Reconstruction of pathogen genomes from ancient DNA has provided important insights into the evolution of major pathogens including Mycobacterium tuberculosis, Yersinia pestis, and Salmonella enterica. I worked on a collaborative project analyzing ancient, calcified nodules found at the base of the ribs of a 30 year old woman in Late Byzantine Troy. These nodules were originally identified by the archaeologist as calcified granulomas (i.e. tubercles) resulting from a M. tuberculosis infection. We collaborated with Dr. Hendrik Poinar’s ancient DNA group at McMaster University to sequence the contents of these nodules, and we found that these nodules were actually the result of a multispecies infection dominated by Staphylococcus saprophyticus and Gardnerella vaginalis. The species found in the nodules as well as results from elemental analysis and electron microscopy led to the conclusion that the nodules were calcified placental abscesses. I compared the ancient genomes to those from extant organisms by sequencing and assembling modern clinical isolates, performing calibrated phylogenetic analysis, and analyzing patterns of recombination among the ancient and modern genomes. The ancient G. vaginalis genome falls within contemporary diversity. G. vaginalis is highly recombinogenic, and temporal signals are obscured by recombination at the time scales examined in this study. In contrast to G. vaginalis, the ancient S. saprophyticus genome is distinct from modern human pathogenic isolates and may be an intermediate step between a host-generalist or bovine-associated lineage and the human pathogenic lineage. S. saprophyticus inhabits several niches, including humans, animals, and the environment, and variation in selection pressures and generation times in these niches may be the cause of the lack of temporal signal we observed in this data.
Check it out in eLife here!