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 particular outbreak to date.
‘New metagenomic analysis tool called MALT, helps obtain traces of ancient pathogen DNA to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico.’
"Given the historical and 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," explains Åshild J. Vågene of the MPI-SHH, co-first author of the study. 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. These circumstances made Teposcolula-Yucundaa an ideal site to test a new method to search for direct evidence of the cause of the disease.
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 particular target beforehand
. This screening method revealed promising evidence of S. enterica DNA traces in 10 of their samples.
Subsequent to this initial finding, a DNA enrichment method specifically designed for this study was applied. With this, the 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 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.
A new tool in discovering past diseases
"A key result of this study is that we were successful in recovering information about a microbial infection that was circulating in this population, and we did not need to specify a particular target in advance," explains Alexander Herbig, also of the MPI-SHH and co-first author of the study. In the past, scientists usually targeted a particular pathogen or a small set of pathogens, for which they had prior indication.
"This new approach allows us to search broadly at the genome level for whatever may be present," added Johannes Krause, director of the Department of Archaeogenetics at the MPI-SHH and last author of the study. Kirsten Bos, also of the MPI-SHH, 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."