Excavated structure at the northern edge of the Grand Plaza at Teposcolula-Yucundaa. Architectural investigations of the Grand Plaza resulted in the unexpected discovery of a large epidemic cemetery associated with the 1545-1550 cocoliztli epidemic. The cemetery was found to contain numerous mass burials, attesting to the catastrophic nature of the epidemic. Photo: Christina Warinner/Teposcolula-Yucundaa Archaeological Project

The natives who lived in the Western Hemisphere at the time of the arrival of European colonists were all but wiped out through decades and then centuries of conquest. But disease did the majority of the work: germs killed off millions of people, from the North Atlantic Coast to the mountains of Peru. Historians believe these illnesses were a wide variety of contagions, from smallpox, chickenpox, influenza, measles, sexually transmitted diseases, and even the common cold – but little physical evidence exists to confirm what outbreak killed off which tribe.

A particularly virulent outbreak that devastated huge swaths of Mexico and Guatemala in 1545 was known only at the time as the “cocolitzli” – a Nahuatl word for “pestilence.” Now a team of scientists using a novel method to scan for clues of disease in the deceased said they have isolated the DNA evidence from bones that points to the bug: a specific enteric fever called Salmonella enterica Paratyphi C, they report in the latest Nature Ecology and Evolution.

“Our study represents a first step toward a molecular understanding of disease exchange in contact-era Medico,” they conclude. “The 1545 cocolitzli epidemic is regarded as one of the most devastating epidemics in New World history.”

Two specific breakthroughs were necessary to pinpoint the underlying cause of the epidemic, which was estimated to have killed anywhere between 60 and 90 percent of the population (native and colonizer) of what was then called New Spain.

First, the cemetery in Oaxaca known as Teposcolula-Yucundaa was a perfect scientific test case, since it left essentially untouched when the epidemic made it into a ghost town. The pulp from within the teeth of these natives was available for testing to provide the DNA information. Twenty-nine individuials resulted in ancient bacterial DNA profiles.

“Given the historical archaeological context of Teposcolula-Yucundaa, it provided us with a unique opportunity to address the question regarding the unknown microbial causes responsible for this epidemic,” said Ashild Vagene, of the Max Plank Institute for the Science of Human History, one of the first authors.

Second, that DNA was subjected to a new kind of analysis by the scientists, from the Max Planck Institute, as well as Harvard University and the Mexican National Institute of Anthropology and History (INAH). Traditional DNA sequencing would mean that the analysts would have had to screen for specific germ DNA within the smorgasbord of genetic information. But the new method, involving next-generation sequencing, was put through a new analytical process called MEGAN alignment tool, called MALT for short. The process involves a statistical method that improves upon the discovery powers of prior tools like the Basic Local Alignment Search Tool (BLAST), whose metagenomic data conclusions would take prohibitive amounts of time and power, they add.

“MALT contains the same taxonomic binning algorithm, that is, the naïve lowest common ancestor algorithm implement in the interactive metagenomics analysis software MEGAN,” they write. “Like BLAST, MALT computes ‘local’ alignments between highly conserved segments of reads and references. MALT can also calculate ‘semi-global’ alignments where reads are aligned end-to-end.”

The analysis was a game-changer, according to the authors.

“This new approach allows us to search broadly at the genomic level for whatever may be present,” said Johannes Krause, another author, also of the Max Planck Institute. “This is a critical advancement in the methods available to us as researchers of ancient diseases.”

Their conclusion: 10 of the individuals sampled showed microbial infections from S. enterica Paratyphic C.