Biotype and molecular fingerprints of metronidazole-resistant strains of Helicobacter pylori from antral gastric mucosa

The Prevalence of Mixed Helicobacter pylori Infections in Symptomatic and Asymptomatic Subjects in Dhaka, Bangladesh

BACKGROUND

Helicobacter pylori is a highly genetically diverse bacterial species, which can persist in the gastric environment for decades. Recent studies have shown that single infections predominate in developed countries, whereas mixed infections are more prevalent in developing countries. Mixed infections of this bacterium may be important for adaptation to the hostile gastric environment and may facilitate dyspeptic symptoms.

MATERIALS AND METHODS

To calculate the prevalence of mixed infections in symptomatic and asymptomatic subjects, 2010 H. pylori isolates collected from 83 symptomatic and 91 asymptomatic subjects from Dhaka, Bangladesh, were analyzed by (i) random amplified polymorphic DNA fingerprinting (RAPD) and (ii) multiplex PCR amplification for cagA and vacA virulence gene alleles.

RESULTS

The overall prevalence of mixed H. pylori infection was 60.15% (77/128), indicating substantial co-colonization in this population. We additionally found that symptomatic subjects (53%) had a significantly higher rate of mixed infection than asymptomatic individuals (36.3%) (p = .016) and that the prevalence of the cagA and vacA and vacA m1/s1 and vacA m2/s1 alleles were higher in subjects with mixed infection.

CONCLUSION

Our findings suggest that an increased diversity of the H. pylori strains in the gastric environment may contribute to the development of disease symptoms.

Characteristics and interactions of Helicobacter pylori and H. pylori-infected human gastroduodenal epithelium in peptic ulcer: a transmission electron microscopy study

Helicobacter pylori (H. pylori) has been presumed to be an initiating factor in a previously recognized chain of events, starting with active chronic gastritis and leading to atrophy of the mucosal membrane, intestinal metaplasia, dysplasia (intraepithelial neoplasia), and finally culminating in gastric carcinoma. Adherence of H. pylori to the gastroduodenal epithelium is believed to be an important step in the induction of active chronic inflammation of the mucosal layer. However, it is not clear how the pathogen chronically colonizes the gastroduodenal epithelium. In this study, 30 biopsy specimens from H. pylori-positive peptic ulcer (15 for gastric ulcer, 15 for duodenal ulcer) patients were examined by transmission electron microscopy (TEM) to observe the structural adherence of H. pylori to gastroduodenal epithelium while ten healthy postulants were served as controls. We also investigated the interaction between H. pylori and gastroduodenal epithelial cells. Morphological appearances of both the pathogen and the cells as well as features of colonization, attachment, and internalization were observed. H. pylori exhibited both spiral and coccoid forms. Cytoplasmic vacuolar degeneration played by the vacuolating toxin (VacA) was apparent in gastroduodenal epithelial cells. Specially, a number of tumor cells were found in H. pylori-positive gastric intestinal metaplasia (IM) mucosa under TEM which provided an ultrastructural evidence of IM carrying a particularly high risk for the development of gastric cancer.

Amplified fragment length polymorphism genotyping of metronidazole-resistant Helicobacter pylori infecting dyspeptics in England

OBJECTIVE

Intra-specific diversity of Helicobacter pylori infecting stomachs of different individuals was investigated by numerical analysis of amplified fragment length polymorphisms (AFLP), to determine the existence of clones within the strain population and the effect that antibiotic treatment, particularly with metronidazole (Mtz), had on the balance of types/subtypes present before and after treatment.

METHODS

The 92 cultures studied comprised 89 single or multiple (pre- and post-treatment) isolates from gastric biopsies from 35 dyspeptic patients at two geographical locations in England, and three reference strains. HindIII restriction fragments tagged with specific adaptors were used as template DNA for AFLP. Patterns were coded in binary format according to deduced sizes of amplified fragments, and numerical analysis was performed.

RESULTS

H. pylori isolated from different individuals were highly diverse (43 AFLP types) with a continuum of similarities that included three putative strain clusters at the 55% similarity level. Twelve sets each comprised identical isolates but subclonal variants with similarities of 82-99% coexisted in isolate sets from 19 patients. Seven sets contained strains with different AFLP types which for several corresponded with vacA/cagA genotypic differences. Mtz resistance was a feature of clonal as well as unrelated isolates.

CONCLUSIONS

AFLP profiling was a robust, reproducible and highly discriminatory means of indexing H. pylori strain diversity, and the numerical analysis enabled clonal/subclonal variants infecting an individual to be defined and contrasted with the general species diversity. The majority (65%) of patients had co-infections with different strain types/subtypes but antibiotic treatment apparently did not markedly modify H. pylori population diversity in individual stomachs. Mtz sensitivity was generally associated with greater strain diversity as several subtypes often coexisted in sensitive pretreatment strain sets. In contrast, Mtz-resistant strain populations were less diverse, which was attributed to selection by previous exposure to nitroimidazoles in the same or a different host.

High prevalence of mixed infections by Helicobacter pylori in Hong Kong: metronidazole sensitivity and overall genotype

BACKGROUND

Diversity in metronidazole susceptibility and genotypes of Helicobacter pylori have been reported with varying results in different areas.

AIMS

To investigate the prevalence of multiple strain infection in a symptomatic Chinese population and to determine the metronidazole susceptibility pattern and genotypic characteristics of these infecting strains.

METHODS

Gastric biopsies from antrum, body and cardia were taken during upper endoscopy in symptomatic patients referred to our department. Pooled cultures and single colony isolates were obtained and tested for metronidazole susceptibility and random amplified polymorphic DNA (RAPD) fingerprint patterns.

RESULTS

A total of 461 isolates were successfully cultured from 46 patients. Fifty-seven per cent of subjects had metronidazole-resistant strains. Among them, 77% carried a mixture of sensitive and resistant strains, non-uniformly distributed in the gastric mucosa. Mixed genotypes were found by RAPD typing in 24% of subjects. These did not correlate with the metronidazole susceptibility/resistance pattern.

CONCLUSION

H. pylori infections with mixed metronidazole sensitive/resistant strains and mixed genotypes are common in Hong Kong. This makes it prudent to use bacterial strains from several biopsy sites when testing for traits such as drug resistance or virulence in relation to disease.

Effect of clarithromycin and omeprazole therapy on the diversity and stability of genotypes of Helicobacter pylori from duodenal ulcer patients

The genotypes of multiple isolates of Helicobacter pylori from 17 duodenal ulcer patients in the United Kingdom were compared to determine reasons for treatment failure. Isolates were from antrum and corpus biopsies taken before and after dual therapy with clarithromycin and omeprazole. All isolates were tested for antibiotic resistance and characterised by a novel scheme combining polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the ureA + ureB and 23S rRNA genes, vacA signal and midregion genotypes, and PCR detection of cagA. Combined genotypes of paired pre- and post-treatment isolates from 8 patients showed an infection with a single strain of H. pylori that had acquired resistance to clarithromycin. In 4 other patients, acquisition of clarithromycin resistance was associated with the presence of different strain types of H. pylori. The remaining 5 patients had clarithromycin-sensitive isolates. Overall, H. pylori from different patients had diverse genotypes, yet most (70%) were colonized by the same predominant and stable strain in both the antrum and corpus. There was no link between the emergence of in vitro clarithromycin resistance and a particular strain genotype for these UK isolates. It was concluded that colonization with a clarithromycin-resistant H. pylori was due to selection of a resistant strain or clonal variant within the infecting population. Present genomic markers had low predictive value for emergence of resistance.

Performance criteria of DNA fingerprinting methods for typing of Helicobacter pylori isolates: experimental results and meta-analysis

Typing systems are used to discriminate between isolates of Helicobacter pylori for epidemiological and clinical purposes. Discriminatory power and typeability are important performance criteria of typing systems. Discriminatory power refers to the ability to differentiate among unrelated isolates; it is quantitatively expressed by the discriminatory index (DI). Typeability refers to the ability of the method to provide an unambiguous result for each isolate analyzed; it is quantitatively expressed by the percentage of typeable isolates. We evaluated the discriminatory power and the typeability of the most currently used DNA fingerprinting methods for the typing of H. pylori isolates: ribotyping, PCR-based restriction fragment length polymorphism (PCR-RFLP) analysis, and random amplified polymorphism DNA (RAPD) analysis. Forty epidemiologically unrelated clinical isolates were selected to constitute a test population adapted to the evaluation of these performance criteria. A meta-analysis of typeability and discriminatory power was conducted retrospectively with raw data from published studies in which ribotyping, PCR-RFLP, RAPD, repetitive extragenic palindromic DNA sequence-based PCR (REP-PCR), or pulsed-field gel electrophoresis (PFGE) was used. Experimental results and the meta-analysis demonstrated the optimal typeability (100%) and the excellent discriminatory powers of PCR-based typing methods: RAPD analysis, DIs, 0.99 to 1; REP-PCR, DI, 0.99; and PCR-RFLP analysis, DIs, 0.70 to 0.97). Chromosome restriction-based typing methods (ribotyping and PFGE) are limited by a low typeability (12.5 to 75%) that strongly decreases their discriminatory powers: ribotyping, DI, 0.92; PFGE, DIs, 0.24 to 0.88. We do not recommend the use of ribotyping and PFGE for the typing of H. pylori isolates. We recommend the use of PCR-based methods.

Molecular methods for typing of Helicobacter pylori and their applications

Microbial typing is a useful tool in clinical epidemiology for defining the source and route of infection, for studying the persistence and reinfection rates, clonal selection in the host and bacterial evolution. Phenotypic methods such as biotyping, serotyping and hemagglutinin typing have little discriminatory power compared to genotypic methods concerning the typing of Helicobacter pylori. Therefore great efforts have been made to establish useful molecular typing methods. In this context, the most frequently used genotypic methods are described based on our own experience and the literature: (1) restriction endonuclease analysis, (2) endonuclease analysis using pulsed-field gel electrophoresis, (3) ribotyping, (4) polymerase chain reaction (using either random primers or repetitive DNA sequence primers), and (5) polymerase chain reaction-restriction fragment length polymorphism analysis of e.g. the urease genes. Furthermore, reproducibility, discriminatory power, ease of performance and interpretation, cost and toxic procedures of each method are assessed. To date no direct comparison of all the molecular typing methods described has been performed in the same study with the same H. pylori strains. However, PCR analysis of the urease gene directly on suspensions of H. pylori or gastric biopsy material seems to be useful for routine use and applicable in specific epidemiological situations.

Rapid genomic diversification of Helicobacter pylori

Helicobacter pylori was cultured from antrum and corpus gastric biopsies from 65 patients originating from two separate groups: (i) a geographically linked group and (ii) a geographically nonlinked group. Genomic DNA was recovered from the clinical isolates and subjected to restriction fragment length polymorphism (RFLP) analysis after digestion with DraI. Southern blots were probed with the oligonucleotide (GTG)5, the riboprobe pKK3535, and the cagA gene probe pMC3. (GTG)5 and cagA DNA fingerprints and ribopatterns suggested that most of the patients were infected with their own unique strain; however, some were infected with multiple strains. Minor genomic differences were detected in many antrum/corpus sample pairs (clonal variants), suggesting rapid evolutionary change in domains detected by (GTG)5. The high degree of genomic diversity detected by (GTG)5 may reflect structural versatility of these domains. The genomic diversity indicates that infection by H. pylori in a defined community does not appear to be limited to certain RFLP types.

Phenotypic diversity in Lewis expression of Helicobacter pylori isolates from the same host

Populations of Helicobacter pylori cells show a stable expression of Lewis surface antigens, although phase variation may occur among individual organisms grown in vitro. We searched for variation in Lewis phenotypes among H. pylori cells of minimally in vitro-passaged isolates. Lewis expression in 180 clonal H. pylori populations from the primary culture of 20 gastric biopsy samples from 12 patients, and that in 160 isolates from primary cultures from 16 experimentally infected rodents, were examined by enzyme immunoassays. Substantial differences in Lewis expression were found among the isolates from 9 (75%) of 12 patients. These differences were unrelated to overall genetic diversity as determined by polymerase chain reactions for random amplified polymorphic DNA or cagA status, and they persisted during subsequent in vitro passage. In contrast, Lewis expression was highly uniform in H. pylori isolates from different rodents infected for up to 20 weeks. Variation in H. pylori Lewis expression in genetically closely related organisms in human subjects may provide a pool of bacterial phenotypes for the continuous selection of optimally host-adapted populations suitable for persistence.

DNA banding pattern polymorphism in vancomycin-resistant Enterococcus faecium and criteria for defining strains

The degree of DNA banding pattern polymorphism exhibited by vancomycin-resistant Enterococcus faecium (VREM) strains isolated on a renal unit over an 11-month period was investigated. Thirty VREM strains from different patients were analyzed by pulsed-field gel electrophoresis (PFGE; with extended run and optimal pulse times), ribotyping, plasmid profile analysis, biotyping, pyrolysis mass spectrometry, and antibiogram analysis. PFGE resolved 17 banding patterns which formed four distinct clusters at the 82% similarity level. Intercluster band differences ranged from 14 to 31 bands. The strains in one cluster, which contained seven patterns that differed from each other by one to seven bands and from the common pattern by five bands, were confirmed to be a single strain by four of the five other typing methods. The strains in a second cluster with eight patterns, which differed from each other by 1 to 12 bands, contained two subclusters. This subdivision was supported by ribotyping and biotyping. However, it was unclear whether these subclusters represented distinct strains. In one strain, marked polymorphism (patterns that differed from each other by up to four bands) was observed in the ribotype pattern. This study demonstrates the high degree of DNA banding pattern polymorphism found for some strains of VREM and illustrates the complexity involved in defining such strains.

Transmission of canine gastric Helicobacter salomonis infection from dam to offspring and between puppies

H. bizzozeronii CCUG 35045, a new canine gastric Helicobacter spp. was used for experimental infection of four weaned puppies at 7 weeks of age. Controls were four nonchallenged puppies. The puppies originated from two dams which had Helicobacter salomonis infection in biopsy samples taken 3 weeks before the delivery but which had urease, brush cytology and culture-negative biopsy samples taken 7 weeks after antimicrobial treatment (metronidazole, amoxicillin, bismuth subcitrate). Both dams were detected urease- and Helicobacter-positive again three and a half months after therapy. Dam B was shown to be colonised with the similar genotype of H. salomonis for more than 2 years. Unexpectedly, H. salomonis was also cultured from gastric biopsy samples of the nonchallenged puppies three times during 7 months. When H. salomonis isolates of dams and puppies were studied by ribotyping (HaeIII, ClaI or PstI) they were shown to be identical although the HaeIII and PstI REA patterns of dam A differed from the patterns of dam B and nonchallenged group by one fragment. PFGE pattern analysis of NotI digests, however, revealed that the isolates of the puppies were identical with the isolates of dam B, and differed from the isolates of dam A. The isolates of the dams and puppies in the nonchallenged group were metronidazole-resistant. The antimicrobial therapy had merely suppressed, but not eradicated, the infection from dams. These studies suggested that puppies may acquire gastric Helicobacter infection from dams during the lactation period and puppies can infect each other during their early life. PFGE pattern analysis was shown to be a more distinguishing method than ribotyping to study the similarity of the isolates.

Influence of a proton pump inhibitor-based therapy on Helicobacter pylori strain selection

The influence of the proton pump inhibitor lansoprazole on strain diversity in Helicobacter pylori infected patients was investigated. Multiple isolates of Helicobacter pylori obtained pre- and post-therapy from gastric antral and body biopsies in 22 patients were compared using the random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) for analysis. Post-therapy strains exhibiting novel RAPD-profiles were found in 5 of 22 patients (4 of 11 patients treated with lansoprazole alone and 1 of 11 patients treated with lansoprazole plus amoxicillin). Proton pump inhibition may affect the microecology of the stomach by influencing the colonisation patterns of specific strains.

Are there susceptible hosts to Helicobacter pylori infection?

Susceptibility to Helicobacter pylori infection may manifest itself as an increased prevalence of H. pylori infection, as reinfection after eradication, or as different clinical outcomes (gastritis, peptic ulcer disease, primary gastric B-cell lymphoma, or gastric cancer). These outcomes are likely to be a result of interaction between environmental and genetic factors. Genetic factors include both host genetic predisposition to infection as well as genetic differences in H. pylori strains. Twin studies indicate that the correlation coefficient for the relative importance of genetic effects (heritability) on acquisition of H. pylori infection is approximately 0.66. The remaining variance is accounted for by shared rearing environmental factors (20%), and non-shared environmental factors (23%), which contribute to the differences and not the similarities seen between family members. Molecular epidemiological studies of both the whole bacterial genome and of amplified regions between specific repetitive DNA sequences also suggest that there are disease-specific strains of H. pylori. There are, therefore, many different facets of susceptibility to H. pylori infection.

Immunological properties of the cell surface haemagglutinins (sHAs) of Helicobacter pylori strain NCTC 11637

Rabbits were immunised with stage 1 and stage 2 soluble haemagglutinins (sHA) of Helicobacter pylori strain NCTC 11637 and with rabbit erythrocytes coated with stage 1 sHA. After adsorption of stage 1 sHA on erythrocytes, SDS-PAGE analysis showed that 4 major protein bands were removed from the preparation. The anti-sHA coated erythrocyte serum had the highest HA inhibition titre of 16. Crossed immunoelectrophoresis of the stage 1 sHA, against stage 1 and 2 antisera showed multiple precipitin arcs; however, the anti-sHA coated erythrocyte serum produced only two arcs. One arc produced by the anti-stage 2 serum was absent with the anti-stage 1 serum. This arc could have been produced against a 20 kDa polypeptide which was absent in the stage 1 sHA. The other arc was stronger when compared with that produced by anti-stage 1 serum. These two arcs corresponded to the two arcs produced by the anti-sHA coated erythrocyte serum, which had the highest inhibition titre. The two arcs were markedly reduced in crossed immunoelectrophoresis with an adsorbed stage 1 sHA preparation, which indicates that these arcs were produced against the sHAs.

Comparison of PCR-based restriction length polymorphism analysis of urease genes with rRNA gene profiling for monitoring Helicobacter pylori infections in patients on triple therapy

Multiple isolates of Helicobacter pylori from antral biopsies of nine patients were examined by DNA fingerprinting. Analysis of rRNA gene patterns and HaeIII restriction fragment length polymorphism of PCR-amplified urease genes were compared and used to study colonization before and after failed triple therapy. H. pylori isolates from a single biopsy shared the same HaeIII DNA fingerprint regardless of the isolation method (plate or broth). DNA pattern types of paired strains of H. pylori were distinct between patients and were not grossly affected by treatment except for one patient with an altered strain type. H. pylori infections were generally associated with several subpopulations of strains, evident from the subtypic variation before and after treatment, detectable by both DNA fingerprinting methods. The urease gene patterns also provided evidence that some cultures of H. pylori probably contained a mixture of genomic subtypes. The study suggests that triple therapy has the effect either of inducing minor genomic variations or of changing the proportions of different subtypes of H. pylori. It was concluded that urease gene profiling provides a simple yet reliable method of establishing whether treatment failures are attributable to incomplete eradication of H. pylori.

Ribotyping patterns and emergence of metronidazole resistance in paired clinical samples of Helicobacter pylori

Metronidazole-susceptible pretreatment isolates and metronidazole-resistant posttreatment isolates of Helicobacter pylori from 11 patients before and after unsuccessful triple therapy consisting of metronidazole, amoxicillin, and colloidal bismuth subcitrate were studied. Ribotyping (rRNA gene restriction pattern analysis) of the isolates demonstrated that all patients except one had identical digest patterns for pre- and posttreatment isolates.

Resistance to the nitroheterocyclic drugs

The nitroheterocyclic drugs have been available since the early 1960's for the treatment of anaerobic protozoa. The application of these drugs has widened since then and they are presently used to treat anaerobic pathogenic bacteria and protozoa. The activity of the nitroheterocyclic drugs depends on the all-important nitro group attached to the imidazole or furan ring. Although the nitro radicals, generated by reduction of the parent drugs, are similar for both families of nitroheterocyclics, the nitroimidazoles and the nitrofurans, the electron potential of each is different and thus the mechanism of action depends on different pathways. The nitroimidazoles depend on reduction by ferredoxin or flavodoxin. The nitrofurans require nitroreductase activity, but the natural substrate of these enzymes has not been identified. Increased use of nitroheterocyclic drugs, in response to drug resistance to other commonly used antibiotics, has in turn resulted in drug resistance to a number of nitroheterocyclic drugs. Bacteroides strains and other bacteria, including Helicobacter, have developed resistance. Among the protozoa, Trichomonas has developed resistance to metronidazole via a number of mechanisms, especially a decrease in drug reduction, as a result of alterations in the electron transport pathways. Resistance to both types of nitroheterocyclic drugs has been reported in Giardia. Although resistance to these drugs is not widespread, their increased use world-wide as a prophylaxis and in chemotherapy will inevitably result in increased resistance in organisms commonly found in asymptomatic infections, including Trichomonas, Giardia and Entamoeba. However, the variety of substitutions which can be attached to the ring structures has led to a great variety of drugs being synthesised, some of which are many-fold more active than the commonly prescribed nitroheterocyclics. With careful administration of currently available drugs and continued interest in synthesising more active compounds, we can optimistically expect to have useful nitroheterocyclic drugs available for some time.

The coccoid forms of Helicobacter pylori. Criteria for their viability

The fact that Helicobacter pylori can revert to a coccoid form has stimulated speculation about its role in transmission and as a possible cause of reinfection in duodenal ulcer disease. Bismuth subcitrate (32 micrograms/ml), bismuth subsalicylate (64 micrograms/ml), amoxicillin (0.05 micrograms/ml) and erythromycin (4 micrograms/ml) inhibited the growth of H. pylori and stimulated the formation of basically respiring but non-culturable coccoid structures. The presence of polyphosphates as energy and phosphorus source permits a certain level of endogenous metabolism to preserve RNA and DNA, as well as structural components like cell wall, cell membrane and cytoplasma for at least 3 months. However, the applied standard laboratory methods were insufficient for regrowth of H. pylori out of the coccoid form.

Differentiation between isolates of Helicobacter pylori by PCR-RFLP analysis of urease A and B genes and comparison with ribosomal RNA gene patterns

Genetic diversity amongst 21 human gastric isolates of Helicobacter pylori was investigated by polymerase chain reaction amplification and HaeIII digest (restriction fragment length polymorphism) analysis of an internal 2.4-kb segment of the urease A and urease B genes. H. pylori from 11 independent individuals yielded nine distinct restriction fragment patterns but only one pattern was common to H. pylori from two individuals. By contrast, multiple isolate sets of H. pylori from two patients each had common urease gene patterns. Most strains with the same urease gene patterns were distinguishable in their ribosomal RNA gene patterns. The study demonstrated diversity amongst H. pylori and established that PCR analysis of urease genes provided a novel method of identifying isolates. The profiles were reproducible and convenient to obtain and analyse, and were almost as discriminatory as HaeIII ribopatterns.

Comparisons between degree of histological gastritis and DNA fingerprints, cytotoxicity and adhesivity of Helicobacter pylori from different gastric sites

Thirty-six isolates of H. pylori from up to three gastric biopsy sites (antrum, corpus and fundus) from 13 patients in Italy with different degrees of histological gastritis were investigated. All strains were tested for motility, cytotoxicity and degree of adhesion, and were typed by analysis of ribosomal RNA gene patterns (ribopatterns). Seventeen different DNA types (ribotypes) were identified, with each patient possessing H. pylori of one or more unique types. Only two patients had identical H. pylori at three sites. Most patients had H. pylori with different ribotypes or subtypes, but nine strains were not typable. Five patients had the same strain colonizing two of the three sites and atypical strains were mostly from the antrum. A complex pattern of H. pylori colonization in the stomach of some individuals was evident and suggested multiple sources of infection. No consistent associations were detected between degree of gastritis and adherence, cytotoxicity and motility but a 2.56Kb rRNA gene fragment that had a higher frequency in strains associated with severe gastritis than mild gastritis, may provide a useful molecular marker for future pathogenicity studies.