The E phylogroup of Escherichia coli is highly diverse and mimics the whole E. coli species population structure
The E phylogroup of Escherichia coli is highly diverse and mimics the whole E. coli species population structure
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DOI：
10.1111/1462-2920.15742
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发表时间：
2021-09-09
影响因子：
5.1
通讯作者：
Denamur, Erick
中科院分区：
文献类型：
--
作者：
Clermont, Olivier;Condamine, Benedicte;Denamur, Erick
为了了解包括O157：H7 EHEC谱系在内的E类大肠杆菌的种群结构的全球图景，我们分析了从不同大陆、宿主和生活方式分离的144株代表种系多样性的菌株的全基因组。这些菌株含有4331~5440个基因，其中核心基因组2771个基因，基因组33722个基因。这些基因在菌株间的分布呈不对称的U型分布。E系统发育株拥有该物种最大的基因组，部分原因是存在可移动的遗传元件。描述了68个谱系，其中一些显示了肠外毒力基因，并在小鼠脓毒症模型中具有毒力。除EHEC谱系和参考菌株EPEC、EIEC和ETEC外，很少有菌株具有肠道毒力基因。大多数菌株缺乏获得性耐药基因，但有8株菌株具有超广谱β-内酰胺酶基因。人类毒株属于特定的谱系，其中一些毒力强，对抗生素具有耐药性[序列类型复合体(STC)350和2064]。E系统群模拟了整个物种的所有特征，这一现象已经在STC水平上观察到，证明了E.Coli的种群结构是分形的。
To get a global picture of the population structure of the Escherichia coli phylogroup E, encompassing the O157:H7 EHEC lineage, we analysed the whole genome of 144 strains isolated from various continents, hosts and lifestyles and representative of the phylogroup diversity. The strains possess 4331 to 5440 genes with a core genome of 2771 genes and a pangenome of 33 722 genes. The distribution of these genes among the strains shows an asymmetric U-shaped distribution. E phylogenetic strains have the largest genomes of the species, partly explained by the presence of mobile genetic elements. Sixty-eight lineages were delineated, some of them exhibiting extra-intestinal virulence genes and being virulent in the mouse sepsis model. Except for the EHEC lineages and the reference EPEC, EIEC and ETEC strains, very few strains possess intestinal virulence genes. Most of the strains were devoid of acquired resistance genes, but eight strains possessed extended-spectrum beta-lactamase genes. Human strains belong to specific lineages, some of them being virulent and antibiotic-resistant [sequence type complexes (STcs) 350 and 2064]. The E phylogroup mimics all the features of the species as a whole, a phenomenon already observed at the STc level, arguing for a fractal population structure of E. coli.