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A comprehensive resource for Bordetella genomic epidemiology and biodiversity studies

Author

Listed:
  • Sébastien Bridel

    (Biodiversity and Epidemiology of Bacterial Pathogens)

  • Valérie Bouchez

    (Biodiversity and Epidemiology of Bacterial Pathogens
    Institut Pasteur)

  • Bryan Brancotte

    (Bioinformatics and Biostatistics Hub)

  • Sofia Hauck

    (University of Oxford)

  • Nathalie Armatys

    (Biodiversity and Epidemiology of Bacterial Pathogens
    Institut Pasteur)

  • Annie Landier

    (Biodiversity and Epidemiology of Bacterial Pathogens
    Institut Pasteur)

  • Estelle Mühle

    (Université Paris Cité)

  • Sophie Guillot

    (Biodiversity and Epidemiology of Bacterial Pathogens
    Institut Pasteur)

  • Julie Toubiana

    (Biodiversity and Epidemiology of Bacterial Pathogens
    Institut Pasteur
    APHP)

  • Martin C. J. Maiden

    (University of Oxford)

  • Keith A. Jolley

    (University of Oxford)

  • Sylvain Brisse

    (Biodiversity and Epidemiology of Bacterial Pathogens
    Institut Pasteur)

Abstract

The genus Bordetella includes bacteria that are found in the environment and/or associated with humans and other animals. A few closely related species, including Bordetella pertussis, are human pathogens that cause diseases such as whooping cough. Here, we present a large database of Bordetella isolates and genomes and develop genotyping systems for the genus and for the B. pertussis clade. To generate the database, we merge previously existing databases from Oxford University and Institut Pasteur, import genomes from public repositories, and add 83 newly sequenced B. bronchiseptica genomes. The public database currently includes 2582 Bordetella isolates and their provenance data, and 2085 genomes ( https://bigsdb.pasteur.fr/bordetella/ ). We use core-genome multilocus sequence typing (cgMLST) to develop genotyping systems for the whole genus and for B. pertussis, as well as specific schemes to define antigenic, virulence and macrolide resistance profiles. Phylogenetic analyses allow us to redefine evolutionary relationships among known Bordetella species, and to propose potential new species. Our database provides an expandable resource for genotyping of environmental and clinical Bordetella isolates, thus facilitating evolutionary and epidemiological research on whooping cough and other Bordetella infections.

Suggested Citation

  • Sébastien Bridel & Valérie Bouchez & Bryan Brancotte & Sofia Hauck & Nathalie Armatys & Annie Landier & Estelle Mühle & Sophie Guillot & Julie Toubiana & Martin C. J. Maiden & Keith A. Jolley & Sylvai, 2022. "A comprehensive resource for Bordetella genomic epidemiology and biodiversity studies," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31517-8
    DOI: 10.1038/s41467-022-31517-8
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    References listed on IDEAS

    as
    1. Chirag Jain & Luis M. Rodriguez-R & Adam M. Phillippy & Konstantinos T. Konstantinidis & Srinivas Aluru, 2018. "High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
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