Ancient DNA reveals possible cause of epidemic in early colonial-era Mexico

While we know that that 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, what exactly was transmitted has remained a mystery. Of all the colonial New World epidemics, the unidentified 1545-1550 ‘cocoliztli’ outbreak was among the most devastating, affecting large parts of Mexico and Guatemala. Its pathogenic cause has been debated for more than a century, but now research, in part funded by the EU, is throwing some light on the tragedy.

A team, one of whom is supported by the EU through the APGREID grant, has used a new, metagenomic analysis tool called MALT to get to the bottom of what caused the disease. Metagenomics came into its own over the last decade and is defined as the direct genetic analysis of genomes contained within an environmental sample. Using these methods applied to ancient DNA analysis, the researchers have identified the Salmonella enterica Paratyphi C, (a pathogen that causes enteric fever), in the skeletons of individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico.

They have just published their results in the journal ‘Nature’. In their paper they present genome-wide data from individuals for Salmonella enterica subsp. Enterica serovar Paratyphi C, and propose that S. Paratyphi C be considered a strong candidate for the epidemic population decline during the 1545 cocoliztli outbreak at Teposcolula-Yucundaa.

A pathogen that scythed through the indigenous population

Prior to the arrival of the Spanish, the señorío (yuhuitayu, or local state) of Teposcolula-Yucundaa controlled a large Mixtec territory with an estimated population of 60 000. The area was well-connected to regional and long-distance trade routes and in 1524 the state became subject to the Spanish crown. While few records survive from the state’s early colonial history, documents from a neighbouring state record a disease outbreak in 1545, which saw 30-40 people dying a day at the epidemic’s height. In Teposcolula-Yucundaa itself, a large plaster covered cemetery is estimated to contain around 800 individuals.

The team revisited the site, and others nearby, collecting the DNA of 29 individuals from their teeth. Each tooth was sectioned at the cementoenamel junction and a sample was drilled from the crown pulp chamber. Samples were processed according to an established protocol tailored for extracting DNA from archaeological bone. They also added an extraction blank for every ten samples processed per batch and a positive control, (bone powder from an ancient cave bear), was included in every batch.

The data generated from all tooth pulp chamber samples, the soil sample and negative controls were screened for ancient bacterial pathogen DNA using the bioinformatics tool MALT which revealed promising evidence of S. enterica DNA traces in 10 of their samples. Once all tests were completed, scientists were able to reconstruct full S. enterica genomes, and 10 of the individuals were found to contain a subspecies of S. enterica that causes enteric fever.

‘This new approach allows us to search broadly at the genome level for whatever may be present,’ says Johannes Krause, director of the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History, one of the authors of the study. Kirsten Bos, also from the Institute, adds, ‘This is a critical advancement in the methods available to us as researchers of ancient diseases. We 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.’

APGREID (Ancient Pathogen Genomics of Re-Emerging Infectious Disease), ended last year. The recent contribution to the work set out in this paper shows that its goal of enabling ‘a direct reconstruction of the evolutionary history of human infectious disease agents by obtaining genome wide data of historic pathogens,’ has helped to reveal long lost secrets. The project set out to provide priceless information within the fields of history, evolutionary biology, anthropology as well as medicine and, in doing so, it aimed to have direct impact on how we manage emerging and re-emerging infectious disease in the future.

For more information, please see:
CORDIS project web page