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Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity

Author

Listed:
  • Arif M. Tanmoy

    (Child Health Research Foundation
    Erasmus University Medical Center)

  • Yogesh Hooda

    (Child Health Research Foundation
    MRC-Laboratory Molecular Biology)

  • Mohammad S. I. Sajib

    (Child Health Research Foundation
    University of Glasgow)

  • Kesia E. Silva

    (Stanford University School of Medicine)

  • Junaid Iqbal

    (Aga Khan University)

  • Farah N. Qamar

    (Aga Khan University)

  • Stephen P. Luby

    (Stanford University School of Medicine)

  • Gordon Dougan

    (Wellcome Trust Sanger Institute, Hinxton)

  • Zoe A. Dyson

    (Wellcome Trust Sanger Institute, Hinxton
    University of Cambridge
    London School of Hygiene and Tropical Medicine
    Monash University)

  • Stephen Baker

    (University of Cambridge)

  • Denise O. Garrett

    (Applied Epidemiology Team, Sabin Vaccine Institute)

  • Jason R. Andrews

    (Stanford University School of Medicine)

  • Samir K. Saha

    (Child Health Research Foundation
    Bangladesh Shishu Hospital and Institute)

  • Senjuti Saha

    (Child Health Research Foundation)

Abstract

Salmonella Paratyphi A, the primary etiology of paratyphoid, is estimated to cause 3.4 million infections annually, worldwide. With rising antimicrobial resistance and no licensed vaccines, genomic surveillance is key to track and monitor transmission, but there is currently no reliable genotyping framework for this pathogen. Here, we sequence 817 isolates from South Asia and add 562 publicly available genomes to build a global database representing 37 countries, covering 1917–2019. We develop a single nucleotide polymorphism-based genotyping scheme, Paratype, that segregates Salmonella Paratyphi A population into three primary and nine secondary clades, and 18 genotypes. Each genotype is assigned a unique allele definition located on an essential gene. Using Paratype, we identify spatiotemporal genomic variation and antimicrobial resistance markers. We release Paratype as an open-access tool that can use raw read files from both Illumina and Nanopore platforms, and thus can assist surveillance studies tracking Salmonella Paratyphi A across the globe.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-35587-6
    DOI: 10.1038/s41467-022-35587-6
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    References listed on IDEAS

    as
    1. Yuki Furuse, 2019. "Analysis of research intensity on infectious disease by disease burden reveals which infectious diseases are neglected by researchers," Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, vol. 116(2), pages 478-483, January.
    2. 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.
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