Refining the pathovar paradigm via phylogenomics of the attaching and effacing Escherichia coli
Refining the pathovar paradigm via phylogenomics of the attaching and effacing Escherichia coli
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DOI：
10.1073/pnas.1306836110
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发表时间：
2013-07-30
影响因子：
11.1
通讯作者：
Rasko, David A.
中科院分区：
文献类型：
--
作者：
Hazen, Tracy H.;Sahl, Jason W.;Rasko, David A.
附着和消失大肠杆菌（AEEC）的特征在于存在由肠上皮细胞消失位点（LEE）编码的III型分泌系统。肠出血性大肠大肠杆菌（EHEC）通常被鉴定为LEE+且携带编码滋贺毒素（stx）的噬菌体的分离物，其被标记为产滋贺毒素的大肠杆菌。coli;而肠致病性E.大肠杆菌（EPEC）是LEE+，并且通常携带EPEC粘附因子质粒编码的菌毛形成（bfp）基因。所有其他LEE+/bfp-/stx-分离株历来被指定为非典型EPEC。这些组已被定义的基础上存在或不存在有限数量的毒力因子，其中许多编码的移动的元件。本研究对114株LEE+ E的基因组进行了比较分析。大肠杆菌分离株。基于全基因组遗传学和III型分泌系统效应子的分析，AEEC被分为五个不同的基因组谱系。LEE+/stx+/bfp-基因组主要分为两个基因组谱系，O 157/O 55 EHEC 1和非O 157 EHEC 2。本研究中测序的LEE+/bfp+/stx- AEEC分离株分为EPEC 1、EPEC 2和EPEC 4基因组谱系。开发了用于鉴定这些AEEC基因组谱系中的每一个的多重PCR测定。在分析的114个AEEC基因组中，31个LEE+分离株不属于任何已知的AEEC谱系，因此代表在大多数情况下与其他E.大肠杆菌致病变种比文本修改AEEC。我们的研究结果表明不同AEEC病原体之间的进化关系和AEEC临床分离株谱系特异性鉴定的基因组学的实用性。
The attaching and effacing Escherichia coli (AEEC) are characterized by the presence of a type III secretion system encoded by the locus of enterocyte effacement (LEE). Enterohemorrhagic E. coli (EHEC) are often identified as isolates that are LEE+ and carry the Shiga toxin (stx)-encoding phage, which are labeled Shiga toxin-producing E. coli; whereas enteropathogenic E. coli (EPEC) are LEE+ and often carry the EPEC adherence factor plasmid-encoded bundle-forming pilus (bfp) genes. All other LEE+/bfp-/stx- isolates have been historically designated atypical EPEC. These groups have been defined based on the presence or absence of a limited number of virulence factors, many of which are encoded on mobile elements. This study describes the comparative analysis of the genomes of 114 LEE+ E. coli isolates. Based on a whole-genome phylogeny and analysis of type III secretion system effectors, the AEEC are divided into five distinct genomic lineages. The LEE+/stx+/bfp- genomes were primarily divided into two genomic lineages, the O157/O55 EHEC1 and non-O157 EHEC2. The LEE+/bfp+/stx- AEEC isolates sequenced in this study separated into the EPEC1, EPEC2, and EPEC4 genomic lineages. A multiplex PCR assay for identification of each of these AEEC genomic lineages was developed. Of the 114 AEEC genomes analyzed, 31 LEE+ isolates were not in any of the known AEEC lineages and thus represent unclassified AEEC that in most cases are more similar to other E. coli pathovars than to text modification AEEC. Our findings demonstrate evolutionary relationships among diverse AEEC pathogens and the utility of phylogenomics for lineage-specific identification of AEEC clinical isolates.