Slow Genetic Divergence of Helicobacter pylori Strains during Long-Term Colonization

ABSTRACT The genetic variability of Helicobacter pylori is known to be high compared to that of many other bacterial species. H. pylori is adapted to the human stomach, where it persists for decades, and adaptation to each host results in every individual harboring a distinctive bacterial population. Although clonal variants may exist within such a population, all isolates are generally genetically related and thus derived from a common ancestor. We sought to determine the rate of genetic change of H. pylori over 9 years in two asymptomatic adult patients. Arbitrary primed PCR confirmed the relatedness of individual subclones within a patient. Furthermore, sequencing of 10 loci (∼6,000 bp) in three subclones per time and patient revealed only two base pair changes among the subclones from patient I. All sequences were identical among the patient II subclones. However, PCR amplification of the highly divergent gene amiA revealed great variation in the size of the gene between the subclones within each patient. Thus, both patients harbored a single strain with clonal variants at both times. We also studied genetic changes in culture- and mouse-passaged strains, and under both conditions no genetic divergence was found. These results suggest that previous estimates of the rate of genetic change in H. pylori within an individual might be overestimates.

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Detection of Helicobacter pylori Microevolution and Multiple Infection from Gastric Biopsies by Housekeeping Gene Amplicon Sequencing

Pathogens ◽

10.3390/pathogens9020097 ◽

2020 ◽

Vol 9 (2) ◽

pp. 97

Author(s):

Montserrat Palau ◽

Núria Piqué ◽

André M. Comeau ◽

Gavin M. Douglas ◽

M. José Ramírez-Lázaro ◽

...

Keyword(s):

Helicobacter Pylori ◽

Pcr Amplification ◽

Housekeeping Genes ◽

Housekeeping Gene ◽

Amplicon Sequencing ◽

Multiple Infection ◽

Multiple Infections ◽

Single Strain ◽

Gastric Biopsies ◽

H Pylori

Despite the great efforts devoted to research on Helicobacter pylori, the prevalence of single-strain infection or H. pylori mixed infection and its implications in the mode of transmission of this bacterium are still controversial. In this study, we explored the usefulness of housekeeping gene amplicon sequencing in the detection of H. pylori microevolution and multiple infections. DNA was extracted from five gastric biopsies from four patients infected with distinct histopathological diagnoses. PCR amplification of six H. pylori-specific housekeeping genes was then assessed on each sample. Optimal results were obtained for the cgt and luxS genes, which were selected for amplicon sequencing. A total of 11,833 cgt and 403 luxS amplicon sequences were obtained, 2042 and 112 of which were unique sequences, respectively. All cgt and luxS sequences were clustered at 97% to 9 and 13 operational taxonomic units (OTUs), respectively. For each sample from a different patient, a single OTU comprised the majority of sequences in both genes, but more than one OTU was detected in all samples. These results suggest that multiple infections with a predominant strain together with other minority strains are the main way by which H. pylori colonizes the human stomach.

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In Vitro Incorporation of Helicobacter pylori into Candida albicans Caused by Acidic pH Stress

Pathogens ◽

10.3390/pathogens9060489 ◽

2020 ◽

Vol 9 (6) ◽

pp. 489 ◽

Cited By ~ 1

Author(s):

Kimberly Sánchez-Alonzo ◽

Cristian Parra-Sepúlveda ◽

Samuel Vega ◽

Humberto Bernasconi ◽

Víctor L. Campos ◽

...

Keyword(s):

Helicobacter Pylori ◽

Candida Albicans ◽

Pcr Amplification ◽

Growth Curves ◽

Acidic Ph ◽

Ph Values ◽

16S Gene ◽

Wide Range ◽

H Pylori

Yeasts can adapt to a wide range of pH fluctuations (2 to 10), while Helicobacter pylori, a facultative intracellular bacterium, can adapt to a range from pH 6 to 8. This work analyzed if H. pylori J99 can protect itself from acidic pH by entering into Candida albicans ATCC 90028. Growth curves were determined for H. pylori and C. albicans at pH 3, 4, and 7. Both microorganisms were co-incubated at the same pH values, and the presence of intra-yeast bacteria was evaluated. Intra-yeast bacteria-like bodies were detected using wet mounting, and intra-yeast binding of anti-H. pylori antibodies was detected using immunofluorescence. The presence of the H. pylori rDNA 16S gene in total DNA from yeasts was demonstrated after PCR amplification. H. pylori showed larger death percentages at pH 3 and 4 than at pH 7. On the contrary, the viability of the yeast was not affected by any of the pHs evaluated. H. pylori entered into C. albicans at all the pH values assayed but to a greater extent at unfavorable pH values (pH 3 or 4, p = 0.014 and p = 0.001, respectively). In conclusion, it is possible to suggest that H. pylori can shelter itself within C. albicans under unfavorable pH conditions.

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Genotyping pattern of the vacuolating cytotoxin A and cytotoxin associated gene A of the Helicobacter pylori strains detected in fecal samples of household dogs

Microbiology Research ◽

10.4081/mr.2017.7289 ◽

2017 ◽

Vol 8 (2) ◽

Author(s):

Asieh Bolandi ◽

Saam Torkan ◽

Iman Alavi

Keyword(s):

Helicobacter Pylori ◽

16S Rrna ◽

16S Rrna Gene ◽

Pcr Amplification ◽

Rrna Gene ◽

Fecal Samples ◽

The Status ◽

Cytotoxin Associated Gene A ◽

H Pylori

In despite of the high clinical impact of Helicobacter pylori, its exact sources and routes of transmission are unknown. Dogs may play an imperative role in the transmission of H. pylori to humans. The current investigation was done to study the status of vacA and cagA genotypes in the H. pylori strains of dogs. One-hundred and fifty fecal samples were collected from healthy and complicated household dogs. Genomic DNA was extracted from fecal samples and presence of 16S rRNA gene was studied using the PCR amplification. Distribution of vacA and cagA genotypes were studied by the multiplex PCR. Thirteen out of 150 fecal samples (8.66%) were positive for H. pylori 16S rRNA gene. Prevalence of H. pylori in healthy and complicated dogs were 5.55% and 8.57%, respectively. Male had the higher prevalence of H. pylori (P=0.038). The most commonly detected genotypes among the H. pylori strains were vacAs1A (61.53%), cagA (38.46%), vacAm1a (38.46%), vacAs2 (30.76%) and vacAm2 (30.76%). The most commonly detected combined genotypes were s1aCagA (30.76%), s1am1a (23.07%), s2m1a (23.07%) and s2CagA (23.07%). Iranian household dogs harbor H. pylori in their fecal samples similar in genotypes of the vacA and cagA alleles which suggest that complicated and even healthy dogs may be the latent host of the H. pylori and its genotypes. However, supplementary studies are required to found the exact role of dogs as a definitive host of the H. pylori.

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Multiple in vivo passages enhance the ability of a clinical Helicobacter pylori isolate to colonize the stomach of Mongolian gerbils and to induce gastritis

Laboratory Animals ◽

10.1258/0023677053739800 ◽

2005 ◽

Vol 39 (2) ◽

pp. 221-229 ◽

Cited By ~ 10

Author(s):

A Bleich ◽

I Köhn ◽

S Glage ◽

W Beil ◽

S Wagner ◽

...

Keyword(s):

Helicobacter Pylori ◽

Bacterial Colonization ◽

Underlying Mechanism ◽

Mongolian Gerbils ◽

Histopathological Changes ◽

Genetic Changes ◽

Colonization Ability ◽

Colonization Factors ◽

H Pylori

The Mongolian gerbil is an excellent animal model for Helicobacter pylori-induced gastritis in humans. In this study, initially low colonization rates of the H. pylori strains ATCC 43504, SS1, or HP87 inoculated into gerbils caused difficulties in establishing this model. In order to increase the colonization ability and pathogenicity, the clinical HP87 isolate was selected for adaptation to the gerbil stomach by multiple in vivo passages through gerbils. Development of gastritis was examined histologically at 4–52 weeks after infection. The proportion of gerbils which tested positive for H. pylori by culture at four weeks after inoculation gradually increased from 11.1% of gerbils inoculated with HP87 without prior in vivo passage (P0) to 100% of gerbils inoculated with HP87 with seven in vivo passages (P7). In addition, adaptation of HP87 resulted in more severe histopathological changes. Gerbils infected with adapted HP87 (P7) exhibited severe infiltration by monomorphonuclear and polymorphonuclear leukocytes in the mucosa, submucosa, and subserosa of the gastric antrum, as well as epithelial changes consisting of hyperplasia, erosion, and ulceration. Histopathological changes increased in severity from four to 52 weeks after infection. Adaptation of HP87 during its passages through gerbils could be due to genetic changes in bacterial colonization factors. Identification of these changes might be useful to understand the underlying mechanism of gastric adaptation and pathogenesis of H. pylori.

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Molecular and Structural Analysis of the Helicobacter pylori cag Type IV Secretion System Core Complex

mBio ◽

10.1128/mbio.02001-15 ◽

2016 ◽

Vol 7 (1) ◽

Cited By ~ 67

Author(s):

Arwen E. Frick-Cheng ◽

Tasia M. Pyburn ◽

Bradley J. Voss ◽

W. Hayes McDonald ◽

Melanie D. Ohi ◽

...

Keyword(s):

Helicobacter Pylori ◽

Bacterial Species ◽

Secretion System ◽

Effector Proteins ◽

Type Iv Secretion ◽

Secretion Systems ◽

Core Complex ◽

Type Iv ◽

Membrane Spanning ◽

H Pylori

ABSTRACT Bacterial type IV secretion systems (T4SSs) can function to export or import DNA, and can deliver effector proteins into a wide range of target cells. Relatively little is known about the structural organization of T4SSs that secrete effector proteins. In this report, we describe the isolation and analysis of a membrane-spanning core complex from the Helicobacter pylori cag T4SS, which has an important role in the pathogenesis of gastric cancer. We show that this complex contains five H. pylori proteins, CagM, CagT, Cag3, CagX, and CagY, each of which is required for cag T4SS activity. CagX and CagY are orthologous to the VirB9 and VirB10 components of T4SSs in other bacterial species, and the other three Cag proteins are unique to H. pylori . Negative stain single-particle electron microscopy revealed complexes 41 nm in diameter, characterized by a 19-nm-diameter central ring linked to an outer ring by spoke-like linkers. Incomplete complexes formed by Δ cag3 or Δ cagT mutants retain the 19-nm-diameter ring but lack an organized outer ring. Immunogold labeling studies confirm that Cag3 is a peripheral component of the complex. The cag T4SS core complex has an overall diameter and structural organization that differ considerably from the corresponding features of conjugative T4SSs. These results highlight specialized features of the H. pylori cag T4SS that are optimized for function in the human gastric mucosal environment. IMPORTANCE Type IV secretion systems (T4SSs) are versatile macromolecular machines that are present in many bacterial species. In this study, we investigated a T4SS found in the bacterium Helicobacter pylori. H. pylori is an important cause of stomach cancer, and the H. pylori T4SS contributes to cancer pathogenesis by mediating entry of CagA (an effector protein regarded as a “bacterial oncoprotein”) into gastric epithelial cells. We isolated and analyzed the membrane-spanning core complex of the H. pylori T4SS and showed that it contains unique proteins unrelated to components of T4SSs in other bacterial species. These results constitute the first structural analysis of the core complex from this important secretion system.

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Quantitative Effect of luxS Gene Inactivation on the Fitness of Helicobacter pylori

Applied and Environmental Microbiology ◽

10.1128/aem.01291-06 ◽

2006 ◽

Vol 72 (10) ◽

pp. 6615-6622 ◽

Cited By ~ 17

Author(s):

Woo-Kon Lee ◽

Keiji Ogura ◽

John T. Loh ◽

Timothy L. Cover ◽

Douglas E. Berg

Keyword(s):

Helicobacter Pylori ◽

Competitive Ability ◽

Reference Strain ◽

Bacterial Species ◽

Soft Agar ◽

Autoinducer 2 ◽

Methyl Cycle ◽

Adenosyl Methionine ◽

Unrelated Strain ◽

H Pylori

ABSTRACT Furanone metabolites called AI-2 (autoinducer 2), used by some bacterial species for signaling and cell density-regulated changes in gene expression, are made while regenerating S-adenosyl methionine (SAM) after its use as a methyl donor. The luxS-encoded enzyme, in particular, participates in this activated methyl cycle by generating both a pentanedione, which is transformed chemically into these AI-2 compounds, and homocysteine, a precursor of methionine and SAM. Helicobacter pylori seems to contain the genes for this activated methyl cycle, including luxS, but not genes for AI-2 uptake and transcriptional regulation. Here we report that deletion of luxS in H. pylori reference strain SS1 diminished its competitive ability in mice and motility in soft agar, whereas no such effect was seen with an equivalent ΔluxS derivative of the unrelated strain X47. These different outcomes are consistent with H. pylori's considerable genetic diversity and are reminiscent of phenotypes seen after deletion of another nonessential metabolic gene, that encoding polyphosphate kinase 1. We suggest that synthesis of AI-2 by H. pylori may be an inadvertent consequence of metabolite flux in its activated methyl cycle and that impairment of this cycle and/or pathways affected by it, rather than loss of quorum sensing, is deleterious for some H. pylori strains. Also tenable is a model in which AI-2 affects other microbes in H. pylori's gastric ecosystem and thereby modulates the gastric environment in ways to which certain H. pylori strains are particularly sensitive.

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Interplay and cooperation of Helicobacter pylori and gut microbiota in gastric carcinogenesis

BMC Microbiology ◽

10.1186/s12866-021-02315-x ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Seyedeh Zahra Bakhti ◽

Saeid Latifi-Navid

Keyword(s):

Helicobacter Pylori ◽

Gut Microbiota ◽

Intestinal Microbiota ◽

Bacterial Species ◽

Short Chain Fatty Acids ◽

Gastric Carcinogenesis ◽

Oncogenic Signaling ◽

Comprehensive Overview ◽

H Pylori ◽

Oncogenic Signaling Pathways

AbstractChronic Helicobacter pylori infection is a critical risk factor for gastric cancer (GC). However, only 1–3 % of people with H. pylori develop GC. In gastric carcinogenesis, non-H. pylori bacteria in the stomach might interact with H. pylori. Bacterial dysbiosis in the stomach can strengthen gastric neoplasia development via generating tumor-promoting metabolites, DNA damaging, suppressing antitumor immunity, and activating oncogenic signaling pathways. Other bacterial species may generate short-chain fatty acids like butyrate that may inhibit carcinogenesis and inflammation in the human stomach. The present article aimed at providing a comprehensive overview of the effects of gut microbiota and H. pylori on the development of GC. Next, the potential mechanisms of intestinal microbiota were discussed in gastric carcinogenesis. We also disserted the complicated interactions between H. pylori, intestinal microbiota, and host in gastric carcinogenesis, thus helping us to design new strategies for preventing, diagnosing, and treating GC.

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Helicobacter pylori Can Be Induced To Assume the Morphology of Helicobacter heilmannii

Journal of Clinical Microbiology ◽

10.1128/jcm.37.4.1045-1048.1999 ◽

1999 ◽

Vol 37 (4) ◽

pp. 1045-1048 ◽

Cited By ~ 14

Author(s):

Paul T. Fawcett ◽

Kathleen M. Gibney ◽

Kathleen M. B. Vinette

Keyword(s):

Helicobacter Pylori ◽

Culture Collection ◽

Blood Agar ◽

Broth Culture ◽

Differential Interference Contrast Microscopy ◽

Single Strain ◽

Helicobacter Heilmannii ◽

Interference Contrast Microscopy ◽

Collection Strain ◽

H Pylori

Cultures of Helicobacter pylori obtained from the American Type Culture Collection (strain 43504) were grown as isolated colonies or lawns on blood agar plates and in broth culture with constant shaking. Examination of bacterial growth with Gram-stained fixed preparation and differential interference contrast microscopy on wet preparations revealed that bacteria grown on blood agar plates had a morphology consistent with that normally reported for H. pylori whereas bacteria from broth cultures had the morphologic appearance of Helicobacter heilmannii. Bacteria harvested from blood agar plates assumed an H. heilmannii-like morphology when transferred to broth cultures, and bacteria from broth cultures grew with morphology typical of H. pylori when grown on blood agar plates. Analysis by PCR of bacteria isolated from blood agar plates and broth cultures indicated that a single strain of bacteria (H. pylori) was responsible for both morphologies.

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Gastric Microbiota in Helicobacter pylori-Negative and -Positive Gastritis Among High Incidence of Gastric Cancer Area

Cancers ◽

10.3390/cancers11040504 ◽

2019 ◽

Vol 11 (4) ◽

pp. 504 ◽

Cited By ~ 14

Author(s):

Boldbaatar Gantuya ◽

Hashem B. El-Serag ◽

Takashi Matsumoto ◽

Nadim J. Ajami ◽

Khasag Oyuntsetseg ◽

...

Keyword(s):

Gastric Cancer ◽

Helicobacter Pylori ◽

Bacterial Species ◽

Rrna Gene ◽

Linear Discriminant ◽

Haemophilus Parainfluenzae ◽

Increased Risk ◽

Comparison Groups ◽

H Pylori ◽

Gastric Microbiota

Helicobacter pylori (H. pylori) related chronic gastritis is a well-known major etiological factor for gastric cancer development. However, H. pylori-negative gastritis (HpN) is not well described. We aimed to examine gastric mucosal microbiota in HpN compared to H. pylori-positive gastritis (HpP) and H. pylori-negative non-gastritis group (control). Here, we studied 11 subjects with HpN, 40 with HpP and 24 controls. We performed endoscopy with six gastric biopsies. Comparison groups were defined based on strict histological criteria for the disease and H. pylori diagnosis. We used 16S rRNA gene amplicon sequencing to profile the gastric microbiota according to comparison groups. These results demonstrate that the HpP group had significantly lower bacterial richness by the operational taxonomic unit (OTU) counts, and Shannon and Simpson indices as compared to HpN or controls. The linear discriminant analysis effect size analysis showed the enrichment of Firmicutes, Fusobacteria, Bacteroidetes and Actinobacteria at phylum level in the HpN group. In the age-adjusted multivariate analysis, Streptococcus sp. and Haemophilus parainfluenzae were at a significantly increased risk for HpN (odds ratio 18.9 and 12.3, respectively) based on abundance. Treponema sp. was uniquely found in HpN based on occurrence. In this paper, we conclude that Streptococcus sp., Haemophilus parainfluenzae and Treponema sp. are candidate pathogenic bacterial species for HpN. These results if confirmed may have important clinical implications.

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Identification of the periplasmic DNA receptor for natural transformation of Helicobacter pylori

Nature Communications ◽

10.1038/s41467-019-13352-6 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 6

Author(s):

Prashant P. Damke ◽

Anne Marie Di Guilmi ◽

Paloma Fernández Varela ◽

Christophe Velours ◽

Stéphanie Marsin ◽

...

Keyword(s):

Helicobacter Pylori ◽

Natural Transformation ◽

Bacterial Species ◽

Dna Binding Protein ◽

Gram Negative Bacteria ◽

Membrane Channel ◽

Inner Membrane ◽

Double Stranded Dna ◽

Periplasmic Domain ◽

H Pylori

AbstractHorizontal gene transfer through natural transformation is a major driver of antibiotic resistance spreading in many pathogenic bacterial species. In the case of Gram-negative bacteria, and in particular of Helicobacter pylori, the mechanisms underlying the handling of the incoming DNA within the periplasm are poorly understood. Here we identify the protein ComH as the periplasmic receptor for the transforming DNA during natural transformation in H. pylori. ComH is a DNA-binding protein required for the import of DNA into the periplasm. Its C-terminal domain displays strong affinity for double-stranded DNA and is sufficient for the accumulation of DNA in the periplasm, but not for DNA internalisation into the cytoplasm. The N-terminal region of the protein allows the interaction of ComH with a periplasmic domain of the inner-membrane channel ComEC, which is known to mediate the translocation of DNA into the cytoplasm. Our results indicate that ComH is involved in the import of DNA into the periplasm and its delivery to the inner membrane translocator ComEC.

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