Yersinia pestis, the causative agent of plague, has been prevalent among humans for at least 5000 years, being accountable for several devastating epidemics in history, including the Black Death. Analyses of the genetic diversity of ancient strains of Y. pestis have shed light on the mechanisms of evolution and the spread of plague in Europe. However, many questions regarding the origins of the pathogen and its long persistence in Europe are still unresolved, especially during the late medieval time period. To address this, we present four newly assembled Y. pestis genomes from Eastern Europe (Poland and Southern Russia), dating from the fifteenth to eighteenth century AD. The analysis of polymorphisms in these genomes and their phylogenetic relationships with other ancient and modern Y. pestis strains may suggest several independent introductions of plague into Eastern Europe or its persistence in different reservoirs. Furthermore, with the reconstruction of a partial Y. pestis genome from rat skeletal remains found in a Polish ossuary, we were able to identify a potential animal reservoir in late medieval Europe. Overall, our results add new information concerning Y. pestis transmission and its evolutionary history in Eastern Europe.

This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

鼠疫耶尔森菌是鼠疫的致病因子，在人类中已经流行了至少5000年，是造成包括黑死病在内的历史上几次毁灭性流行的原因。对古老的鼠疫耶尔森氏菌菌株的遗传多样性的分析揭示了鼠疫在欧洲的进化和传播机制。但是，关于病原体的起源及其在欧洲的长期存在的许多问题仍未解决，特别是在中世纪后期。为了解决这个问题，我们提出了四个新组装的鼠疫耶尔森菌东欧（波兰和俄罗斯南部）的基因组，其历史可追溯到公元15世纪至18世纪。分析这些基因组中的多态性及其与其他古代和现代鼠疫耶尔森菌菌株的系统发育关系，可能表明鼠疫多次独立地传入东欧或在不同的水库中持续存在。此外，通过从在波兰藏骨骨库中发现的大鼠骨骼残骸重建鼠疫耶尔森氏菌的部分基因组，我们得以确定中世纪晚期欧洲的潜在动物库。总体而言，我们的结果为有关鼠疫耶尔森菌的传播及其在东欧的进化史提供了新的信息。

本文是“从古代生物分子对健康和疾病的洞察”这一主题问题的一部分。