Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico.

Åshild J Vågene,Alexander Herbig,Nelly M Robles García,Daniel Huson,Michael G Campana,Susanna Sabin,Christina Warinner,Johannes Krause,Aida Andrades Valtueña,Noreen Tuross,Maria A Spyrou,Kirsten I Bos

doi:10.1038/s41559-017-0446-6

Abstract

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. Through the introduction of a new metagenomic analysis tool called MALT, applied here 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, based on historical and archaeological evidence, to the 1545-1550 CE epidemic that affected large parts of Mexico. Locally, this epidemic was known as 'cocoliztli', the pathogenic cause of which has been debated for more than a century. Here, we present genome-wide data from ten individuals for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C be considered a strong candidate for the epidemic population decline during the 1545 cocoliztli outbreak at Teposcolula-Yucundaa.

Highlights

A variety of plants, animals, cultures, technologies and infectious diseases accompanied the movement of people from the Old World to the New World immediately following initial contact, in a process commonly known as the “Columbian exchange” [1]
One hypothesis assumes that the increased susceptibility of New World populations to Old World diseases facilitated European conquest, whereby rapidly disseminating diseases severely weakened indigenous populations [3], in some cases even in advance of European presence in the region [3, 9]
While the pathogenic cause of the cocoliztli epidemic is ambiguous based on ethnohistorical evidence [10, 12, 28, 30], we report the first molecular evidence of microbial infection with the reconstruction of two ancient S. enterica subsp. enterica serovar Paratyphi C genomes isolated from epidemic-associated contact era burials

Summary

Introduction

A variety of plants, animals, cultures, technologies and infectious diseases accompanied the movement of people from the Old World to the New World immediately following initial contact, in a process commonly known as the “Columbian exchange” [1]. The individuals included in this investigation were excavated from the contact era epidemic cemetery located in the Grand Plaza (administrative square) (n=24) and the pre-contact churchyard cemetery (n=5) at Teposcolula-Yucundaa between 2004 and 2010 [28] (Fig. 1; table S1; Supplementary materials S1).

Results

Conclusion