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Ancient genomic studies have identified  Yersinia pestis  ( Y. pestis ) as the causative agent of the second plague pandemic (fourteenth–eighteenth century) that started with the Black Death (1,347–1,353). Most of the  Y. pestis  strains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence of  Y. pestis  sequences in four remains, confirming that the buried individuals were victims of plague. In two samples,  Y. pestis  DNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the Riga strains fell within the diversity of the already known post-Black Death genomes. Interestingly, the two Latvian isolates did not cluster together. Moreover, we detected a drop in coverage of the pPCP1 plasmid region containing the  pla  gene. Further analysis indicated the presence of two pPCP1 plasmids, one with and one without the  pla  gene region, and only one bacterial chromosome, indicating that the same bacterium carried two distinct pPCP1 plasmids. In addition, we found the same pattern in the majority of previously published post-Black Death strains, but not in the Black Death strains. The  pla  gene is an important virulence factor for the infection of and transmission in humans. Thus, the spread of  pla -depleted strains may, among other causes, have contributed to the disappearance of the second plague pandemic in eighteenth century Europe.

Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic