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Salmonella Paratyphi A, one of the major etiologic agents of enteric fever, has increased in prevalence in recent decades in certain endemic regions in comparison to S. Typhi, the most prevalent cause of enteric fever. Despite this increase, data on the prevalence and molecular epidemiology of S. Paratyphi A remain generally scarce. Here, we analysed the whole genome sequences of 216 S. Paratyphi A isolates originating from Kathmandu, Nepal between 2005 and 2014, of which 200 were from patients with acute enteric fever and 16 from the gallbladder of people with suspected chronic carriage. By exploiting the recently developed genotyping framework for S. Paratyphi A (Paratype), we identified several genotypes circulating in Kathmandu. Notably, we observed an unusual clonal expansion of genotype 2.4.3 over a four-year period that spread geographically and systematically replaced other genotypes. This rapid genotype replacement is hypothesised to have been driven by both reduced susceptibility to fluoroquinolones and genetic changes to virulence factors, such as functional and structural genes encoding the type 3 secretion systems. Finally, we show that person-to-person is likely the most common mode of transmission and chronic carriers seem to play a limited role in maintaining disease circulation.

Original publication

DOI

10.1371/journal.pntd.0011864

Type

Journal article

Journal

PLoS Negl Trop Dis

Publication Date

06/2024

Volume

18

Keywords

Nepal, Humans, Salmonella paratyphi A, Genotype, Retrospective Studies, Paratyphoid Fever, Male, Adult, Female, Young Adult, Adolescent, Child, Prevalence, Middle Aged, Molecular Epidemiology, Child, Preschool, Whole Genome Sequencing, Anti-Bacterial Agents, Phylogeny