High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

Abstract

Isolates of Salmonella enterica serovar Typhi (Typhi), a human-restricted bacterial pathogen that causes typhoid, show limited genetic variation. We generated whole-genome sequences for 19 Typhi isolates using 454 (Roche) and Solexa (Illumina) technologies. Isolates, including the previously sequenced CT18 and Ty2 isolates, were selected to represent major nodes in the phylogenetic tree. Comparative analysis showed little evidence of purifying selection, antigenic variation or recombination between isolates. Rather, evolution in the Typhi population seems to be characterized by ongoing loss of gene function, consistent with a small effective population size. The lack of evidence for antigenic variation driven by immune selection is in contrast to strong adaptive selection for mutations conferring antibiotic resistance in Typhi. The observed patterns of genetic isolation and drift are consistent with the proposed key role of asymptomatic carriers of Typhi as the main reservoir of this pathogen, highlighting the need for identification and treatment of carriers.

Figure 1

Phylogenetic tree based on SNP data. Branch colors indicate different lineages of Typhi; branch lengths are measured in number of SNPs, scale as indicated. Central, small black circle indicates the ancestral root, dashed line represents Salmonella lineage; phage (ST) and SPI15 insertion events are shown along branches; plasmids detected in each isolate are indicated by filled circles (IncHI1 multidrug resistance plasmids), open circles (cryptic plasmid) and filled lines (linear plasmid carrying z66 flagella variant).

Figure 2

Trajectory of dN/dS over time. y axis is the reciprocal of dN/dS, or 1/(dN/dS). (a) Pairwise dN/dS between 19 Typhi isolates. (b) dN/dS for SNPs in three relative age groups (i-iii, youngest-oldest), calculated from SNPs with complete allele data in 19 isolates (purple circles) and SNPs with incomplete allele data (green squares).

Figure 3

Distribution of number of SNPs per gene. Lines indicate 95% confidence interval of mean predicted values under a Poisson distribution fitted to the data shown in green. Inset shows gene count on a log scale to better show deviation from the Poisson model at high numbers of SNPs per gene.

Figure 4

Accumulation of gene-inactivating mutations in Typhi lineages. Points correspond to bifurcations in the phylogenetic tree in Figure 1; y axis shows the total number of genes inactivated by deletion or nonsense mutation up to that bifurcation. Each line represents the accumulation of mutations in a particular isolate; different lineages of Typhi are colored as in Figure 1. LCA, last common ancestor.