Scientists have never been able to pinpoint the exact disease that killed millions of native Aztecs in the middle 1500s, which in turn helped Europeans dominate the region during their conquest of the “New World.” In 1545, between 7 and 17 million people died during an outbreak in the Mexican highlands, and one group of scientists believe they may have figured out the specific pathogen that led to the death of so many.
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 entericasubsp. 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.
Salmonella was the likely culprit. Science Alert explains that it was during this specific outbreak that the overwhelming majority of the native population perished.