Gallbladder carriage generates genetic variation and genome degradation in Salmonella Typhi

Abstract

Despite recent advances in typhoid fever control, asymptomatic carriage of Salmonella Typhi in the gallbladder remains poorly understood. Aiming to understand if S. Typhi becomes genetically adapted for long-term colonisation in the gallbladder, we performed whole genome sequencing on a collection of S. Typhi isolated from the gallbladders of typhoid carriers. These sequences were compared to contemporaneously sampled sequences from organisms isolated from the blood of acute patients within the same population. We found that S. Typhi carriage was not restricted to any particular genotype or conformation of antimicrobial resistance genes, but was largely reflective of S. Typhi circulating in the general population. However, gallbladder isolates showed a higher genetic variability than acute isolates, with median pairwise SNP distances of 21 and 13 SNPs (p = 2.8x10-9), respectively. Within gallbladder isolates of the predominant H58 genotype, variation was associated with a higher prevalence of nonsense mutations. Notably, gallbladder isolates displayed a higher frequency of non-synonymous mutations in genes encoding hypothetical proteins, membrane lipoproteins, transport/binding proteins, surface antigens, and carbohydrate degradation. Specifically, we identified several gallbladder-specific non-synonymous mutations involved in LPS synthesis and modification, with some isolates lacking the Vi capsular polysaccharide vaccine target due to the 134Kb deletion of SPI-7. S. Typhi is under strong selective pressure in the human gallbladder, which may be reflected phylogenetically by long terminal branches that may distinguish organisms from chronic and acute infections. Our work shows that selective pressures asserted by the hostile environment of the human gallbladder generate new antigenic variants and raises questions regarding the role of carriage in the epidemiology of typhoid fever.

Fig 1. The phylogenetic structure of gallbladder and acute S. Typhi isolates collected between 2007 and 2010.

Rooted maximum likelihood tree (S. Paratyphi A used as an outgroup to root the tree and pruned for visualization) based on core-genome SNPs of 120 S. Typhi isolates with the corresponding metadata: genotype, gyrA mutation. Gallbladder and acute isolates are shown as red and dark circles at the terminal nodes, respectively. Acute isolates originating from importation are also highlighted by turquoise circles at the terminal nodes. Terminal branches leading to gallbladder isolates are highlighted in red. Red triangles show gallbladder isolates associated with unusually long terminal branches.

Fig 2. The Distribution of nearest phylogenetic distances of gallbladder and acute H58 isolates over the study period.

Each circle represents the phylogenetic distance from each isolate to its nearest neighbour on the phylogenetic tree. The error bar represents the average phylogenetic distance to the nearest neighbour (± standard deviation) for acute H58 isolates. Gallbladder and acute isolates estimated to have originated from chronic carriers are labelled with their corresponding strain names.

Fig 3. Functional classes of Salmonella Typhi genes associated with the highest prevalence of gallbladder-specific nonsynonymous SNPs versus acute-specific nonsynonymous SNPs.

Functional classes are shown on the outermost circle. Four circles from the middle represent 5–10–15–20 percent of the cumulative percentage of functional classes. Red and blue blocks are representatives of gallbladder and acute isolates, respectively.