Fig. 2

A tree showing the relationship between the core genomes of 77 phylogroup 1 S. flexneri isolates from Connor et al. [23] and isolate SF1 (in blue) (metadata can be found in Additional file 1: Table S1). The S. flexneri 2a str. 301 genome sequence (Chr: NC_004,337 and pCP301: NC_004851) was used as a reference for the core genome alignment and is represented in the tree as the unlabeled outgroup. The tree was inferred using IQtree version 1.6.12. Approximately, 80% of the S. flexneri 2a str. 301 genome sequence was used for the core genome and the greatest pairwise SNP distance was 2151 bases. Taxon labels include serotype, isolate name, country (abbreviated using ISO3166 three letter code; note EU = Europe, and UNK = Unknown) and year of isolation. The close relationship of the Kuwaiti isolate with those from Pakistan and Bangladesh is indicated in purple lines. A genotypic antimicrobial resistance profile for 13 resistance genes is shown at the right of the taxon label where an open box or circle (for β-lactamases) indicates gene absence and closed one indicates gene presence. The figure was produced using the interactive tree of life website (https://itol.embl.de)