(A) A minimal spanning tree of 169 S. sonnei isolates using the data from 97 chromosomal SNPs. Haplotypes were clustered into groups by sharing at least 92 alleles. Nodes including isolates described by Holt et al. () are shown in gray and do not reflect the number of isolates. Nodes containing 68 isolates that were HRM typed are displayed as pie charts whose sizes correspond to the numbers of isolates. Distances between haplotypes (nodes) reflect the numbers of polymorphic SNPs and are shown in log scale. (B) Major S. sonnei clones defined by a minimal set of six SNPs. Lineages are labeled as identified from the whole genomic variation presented by Holt et al. () and their corresponding MLVA groups as described by Filliol-Toutain et al. ().