Single nucleotide polymorphisms caused by cultivation among Shiga toxin producing Escherichia coli O157:H7/H- strains

The whole genome sequence (WGS) data were obtained from nine Shiga toxin producing Escherichia coli O157:H7/H- (O157) strains after three times subcultivation on LB agar plates. In each subculture, five colonies were picked up and DNAs were extracted for next generation sequencer analysis. After exclusion of possible recombination-related SNPs from WGS data, several SNPs were detected in genes in the backbone, O-island, and mobile elements gene categories. This suggested that those SNPs caused by cultivation could influence the molecular epidemiology and phylogenetic analysis of O157. Significant differences were observed by the Kruskal-Wallis test (P < 0.01) when the number of the SNPs in a strain was compared to that in other strains, indicating that the influence of SNPs caused by cultivation would be different using different strains for those analyses.