Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause in humans of urinary tract infection and bacteremia. The previously published web tool VirulenceFinder (http://cge.cbs.dtu.dk/services/VirulenceFinder/) uses whole-genome sequencing (WGS) data for in silico characterization of E. coli isolates and enables researchers and clinical health personnel to quickly extract and interpret virulence-relevant information from WGS data. In this study, 38 ExPEC-associated virulence genes were added to the existing E. coli VirulenceFinder database. In total, 14,441 alleles were downloaded. A total of 1,890 distinct alleles were added to the database after removal of redundant sequences and analysis of the remaining alleles for open reading frames (ORFs). The database now contains 139 genes—of which 44 are related to ExPEC—and 2,826 corresponding alleles. Construction of the database included validation against 27 primer pairs from previous studies, a search for serotype-specific P fimbriae papA alleles, and a BLASTn confirmation of seven genes (etsC, iucC, kpsE, neuC, sitA, tcpC, and terC) not covered by the primers. The augmented database was evaluated using (i) a panel of nine control strains and (ii) 288 human-source E. coli strains classified by PCR as ExPEC and non-ExPEC. We observed very high concordance (average, 93.4%) between PCR and WGS findings, but WGS identified more alleles. In conclusion, the addition of 38 ExPEC-associated genes and the associated alleles to the E. coli VirulenceFinder database allows for a more complete characterization of E. coli isolates based on WGS data, which has become increasingly important considering the plasticity of the E. coli genome.

中文翻译：

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使用全基因组测序数据对肠外毒力基因的大肠杆菌分离株进行计算机基因分型。

肠外致病性大肠杆菌(ExPEC) 是人类尿路感染和菌血症的主要原因。先前发布的网络工具 VirulenceFinder (http://cge.cbs.dtu.dk/services/VirulenceFinder/) 使用全基因组测序 (WGS) 数据对大肠杆菌分离株进行计算机表征，并使研究人员和临床卫生人员能够从 WGS 数据中快速提取和解释毒力相关信息。在这项研究中，将 38 个与 ExPEC 相关的毒力基因添加到现有的大肠杆菌中VirulenceFinder 数据库。总共下载了 14,441 个等位基因。在去除冗余序列并分析剩余等位基因的开放阅读框 (ORF) 后，共有 1,890 个不同的等位基因被添加到数据库中。该数据库现在包含 139 个基因（其中 44 个与 ExPEC 相关）和 2,826 个相应的等位基因。数据库的构建包括针对先前研究中的 27 对引物进行验证，搜索血清型特异性 P fimbriae papA等位基因，以及对七个基因（etsC、iucC、kpsE、neuC、satA、tcpC和terC ）的 BLASTn 确认) 没有被引物覆盖。使用 (i) 一组 9 个对照菌株和 (ii) 288 种人源大肠杆菌菌株（通过 PCR 分类为 ExPEC 和非 ExPEC ）对增强的数据库进行了评估。我们观察到 PCR 和 WGS 结果之间非常高的一致性（平均为 93.4%），但 WGS 鉴定了更多的等位基因。总之，将 38 个 ExPEC 相关基因和相关等位基因添加到E.coli VirulenceFinder 数据库允许基于 WGS 数据更完整地表征大肠杆菌分离株，考虑到E.coli的可塑性，这变得越来越重要。大肠杆菌基因组。