A comprehensive resource for Bordetella genomic epidemiology and biodiversity studies.
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, Sylvain Brisse
Author Information
Sébastien Bridel: Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France. ORCID
Valérie Bouchez: Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France. ORCID
Bryan Brancotte: Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015, Paris, France. ORCID
Sofia Hauck: Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
Nathalie Armatys: Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.
Annie Landier: Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France. ORCID
Estelle Mühle: Collection de l´Institut Pasteur, Institut Pasteur, Université Paris Cité, Paris, France. ORCID
Sophie Guillot: Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.
Julie Toubiana: Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France. ORCID
Martin C J Maiden: Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
Keith A Jolley: Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK. ORCID
Sylvain Brisse: Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France. sylvain.brisse@pasteur.fr. ORCID
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.
