Fig. 1.

Maximum likelihood tree of 1005 S. Typhi (H58 and non—H58) inferred from 2072 SNPs and rooted against the reference genome CT18. Light shaded box indicates H58 population, while the rest are non-H58 group. The tips of the tree are colored according to the geographical origin of the genomes. Red colored squared boxes with arrows indicates the position of ceftriaxone resistant S. Typhi in the context of global phylogeny, indicating relatedness with respect to the geographical locations. Tree scale indicates the number of substitutions per genome. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)