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

Abstract

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.

A hotspot of Toxoplasma gondii Africa 1 lineage in Benin: How new genotypes from West Africa contribute to understand the parasite genetic diversity worldwide

“…Recent evidence has shown that T . gondii was already present in Africa 2,000 years ago [ 21 ]. However, such extensive and long-term intercontinental exchanges may have fueled the dissemination of many organisms to and from coastal Africa, and this could include pathogens such as non-autochtonous lineages of T .…”

Toxoplasma gondii Infections in Animals and Humans in Southern Africa: A Systematic Review and Meta-Analysis

“…Although serological methods seem to lack sensitivity and specificity, they remain a standard tool for the qualitative detection of antibodies [64]. Studies that used LAT [3,56,60], histology [28,33,34], and molecular techniques [48,50,92] were few, while others used the combination of one or two of LAT, MAT, ELISA, IFAT, DT, CF, Wolstenholme's modification, and Sabin-Feldman dye test techniques [30,32,35,41,42,54,59,93,94]. A recent study comparing three serological diagnostic tools showed that ELISA and IFAT had relatively higher sensitivity and specificity than MAT [95].…”

Homo medicus: The transition to meat eating, increased pathogen pressure, and the constitutive and inducible use of pharmacological plants in Homo

“…A large population study found an association between seropositivity for T. gondii and schizophrenia (Burgdorf et al, 2019). A study of ancient DNA from a 2000-year-old hunter gatherer boy from South Africa found evidence that he died of complications of co-infection with T. gondii and typhus-like flea-borne rickettsioses (Rifkin et al, 2020). Interestingly, a study of T. gondii-infected chimpanzees found they had a morbid attraction to leopard urine, hinting that T. gondii has long manipulated hominids, perhaps including human ancestors, to lose fear of their felid predators and thus serve as viable intermediate hosts (Poirotte et al, 2016).…”