Use of optical mapping to sort uropathogenic Escherichia coli strains into distinct subgroups
Use of optical mapping to sort uropathogenic Escherichia coli strains into distinct subgroups
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DOI：
10.1099/mic.0.033977-0
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发表时间：
2010-07-01
期刊：
影响因子：
2.8
通讯作者：
Dykes, Colin W.
中科院分区：
文献类型：
--
作者：
Schwan, William R.;Briska, Adam;Dykes, Colin W.
光学地图生成33尿路致病性大肠杆菌（UPEC）分离株。对于单个基因组，Ncol限制性片段与每个分离株的独特染色体图谱对齐，然后将其与所有测序的E.大肠杆菌和志贺氏菌菌株。所有UPEC分离株与志贺氏菌菌株以及实验室和肠出血性大肠杆菌菌株分开聚类。大肠杆菌菌株。此外，个别菌株似乎聚类成不同的亚组的树状图分析的基础上。33株菌的系统发育分型结果表明，32/33株为B2亚群，1/33株为A亚群。为了进一步研究33株分离株之间的相似性和差异性，进行了致病力岛（派），溶血素和毒力基因的比较。观察到个体亚组与毒力因子基因以及溶血活性之间存在强相关性。此外，有相当大的保守性测序菌株PAI在特定的亚组。具有不同耐药性模式的菌株似乎也分为不同的亚组。因此，光学图谱将UPEC菌株与其他E.大肠杆菌菌株，并进一步细分为不同的亚群。这种光学映射过程有望作为一种替代方法来分组所有E。大肠杆菌菌株，包括涉及肠道外感染的菌株和具有不同抗生素耐药性模式的流行菌株。
Optical maps were generated for 33 uropathogenic Escherichia coli (UPEC) isolates. For individual genomes, the Ncol restriction fragments aligned into a unique chromosome map for each individual isolate, which was then compared with the in silico restriction maps of all of the sequenced E. coli and Shigella strains. All of the UPEC isolates clustered separately from the Shigella strains as well as the laboratory and enterohaemorrhagic E. coli strains. Moreover, the individual strains appeared to cluster into distinct subgroups based on the dendrogram analyses. Phylogenetic grouping of these 33 strains showed that 32/33 were the B2 subgroup and 1/33 was subgroup A. To further characterize the similarities and differences among the 33 isolates, pathogenicity island (PAI), haemolysin and virulence gene comparisons were performed. A strong correlation was observed between individual subgroups and virulence factor genes as well as haemolysis activity. Furthermore, there was considerable conservation of sequenced-strain PAIs in the specific subgroups. Strains with different antibiotic-resistance patterns also appeared to sort into separate subgroups. Thus, the optical maps distinguished the UPEC strains from other E. coli strains and further subdivided the strains into distinct subgroups. This optical mapping procedure holds promise as an alternative way to subgroup all E. coli strains, including those involved in infections outside of the intestinal tract and epidemic strains with distinct patterns of antibiotic resistance.