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

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. pylor...

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Bibliographic Details
Published in:	Nature communications Vol. 10; no. 1; pp. 2273 - 13
Main Authors:	Ailloud, Florent, Didelot, Xavier, Woltemate, Sabrina, Pfaffinger, Gudrun, Overmann, Jörg, Bader, Ruth Christiane, Schulz, Christian, Malfertheiner, Peter, Suerbaum, Sebastian
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 22-05-2019 Nature Publishing Group Nature Portfolio
Subjects:	45/23 45/43 631/181 631/326 Adaptation Adaptation, Biological - genetics Adult Aged Antibiotics Biological evolution Biopsy Cell migration Chemotaxis Chemotaxis - genetics Evolution Gastric Mucosa - microbiology Gastric Mucosa - pathology Genetic diversity Genome, Bacterial - genetics Genomes Helicobacter Infections - microbiology Helicobacter Infections - pathology Helicobacter pylori Helicobacter pylori - genetics Helicobacter pylori - isolation & purification Helicobacter pylori - pathogenicity Humanities and Social Sciences Humans Membrane proteins Middle Aged Mucosa multidisciplinary Mutation Rate Niches Outer membrane proteins Pathogens Phylogeny Polymorphism, Genetic Population dynamics Population structure Science Science (multidisciplinary) Stomach
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Summary:	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 . Helicobacter pylori , a bacterial pathogen that infects human stomachs, has high genetic diversity across hosts. Here, Ailloud et al. reveal genetic structuring of H. pylori populations among different stomach regions of individual hosts and find signals of genetic associations with stomach region.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	2041-1723 2041-1723
DOI:	10.1038/s41467-019-10050-1