Skeleton bones on the floor of a burial site

Epidemics have plagued human populations for thousands of years, but there are very few clues as to what pathogens may have caused massive epidemics in the past. Scientists are using new techniques to extract and analyze ancient DNA, and what they have found may give us information about how things happened nearly 500 years ago.

Through the pairing of archeological and genomic evidence, there is new knowledge of the historical circumstances and potential impact of pathogens on ancient human communities. Traces of the ancient DNA of Salmonella enterica subspecies serovar Paratyphi C were found from individuals excavated from a specific cemetery Teposcolula-Yucundaa, Oaxaca in southern Mexico that is linked to the 1545–1550 CE epidemic.

In a recent paper, scientists isolated S. Paratyphi C in human remains of ten individuals in Mexico using a new metagenomic analysis tool called MALT. Scientists suggest that this bacterial cause for enteric fever may have been the pathogen of the 1545 epidemic in this community.

Much of what we know today about past human populations comes from remains that can be found in burial sites. Modern DNA extraction and sequencing techniques make it possible to determine what microbes and remnants of DNA exist on bones and teeth.

Tooth samples were taken from individuals buried in sites that have been identified as pre-contact and post-contact with the epidemic causing agent. The ancient DNA samples were sequenced and compared with bacterial genomes available from the National Center for Biotechnology Information (NCBI) RefSeq. Soil samples were also taken to assess the background DNA.

A new analysis technique is introduced by these authors, the MEGAN alignment tool or MALT. MALT was used for alignment and analysis of metagenomic DNA-sequencing data. MALT is similar to Basic Local Alignment Search Tool (BLAST) in that it computes alignments of highly conserved segments and references, but has been built to make these computations much faster.

Much like detectives hoping to find clues at a murder site, these scientists hoped that their analysis would reveal what pathogens were at the burial site. The results show that all individuals from the post-contact burial site had DNA segments that aligned with S. Paratyphi C DNA. No matches were found in individuals from the pre-contact burial site.

Seems like an open and shut case, but while all of the individuals from the post-contact time period show DNA that matched with S. Paratyphi C, it may be only one part of the epidemic picture.

“The historical records match a hemorrhagic fever, but we shouldn’t be too dismissive on what biologic agent it really was,” Kirsten Bos told Science.

We may still be far from seeing the whole epidemic picture. This study compared DNA samples from humans with known complete bacterial DNA genomes, therefore excluding RNA genomes. Future studies may also investigate the potential for multiple pathogens circulating at the time to have compounding and synergistic effects on the human population.

Ancient evidence of S. Paratyphi C has also been explored in Europe. A study in 2017 found the strain in an 800-year-old skeleton in Norway. Scientists are estimating that this pathogen has circulated in human populations for at least 1,000 years, and originated in swine.

Although this bacterial pathogen was only found in bodies buried during the epidemic around the time the Europeans arrived in Mexico, it may not necessarily imply that the Europeans brought the disease with them.

This groundbreaking research helps to clarify the presence of certain pathogens at the time and place of the epidemic, but further investigative work is needed to understand the full story!

Learn more about how researchers are working with ancient DNA:

By Chia-Yi Hou, PhD