IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-31517-8.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-31517-8
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-31517-8?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    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.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Danruo Deng & Wuqin Xu & Bian Wu & Hans Peter Comes & Yu Feng & Pan Li & Jinfang Zheng & Guangyong Chen & Pheng-Ann Heng, 2025. "PhyloTune: An efficient method to accelerate phylogenetic updates using a pretrained DNA language model," Nature Communications, Nature, vol. 16(1), pages 1-13, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Minghui Cheng & Yingjie Xu & Xiao Cui & Xin Wei & Yundi Chang & Jun Xu & Cheng Lei & Lei Xue & Yifan Zheng & Zhang Wang & Lingtong Huang & Min Zheng & Hong Luo & Yuxin Leng & Chao Jiang, 2024. "Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Awa Diop & Gavin M. Douglas & Louis-Marie Bobay, 2025. "Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
    3. M. C. Rühlemann & C. Bang & J. F. Gogarten & B. M. Hermes & M. Groussin & S. Waschina & M. Poyet & M. Ulrich & C. Akoua-Koffi & T. Deschner & J. J. Muyembe-Tamfum & M. M. Robbins & M. Surbeck & R. M. , 2024. "Functional host-specific adaptation of the intestinal microbiome in hominids," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    4. Lucas Serra Moncadas & Cyrill Hofer & Paul-Adrian Bulzu & Jakob Pernthaler & Adrian-Stefan Andrei, 2024. "Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    5. Ling Zhong & Menghan Zhang & Libing Sun & Yu Yang & Bo Wang & Haibing Yang & Qiang Shen & Yu Xia & Jiarui Cui & Hui Hang & Yi Ren & Bo Pang & Xiangyu Deng & Yahui Zhan & Heng Li & Zhemin Zhou, 2023. "Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    6. Aleksandar Stanojković & Svatopluk Skoupý & Hanna Johannesson & Petr Dvořák, 2024. "The global speciation continuum of the cyanobacterium Microcoleus," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    7. Xiaoqing Xu & Yunqi Lin & Yu Deng & Lei Liu & Dou Wang & Qinling Tang & Chunxiao Wang & Xi Chen & You Che & Ethan R. Wyrsch & Veronica M. Jarocki & Steven P. Djordjevic & Tong Zhang, 2025. "Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    8. Kyung Mo Kim & Kyuin Hwang & Hanbyul Lee & Ahnna Cho & Christina L. Davis & Brent C. Christner & John C. Priscu & Ok-Sun Kim, 2025. "Genetic isolation and metabolic complexity of an Antarctic subglacial microbiome," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    9. Xin Fan & Rong-Chen Dai & Shu Zhang & Yuan-Yuan Geng & Mei Kang & Da-Wen Guo & Ya-Ning Mei & Yu-Hong Pan & Zi-Yong Sun & Ying-Chun Xu & Jie Gong & Meng Xiao, 2023. "Tandem gene duplications contributed to high-level azole resistance in a rapidly expanding Candida tropicalis population," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    10. Lucie Semenec & Amy K. Cain & Catherine J. Dawson & Qi Liu & Hue Dinh & Hannah Lott & Anahit Penesyan & Ram Maharjan & Francesca L. Short & Karl A. Hassan & Ian T. Paulsen, 2023. "Cross-protection and cross-feeding between Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    11. Corentin Hochart & Lucas Paoli & Hans-Joachim Ruscheweyh & Guillem Salazar & Emilie Boissin & Sarah Romac & Julie Poulain & Guillaume Bourdin & Guillaume Iwankow & Clémentine Moulin & Maren Ziegler & , 2023. "Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    12. Daniel P. Morreale & Eric A. Porsch & Brad K. Kern & Joseph W. Geme & Paul J. Planet, 2023. "Acquisition, co-option, and duplication of the rtx toxin system and the emergence of virulence in Kingella," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    13. Robby Concha-Eloko & Beatriz Beamud & Pilar Domingo-Calap & Rafael Sanjuán, 2025. "Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    14. Xiyang Dong & Yongyi Peng & Muhua Wang & Laura Woods & Wenxue Wu & Yong Wang & Xi Xiao & Jiwei Li & Kuntong Jia & Chris Greening & Zongze Shao & Casey R. J. Hubert, 2023. "Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    15. Katherine Duchesneau & Borja Aldeguer-Riquelme & Caitlin Petro & Ghiwa Makke & Madison Green & Malak Tfaily & Rachel Wilson & Spencer W. Roth & Eric R. Johnston & Laurel A. Kluber & Christopher W. Sch, 2025. "Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    16. Akuzike Kalizang’oma & Damien Richard & Brenda Kwambana-Adams & Juliana Coelho & Karen Broughton & Bruno Pichon & Katie L. Hopkins & Victoria Chalker & Sandra Beleza & Stephen D. Bentley & Chrispin Ch, 2024. "Population genomics of Streptococcus mitis in UK and Ireland bloodstream infection and infective endocarditis cases," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    17. Xuanji Li & Asker Brejnrod & Jonathan Thorsen & Trine Zachariasen & Urvish Trivedi & Jakob Russel & Gisle Alberg Vestergaard & Jakob Stokholm & Morten Arendt Rasmussen & Søren Johannes Sørensen, 2023. "Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    18. Thomas C. A. Hitch & Johannes M. Masson & Charlie Pauvert & Johanna Bosch & Selina Nüchtern & Nicole S. Treichel & Marko Baloh & Soheila Razavi & Afrizal Afrizal & Ntana Kousetzi & Andrea M. Aguirre &, 2025. "HiBC: a publicly available collection of bacterial strains isolated from the human gut," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
    19. Wenxiu Wang & Weizhi Song & Marwan E. Majzoub & Xiaoyuan Feng & Bu Xu & Jianchang Tao & Yuanqing Zhu & Zhiyong Li & Pei-Yuan Qian & Nicole S. Webster & Torsten Thomas & Lu Fan, 2024. "Decoupling of strain- and intrastrain-level interactions of microbiomes in a sponge holobiont," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    20. Raymond Kiu & Elizabeth M. Darby & Cristina Alcon-Giner & Antia Acuna-Gonzalez & Anny Camargo & Lisa E. Lamberte & Sarah Phillips & Kathleen Sim & Alexander G. Shaw & Paul Clarke & Willem Schaik & J. , 2025. "Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants," Nature Communications, Nature, vol. 16(1), pages 1-16, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31517-8. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.