The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone.
The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone.
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DOI：
10.1371/journal.pone.0104400
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Beatson SA
中科院分区：
文献类型：
--
作者：
Forde BM;Ben Zakour NL;Stanton-Cook M;Phan MD;Totsika M;Peters KM;Chan KG;Schembri MA;Upton M;Beatson SA
大肠杆菌ST 131现在被认为是社区和临床环境中尿路和血流感染的主要贡献者。在这里，我们提出了完整的，注释的基因组E。大肠杆菌EC 958，其分离自英格兰西北地区出现泌尿道感染的患者的尿，并且代表最充分表征的ST 131菌株。测序使用Pacific Biosciences平台进行，该平台提供足够的深度和读取长度以产生完整的基因组，而不需要其他技术。假重叠群内的组装，对应于位点特异性倒位在尾纤维区的原噬菌体的发现表明了这种技术的潜力，以揭示动态的进化机制。E.大肠杆菌EC 958属于ST 131菌株的主要亚群，其产生CTX-M-15超广谱β-内酰胺酶，对氟喹诺酮耐药，编码fimH 30 1型菌毛粘附素。该亚群包括印度株NA 114和北美株JJ 1886。比较EC 958、JJ 1886和NA 114的基因组显示，NA 114基因组中基因组岛、原噬菌体和其他重复元件的排列差异与生物学无关，而是由于错误组装造成的。高质量的尿路致病性E. coli ST 131的基因组为了解这种多重耐药病原体提供了参考，并将促进新的功能，比较和临床研究。coliST 131克隆谱系。
Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage.
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影响因子：
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