Figure 1

Phylogenetic trees based upon SNPs, demonstrating the relationship of 62 S . Typhi isolates from Nepalese children. A) Phylogenetic tree showing haplotypes detected in pediatric samples from Nepal (highlighted in red, white, blue and yellow circles). The tree root (representing other Salmonella serotypes) is shown in grey. Branch lengths indicate an estimated rate of substitutions per assayed SNP locus, as calculated by RAxML. Length of the scale bar is 0.01 substitutions per site, equivalent to approximately 15 SNPs. B) Zoomed-in view of the H58 group in (A). The root of the H58 clonal group is shown in grey; the dashed line represents the link to the remainder of the S. Typhi phylogenetic tree. The division between lineage I and lineage II is indicated using grey vs white background. Leaves of the tree correspond to previously sequenced S. Typih isolates; 8(04)N (Vietnam, 2004), E03-9804 (Nepal, 2003), E02-2759 (India, 2002), ISP-03-07467 (Morocco, 2003), ISP-04-06979 (Central Africa, 2004), AG3 (Vietnam, 2004) and 150(98)S (Vietnam, 1998).