Molecular detection of medically important rickettsiae, including Rickettsia prowazekii in Rhipicephalus appendiculatus and Hyalomma rufipes: A microbiome perspective

The East African region hosts more than 50 % of Africa livestock and 9 % of global cattle, creating an ideal environment for ticks to thrive and transmit pathogens. Little is known of the full spectrum of tick-associated bacterial pathogens that circulate in the vast pastoralist-intense regions of East Africa, the range of the pathogens and their genetic relationships. To define this, we need to first delineate the microbial composition of the medically and veterinary important East African tick species. This study focused on the likely vectors of Orthonairovirus haemorrhagiae in Kenya and Uganda, specifically H. rufipes and R. appendiculatus. To characterize the bacterial microbiome associated with these two tick species, the V3-V4 hypervariable region of the 16S rRNA gene was sequenced from a total of 25 R. appendiculatus and 24 H rufipes specimens using the Illumina MiSeq platform. Microbial abundance and diversity were subsequently analysed to assess the composition and structure of their bacterial communities. We observed a richer and balanced bacterial microbiome profile among the H. rufipes compared to that of the R. appendiculatus, which was mainly dominated by Coxiella-like endosymbionts. Furthermore, a few bacterial taxa were unique to each sampling site, while several were common across all sampling sites. This study identified several medically important Rickettsia species, including R. aeschlimannii, R. conorii, and, for the first time, R. prowazekii, the causative agent of epidemic typhus, in H. rufipes sampled from Northeast Kenya. Furthermore, our findings demonstrate that R. africae exhibits a broad tick host tropism. Our present findings provide insights into the microbial community of medically important tick species of East Africa. The observation of a significant level of Coxiella-like endosymbionts in R. appendiculatus warrants an investigation into their transmissibility and impacts on the transmission of other pathogens. The identification of R. prowazekii in H. rufipes suggest that R. prowazekii is broadening its host tropism in Kenya.