Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete

During the late 3rd millennium BCE (before common era), the Eastern Mediterranean and Near East witnessed societal changes in many regions, which have usually been explained with a combination of social and climatic factors1-4. However, recent archaeogenetic research forces us to rethink models regarding the role of infectious diseases in past societal trajectories5. The plague bacterium Yersinia pestis, which has been involved in some of the most destructive historical pandemics5-8 was shown to have been present across Eurasia at least from the onset of the 3rd millennium BCE9-13, but the challenging preservation of ancient DNA (aDNA) in warmer climates has restricted its identification from this period to temperate climatic regions. As such, evidence from culturally prominent regions such as the eastern Mediterranean is currently lacking. Here, we present genetic evidence for the presence of Y. pestis as well as Salmonella enterica subsp. enterica, the causative agent of typhoid/enteric fever, from this period of transformation in Crete, detected at the burial cave site of Hagios Charalambos. We were able to reconstruct one Y. pestis genome that forms part of a now extinct lineage, clustering together with other Y. pestis strains from the Late Neolithic and Bronze Age (LNBA) that were likely not yet adapted for transmission via fleas. We were furthermore able to reconstruct two ancient S. enterica genomes that fall on the Para C lineage and cluster with strains isolated from the Neolithic and Bronze Age that were likely not yet fully adapted to humans as a host. The occurrence of these two virulent pathogens at the end of the Early Minoan period in Crete emphasizes the necessity to re-introduce infectious diseases as an additional factor possibly contributing to the transformation of early complex societies in the Aegean and possibly beyond.