Epidemics swept through the Americas after Europeans began their conquest of the continents, decimating native populations. While many accounts of the events have survived, it has been nearly impossible for researchers to pinpoint the exact causes. Now an international team of scientists, including investigators 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 identified a likely cause of an outbreak in Mexico that occurred in colonial times. The pathogen Salmonella enterica Paratyphi C, which causes enteric fever, has been found in the skeletal remains of victims that died during the 1545-1550 cocoliztli epidemic. The report has been published in Nature Ecology & Evolution.
Historical descriptions of such illnesses are not definitive enough to nail down an exact cause; technological advancements have now helped fill in the gaps in our knowledge. Bacterial infections can result in very similar symptoms, and we also cannot know if the pathogens have changed over 500 years; they may now present differently in patients. Genetic analysis has improved to the point where can reveal the details of how these epidemics started. This study marks the first time that a cause of the 1545-1550 cocoliztli epidemic has been found.
For this work, DNA was taken from 29 skeletons that had been excavated from the site of the outbreak. Computational tools were used to pick out the bacterial DNA in the skeletons indiscriminately. That allowed the researchers to find the bacterium common to many victims; bits of S. enterica DNA was present in ten of the samples. After focusing on the genome of that bacterium, the investigators reconstructed the complete genome. They determined that ten of the victims carried S. enterica that results in fever.
"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," explained co-first author Alexander Herbig.
Typhoid fever is the most common enteric fever in modern times. Very little is known about it, however, though it sickens around 27 million people every year.
Back in colonial times, the cocoliztli epidemic of 1545-1550 was devastating, impacting many people in swaths of Mexico and Guatemala. The town of Teposcolula-Yucundaa, in Oaxaca, Mexico, is the site of the only cemetery definitively linked to the outbreak.
"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," noted co-first-author Åshild J. Vågene of the MPI-SHH.
"This new approach allows us to search broadly at the genome level for whatever may be present," added senior author Johannes Krause, director of the Department of Archaeogenetics at the MPI-SHH. Kirsten Bos, of the MPI-SHH noted that "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."