Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28
Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28
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DOI：
10.1099/mgen.0.000323
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发表时间：
2020-01-01
影响因子：
3.9
通讯作者：
Hayashi, Tetsuya
中科院分区：
文献类型：
--
作者：
Nakamura, Keiji;Murase, Kazunori;Hayashi, Tetsuya
噬菌体和质粒在细菌进化和多样化中发挥着重要作用。尽管已经生成了许多基因组草案，但噬菌体和质粒基因组通常是碎片化的，限制了我们对其动态的理解。在这里，我们对产志贺毒素（Stx）大肠杆菌O145:H28的239个基因组草案和7个完整基因组进行了系统分析，其主要毒力因子由原噬菌体（PP）或质粒编码。结果表明，PP 比质粒更稳定地维持。一组祖先获得的 PP 得到了很好的保存，而包括 Stx 噬菌体在内的各种 PP 是由多个亚系获得的。相比之下，O145:H28谱系中经常发生多种质粒的获得和丢失，并且只有毒力质粒保存完好。 PP 和质粒的不同动态对 O145:H28 的全基因组产生了不同的影响，在可变存在和稀有基因部分中分别存在高比例的 PP 和质粒相关基因。 PP和质粒的动态也强烈影响毒力基因库，例如stx基因的高度可变分布和一组III型分泌效应子的高度保守，这可能代表O145:H28的核心效应子和整个O145:H28群体中毒力质粒上的基因。这些结果提供了对 PP 和质粒动态的详细了解，并展示了使用大量基因组草案和适当选择的完整基因组进行基因组分析的应用。
Phages and plasmids play important roles in bacterial evolution and diversification. Although many draft genomes have been generated, phage and plasmid genomes are usually fragmented, limiting our understanding of their dynamics. Here, we performed a systematic analysis of 239 draft genomes and 7 complete genomes of Shiga toxin (Stx)-producing Escherichia coli O145:H28, the major virulence factors of which are encoded by prophages (PPs) or plasmids. The results indicated that PPs are more stably maintained than plasmids. A set of ancestrally acquired PPs was well conserved, while various PPs, including Stx phages, were acquired by multiple sublineages. In contrast, gains and losses of a wide range of plasmids have frequently occurred across the O145:H28 lineage, and only the virulence plasmid was well conserved. The different dynamics of PPs and plasmids have differentially impacted the pangenome of O145:H28, with high proportions of PP- and plasmid-associated genes in the variably present and rare gene fractions, respectively. The dynamics of PPs and plasmids have also strongly impacted virulence gene repertoires, such as the highly variable distribution of stx genes and the high conservation of a set of type III secretion effectors, which probably represents the core effectors of O145:H28 and the genes on the virulence plasmid in the entire O145:H28 population. These results provide detailed insights into the dynamics of PPs and plasmids, and show the application of genomic analyses using a large set of draft genomes and appropriately selected complete genomes.