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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
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    References listed on IDEAS

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    1. 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.
    2. 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.
    3. 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.
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