Figure 2.

Timeline of Salmonella Typhi genomic clusters in Fiji. A) Each typhoid case is represented by a single dot and are classified as being sporadic single genomic cases (top box) or belonging to 27 genomic clusters (defined as containing 3 or more isolates related by <=2 core chromosomal SNPs). Cases are plotted by date of sampling (x-axis) and genomic cluster (y-axis) with size of cluster relative to total number of isolates in the cluster. Dotted lines refer to exact clones (no SNP differences). Triangle refer to isolates collected before case-control study where date of collection was estimated. B) Phylogenetic relationship of 251 Central Division isolates built from 252 SNPs and color coded by genomic cluster represented in (A). Multiple genomic outbreak clusters are represented at any one time some of which can persist for several years, some of which can spread between geographical regions (Supplementary Figure 4).