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

Vanessa K. Wong, Stephen Baker, Thomas R Connor, Derek Pickard, Andrew J. Page, Jayshree Dave, Niamh C Murphy, Richard Holliman, Armine Sefton, Michael Millar, Zoe A. Dyson, Gordon Dougan, Kathryn E Holt, International Typhoid Consortium

Research output: Contribution to journalArticleResearchpeer-review

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.

Original languageEnglish
Article number12827
Number of pages11
JournalNature Communications
Volume7
DOIs
Publication statusPublished - 5 Oct 2016
Externally publishedYes

Keywords

  • epidemiology
  • genome
  • infectious-disease diagnostics
  • microbial genetics

Cite this

Wong, V. K., Baker, S., Connor, T. R., Pickard, D., Page, A. J., Dave, J., ... International Typhoid Consortium (2016). An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Nature Communications, 7, [12827]. https://doi.org/10.1038/ncomms12827
Wong, Vanessa K. ; Baker, Stephen ; Connor, Thomas R ; Pickard, Derek ; Page, Andrew J. ; Dave, Jayshree ; Murphy, Niamh C ; Holliman, Richard ; Sefton, Armine ; Millar, Michael ; Dyson, Zoe A. ; Dougan, Gordon ; Holt, Kathryn E ; International Typhoid Consortium. / An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. In: Nature Communications. 2016 ; Vol. 7.
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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.",
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author = "Wong, {Vanessa K.} and Stephen Baker and Connor, {Thomas R} and Derek Pickard and Page, {Andrew J.} and Jayshree Dave and Murphy, {Niamh C} and Richard Holliman and Armine Sefton and Michael Millar and Dyson, {Zoe A.} and Gordon Dougan and Holt, {Kathryn E} and {International Typhoid Consortium} and Jane Hawkey",
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Wong, VK, Baker, S, Connor, TR, Pickard, D, Page, AJ, Dave, J, Murphy, NC, Holliman, R, Sefton, A, Millar, M, Dyson, ZA, Dougan, G, Holt, KE & International Typhoid Consortium 2016, 'An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid' Nature Communications, vol. 7, 12827. https://doi.org/10.1038/ncomms12827

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. / Wong, Vanessa K.; Baker, Stephen; Connor, Thomas R; Pickard, Derek; Page, Andrew J.; Dave, Jayshree; Murphy, Niamh C; Holliman, Richard; Sefton, Armine; Millar, Michael; Dyson, Zoe A.; Dougan, Gordon; Holt, Kathryn E; International Typhoid Consortium.

In: Nature Communications, Vol. 7, 12827, 05.10.2016.

Research output: Contribution to journalArticleResearchpeer-review

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