IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-35178-5.html
   My bibliography  Save this article

Strong pathogen competition in neonatal gut colonisation

Author

Listed:
  • Tommi Mäklin

    (University of Helsinki)

  • Harry A. Thorpe

    (University of Oslo)

  • Anna K. Pöntinen

    (University of Oslo
    University Hospital of North Norway)

  • Rebecca A. Gladstone

    (University of Oslo)

  • Yan Shao

    (Wellcome Sanger Institute)

  • Maiju Pesonen

    (University of Oslo)

  • Alan McNally

    (University of Birmingham)

  • Pål J. Johnsen

    (UiT The Arctic University of Norway)

  • Ørjan Samuelsen

    (University Hospital of North Norway
    UiT The Arctic University of Norway)

  • Trevor D. Lawley

    (Wellcome Sanger Institute)

  • Antti Honkela

    (University of Helsinki)

  • Jukka Corander

    (University of Oslo
    Wellcome Sanger Institute
    University of Helsinki)

Abstract

Opportunistic bacterial pathogen species and their strains that colonise the human gut are generally understood to compete against both each other and the commensal species colonising this ecosystem. Currently we are lacking a population-wide quantification of strain-level colonisation dynamics and the relationship of colonisation potential to prevalence in disease, and how ecological factors might be modulating these. Here, using a combination of latest high-resolution metagenomics and strain-level genomic epidemiology methods we performed a characterisation of the competition and colonisation dynamics for a longitudinal cohort of neonatal gut microbiomes. We found strong inter- and intra-species competition dynamics in the gut colonisation process, but also a number of synergistic relationships among several species belonging to genus Klebsiella, which includes the prominent human pathogen Klebsiella pneumoniae. No evidence of preferential colonisation by hospital-adapted pathogen lineages in either vaginal or caesarean section birth groups was detected. Our analysis further enabled unbiased assessment of strain-level colonisation potential of extra-intestinal pathogenic Escherichia coli (ExPEC) in comparison with their propensity to cause bloodstream infections. Our study highlights the importance of systematic surveillance of bacterial gut pathogens, not only from disease but also from carriage state, to better inform therapies and preventive medicine in the future.

Suggested Citation

  • Tommi Mäklin & Harry A. Thorpe & Anna K. Pöntinen & Rebecca A. Gladstone & Yan Shao & Maiju Pesonen & Alan McNally & Pål J. Johnsen & Ørjan Samuelsen & Trevor D. Lawley & Antti Honkela & Jukka Corande, 2022. "Strong pathogen competition in neonatal gut colonisation," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-35178-5
    DOI: 10.1038/s41467-022-35178-5
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-35178-5
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-35178-5?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. John R. Brannon & Taryn L. Dunigan & Connor J. Beebout & Tamia Ross & Michelle A. Wiebe & William S. Reynolds & Maria Hadjifrangiskou, 2020. "Invasion of vaginal epithelial cells by uropathogenic Escherichia coli," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    2. Yan Shao & Samuel C. Forster & Evdokia Tsaliki & Kevin Vervier & Angela Strang & Nandi Simpson & Nitin Kumar & Mark D. Stares & Alison Rodger & Peter Brocklehurst & Nigel Field & Trevor D. Lawley, 2019. "Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth," Nature, Nature, vol. 574(7776), pages 117-121, October.
    3. Claire L. Gorrie & Mirjana Mirčeta & Ryan R. Wick & Louise M. Judd & Margaret M. C. Lam & Ryota Gomi & Iain J. Abbott & Nicholas R. Thomson & Richard A. Strugnell & Nigel F. Pratt & Jill S. Garlick & , 2022. "Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen," Nature Communications, Nature, vol. 13(1), pages 1-17, 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. Aneta Słabuszewska-Jóźwiak & Jacek Krzysztof Szymański & Michał Ciebiera & Beata Sarecka-Hujar & Grzegorz Jakiel, 2020. "Pediatrics Consequences of Caesarean Section—A Systematic Review and Meta-Analysis," IJERPH, MDPI, vol. 17(21), pages 1-17, October.
    2. Kerstin Thriene & Karin B. Michels, 2023. "Human Gut Microbiota Plasticity throughout the Life Course," IJERPH, MDPI, vol. 20(2), pages 1-14, January.
    3. Kai Zhou & Chun-Xu Xue & Tingting Xu & Ping Shen & Sha Wei & Kelly L. Wyres & Margaret M. C. Lam & Jinquan Liu & Haoyun Lin & Yunbo Chen & Kathryn E. Holt & Yonghong Xiao, 2023. "A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Justine Tanoey & Christina Baechle & Hermann Brenner & Andreas Deckert & Julia Fricke & Kathrin Günther & André Karch & Thomas Keil & Alexander Kluttig & Michael Leitzmann & Rafael Mikolajczyk & Nadia, 2022. "Birth Order, Caesarean Section, or Daycare Attendance in Relation to Child- and Adult-Onset Type 1 Diabetes: Results from the German National Cohort," IJERPH, MDPI, vol. 19(17), pages 1-14, August.
    5. Maria Nieto-Rosado & Kirsty Sands & Edward A. R. Portal & Kathryn M. Thomson & Maria J. Carvalho & Jordan Mathias & Rebecca Milton & Calie Dyer & Chinenye Akpulu & Ian Boostrom & Patrick Hogan & Habib, 2024. "Colonisation of hospital surfaces from low- and middle-income countries by extended spectrum β-lactamase- and carbapenemase-producing bacteria," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    6. Chiara Tarracchini & Giulia Alessandri & Federico Fontana & Sonia Mirjam Rizzo & Gabriele Andrea Lugli & Massimiliano Giovanni Bianchi & Leonardo Mancabelli & Giulia Longhi & Chiara Argentini & Laura , 2023. "Genetic strategies for sex-biased persistence of gut microbes across human life," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    7. 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.
    8. Shuqin Zeng & Alexandre Almeida & Shiping Li & Junjie Ying & Hua Wang & Yi Qu & R. Paul Ross & Catherine Stanton & Zhemin Zhou & Xiaoyu Niu & Dezhi Mu & Shaopu Wang, 2024. "A metagenomic catalog of the early-life human gut virome," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    9. Bin Zhu & David J. Edwards & Katherine M. Spaine & Laahirie Edupuganti & Andrey Matveyev & Myrna G. Serrano & Gregory A. Buck, 2024. "The association of maternal factors with the neonatal microbiota and health," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    10. Na Chen & Lilan Hao & Zhe Zhang & Chenglu Qin & Zhuye Jie & Hongxin Pan & Jiali Duan & Xincheng Huang & Yunhong Zhang & Hongqin Gao & Ruike Lu & Tianshu Sun & Hua Yang & Jinqiu Shi & Maolian Liang & J, 2024. "Insights into the assembly of the neovaginal microbiota in Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome patients," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    11. Shuqin Zeng & Dhrati Patangia & Alexandre Almeida & Zhemin Zhou & Dezhi Mu & R. Paul Ross & Catherine Stanton & Shaopu Wang, 2022. "A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    12. Dena Ennis & Shimrit Shmorak & Evelyn Jantscher-Krenn & Moran Yassour, 2024. "Longitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition," Nature Communications, Nature, vol. 15(1), pages 1-12, 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_s41467-022-35178-5. 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.