Typhoid in Kenya Is Associated with a Dominant Multidrug-Resistant Salmonellaenterica Serovar Typhi Haplotype That Is Also Widespread in Southeast Asia

Subtypes of Kenyan S. Typhi isolates of haplotype H58. (a) Radial phylogram of the H58 cluster of S. Typhi; the dashed line indicates where this phylogram links back to the broader S. Typhi phylogram shown in Fig. 1. Black nodes, genotyped control isolates, including seven genomes sequenced (labeled with strain names [11]) or previously defined (labeled with H groups [27]); colored nodes, nodes to which Kenyan isolates were mapped by SNP typing (colors were randomly assigned to the nodes), labeled with letters. The oval shading highlights two distinct H58 lineages, I and II. (b) Distribution of H58 subtypes of Kenyan S. Typhi by year of isolation, split by the presence of MDR IncHI1 plasmids (note than no non-H58 isolates contained plasmids). The labels and colors correspond to those defined in panel a.