Enteric fever in sixteenth-century Mexico

Ancient DNA coupled with metagenomic analyses shed light on the longstanding question of the cause of a major sixteenth-century epidemic in Mexico.
Enteric fever in sixteenth-century Mexico

The paper in Nature Ecology & Evolution is here: http://go.nature.com/2mENZSa

After the arrival of Europeans in the New World dozens of epidemics devastated its indigenous inhabitants. One such epidemic outbreak was the 1545-1550 ‘cocoliztli’ epidemic (cocoliztli means 'pestilence' in Nahuatl) that heavily affected Mexico and Guatemala, the pathogenic cause of which has been debated for over a century.

Teposcolula-Yucundaa, an ancient Mixtec town situated in the Oaxaca region of southern Mexico, contains the only known cemetery linked to this epidemic. Archaeologists estimate that more than 800 individuals are buried here, in what was the town’s main square or “Grand Plaza”, many of whom were victims of the cocoliztli. Shortly after the epidemic, Teposcolula-Yucundaa was abandoned and the town was relocated. The epidemic cemetery was left untouched until a team of archaeologists, led by Nelly Robles García of the Mexican National Institute of Anthropology and History (INAH), excavated the site between 2004 and 2010. Also located at this site is a second cemetery in the town’s churchyard that contains individuals who died prior to European contact in the region.

In 2013 we formed a collaborative team comprising researchers from the Max Planck Institute for the Science of Human History, Harvard University, INAH, and the University of Tübingen with the aim of using ancient DNA to shed light on the question:

Can ancient DNA help us to determine the pathogenic cause of the 1545-1550 cocoliztli epidemic at Teposcolula-Yucundaa? 

Archaeological excavations at the site of Teposcolula-Yucundaa, a major political center of the ancient Mixtecs. After the epidemic, the city was relocated to the valley and the mountain-top site was abandoned. Photo: Christina Warinner. Image courtesy of the Teposcolula-Yucundaa Archaeological Project.

Visual clues as to what caused this epidemic were absent from the excavated skeletons. This was perhaps not surprising, as only a handful of infectious diseases leave visibly distinctive lesions on bone – the most common biological material to survive in the archaeological record. Although historical documents by both indigenous and European authors describe first-hand accounts of the disease symptoms, historians have not been able to reach a consensus on its pathogenic cause. The historical evidence alone suggests that the cause of the epidemic was some sort of malady that produced a body rash and could lead to bleeding from facial orifices. However, these symptoms are not specific to one particular disease. Over the years suggestions have accumulated, including: typhus, measles, enteric (typhoid) fever, viral haemorrhagic fever and pneumonic plague, to name a few. 

Indigenous Mexican people recorded their histories in codices, which contain mostly images and pictograms. The depictions shown here are of the 1545 epidemic from 16th century documents. (a) Codex en Cruz, (b) Codex Mexicanus, (c) Codex Aubin, (d) Tira de Tepechpan, (e) Codex Telleriano-Remensis. All of the images depict bleeding from the face (or the vomiting of blood), with the exception of the Codex Telleriano-Remensis, which shows a stack of shrouded corpses. All images were re-drawn by Annette Günzel. This figure appears as Supplementary Figure 10 in our paper.

We collected teeth from 24 individuals from the epidemic Grand Plaza cemetery and 5 from the churchyard cemetery and brought them to the University of Tübingen, where the tooth pulp-chambers were sampled for DNA extraction. Based on previous experience we knew that our extracts would contain DNA from many different sources, including from the bacterial, fungal, viral, plant, insect and animal communities present in the soil in which the individuals were buried. This complex environmental background greatly confounds our attempts to find ancient pathogen DNA, which is usually preserved in very low abundance. However, the interiors of teeth are shielded to some degree from the burial environment by their hard enamel surface. Thus, we determined that teeth would be our best bet to detect traces of DNA from any blood-borne pathogens infecting the individuals at their time of death.

A mass burial in the Teposcolula-Yucundaa Grand Plaza, shown prior to excavation. It contained the remains of three individuals, all of whom tested positive for Salmonella enterica. A second grave, visible at the top right, contained an additional two individuals who tested positive for S. enterica. Mass graves in the Grand Plaza were densely spaced and roughly cut into the plaster floor. The floor was never repaired, indicating the haste with which the site was abandoned shortly after the epidemic. Photo: Christina Warinner. Image courtesy of the Teposcolula-Yucundaa Archaeological Project.

We needed a strategy that would handle two issues: the fact that we would be dealing with DNA from a large number of environmental sources that could hinder our ability to find the pathogen, and the fact that we did not know which pathogen we were looking for. Therefore, approaches targeting one or a selected set of pathogens were out of the question. We needed a broad scale screening approach – the more unbiased and broader, the better.   Like others before us who have faced similar predicaments, we chose a metagenomic approach and made use of a novel computational tool, termed MALT (MEGAN ALignment Tool), developed by Daniel Huson at the University of Tübingen and adapted for our screening purposes by Alexander Herbig (available to download here). MALT works by placing all sequenced DNA fragments at the taxonomic position of best fit by comparing every read to every possible position in every genome included in your database of choice. Ours contained all complete bacterial genomes available through NCBI RefSeq, providing us with a screening approach for bacterial pathogens that was both of limited bias and would also categorize and filter out DNA from soil-dwelling species that had made it into our data.

Listed in our results, amongst hundreds of environmental bacterial species, we discovered Salmonella enterica subsp. enterica serovar Paratyphi C, a cause of enteric fever, as a potential candidate pathogen in ten of our individuals from the epidemic cemetery. This was unexpected as S. Paratyphi C rarely causes human infection today. However, further experiments and analyses confirmed our S. Paratyphi C finding in all ten individuals from the epidemic cemetery. For five individuals, we were able to reconstruct complete S. Paratyphi C genomes. The pre-contact samples, and a soil sample included as a measure of the environmental background, did not test positive for S. Paratyphi C, indicating that S. Paratyphi C was not an environmental contaminant, and was not present in the pre-contact community.

Åshild Vågene conducting lab work at the Max Planck Institute for the Science of Human History. Working with ancient DNA requires dedicated cleanroom facilities, where we have to cover ourselves from head to toe in order to prevent contamination of our samples with our own DNA – the gear is worn for the samples’ protection, not ours! Ancient DNA is usually preserved in very low abundance and the further introduction of ‘modern’ DNA might swamp out the ancient to undetectable levels. Photo: Elizabeth Nelson.

Now we are able to say, through direct ancient DNA evidence, that S. Paratyphi C was at least one of the pathogens circulating in the indigenous population at Teposcolula-Yucundaa during the 1545-1550 cocoliztli epidemic. Whether enteric fever affected people in other parts of Mexico or Guatemala during this epidemic remains to be seen. Being able to contribute to a longstanding historical epidemic mystery via ancient DNA, as well as the proof of principal that we can indeed look for ancient pathogens without having to specify a target organism, has made this an extremely exciting project. We hope others will use these methods to tackle similar ancient and modern mysteries in the future.

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Go to the profile of Ben Johnson
over 5 years ago

The authors have written an additional post clarifying some of the results in their study, and available here: https://natureecoevocommunity.nature.com/posts/30037-mixtecs-aztecs-and-the-great-cocoliztli-epidemic-of-ad-1545-1550

Go to the profile of John Cathey
about 3 years ago

Dear Dr. Vågene and colleagues 


We apologize for the delayed response in commenting on your 2018 article. The advent of the COVID-19 epidemic has concentrated our minds somewhat, and we’ve realized we better do it before it’s too late. We submitted a comment to Matters Arising, but they declined since our comment is not on technical matters, but primarily on your remarks about other explanations for the cocolitzli  events of the 16th century. In the supplementary discussion you dismissed analyses using historical accounts of clinical manifestations and suggested specifically that “...the historical symptoms of cocoliztli are also not consistent with any known viral disease...”.   We take issue with that and with the idea that all analyses based on historical description are of the same flavor and of little value. Marr and Kiracofe (2000),1  who focused primarily on the epidemic of 1576-80, concluded that contemporaneous historical descriptions by  Francisco Hernandez were consistent with a viral hemorrhagic fever, specifically one of the diseases caused by an arenavirus, a family of mostly murid viruses with single-stranded RNA.2  Francisco Hernandez was the Spanish physician in charge of the Royal Hospital in Mexico City during the outbreak of 1576-77. The 16th-century document written by Hernandez, thought to have been lost, was discovered  in archives in Madrid in the 1950s. While most other accounts from the time are not useful, those of Hernandez, “... stand out as an exception [to the humoral theory of the time] in his remarkably full statement of the symptoms of the 1576-81 epidemic…”3 Unlike the  writers of most early accounts of the epidemics, Fernandez was a trained, experienced physician who  was familiar with typhus, smallpox and other epidemic diseases. His descriptions included Nahuatal terms, suggesting that he was attempting to describe  a disease unfamiliar to European colleagues. Marr and Kiracofe carefully compared the symptomatology of smallpox and typhus with arenaviral diseases. Their  analysis involved an approach similar to the comparative methodology described by Joralemon (1982),4 which is described as “a base from which to proceed with external sources of evidence” in analyzing historical epidemics. In addition to the Hernandez document, they used translations of Nahuatl codices and graphical codices illustrating the symptoms, studied the bionomics of Mexican rodents, reviewed historical and anthropological data on post-contact Aztec agrarian practices, considered recent phylogenetic hypotheses and the epidemiology of the New World (Tacaribe) arenaviral diseases.  The first New World arenavirus was discovered and characterized in 1956,5 and thus would not have been among alternatives considered  by early writers such as Nicolle and Zinsser.6,7

As you say, your methodology was limited to detection of bacterial pathogens and DNA viruses since the technology for study of RNA viruses in ancient samples is not well developed.8 There is also the point that Salmonella is widely prevalent in many human populations, particularly rural agrarian workers,9  and that many die with the disease, not because of it.  We agree with others who think a more definitive conclusion on the cause of the Huey Cocoliztli  awaits further developments in the field of ancient RNA analysis.10

John T. Cathey (jt.cathey@gmail.com), John S. Marr (john.marr@marr-online.com)





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