Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany.
Institute of Latvian History, University of Latvia, Kalpaka bulvāris 4, Riga, 1050, Latvia.
Sci Rep. 2020 Sep 3;10(1):14628. doi: 10.1038/s41598-020-71530-9.
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.
古代基因组研究已经确定了鼠疫耶尔森菌（Yersinia pestis，Y. pestis）是第二次鼠疫大流行（14 至 18 世纪）的病原体，这次大流行始于黑死病（1347-1353 年）。从这次大流行中调查的大多数鼠疫耶尔森菌菌株都分离自西欧，而对东欧国家这种细菌的多样性和微观进化知之甚少。在这项研究中，我们研究了从里加（拉脱维亚）的两个墓地中挖掘出的人类遗骸。历史证据表明，这些埋葬是 17 世纪鼠疫爆发的结果。从 16 个人的牙齿中提取 DNA，并进行鸟枪法测序。对宏基因组数据的分析显示，有 4 具遗骸中存在鼠疫耶尔森菌序列，证实这些被埋葬的个体是鼠疫的受害者。在两个样本中，鼠疫耶尔森菌 DNA 的覆盖度足以进行基因组重建。随后的系统发育分析表明，里加株落在已经已知的黑死病后基因组的多样性范围内。有趣的是，这两个拉脱维亚分离株没有聚集在一起。此外，我们检测到含有 pla 基因的 pPCP1 质粒区域的覆盖度下降。进一步分析表明存在两种 pPCP1 质粒，一种带有 pla 基因区域，一种没有，只有一条细菌染色体，这表明同一细菌携带两种不同的 pPCP1 质粒。此外，我们在大多数以前发表的黑死病后菌株中也发现了相同的模式，但在黑死病菌株中没有发现。pla 基因是感染和在人类中传播的重要毒力因子。因此，pla 缺失菌株的传播可能是导致 18 世纪欧洲第二次鼠疫大流行消失的原因之一。
