Comparative Genomics of E. coli O157:H7

The closed genomes of the representative O157:H7 strains (Supplemental Table S1) were imported into SeqSphere+ (v.8.3) (Ridom GmbH, Münster, Germany) for gene-by-gene alignment, allele calling, and comparison [121 (link)]. A core genome MLST (cgMLST) schema was developed using the closed chromosome of E. coli K-12 substrain, MG1655, (GenBank accession U00096) [122 (link)] as a seed and queried against 11 closed genomes representing the 9 distinct O157:H7 phylogenetic clades [68 (link),88 (link),106 (link),107 (link)]. Core and accessory MLST targets were identified according to the inclusion/exclusion criteria of the SeqSphere+ Target Definer. The allele information from the defined core genome gene of the queried strains was used to establish phylogenetic hypotheses using the minimum-spanning method [123 (link),124 (link)] with default settings in Ridom SeqSphere+ (v.8.3).