Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago

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, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection 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. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome. Ancient genomic evidence for Rickettsia felis presence in human remains from 2000 years ago reframes previous hypotheses of R. felis as a novel or emergent pathogen in modern humans.

Automated summary

By analyzing metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, about 2000 years ago, ancient DNA sequences homologous to the flea-borne typhus-like pathogen Rickettsia felis were identified, and an ancient R. felis genome was reconstructed. This provides ancient genomic evidence for the presence of Rickettsia felis in human remains from 2000 years ago, reframing previous hypotheses of R. felis as a novel or emergent pathogen in modern humans.