Abstract
Yersinia pestis, the bacterium responsible for plague, has caused three major pandemics throughout recorded history. Paleogenetic studies of human skeletons have also traced the presence of Y. pestis back to prehistoric times, as early as the Neolithic period, though these discoveries have been geographically confined to Eurasia.
In this study, we present evidence of Y. pestis DNA in an ancient Egyptian mummy, an adult male from the Museo Egizio collection in Turin, Italy. The individual, anthropogenically mummified, has been radiocarbon-dated to the transitional period between the end of the Second Intermediate Period and the beginning of the New Kingdom (3290 ± 45 years BP; 1686–1449 cal. BC). While the mummified individual's exact provenance within Egypt remains uncertain, analyses of bone tissue and intestinal content using shotgun metagenomics revealed the presence of Y. pestis DNA in both samples. This might suggest a broad tissue tropism of the pathogen during an advanced stage of infection.
Subsequent targeted enrichment methods yielded low-coverage genome-wide data for both the human host and the Y. pestis pathogen. This marks the first protohistoric Y. pestis genome discovered outside Eurasia, providing molecular evidence of plague in ancient Egypt. Nevertheless, the prevalence of the disease during this time remains unclear. Further genomic analysis aims to position this ancient strain within the known diversity of Y. pestis, examine virulence-associated genes, and explore potential modes of transmission and pathology.