The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens . While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, there is insufficient evidence for ancient human-pathogen interactions in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c . 2,000 years ago. This resulted in the identification of DNA sequence reads homologous to Rickettsia felis , and the reconstruction of an ancient R. felis genome, the causative agent of typhus-like flea-borne rickettsioses. The concurrent detection of DNA reads derived from Toxoplasma gondii , the causative agent of toxoplasmosis, confirms the pre-Neolithic incidence of these pathogens in southern Africa. We demonstrate that an R. felis and T. gondii co-infection, exacerbated by various additional bacterial and parasitic pathogens, contributed to the ill-health and subsequent demise of the boy from Ballito Bay.

Ancient DNA of <i>Rickettsia felis</i> and <i>Toxoplasma gondii</i> implicated in the death of a hunter-gatherer boy from South Africa, 2,000 years ago

Ancient DNA of Rickettsia felis and Toxoplasma gondii implicated in the death of a hunter-gatherer boy from South Africa, 2,000 years ago