首页> 外文期刊>Frontiers in Microbiology >Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation
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Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation

机译:系统识别的志贺氏菌和肠侵袭性大肠杆菌用于分子流行病学标记的鉴定:全基因组比较分析不支持不同的属称

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摘要

As a leading cause of bacterial dysentery, Shigella represents a significant threat to public health and food safety. Related, but often overlooked, enteroinvasive Escherichia coli (EIEC) can also cause dysentery. Current typing methods have limited ability to identify and differentiate between these pathogens despite the need for rapid and accurate identification of pathogens for clinical treatment and outbreak response. We present a comprehensive phylogeny of Shigella and EIEC using whole genome sequencing of 169 samples, constituting unparalleled strain diversity, and observe a lack of monophyly between Shigella and EIEC and among Shigella taxonomic groups. The evolutionary relationships in the phylogeny are supported by analyses of population structure and hierarchical clustering patterns of translated gene homolog abundance. Lastly, we identified a panel of 254 single nucleotide polymorphism (SNP) markers specific to each phylogenetic cluster for more accurate identification of Shigella and EIEC. Our findings show that Shigella and EIEC are not distinct evolutionary groups within the E. coli genus and, thus, EIEC as a group is not the ancestor to Shigella . The multiple analyses presented provide evidence for reconsidering the taxonomic placement of Shigella . The SNP markers offer more discriminatory power to molecular epidemiological typing methods involving these bacterial pathogens.
机译:作为细菌性痢疾的主要原因,志贺氏菌对公共卫生和食品安全构成了重大威胁。相关但常常被忽视的肠侵袭性大肠杆菌(EIEC)也可引起痢疾。尽管需要快速,准确地识别病原体以进行临床治疗和暴发反应,但目前的分型方法在这些病原体之间进行识别和区分的能力有限。我们使用169个样品的全基因组测序,对志贺氏菌和EIEC进行了全面的系统发育分析,构成了无与伦比的菌株多样性,并观察到志贺氏菌和EIEC之间以及志贺氏菌分类群之间缺乏单一性。系统发育中的进化关系得到人口结构分析和翻译基因同源物丰度的分层聚类模式的支持。最后,我们确定了一组254个单核苷酸多态性(SNP)标记物,这些标记物对每个系统发育簇具有特异性,可更准确地鉴定志贺氏菌和EIEC。我们的发现表明,志贺氏菌和EIEC在大肠杆菌属中不是不同的进化组,因此,EIEC作为一个组不是志贺氏菌的祖先。提出的多种分析为重新考虑志贺氏菌的分类位置提供了证据。 SNP标记为涉及这些细菌病原体的分子流行病学分型方法提供了更大的区分能力。

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