Johannes Krause (Director, Department of Archaeogenetics, MPISSH Jena, Univ. Tübingen),

With comments by Edward T. Ryan, Director of Global Infectious Disease, Massachusetts General Hospital, Professor of Medicine, Harvard Medical School, Professor of Immunology and Infectious Diseases, Harvard School of Public Health, and Principal Investigator, Harvard collaboration with the International Centre for Diarrhoeal Disease Research in Dhaka, Bangladesh
Noreen Tuross, Landon T. Clay Professor of Scientific Archaeology, Department of Human Evolutionary Biology, Harvard University.

Genome-wide data from ancient microbes may help to understand mechanisms of pathogen evolution and adaptation for today’s emerging and re-emerging infectious diseases. Ancient pathogen genomes provide, furthermore, the possibility to identify causative agents of past pandemics and therefore elucidate mortality crisis such as those that marked the early contact period in the New World. In order to identify the presence of pathogens in past populations our group 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. entericaserovar 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.

"Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico,"
Nature, 15 January 2018