An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid.


Type
Article
Change log
Authors
Wong, Vanessa K 
Baker, Stephen 
Connor, Thomas R 
Pickard, Derek 
Page, Andrew J 
Abstract

The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations.

Description
Keywords
Cluster Analysis, DNA, Bacterial, Genotype, Geography, Haplotypes, Humans, Phylogeny, Polymorphism, Single Nucleotide, Salmonella typhi, Sequence Analysis, DNA, Typhoid Fever
Journal Title
Nat Commun
Conference Name
Journal ISSN
2041-1723
2041-1723
Volume Title
7
Publisher
Springer Science and Business Media LLC
Sponsorship
Biotechnology and Biological Sciences Research Council (BB/M014088/1)
Medical Research Council (G1100100)