Historical Y. pestis genomes reveal the European Black Death as the source of ancient and modern plague pandemics

Yersinia pestis is one of the most virulent bacterial pathogens known to humans. Here we deepen our knowledge of its history through the analysis of Y. pestis genomes from plague victims of the Black Death and two subsequent historical outbreaks. Our sample range spans Europe and its vicinity, namely Barcelona, Spain (1300-1420 cal AD), Bolgar City, Russia (1298-1388 cal AD), and Ellwangen, Germany (1485-1627 cal AD). Our results provide support for a single entry of plague during the Black Death, followed by a medieval wave of plague that traveled towards Asia to later become the source population for contemporary worldwide epidemics. In addition, our data from post-Black Death outbreaks are best explained by the presence of an historical European plague focus that is now likely extinct.