Detection of Multiple Microorganisms in Ruminant Ticks in Senegal Using High-Throughput Microfluidic Real-Time PCR

Ticks are major vectors of numerous pathogens affecting both livestock and humans. In Senegal, data on the diversity of tick-borne pathogens (TBPs) in ruminant-associated ticks remain limited. In total, 1703 ticks were collected from goats, sheep, and cattle across three ecological zones of Senegal (Sudanian, Sahelian, and Sudano-Sahelian). Tick species were identified morphologically, and 300 individuals were screened for 36 microorganisms using a high-throughput microfluidic real-time PCR system. DNA was successfully extracted and amplified from 289 ticks. The most abundant species were Rhipicephalus evertsi evertsi (32.3%), Hyalomma truncatum (19.6%), R. guilhoni (15.6%), H. rufipes (11.6%), and Amblyomma variegatum (11.0%). Among the screened ticks, 226 (78.9%) were positive for at least one microorganism. True pathogens of veterinary and/or zoonotic importance included Anaplasma ovis (30.8%), Coxiella spp. (23.9%), Rickettsia aeschlimannii (13.1%), Theileria spp. (11.1%), and Ehrlichia canis (4.8%), with sporadic detections of Anaplasma marginale, A. bovis, and Babesia spp. (0.3% each). In addition, non-pathogenic Francisella-like endosymbionts (FLEs) were detected at high prevalence (37.4%) across all ecological zones. The presence of TBPs and/or endosymbionts was significantly associated only with the tick's host in the multivariable logistic regression model. Ticks collected from goats (OR = 7.82; p = 0.024) and sheep (OR = 7.70; p = 0.015) were significantly more likely to be infected than those collected from cattle (reference group). A total of 96 cases of microorganism co-occurrence were recorded across different tick species. Co-infections were more frequent in ticks collected from the Sudano-Sahelian zone (48.2%) and in those from sheep (32.0%). None of the detected microorganism species showed a significant associated with tick sex. This study represents the first large-scale molecular survey of TBPs in ruminant-associated ticks in Senegal, revealing both a high diversity of pathogens and a widespread presence of tick endosymbionts. While endosymbionts, such as FLEs, are not known to be pathogenic, their abundance may influence tick physiology and vector competence. The detection of zoonotic pathogens, such as E. canis and R. aeschlimannii, underscores the need to strengthen tick surveillance and investigate their potential public health implications.