Comparative Genomic Analysis of E. coli Strains

The assembled ATCC MP-9 genomes along with E. coli strains EC4115 (O157:H7; Eppinger et al., 2011 (link)) and K-12 substrain MG1655 (Blattner et al., 1997 (link)) were imported into SeqSphere+ (v.8.3; Ridom GmbH, Münster, Germany) for gene-by-gene alignment, allele calling, and comparison (Jünemann et al., 2013 (link)). MLST typing was performed using targeted and whole genome schemas developed for E. coli (Foley et al., 2009 (link); Zhou et al., 2020 (link)). We determined the Sequence Type (ST) by applying the 7-gene ST Achtman schema (Zhou et al., 2020 (link)). Allele sequences for the 7 genes (adk, fumC, gyrB, icd, mdh, purA, and recA) were accessed on the EnteroBase website⁵ and imported into Ridom SeqSphere+. A core genome (cg) MLST schema was developed using the closed chromosome of K-12 substrain MG1655 (GenBank accession U00096; Riley et al., 2006 (link)) as seed as previously described (Díaz et al., 2021 (link)). Core and accessory MLST targets were identified according to the inclusion/exclusion criteria of the SeqSphere+ Target Definer. The allele information from the targeted seven-gene schema and the defined core genome gene of the panel strains were used to establish phylogenetic hypotheses using the minimum-spanning method (Kruskal, 1956 (link); Francisco et al., 2009 (link)) with default settings in Ridom SeqSphere+ (v.8.3).