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Sixteenth Century Outbreak Linked by Metagenomic DNA to Salmonella Paratyphi

NEW YORK (GenomeWeb) – Researchers have recovered Salmonella enterica DNA from individuals buried in a 16th century cemetery in Mexico, hinting that the bacterium may have been behind an outbreak that swept the region at that time.

Waves of disease followed the arrival of Europeans to the New World, including one called cocoliztli that affected large parts of Mexico between 1545 CE and 1550 CE and led to a sharp population decline in the region. While the symptoms of cocoliztli included red spots on the skin and vomiting, according to historical sources, the causative agent of the outbreak has been unclear.

Researchers led by Johannes Krause from the Max Planck Institute for the Science of Human History used a new metagenomic tool they developed to search for pathogen DNA among samples collected from a 16th century cemetery in Teposcolula-Yucundaa in Oaxaca, Mexico. As they reported in Nature Ecology & Evolution today, the researchers uncovered genome-wide data from 10 individuals that implicated S. enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever.

"Our findings contribute to the debate concerning the causative agent of this epidemic at Teposcolula-Yucundaa, where we propose that S. Paratyphi C be considered," Krause and his colleagues wrote in their paper.

The researchers collected samples from two sites in Teposcolula-Yucundaa, one cemetery that pre-dated European arrival in the area and one from the time of the cocoliztli outbreak. In particular, they gathered DNA from tooth samples from 24 indigenous individuals buried in the outbreak-era cemetery and from five individuals buried in the pre-contact cemetery for sequencing. They generated about a million pair-end reads per tooth.

With their MEGAN Alignment tool (MALT), a screening pipeline, the researchers analyzed and aligned non-enriched metagenomic sequencing data they generated by comparing it to all the entries in the National Center for Biotechnology Information's RefSeq database, about 6,247 complete bacterial genomes.

From this, they noticed that three tooth samples had between 365 reads and 659 reads the tool assigned to S. enterica. Of the S. enterica strains in the database, Krause and his colleagues said S. Paratyphi C matched the highest number of reads. When they mapped these three samples' reads to the S. Paratyphi C RKS4594 genome, they found that they harbored a damage pattern that is characteristic of ancient DNA, supporting their ancient origin.

Seven additional individuals from the outbreak-era cemetery and one negative control had low levels of S. enterica-assigned reads, the researchers noted, adding that the remaining samples including soil samples from the cemeteries, lacked S. enterica reads. The researchers confirmed the MALT results using a whole-genome targeted array.

Krause and his colleagues constructed complete genomes for the five ancient samples, and phylogenetic analysis clustered them with S. Paratyphi C.

But the ancient samples differed from the modern strains at some 200,000 SNPs, including 133 found only in the ancient samples. The ancient genomes also carried a region in the pil operon that the modern reference genome lacks. According to the researchers, the ancient version of pilV is suspected to help bacteria self-aggregate, which could help them infect host tissue.

These findings suggest that enteric fever was circulating at the time of the cocoliztli outbreak. The researchers noted that while most cases of modern enteric fever are caused by S. Typhi and S. Paratyphi A, S. Paratyphi C was present around 1200 CE in Norway, indicating that strain was present in pre-contact era Europe.

"We propose that S. Paratyphi C be considered a strong candidate for the epidemic population decline during the 1545 cocoliztli outbreak at Teposcolula-Yucundaa," Krause and his colleagues wrote in their paper.