Phylogeographical Analysis of the Dominant Multidrug-Resistant H58 Clade of Salmonella Typhi Identifies Inter- And Intracontinental Transmission Events

Nat Genet. 2015 Jun;47(6):632-9. doi: 10.1038/ng.3281. Epub 2015 May 11.

Abstract

The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Anti-Bacterial Agents / therapeutic use
  • Drug Resistance, Multiple, Bacterial
  • Genome, Bacterial
  • Humans
  • Molecular Sequence Data
  • Phylogeny
  • Phylogeography
  • Quinolines / pharmacology
  • Quinolines / therapeutic use
  • Salmonella typhi / genetics*
  • Sequence Analysis, DNA
  • Typhoid Fever / drug therapy
  • Typhoid Fever / microbiology*
  • Typhoid Fever / transmission

Substances

  • Anti-Bacterial Agents
  • Quinolines
  • quinoline