endemic circulation of zoonotic abortifacient pathogens and highlighted the added value of molecular diagnostics for effective surveillance. These findings provide an essential scientific basis for revising national control strategies to reduce economic losses and to limit zoonotic transmission to humans in a context of limited resources.