Phylogenomic tree inferred by approximately-maximum-likelihood method from the aligned core genomes. Multiple genomes alignments were generated by mapping genome sequences of the 20 global S. Typhi strains against CT18 at all sites relevant for phylogenomic analysis using RealPhy . Phylogenetic tree (unrooted) was inferred via approximately-maximum-likelihood method using FastTreeMP . Strains studied were labelled in blue. Bootstrap support values shown at each node.