Genome and Methylome Variation in Helicobacter pylori With a cag Pathogenicity Island During Early Stages of Human Infection

Gastroenterology. 2018 Feb;154(3):612-623.e7. doi: 10.1053/j.gastro.2017.10.014. Epub 2017 Oct 21.


Background & aims: Helicobacter pylori is remarkable for its genetic variation; yet, little is known about its genetic changes during early stages of human infection, as the bacteria adapt to their new environment. We analyzed genome and methylome variations in a fully virulent strain of H pylori during experimental infection.

Methods: We performed a randomized Phase I/II, observer-blind, placebo-controlled study of 12 healthy, H pylori-negative adults in Germany from October 2008 through March 2010. The volunteers were given a prophylactic vaccine candidate (n = 7) or placebo (n = 5) and then challenged with H pylori strain BCM-300. Biopsy samples were collected and H pylori were isolated. Genomes of the challenge strain and 12 reisolates, obtained 12 weeks after (or in 1 case, 62 weeks after) infection were sequenced by single-molecule, real-time technology, which, in parallel, permitted determination of genome-wide methylation patterns for all strains. Functional effects of genetic changes observed in H pylori strains during human infection were assessed by measuring release of interleukin 8 from AGS cells (to detect cag pathogenicity island function), neutral red uptake (to detect vacuolating cytotoxin activity), and adhesion assays.

Results: The observed mutation rate was in agreement with rates previously determined from patients with chronic H pylori infections, without evidence of a mutation burst. A loss of cag pathogenicity island function was observed in 3 reisolates. In addition, 3 reisolates from the vaccine group acquired mutations in the vacuolating cytotoxin gene vacA, resulting in loss of vacuolization activity. We observed interstrain variation in methylomes due to phase variation in genes encoding methyltransferases.

Conclusions: We analyzed adaptation of a fully virulent strain of H pylori to 12 different volunteers to obtain a robust estimate of the frequency of genetic and epigenetic changes in the absence of interstrain recombination. Our findings indicate that the large amount of genetic variation in H pylori poses a challenge to vaccine development. no: NCT00736476.

Keywords: Cancer; Microbe; Pathogen; Stomach.

Publication types

  • Clinical Trial, Phase I
  • Clinical Trial, Phase II
  • Randomized Controlled Trial
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antigens, Bacterial / administration & dosage
  • Antigens, Bacterial / genetics
  • Antigens, Bacterial / immunology
  • Bacterial Adhesion
  • Bacterial Proteins / administration & dosage
  • Bacterial Proteins / genetics
  • Bacterial Proteins / immunology
  • Bacterial Vaccines / administration & dosage
  • Bacterial Vaccines / genetics
  • Bacterial Vaccines / immunology
  • Biopsy
  • DNA Methylation*
  • Epigenesis, Genetic*
  • Gene Expression Regulation, Bacterial
  • Genome, Bacterial*
  • Genomic Islands*
  • Genotype
  • Germany
  • Helicobacter Infections / diagnosis
  • Helicobacter Infections / immunology
  • Helicobacter Infections / microbiology*
  • Helicobacter Infections / prevention & control
  • Helicobacter pylori / genetics*
  • Helicobacter pylori / immunology
  • Helicobacter pylori / pathogenicity
  • Host-Pathogen Interactions
  • Humans
  • Interleukin-8 / immunology
  • Interleukin-8 / metabolism
  • Mutation
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Time Factors
  • Virulence


  • Antigens, Bacterial
  • Bacterial Proteins
  • Bacterial Vaccines
  • CXCL8 protein, human
  • Interleukin-8
  • VacA protein, Helicobacter pylori
  • cagA protein, Helicobacter pylori
  • neutrophil-activating protein A, Helicobacter pylori

Associated data