An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

Abstract

The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations.

Figure 1. Population structure of S. Typhi based on genome-wide SNPs.

(a) Whole-genome tree of 1,831 global S. Typhi isolates. Primary clusters 1–4 are indicated in the outer coloured ring; branches defining these groups are coloured in the tree. These groups are further divided into clades, which are shaded and labelled. The location of S. Typhi reference genomes CT18 (accession number AL513382) and Ty2 (accession number AE014613) are indicated on the tree. Subclade 4.3.1 (H58, marked in red), which comprises half of the global collection, is represented by just 50 (6%) randomly selected isolates out of the total 852 belonging to this subclade, so that the relationships between other clades can be visualized. (b) Tree backbone showing further division of 16 S. Typhi clades (shaded) into 49 subclades (labelled; note 12 undifferentiated clade groups shown in brackets). Branches are coloured by primary cluster. (c) Map of the world showing subclade diversity of S. Typhi isolates in the global collection, by region. Where groups of isolates from the same country and year belonged to the same subclade, this was classified as an ‘outbreak' and the group is only represented once in the pie graphs. Pies are sized to indicate number of isolates; slices are coloured by clade; multiple slices of the same colour indicate multiple subclades belonging to the same clade.

Figure 2. Geographical clustering of S. Typhi subclades.

Heatmap shows, for each subclade, the percentage of unique isolates originating from each of the geographical regions. Where groups of isolates from the same country and year belonged to the same subclade, this was classified as an ‘outbreak' and the group is only represented once. The same data are represented as a scaled bar graph to the right. The full list of isolates by country and subclade is provided in Supplementary Data 1.

Figure 3. Phylogeny of 99 travel-associated S. Typhi in comparison with the global genomic framework containing 1,831 isolates.

Whole-genome SNP tree is shown in the centre and branches are coloured by clade. Rings indicate region of origin: inner ring, global collection; outer ring, travel-associated isolates. Subclades that contain travel-associated isolates are highlighted within the tree (shaded in alternating colours) and labelled around the outside; intrasubclade phylogenies are provided in Supplementary Fig. 4.