Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011
Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011
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DOI：
10.1073/pnas.1121491109
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发表时间：
2012-02-21
影响因子：
11.1
通讯作者：
Hanage, William P.
中科院分区：
文献类型：
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作者：
Grad, Yonatan H.;Lipsitch, Marc;Hanage, William P.
分子流行病学揭示有关疫情来源和传播模式信息的程度取决于所使用技术和研究样本的分辨率。通过标准测试，无法区分 2011 年 5 月至 7 月德国爆发的疫情和 2011 年 6 月法国西南部规模小得多的疫情中分离出的大肠杆菌 O104:H4。我们报告了使用多平台全基因组测序和对德国和法国疫情中的多种分离株进行分析的分子流行病学分析。德国疫情中的分离株表现出非常小的多样性，在四个个体的分离株中仅发现了两个单核苷酸多态性 (SNP)。令人惊讶的是，我们在法国疫情爆发中感染的 7 个人的分离株中发现了更大的多样性（19 个 SNP）。德国分离株在更为多样化的法国爆发菌株中形成了一个进化枝。此外，来自法国爆发的单个感染者的五个分离株的多样性极其有限。德国和法国爆发样本之间多样性的显着差异与几个假设是一致的，包括消除德国分离株多样性的瓶颈、两个大肠杆菌爆发群体中突变率的变化，或者导致每次爆发的种子群体多样性分布不均匀。
The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak.