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)

    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. 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.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. Sanjam S. Sawhney & Rhiannon C. Vargas & Meghan A. Wallace & Carol E. Muenks & Brian V. Lubbers & Stephanie A. Fritz & Carey-Ann D. Burnham & Gautam Dantas, 2023. "Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    11. Harold P. Hodgins & Pengsheng Chen & Briallen Lobb & Xin Wei & Benjamin J. M. Tremblay & Michael J. Mansfield & Victoria C. Y. Lee & Pyung-Gang Lee & Jeffrey Coffin & Ana T. Duggan & Alexis E. Dolphin, 2023. "Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    12. Conor Feehily & Ian J. O’Neill & Calum J. Walsh & Rebecca L. Moore & Sarah Louise Killeen & Aisling A. Geraghty & Elaine M. Lawton & David Byrne & Rocio Sanchez-Gallardo & Sai Ravi Chandra Nori & Ida , 2023. "Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    13. Yuval Bussi & Ruti Kapon & Ziv Reich, 2021. "Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy," PLOS ONE, Public Library of Science, vol. 16(10), pages 1-27, October.
    14. Max E. Schön & Vasily V. Zlatogursky & Rohan P. Singh & Camille Poirier & Susanne Wilken & Varsha Mathur & Jürgen F. H. Strassert & Jarone Pinhassi & Alexandra Z. Worden & Patrick J. Keeling & Thijs J, 2021. "Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    15. Nenad Macesic & Jane Hawkey & Ben Vezina & Jessica A. Wisniewski & Hugh Cottingham & Luke V. Blakeway & Taylor Harshegyi & Katherine Pragastis & Gnei Zweena Badoordeen & Amanda Dennison & Denis W. Spe, 2023. "Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    16. Jean-Sebastien Gounot & Minghao Chia & Denis Bertrand & Woei-Yuh Saw & Aarthi Ravikrishnan & Adrian Low & Yichen Ding & Amanda Hui Qi Ng & Linda Wei Lin Tan & Yik-Ying Teo & Henning Seedorf & Niranjan, 2022. "Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    17. Ruobing Wang & Anru Zhang & Shijun Sun & Guankun Yin & Xingyu Wu & Qi Ding & Qi Wang & Fengning Chen & Shuyi Wang & Lucy Dorp & Yawei Zhang & Longyang Jin & Xiaojuan Wang & Francois Balloux & Hui Wang, 2024. "Increase in antioxidant capacity associated with the successful subclone of hypervirulent carbapenem-resistant Klebsiella pneumoniae ST11-KL64," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    18. Nils Giordano & Marinna Gaudin & Camille Trottier & Erwan Delage & Charlotte Nef & Chris Bowler & Samuel Chaffron, 2024. "Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    19. Wei Ding & Shougang Wang & Peng Qin & Shen Fan & Xiaoyan Su & Peiyan Cai & Jie Lu & Han Cui & Meng Wang & Yi Shu & Yongming Wang & Hui-Hui Fu & Yu-Zhong Zhang & Yong-Xin Li & Weipeng Zhang, 2023. "Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    20. Roxana Zamudio & Patrick Boerlin & Racha Beyrouthy & Jean-Yves Madec & Stefan Schwarz & Michael R. Mulvey & George G. Zhanel & Ashley Cormier & Gabhan Chalmers & Richard Bonnet & Marisa Haenni & Inga , 2022. "Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America," Nature Communications, Nature, vol. 13(1), pages 1-15, 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.