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

Author

Listed:
  • Vanessa K. Wong

    (The Wellcome Trust Sanger Institute
    Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust)

  • Stephen Baker

    (The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme
    Centre for Tropical Medicine and Global Health, Oxford University
    London School of Hygiene and Tropical Medicine)

  • Thomas R. Connor

    (Cardiff University School of Biosciences, Cardiff University)

  • Derek Pickard

    (The Wellcome Trust Sanger Institute)

  • Andrew J. Page

    (The Wellcome Trust Sanger Institute)

  • Jayshree Dave

    (Public Health Laboratory London, Public Health England)

  • Niamh Murphy

    (Public Health Laboratory London, Public Health England)

  • Richard Holliman

    (Public Health Laboratory London, Public Health England)

  • Armine Sefton

    (Barts Health NHS Trust)

  • Michael Millar

    (Barts Health NHS Trust)

  • Zoe A. Dyson

    (Centre for Systems Genomics, University of Melbourne
    Bio21 Molecular Science and Biotechnology Institute, University of Melbourne)

  • Gordon Dougan

    (The Wellcome Trust Sanger Institute)

  • Kathryn E. Holt

    (Centre for Systems Genomics, University of Melbourne
    Bio21 Molecular Science and Biotechnology Institute, University of Melbourne)

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.

Suggested Citation

  • Vanessa K. Wong & Stephen Baker & Thomas R. Connor & Derek Pickard & Andrew J. Page & Jayshree Dave & Niamh Murphy & Richard Holliman & Armine Sefton & Michael Millar & Zoe A. Dyson & Gordon Dougan & , 2016. "An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid," Nature Communications, Nature, vol. 7(1), pages 1-11, November.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms12827
    DOI: 10.1038/ncomms12827
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    Cited by:

    1. Jane Hawkey & Lise Frézal & Alicia Tran Dien & Anna Zhukova & Derek Brown & Marie Anne Chattaway & Sandra Simon & Hidemasa Izumiya & Patricia I. Fields & Niall De Lappe & Lidia Kaftyreva & Xuebin Xu &, 2024. "Genomic perspective on the bacillus causing paratyphoid B fever," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Shengkai Li & Guilai Jiang & Shengke Wang & Min Wang & Yilei Wu & Jinzhi Zhang & Xiao Liu & Ling Zhong & Min Zhou & Shichang Xie & Yi Ren & Ping He & Yongliang Lou & Heng Li & Jimei Du & Zhemin Zhou, 2025. "Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    3. Arif M. Tanmoy & Yogesh Hooda & Mohammad S. I. Sajib & Kesia E. Silva & Junaid Iqbal & Farah N. Qamar & Stephen P. Luby & Gordon Dougan & Zoe A. Dyson & Stephen Baker & Denise O. Garrett & Jason R. An, 2022. "Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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