Alnajar Seema, Gupta Radhey S
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
Infect Genet Evol. 2017 Oct;54:108-127. doi: 10.1016/j.meegid.2017.06.024. Epub 2017 Jun 26.
The family Enterobacteriaceae harbors many important pathogens, however it has proven difficult to reliably distinguish different members of this family or discern their interrelationships. To understand the interrelationships among the Enterobacteriaceae species, we have constructed two comprehensive phylogenetic trees for 78 genome-sequenced Enterobacteriaceae species based on 2487 core genome proteins, and another set of 118 conserved proteins. The genome sequences of Enterobacteriaceae species were also analyzed for genetic relatedness based on average amino acid identity and 16S rRNA sequence similarity. In parallel, comparative genomic studies on protein sequences from the Enterobacteriaceae have identified 88 molecular markers in the form of conserved signature indels (CSIs) that are uniquely shared by specific members of the family. All of these multiple lines of investigations provide consistent evidence that most of the species/genera within the family can be assigned to 6 different subfamily level clades which are designated as the "Escherichia clade", "Klebsiella clade", "Enterobacter clade", "Kosakonia clade", "Cronobacter clade" and "Cedecea clade". The members of the six described clades, in addition to their distinct branching in phylogenetic trees, can now be reliably demarcated in molecular terms on the basis of multiple identified CSIs that are exclusively shared by the group members. Several additional CSIs identified in this work that are either specific for individual genera (viz. Kosakonia, Kluyvera and Escherichia-Shigella), or are present at various taxonomic depths, offer information regarding the interrelationships among the different clades. The described molecular markers provide novel means for diagnostic as well as genetic and biochemical studies on the Enterobacteriaceae species and for resolving the polyphyly of its several genera viz. Escherichia, Enterobacter and Kluyvera. On the bases of our results, we are proposing the reclassification of Escherichia vulneris and Enterobacter massiliensis into two novel genera viz. Pseudescherichia gen. nov. and Metakosakonia gen. nov., respectively. Additionally, our results also support the transfer of "Enterobacter lignolyticus" and "Kluyvera intestini" to the genera Pluralibacter and Metakosakonia, respectively.
肠杆菌科包含许多重要的病原体，然而，事实证明，要可靠地区分该科的不同成员或辨别它们之间的相互关系是很困难的。为了了解肠杆菌科物种之间的相互关系，我们基于2487个核心基因组蛋白以及另一组118个保守蛋白，为78个已进行基因组测序的肠杆菌科物种构建了两个综合系统发育树。还基于平均氨基酸同一性和16S rRNA序列相似性对肠杆菌科物种的基因组序列进行了遗传相关性分析。同时，对肠杆菌科蛋白质序列的比较基因组研究已经鉴定出88个以保守特征插入缺失（CSIs）形式存在的分子标记，这些标记是该科特定成员所特有的。所有这些多方面的研究都提供了一致的证据，表明该科内的大多数物种/属可以归为6个不同的亚科水平分支，分别命名为“大肠杆菌分支”、“克雷伯菌分支”、“肠杆菌分支”、“科萨科尼亚分支”、“克罗诺杆菌分支”和“西地西菌分支”。上述六个分支的成员，除了在系统发育树中有明显的分支外，现在还可以根据该组成员特有的多个已鉴定的CSIs在分子层面上可靠地划分。在这项工作中鉴定出的其他几个CSIs，要么是个别属（即科萨科尼亚属、克吕韦拉属和大肠杆菌-志贺菌属）所特有的，要么存在于不同的分类深度，提供了有关不同分支之间相互关系的信息。所描述的分子标记为肠杆菌科物种的诊断以及遗传和生化研究提供了新方法，也为解决其几个属（即大肠杆菌属、肠杆菌属和克吕韦拉属）的多系性问题提供了新方法。基于我们的研究结果，我们建议将脆弱大肠杆菌和马赛肠杆菌分别重新分类为两个新属，即新拟大肠杆菌属和新元科萨科尼亚属。此外，我们的研究结果还支持将“解木聚糖肠杆菌”和“肠道克吕韦拉菌”分别转移到普氏菌属和新元科萨科尼亚属。
