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Nat Ecol Evol. 2018 Mar;2(3):520-528. doi: 10.1038/s41559-017-0446-6. Epub 2018 Jan 15.

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

Author information

1
Max Planck Institute for the Science of Human History, Jena, Germany.
2
Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.
3
Max Planck Institute for the Science of Human History, Jena, Germany. herbig@shh.mpg.de.
4
Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany. herbig@shh.mpg.de.
5
Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
6
Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.
7
Smithsonian Conservation Biology Institute, Center for Conservation Genomics, Washington DC, USA.
8
National Institute of Anthropology and History (INAH), Mexico, Teposcolula-Yucundaa Archaeological Project, Mexico City, Mexico.
9
Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Tübingen, Germany.

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.

PMID:
29335577
DOI:
10.1038/s41559-017-0446-6

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