Five Years of GenoTyphi: Updates to the Global Salmonella Typhi Genotyping Framework

J Infect Dis. 2021 Dec 20;224(12 Suppl 2):S775-S780. doi: 10.1093/infdis/jiab414.

Abstract

In 2016, a whole-genome sequence (WGS)-based genotyping framework (GenoTyphi) was developed and provided a phylogenetically informative nomenclature for lineages of Salmonella Typhi, the etiological agent of typhoid fever. Subsequent surveillance studies have revealed additional epidemiologically important subpopulations, which require the definition of new genotypes and extension of associated software to facilitate the detection of antimicrobial resistance (AMR) mutations. Analysis of 4632 WGS provide an updated overview of the global S Typhi population structure and genotyping framework, revealing the widespread nature of haplotype 58 ([H58] 4.3.1) genotypes and the diverse range of genotypes carrying AMR mutations.

Keywords: Salmonella Typhi; AMR; WGS; pathogen genotyping; typhoid fever.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Drug Resistance, Bacterial / genetics*
  • Genotype
  • Haplotypes
  • Humans
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • Salmonella typhi / drug effects
  • Salmonella typhi / genetics*
  • Salmonella typhi / isolation & purification
  • Typhoid Fever / epidemiology
  • Typhoid Fever / microbiology*
  • Whole Genome Sequencing

Substances

  • Anti-Bacterial Agents