Helicobacter pylori genetic diversity within the gastric niche of a single human host

Isolates of the gastric pathogen Helicobacter pylori harvested from different individuals are highly polymorphic. Strain variation also has been observed within a single host. To more fully ascertain the extent of H. pylori genetic diversity within the ecological niche of its natural host, we harvested additional isolates of the sequenced H. pylori strain J99 from its human source patient after a 6-year interval. Randomly amplified polymorphic DNA PCR and DNA sequencing of four unlinked loci indicated that these isolates were closely related to the original strain. In contrast, microarray analysis revealed differences in genetic content among all of the isolates that were not detected by randomly amplified polymorphic DNA PCR or sequence analysis. Several ORFs from loci scattered throughout the chromosome in the archival strain did not hybridize with DNA from the recent strains, including multiple ORFs within the J99 plasticity zone. In addition, DNA from the recent isolates hybridized with probes for ORFs specific for the other fully sequenced H. pylori strain 26695, including a putative traG homolog. Among the additional J99 isolates, patterns of genetic diversity were distinct both when compared with each other and to the original prototype isolate. These results indicate that within an apparently homogeneous population, as determined by macroscale comparison and nucleotide sequence analysis, remarkable genetic differences exist among single-colony isolates of H. pylori. Direct evidence that H. pylori has the capacity to lose and possibly acquire exogenous DNA is consistent with a model of continuous microevolution within its cognate host.

[1]  C. Vandenbroucke-Grauls,et al.  Mechanism of clarithromycin resistance in clinical isolates of Helicobacter pylori. , 1996, FEMS microbiology letters.

[2]  B. Roe,et al.  Analyses of the cag pathogenicity island of Helicobacter pylori , 1998, Molecular microbiology.

[3]  J. M. Smith,et al.  Free recombination within Helicobacter pylori. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[4]  R. Rappuoli,et al.  Helicobacter pylori: molecular evolution of a bacterial quasi-species. , 1998, Current opinion in microbiology.

[5]  J Hacker,et al.  Evolution of microbial pathogens. , 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[6]  M. Blaser.  Ecology of Helicobacter pylori in the human stomach. , 1997, The Journal of clinical investigation.

[7]  M. Borodovsky,et al.  cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[8]  A. Thomson,et al.  Helicobacter pylori: Basic Mechanisms to Clinical Cure , 1995 .

[9]  E. Kuipers,et al.  Quasispecies development of Helicobacter pylori observed in paired isolates obtained years apart from the same host. , 2000, The Journal of infectious diseases.

[10]  D. Berg,et al.  Emergence of recombinant strains of Helicobacter pylori during human infection , 1999, Molecular microbiology.

[11]  J. Hacker,et al.  Pathogenicity islands and the evolution of microbes. , 2000, Annual review of microbiology.

[12]  D. Graham,et al.  Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure , 1996, Journal of bacteriology.

[13]  F. Mégraud,et al.  Direct detection of Helicobacter pylori resistance to macrolides by a polymerase chain reaction/DNA enzyme immunoassay in gastric biopsy specimens , 1999, Gut.

[14]  G. Daskalopoulos,et al.  Multiple strain colonization and metronidazole resistance in Helicobacter pylori-infected patients: identification from sequential and multiple biopsy specimens. , 1996, The Journal of infectious diseases.

[15]  D. Graham,et al.  Mutations in 23S rRNA are associated with clarithromycin resistance in Helicobacter pylori , 1996, Antimicrobial agents and chemotherapy.

[16]  E. Kuipers,et al.  Genomic DNA fingerprinting of clinical isolates of Helicobacter pylori by REP-PCR and restriction fragment end-labelling. , 1998, FEMS microbiology letters.

[17]  M. Blaser,et al.  The epidemiology of Helicobacter pylori infection. , 1991, Epidemiologic reviews.

[18]  Y. Shiratori,et al.  Detection of Clarithromycin-ResistantHelicobacter pylori Strains by a Preferential Homoduplex Formation Assay , 2000, Journal of Clinical Microbiology.

[19]  D. Taylor,et al.  Cloning and sequence analysis of two copies of a 23S rRNA gene from Helicobacter pylori and association of clarithromycin resistance with 23S rRNA mutations , 1997, Antimicrobial agents and chemotherapy.

[20]  F. Mégraud,et al.  Distribution of Open Reading Frames of Plasticity Region of Strain J99 in Helicobacter pylori Strains Isolated from Gastric Carcinoma and Gastritis Patients in Costa Rica , 2000, Infection and Immunity.

[21]  A. van der Ende,et al.  Clarithromycin-Susceptible and -ResistantHelicobacter pylori Isolates with Identical Randomly Amplified Polymorphic DNA-PCR Genotypes Cultured from Single Gastric Biopsy Specimens Prior to Antibiotic Therapy , 2001, Journal of Clinical Microbiology.

[22]  S. Kresovich,et al.  DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. , 1992, Nucleic acids research.

[23]  Q. Jiang,et al.  Variability of gene order in different Helicobacter pylori strains contributes to genome diversity , 1996, Molecular microbiology.

[24]  E. El-Omar.  The importance of interleukin 1β inHelicobacter pylori associated disease , 2001, Gut.

[25]  M. Blaser,et al.  Adherence to gastric epithelial cells induces expression of a Helicobacter pylori gene, iceA, that is associated with clinical outcome. , 1998, Proceedings of the Association of American Physicians.

[26]  M. Z. Humayun,et al.  Mutation as an origin of genetic variability in Helicobacter pylori. , 1999, Trends in microbiology.

[27]  M. Dore,et al.  Demonstration of unexpected antibiotic resistance of genotypically identical Helicobacter pylori isolates. , 1998, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[28]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[29]  M. Achtman,et al.  Recombination and clonal groupings within Helicobacter pylori from different geographical regions , 2012 .

[30]  W. Doolittle,et al.  Microbial genomes: dealing with diversity. , 2001, Current opinion in microbiology.

[31]  R. Hunt,et al.  Helicobacter pylori : basic mechanisms to clinical cure 2000 : the proceedings of a symposium organised by Axcan Pharma, held in Bermuda, March 26-29, 2000 , 2000 .

[32]  P. Christie.  Agrobacterium tumefaciens T-complex transport apparatus: a paradigm for a new family of multifunctional transporters in eubacteria , 1997, Journal of bacteriology.

[33]  D. Berg,et al.  Helicobacter pylori populations in Peruvian patients. , 1997, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[34]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[35]  P. Reeves,et al.  Intraspecies variation in bacterial genomes: the need for a species genome concept. , 2000, Trends in microbiology.

[36]  M. Blaser,et al.  Helicobacter pylori genetic diversity and risk of human disease. , 2001, The Journal of clinical investigation.

[37]  D. Taylor,et al.  Construction of a Helicobacter pylori genome map and demonstration of diversity at the genome level , 1992, Journal of bacteriology.

[38]  D. Berg,et al.  Long-term colonization with single and multiple strains of Helicobacter pylori assessed by DNA fingerprinting , 1995, Journal of clinical microbiology.

[39]  M. Blaser,et al.  Allelic Variation within Helicobacter pylori babA and babB , 2001, Infection and Immunity.

[40]  E. Kuipers,et al.  Evidence for a Conjugation-Like Mechanism of DNA Transfer in Helicobacter pylori , 1998, Journal of bacteriology.

[41]  M. Blaser,et al.  Infection with Helicobacter pylori strains possessing cagA is associated with an increased risk of developing adenocarcinoma of the stomach. , 1995, Cancer research.

[42]  M. Couturier,et al.  Interaction between the RP4 coupling protein TraG and the pBHR1 mobilization protein Mob , 2000, Molecular microbiology.

[43]  E. Kuipers,et al.  The dprA gene is required for natural transformation of Helicobacter pylori. , 2000, FEMS immunology and medical microbiology.

[44]  W. Peterson,et al.  Helicobacter pylori and peptic ulcer disease. , 1991, The Western journal of medicine.

[45]  G. Friedman,et al.  Helicobacter pylori infection and the risk of gastric carcinoma. , 1991, The New England journal of medicine.

[46]  S. Garcia-Vallvé,et al.  Horizontal gene transfer in bacterial and archaeal complete genomes. , 2000, Genome research.

[47]  G. Sherlock,et al.  A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[48]  F. de la Cruz,et al.  Genetic evidence of a coupling role for the TraG protein family in bacterial conjugation , 1997, Molecular and General Genetics MGG.

[49]  M. Blaser,et al.  Detection of Helicobacter pylori gene expression in human gastric mucosa , 1995, Journal of clinical microbiology.

[50]  W. Wong,et al.  High prevalence of mixed infections by Helicobacter pylori in Hong Kong: metronidazole sensitivity and overall genotype , 2001, Alimentary pharmacology & therapeutics.

[51]  B. Picard,et al.  Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers. , 1998, FEMS microbiology letters.

[52]  F. Mégraud,et al.  Rapid Detection, by PCR and Reverse Hybridization, of Mutations in the Helicobacter pylori 23S rRNA Gene, Associated with Macrolide Resistance , 1999, Antimicrobial Agents and Chemotherapy.

[53]  Ende,et al.  Heterogeneity in susceptibility to metronidazole among Helicobacter pylori isolates from patients with gastritis or peptic ulcer disease , 1996, Journal of clinical microbiology.

[54]  M. Blaser,et al.  Helicobacter pylori strain-specific differences in genetic content, identified by microarray, influence host inflammatory responses. , 2001, The Journal of clinical investigation.

[55]  J. Hacker,et al.  Ecological fitness, genomic islands and bacterial pathogenicity , 2001, EMBO reports.

[56]  A. Labigne,et al.  Genotyping of Helicobacter pylori isolates by sequencing of PCR products and comparison with the RAPD technique. , 1996, Research in microbiology.

[57]  M. Blaser,et al.  Helicobacter pylori infection and gastric carcinoma among Japanese Americans in Hawaii. , 1991, The New England journal of medicine.

[58]  Benjamin L. King,et al.  Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori , 1999, Nature.

[59]  Mark Borodovsky,et al.  The complete genome sequence of the gastric pathogen Helicobacter pylori , 1997, Nature.