Molecular epidemiology of Shiga toxin producing Escherichia coli O157:H7/H- strains using whole genome sequence data.

The whole genome sequence (WGS) data were used for molecular epidemiology of Shiga toxin producing Escherichia coli O157:H7/H- (O157) strains. All WGS data were obtained using Hiseq2500 (Illumina). The WGS data were analyzed using CLC Genomics Workbench and single nucleotide polymorphisms (SNPs) were detected by direct mapping of short read data to a reference genome and de novo assembling of the read data. The collected SNPs were further divided according to their location, e.g. backbone, O-island, mobile elements, and non-coding regions. All SNP sets were analyzed using BioNumerics software. When SNPs in backbone region were used, maximum pair-wise distances of O157 strains isolated from single source derived strains were significantly lower than those of the other SNPs (Steel-Dwaas test, P < 0.01). In contrast, SNPs in mobile elements and non-coding regions showed poor results for strain differentiation. The Hunter-Gaston Discriminatory Power Index was 0.9303 when SNPs in backbone regions were analyzed.