Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750)
Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750)
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DOI：
10.1073/pnas.1820447116
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发表时间：
2019-06-18
影响因子：
11.1
通讯作者：
Krause, Johannes
中科院分区：
文献类型：
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作者：
Keller, Marcel;Spyrou, Maria A.;Krause, Johannes
历史上记载的第一次由鼠疫耶尔森氏菌引起的大流行始于 541 年罗马帝国的查士丁尼瘟疫，一直持续到 750 年，即所谓的第一次大流行。尽管古基因组研究之前已将病原体确定为鼠疫耶尔森氏菌，但人们对该细菌在大流行过程中的传播、多样性和遗传历史知之甚少。为了阐明这一时期细菌的微观进化，我们对奥地利、英国、德国、法国和西班牙 21 个地点的人类遗骸进行了鼠疫杆菌 DNA 筛查，并重建了 8 个基因组。我们提出了一种评估古代细菌基因组中单核苷酸多态性（SNP）的方法，有助于从宏基因组背景中对低覆盖率基因组进行定性分析。对八个重建基因组的系统发育分析揭示了六至八世纪期间先前未记录的鼠疫耶尔森氏菌多样性的存在，并为欧洲存在多种不同的鼠疫耶尔森氏菌菌株提供了证据。我们提供了查士丁尼瘟疫在不列颠群岛存在的遗传证据，此前仅根据模糊的文献记载进行假设，并且在法国中部和南部、西班牙和德国南部同时出现了多种衍生菌株。所报道的四种菌株形成了与鼠疫耶尔森氏菌系统发育中的其他菌株类似的多态性，与第二次和第三次大流行有关。我们在最近的第一次大流行菌株中发现了一个 45 kb 基因组区域的缺失，影响了两个毒力因子，有趣的是，该区域与 17 至 18 世纪第二次大流行的基因组中发现的缺失重叠。
The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleo-genomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymor-phisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.