RT Journal Article SR Electronic T1 Salmonella enterica genomes recovered from victims of a major 16th century epidemic in Mexico JF bioRxiv FD Cold Spring Harbor Laboratory SP 106740 DO 10.1101/106740 A1 Åshild J. Vågene A1 Michael G. Campana A1 Nelly M. Robles García A1 Christina Warinner A1 Maria A. Spyrou A1 Aida Andrades Valtueña A1 Daniel Huson A1 Noreen Tuross A1 Alexander Herbig A1 Kirsten I. Bos A1 Johannes Krause YR 2017 UL http://biorxiv.org/content/early/2017/02/08/106740.1.abstract AB Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Using a metagenomic tool called MALT to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica 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 locally known as “cocoliztli”, the cause of which has been debated for over a century. Here we present two reconstructed ancient genomes for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C contributed to the population decline during the 1545 cocoliztli outbreak in Mexico.One Sentence Summary Genomic evidence of enteric fever identified in an indigenous population from early contact period Mexico.