In addition to several emerging viruses, bats have been reported to host multiple bacteria
but their zoonotic threats remain poorly understood, especially in Africa where the diversity
of bats is important. Here, we investigated the presence and diversity of Bartonella and
Rickettsia spp. in bats and their ectoparasites (Diptera and Siphonaptera) collected across
South Africa and Swaziland. We collected 384 blood samples and 14 ectoparasites across
29 different bat species and found positive samples in four insectivorous and two frugivorous
bat species, as well as their Nycteribiidae flies. Phylogenetic analyses revealed
diverse Bartonella genotypes and one main group of Rickettsia, distinct from those previously
reported in bats and their ectoparasites, and for some closely related to human pathogens.
Our results suggest a differential pattern of host specificity depending on bat species.
Bartonella spp. identified in bat flies and blood were identical supporting that bat flies may
serve as vectors. Our results represent the first report of bat-borne Bartonella and Rickettsia
spp. in these countries and highlight the potential role of bats as reservoirs of human bacterial