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Local Salmonella may have killed millions of indigenous Mexicans

An ancient burial ground in Oaxaca, Mexico.
A new DNA analyzing technology can find infectious pathogens in ancient graves like this one.
Published Last updated This article is more than 2 years old.

During the 16th century in the southern part of Mexico, a mysterious illness killed some 18 million indigenous Mixtec people. The disease, which was referred to by the name cocoliztli in historic records, caused headaches, fever, liver damage, and bleeding from the eyes, nose, and mouth.

Historically, cocoliztli was believed to be a disease brought over by European settlers, although scientists were never sure what could have caused these symptoms. Native people weren’t immune to new pathogens brought by ships, so sky-high death rates were the norm.

New research, however, suggests that cocoliztili was not a European disease, but rather a form of salmonella endemic to the region. In a paper paper published (paywall) Jan. 15 in Nature Ecology and Evolution Kristen Bos, an anthropologist at the Max Planck Institute in Munich, Germany, and her team identified the pathogen Salmonella enterica as a strong candidate for the pathogen that caused these deadly outbreaks. This particular strain of bacteria causes paratyphoid fever, which presents with the same symptoms consistent with accounts of cocoliztili.

The trouble with picking out individual pathogens responsible for ancient diseases, Bos said, is that you’re working with bits of microbial DNA that have degraded and fragmented over time, and been mixed with all sorts of naturally occurring bacteria in the ground. “In the past when we have looked at infectious disease in archeological material, we’ve had to have had a particular…candidate in mind,” she says. DNA analysis was limited to confirming that a particular pathogen was present, but could do little to find an original disease. All Bos and her team  had to go on were samples from 11 unearthed bodies that had died of cocoliztili, which left no clues on the body other than some small whisps of DNA left deep within tooth enamel. 

Enter, MALT, or a metagenomics analysis alignment tool. This particular program is an algorithm that contains data on known microbial genomes, and can then can match up individual fragments of DNA to the rest of the species. It’s like picking up a puzzle piece, and then matching it to the original box it came from, Bos says.

Among the expected samples of soil bacteria the team identified using MALT, the team also found evidence of S. enterica. They were able to use traditional DNA analysis techniques to confirm that more snippets of S. enterica were present.

S. enterica is spread through through food or water contaminated with fecal matter, and was likely endemic to the land. Bos told NPR that the historical records show that Europeans were getting just as sick from cocoliztili, and had no idea what it was. Plus, there was a drought in the area around the same time as the outbreaks, which could have made it easier for rodents or new European livestock to contribute to disease spread.

The research team was only looking for microbes that have double-stranded genetic material. Viruses like the flu, which only have one, would have been impossible to detect using MALT. It could be that S. enterica could have had several other pathogenic partners in crime. “We can’t say definitively that the epidemic is caused by this particular pathogen, we can say it’s a strong candidate,” Bos says.

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