Johannes Krause (Max Planck Institute for the Science of Human History, Jena), Death by Contact: Ancient Pathogen Genomes from Epidemics in Early Mexico. Sponsored by the Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM) and the Harvard Initiative for the Science of the Human Past.

Genome-wide data from ancient microbes may help to understand mechanisms of pathogen evolution and adaptation for emerging and re-emerging infectious disease. Ancient pathogen genomes provide, furthermore, the possibility to identify causative agents of past pandemics and therefore elucidate mortality crisis such as the early contact period in the New World. In order to identify the presence of pathogens in past populations we used a novel high-throughput DNA sequence alignment and taxonomic assignment tool MALT (MEGAN ALignment Tool) and were able to identify traces of Salmonella enterica DNA in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in Southern Mexico. This cemetery is linked to the 1545–1550 CE epidemic that affected large parts of Mexico, the pathogenic cause of which has been debated for more than a century. After application of a specifically designed targeted DNA enrichment procedure we generated genome-wide data from ten individuals for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose S. Paratyphi C as a strong candidate for the epidemic population decline during the 1545 outbreak at Teposcolula-Yucundaa and provide evidence that it was likely introduced by Europeans.