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Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps

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  • Florent Ailloud

    (Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich
    MHH Hannover Medical School
    DZIF German Center for Infection Research, Munich Site
    DZIF German Center for Infection Research, Hannover-Braunschweig Site)

  • Xavier Didelot

    (University of Warwick
    University of Warwick)

  • Sabrina Woltemate

    (MHH Hannover Medical School)

  • Gudrun Pfaffinger

    (Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich)

  • Jörg Overmann

    (DZIF German Center for Infection Research, Hannover-Braunschweig Site
    Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures)

  • Ruth Christiane Bader

    (Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich
    Max von Pettenkofer Institute)

  • Christian Schulz

    (Otto von Guericke University
    University Hospital, LMU Munich)

  • Peter Malfertheiner

    (Otto von Guericke University
    University Hospital, LMU Munich)

  • Sebastian Suerbaum

    (Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich
    MHH Hannover Medical School
    DZIF German Center for Infection Research, Munich Site
    DZIF German Center for Infection Research, Hannover-Braunschweig Site)

Abstract

The human pathogen Helicobacter pylori displays extensive genetic diversity. While H. pylori is known to evolve during infection, population dynamics inside the gastric environment have not been extensively investigated. Here we obtained gastric biopsies from multiple stomach regions of 16 H. pylori-infected adults, and analyze the genomes of 10 H. pylori isolates from each biopsy. Phylogenetic analyses suggest location-specific evolution and bacterial migration between gastric regions. Migration is significantly more frequent between the corpus and the fundus than with the antrum, suggesting that physiological differences between antral and oxyntic mucosa contribute to spatial partitioning of H. pylori populations. Associations between H. pylori gene polymorphisms and stomach niches suggest that chemotaxis, regulatory functions and outer membrane proteins contribute to specific adaptation to the antral and oxyntic mucosa. Moreover, we show that antibiotics can induce severe population bottlenecks and likely play a role in shaping the population structure of H. pylori.

Suggested Citation

  • Florent Ailloud & Xavier Didelot & Sabrina Woltemate & Gudrun Pfaffinger & Jörg Overmann & Ruth Christiane Bader & Christian Schulz & Peter Malfertheiner & Sebastian Suerbaum, 2019. "Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10050-1
    DOI: 10.1038/s41467-019-10050-1
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    Cited by:

    1. Xiaoyue Xi & Simon E. F. Spencer & Matthew Hall & M. Kate Grabowski & Joseph Kagaayi & Oliver Ratmann & Rakai Health Sciences Program and PANGEA‐HIV, 2022. "Inferring the sources of HIV infection in Africa from deep‐sequence data with semi‐parametric Bayesian Poisson flow models," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 71(3), pages 517-540, June.

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