A team of researchers from the Max Planck Institute for the Science of Human History (MPI-SHH), Harvard University and the Mexican National Institute of Anthropology and History (INAH), has used ancient DNA and a new data processing program to identify the possible cause of a colonial-era epidemic in Mexico. This study is published in Nature Ecology and Evolution.

Many large-scale epidemics spread through the New World during the 16th century but their biological causes are difficult to determine based on symptoms described in contemporaneous historical accounts. Researchers have used new methods in ancient DNA research to identify Salmonella enterica Paratyphi C, a pathogen that causes enteric fever, in the skeletons of victims of the 1545-1550 cocoliztli epidemic in Mexico, identifying a possible cause of this devastating colonial epidemic.

Of all the colonial New World epidemics, the unidentified 1545-1550 "cocoliztli" epidemic was among the most devastating, affecting large parts of Mexico and Guatemala, including the Mixtec town of Teposcolula-Yucundaa, located in Oaxaca, Mexico. Archaeological excavations at the site have unearthed the only known cemetery linked to this outbreak to date.

After the epidemic, the city of Teposcolula-Yucundaa was relocated from the top of a mountain to the neighboring valley, leaving the epidemic cemetery essentially untouched prior to recent archaeological excavations. The scientists analyzed ancient DNA extracted from 29 skeletons excavated at the site, and used a new computational program to characterize the ancient bacterial DNA.

This technique allowed the scientists to search for all bacterial DNA present in their samples, without having to specify a target beforehand. After this initial finding, a DNA enrichment method specifically designed for this study was applied. With this, the scientists could reconstruct full S. enterica genomes, and 10 of the individuals were found to contain a subspecies of S. enterica that causes enteric fever.

This is the first-time scientists have recovered molecular evidence of a microbial infection from this bacterium using ancient material from the New World. Enteric fever, of which typhoid fever is the best-known variety today, causes high fevers, dehydration, and gastro-intestinal complications.

 Today, the disease is considered a major health threat around the world, having caused an estimated 27 million illnesses in the year 2000 alone. However, little is known about its past severity or worldwide prevalence.

Kirsten Bos concludes that serious advancement in the methods available to researchers of ancient diseases. They can now look for the molecular traces of many infectious agents in the archaeological record, which is especially relevant to typical cases where the cause of an illness is not known a priori.