Seqsphere v 8

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).

Assembled genomes were imported into SeqSphere + v. 8.3 (Ridom GmbH, Münster, Germany) for gene-by-gene alignment, allele calling, and comparison (Junemann et al., 2013 (link)). A core genome (cg) MLST schema was developed using the closed chromosome of S. suis (serotype 2; ST 1) strain ISU1606 (GenBank accession CP030017) as seed. Core genome and accessory MLST targets were identified according to the inclusion/exclusion criteria of the SeqSphere + Target Definer. The allele information from core, accessory, and combined gene sets were used to establish phylogenetic hypotheses using the neighbor-joining method (Saitou and Nei, 1987 (link)). The resulting tree was visualized and decorated in iTol v. 6.7.4 (Letunic and Bork, 2021 (link)).