There’s an interesting study in this month’s Nature Genetics in which the authors performed 454 and Solexa whole-genome sequencing on 19 isolates of Salmonella enterica serovar Typhi, the pathogen that causes typhoid fever. Typhi is different from many other Salmonella pathogens in that it’s human-restricted; the main reservoir driving transmission of Typhi is thought to be human carriers. Also, Typhi isolates exhibit very low levels of genetic variation (something like 1 SNP every 2,300 bp).
Among the 19 isolates selected for this study, 10 were sequenced on 454 (average depth: 10.8x) and 12 were sequenced on Solexa (average depth: 20.4x) with 3 isolates done on both platforms. Following Newbler assembly, 454 contigs were aligned to the finished Typhi sequence with MUMmer. Solexa reads were “too short to be assembled effectively using current software” and thus were mapped directly to the finished sequence with Maq (v0.6.0). Cut-offs for SNP calling were determined by comparing data from 454, Solexa, and published sequences for the three strains done on both platforms.
The authors offered little discussion of the relative performance of 454 and Solexa technology for the three strains sequenced on both platforms. However, I got the scoop from Supplemental Table 1. After applying their filtering criteria, the platform-specific performance was as follows. On 454, the mean false positive rate was 1.8% and the mean sensitivity was 85.0%. On Solexa, the mean false positive rate was higher (2.7%) and the sensitivity lower (77.1%). These estimates, by the way, are based on the assumption that the SNPs detected independently by *both* platforms represent the true set of SNPs for each isolate.
The authors claim that a careful sampling strategy designed to capture the full phylogenetic tree, coupled with whole-genome sequencing, allowed them to capture much of the variation present in the Typhi population. Their analysis supports the previously proposed small population size and genetic drift, with little evidence for purifying selection, antigenic variation, or recombination between isolates. The vast majority of genes (72%) contained no SNPs; for the remainder, the distribution of SNPs per gene followed a Poisson distribution. The only gene with a strong signal of positive selection was gyrA, where mutations at codons 83 and 87 are associated with fluoroquinolone resistance; this no doubt reflects selective pressure on Typhi associated with antibiotic use in human populations. However, the sparse evidence for antigenic variation within Typhi suggests that this pathogen is not under strong selective pressure from the human immune system.
The low levels of purifying selection, antigenic variation, and recombination in Typhi are consistent with the role of human carriers as the main consistent reservoir for the pathogen. In other words, the disease persists because there are a number of people who are infected, but asymptomatic. The authors conclude that vaccination may be a crucial long-term strategy for control of typhoid fever because it would treat asymptomatic carriers as well as the infirm. I might add that the apparently-healthy carriers of the Typhi pathogen might be a promising population for immunogenetics studies.