Genomic DNA was extracted from all S. sonnei isolates using a Wizard Genomic DNA Extraction kit (Promega) according to the manufacturer's recommendations. For each sample, 2 μg genomic DNA was subjected to WGS on an Illumina HiSeq2000 platform, following the manufacturer's protocols to generate 100 bp paired-end reads (Quail et al., 2008). All reads were mapped to the reference sequence of S. sonnei Ss046 (GenBank accession number NC_007384) using smalt (version 0.7.4). Candidate SNPs were called against the reference sequence and filtered using SAMtools (Li et al., 2009). Low-quality SNPs were removed according to the following criteria: consensus quality < 50, mapping quality < 30, ratio of SNPs to reads at a position < 75 %, read depth < 4, number of reads per strand < 2, strand bias < 0.001, mapping bias < 0.001 or tail bias < 0.001. Three samples failed due to insufficient read depth, resulting in a final sample set including 71 S. sonnei whole-genome sequences from Bhutan.