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

Impact of mixed-infection rate of clarithromycin-susceptible and clarithromycin-resistant Helicobacter pylori strains on the success rate of clarithromycin-based eradication treatment

BACKGROUND

Clarithromycin (CAM) resistance is a major contributor to the failure to eradicate Helicobacter pylori (H. pylori). The mixed-infection ratio of CAM-susceptible and CAM-resistant H. pylori strains differs among individuals. Pyrosequencing analysis can be used to quantify gene mutations at position each 2142 and 2143 of the H. pylori 23S rRNA gene in intragastric fluid samples. Herein, we aimed to clarify the impact of the rate of mixed infection with CAM-susceptible and CAM-resistant H. pylori strains on the success rate of CAM-containing eradication therapy.

MATERIALS AND METHODS

Sixty-four H. pylori-positive participants who received CAM-based eradication therapy, also comprising vonoprazan and amoxicillin, were enrolled in this prospective cohort study. Biopsy and intragastric fluid samples were collected during esophagogastroduodenoscopy. H. pylori culture and CAM-susceptibility tests were performed on the biopsy samples, and real-time PCR and pyrosequencing analyses were performed on the intragastric fluid samples. The mutation rates and eradication success rates were compared.

RESULTS

The overall CAM-based eradication success rate was 84% (54/64): 62% (13/21) for CAM-resistant strains, and 95% (39/41) for CAM-sensitive strains. When the mutation rate of the 23S rRNA gene was 20% or lower for both positions (2142 and 2143), the eradication success rate was 90% or more. However, when the mutation rate was 20% or higher, the eradication success rate was lower (60%).

CONCLUSIONS

The mutation rate of the CAM-resistance gene was related to the success of eradication therapy, as determined via pyrosequencing analysis.

High prevalence of Helicobacter pylori mixed infections identified by multilocus sequence typing in Ningbo, China

This study used multilocus sequence typing (MLST) to investigate the prevalence of Helicobacter pylori (H. pylori) mixed infections and H. pylori mixed infections involving unrelated strains; and determined the phylogeographic groups of H. pylori recovered from patients in Ningbo, China. A total of 156 H. pylori isolates were obtained from a convenience sample of 33 patients with culture-positive H. pylori infection. MLST was used to classify 150 H. pylori clinical isolates and 12 methodological control strains (6 clinical isolates and 6 strains of American Type Culture Collection H. pylori) into 43 and 12 sequence types (STs), respectively. In this study, 246 new alleles and 53 new STs were identified by MLST. The prevalence of mixed infections was 41% (11/27). The prevalence of H. pylori mixed infections involving unrelated strains was 46% (5/11) and the prevalence of H. pylori mixed infections involving completely unrelated strains (strains with all 7 housekeeping genes different) was 36% (4/11). A phylogenetic tree was created to determine the evolutionary relationships between different strains. The STs in this study were clustered within the hspEAsia subgroup (98%) and hpEurope group (2%). H. pylori mixed infections were common in Ningbo, China. The H. pylori isolates belonging to the hpEurope group were recovered from three different biopsy samples in a native Chinese patient. Most of H. pylori strains colonizing the antrum, corpus, and duodenum bulb were homologous.

Heterogeneity of Helicobacter pylori Strains Isolated from Patients with Gastric Disorders in Guiyang, China

Purpose

Chronic Helicobacter pylori infection causes peptic ulcers in a subpopulation of individuals and is a risk factor for the development of gastric cancer. Multiple infections and heteroresistant H. pylori contribute to poor treatment efficacy. Here, we investigated the extent of genetic diversity among H. pylori strains within a given host and its influence on the results of antibiotic (metronidazole, levofloxacin, clarithromycin, amoxicillin, and tetracycline) susceptibility testing.

Materials and Methods

Gastric mucosa biopsy samples were obtained from patients with gastric disorders, including 48 H. pylori positive patients, who were never previously treated for H. pylori infection. Five potential H. pylori colonies isolated from each sample were subcultured for enrichment. Enriched H. pylori colonies were identified through Gram staining and assays for urease, oxidase, and catalase. For each H. pylori monoclonal colony, the antibiotic susceptibility was assessed, genomic DNA was sequenced, and the cytotoxin-associated gene A (cagA) genotype was verified. Co-infection with multiple H. pylori strains was determined using random amplified polymorphic DNA (RAPD)-polymerase chain reaction (PCR).

Results

Thirteen gastric mucosa biopsy samples were positive for H. pylori. Five monoclonal strains isolated from each of these 13 patients were identified as H. pylori. RAPD-PCR indicated that intra-patient monoclonal strains of H. pylori in 10 of the 13 samples exhibited heterogeneity. Among the 13 patients, intra-patient monoclonal strains isolated from 4 patients had identical cagA genotype, whereas intra-patient monoclonal strains isolated from the other 9 patients harbored more than one cagA genotype. The antibiotic susceptibility of five intra-patient monoclonal strains from seven patients was inconsistent.

Conclusion

The existence of heterogeneous H. pylori strains with resistance to different drugs and virulence were common within the gastric mucosa of an individual patient.

Differential Helicobacter pylori Plasticity in the Gastric Niche of Subjects at Increased Gastric Cancer Risk

Helicobacter pylori (H. pylori) represents an independent risk factor for Gastric Cancer (GC). First Degree Relatives (FDR) of GC subjects and Autoimmune Gastritis (AG) patients are both at increased risk for GC. H. pylori genetic heterogeneity within the gastric niche of FDR and AG individuals has been little explored. To understand whether they exploit an increased H. pylori stability and virulence, 14 AG, 25 FDR, 39 GC and 13 dyspeptic patients (D) were investigated by a cultural PCR-based approach characterizing single colonies-forming-units. We chose three loci within the Cytotoxin-associated gene-A Pathogenicity Island (CagPAI) (cagA,cagE,virB11), vacA, homA and homB as markers of virulence with reported association to GC. Inflammatory/precancerous lesions were staged according to Sydney System. When compared to D, FDR, similarly to GC patients, were associated to higher atrophy (OR = 6.29; 95% CI:1.23-31.96 in FDR; OR = 7.50; 95% CI:1.67-33.72 in GC) and a lower frequency of mixed infections (OR = 0.16; 95% CI:0.03-0.81 in FDR; OR = 0.10; 95% CI:0.02-0.48 in GC). FDR presented also an increased neutrophil infiltration (OR = 7.19; 95% CI:1.16-44.65). Both FDR and GC carried a higher proportion of CagPAI⁺vacAs1i1mx⁺homB⁺ profiles (OR = 2.71; 95% CI: 1.66-4.41 and OR = 3.43; 95% CI: 2.16-5.44, respectively). Conversely, AG patients presented a lower frequency of subtypes carrying a stable CagPAI and vacAs1i1mx. These results underline different H. pylori plasticity in FDR and AG individuals, and thus, a different host-bacterium interaction capacity that should be considered in the context of eradication therapies.

Mixed Infections of Helicobacter pylori Isolated from Patients with Gastrointestinal Diseases in Taiwan

Background. Persistent Helicobacter pylori infection may induce several upper gastrointestinal diseases. Two major virulence factors of H. pylori, vacuolating cytotoxin A (VacA) and cytotoxin-associated gene A (CagA), are thought to be associated with the severity of disease progression. The distribution of vacA and cag-pathogenicity island (cag-PAI) alleles varies in H. pylori isolated from patients in different geographic regions. Aim. To assess the association between mixed infection of H. pylori clinical isolates from Taiwanese patients and the severity of gastrointestinal diseases. Methods. A total of 70 patients were enrolled in this study. Six distinct and well-separated colonies were isolated from each patient and 420 colonies were analyzed to determine the genotypes of virulence genes. Results. The prevalence of mixed infections of all H. pylori-infected patients was 28.6% (20/70). The rate of mixed infections in patients with duodenal ulcer (47.6%) was much higher than that with other gastrointestinal diseases (P < 0.05). Conclusions. H. pylori mixed infections show high genetic diversity that may enhance bacterial adaptation to the hostile environment of the stomach and contribute to disease development.

Helicobacter pylori vacA Genotypes in Chronic Gastritis and Gastric Carcinoma Patients from Macau, China

Helicobacter pylori is the major triggering factor for gastric carcinoma, but only a small proportion of infected patients develop this disease. Differences in virulence observed among H. pylori strains, namely in the vacuolating cytotoxin vacA gene, may contribute to this discrepancy. Infection with vacA s1, i1 and m1 strains increases the risk for progression of gastric premalignant lesions and for gastric carcinoma. However, in East Asian countries most of the H. pylori strains are vacA s1, regardless of the patients’ clinical status, and the significance of the vacA i1 and m1 genotypes for gastric carcinoma in this geographic area remains to be fully elucidated. The aim of the present study was to investigate this relationship in 290 patients from Macau, China. Using very sensitive and accurate genotyping methods, we detected infection with vacA i1 and with vacA m1 strains in, respectively, 85.2% and 52.6% of the patients that were infected with single genotypes. The prevalence of cagA-positive strains was 87.5%. No significant associations were observed between vacA genotypes or cagA and gastric carcinoma. It is worth noting that 37.5% of the infected patients had coexistence of H. pylori strains with different vacA genotypes. Additional studies directed to other H. pylori virulence factors should be performed to identify high risk patients in East Asia.

Genotype Diversity and Quasispecies Development of Helicobacter pylori in a Single Host

Infection with different strains of Helocobacter pylori and emergence of new genomic variants during their long-term gastric colonization are assumed to be the main reasons for eradication failure. We used genotyping and arbitrarily primed PCR fingerprinting (RAPD) to detect relatedness and genetic variations among H. pylori single isolates from each patient in Iran. Multiplex-PCR amplification of gene alleles encoding the virulence factors vacA (m/s), cagA, and iceA (A1/A2) and comparison of RAPD patterns of different singles colonies were performed for each individual patient's isolate. Results showed a high frequency of diversity among the H. pylori strains. Nearly 23% of infected patients showed a single type infection. The infection types related, unrelated, and related/unrelated were found among 25.6%, 12.8%, and 38.5% of patients, respectively. Both mixed type infections (77%) and quasispecies development (15.4%) were detected in these patients. Genotype conversion among vacA (41.6%), cagA (41.6%), and iceA (50%) alleles was observed for the strains with identical or related RAPD patterns. Coevolution of different alleles was also detected in a patient infected with strains presenting the same RAPD patterns. Collectively, results of this study revealed the occurrence of quasispecies development, mixed type infections, and changes in virulence properties of H. pylori strains among the studied patients.

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.

[Clinical Usefulness of Antimicrobial Susceptibility Test for Helicobacter pylori.]

BACKGROUND

Antimicrobial resistance of Helicobacter pylori is considered as the main cause of failure of eradication therapy. Because resistance to metronidazole has been reported in 25.8% to 66.2% of H. pylori, a combination of proton pump inhibitors (PPI), amoxicillin, and clarithromycin is currently recommended as a primary therapy. We investigated the prevalence of antimicrobial resistance to the primary drugs and the impact of antimicrobial resistance on eradication rates.

METHODS

Between May and August 2005, H. pylori isolates from 93 patients were tested for antimicrobial susceptibility at Asan Medical Center. Susceptibility tests of clarithromycin and amoxicillin were performed by the disk diffusion method and those of metronidazole and tetracycline by Etest (AB Biodisk, Solna, Sweden). The medical records of the patients were reviewed to collect the data such as demographic findings, previous and current eradication therapies, and bacteriological outcome. The appropriate therapy was defined as three-drug-combination including susceptible drugs only, or four-drug-combination including metronidazole in the case of metronidazole-resistance.

RESULTS

Resistance rates to clarithromycin and metronidazole were 17.2% and 33.3%, respectively, but there was no resistance to tetracycline and amoxicillin. The eradication was successful in 32 of the 36 patients (88.9%) who received the appropriate therapy, but none of 4 patients who received an inappropriate therapy (P<0.01).

CONCLUSIONS

Resistance to clarithromycin seemed to increase and contribute to the failure of eradication therapy. For the appropriate therapy of H. pylori infection, the susceptibility results should be reported before initiation of the eradication therapy.

Aqueous and organic solvent-extracts of selected south African medicinal plants possess antimicrobial activity against drug-resistant strains of Helicobacter pylori: inhibitory and bactericidal potential

The aim of this study was to identify sources of cheap starting materials for the synthesis of new drugs against Helicobacter pylori. Solvent-extracts of selected medicinal plants; Combretum molle, Sclerocarya birrea, Garcinia kola, Alepidea amatymbica and a single Strychnos species were investigated against 30 clinical strains of H. pylori alongside a reference control strain (NCTC 11638) using standard microbiological techniques. Metronidazole and amoxicillin were included in these experiments as positive control antibiotics. All the plants demonstrated anti-H. pylori activity with zone diameters of inhibition between 0 and 38 mm and 50% minimum inhibitory concentration (MIC₅₀) values ranging from 0.06 to 5.0 mg/mL. MIC₅₀ values for amoxicillin and metronidazole ranged from 0.001 to 0.63 mg/mL and 0.004 to 5.0 mg/mL respectively. The acetone extracts of C. molle and S. birrea exhibited a remarkable bactericidal activity against H. pylori killing more than 50% of the strains within 18 h at 4× MIC and complete elimination of the organisms within 24 h. Their antimicrobial activity was comparable to the control antibiotics. However, the activity of the ethanol extract of G. kola was lower than amoxicillin (P < 0.05) as opposed to metronidazole (P > 0.05). These results demonstrate that S. birrea, C. molle and G. kola may represent good sources of compounds with anti-H. pylori activity.

Resistance to antibiotics and characterization of Helicobacter pylori strains isolated from antrum and body from adults in Mexico

BACKGROUND AND AIMS

Resistance to antibiotics is common in patients with Helicobacter pylori infection in more than one anatomic stomach site. We assessed whether the antibiotic resistance varies according to virulence factors of the bacteria as well as to the age and gender of individuals infected in two anatomic sites.

METHODS

H. pylori strains were isolated from an antral and corpus biopsy from 90 patients with gastric ambulatory who had not received any previous therapy. Susceptibility to metronidazole and clarithromycin was assessed by E-test, and vacA and cagA genotypes were determined by polymerase chain reaction.

RESULTS

Dual resistance to metronidazole and clarithromycin was 3.3% in antrum and 4.4% in the corpus; heteroresistance was 19% and 5.5% for metronidazole and clarithromycin, respectively. Clarithromycin resistance significantly increased with age. Women showed a twofold increased risk for metronidazole-resistant strains in antrum (odds ratio = 2.85, 95% confidence interval 1.09 to 7.42). Virulence factors were not associated with antimicrobial resistance.

CONCLUSION

Prevalence of resistance to clarithromycin may be increasing in this country. Antimicrobial susceptibility tests from different biopsy sites deserve attention.

Analysis of antibiotic susceptibility patterns of Helicobacter pylori isolates from Malaysia

BACKGROUND

The prevalence of antibiotic resistance varies in geographic areas. The information on the antibiotic susceptibility patterns of Helicobacter pylori (H. pylori) in our local setting is therefore relevant as a guide for the treatment options.

OBJECTIVE

This study was conducted to determine the primary resistance rates among H. pylori isolated from Malaysian patients.

MATERIALS AND METHODS

Biopsy samples were obtained from the stomach antrum and corpus of 777 patients from September 2004 until 2007. H. pylori isolated from these patients were then subjected to minimum inhibitory concentration (MICs) determination using E-test method, against metronidazole, clarithromycin, levofloxacin, ciprofloxacin, amoxicillin, and tetracycline.

RESULTS

From 777 patients, 119 were positive for H. pylori where a total of 187 strains were isolated. The resistance rates were noted to be 37.4% (metronidazole), 2.1% (clarithromycin), 1% (levofloxacin and ciprofloxacin), and 0% (amoxicillin and tetracycline). Different resistance profiles were observed among isolates from the antrum and corpus of 13 patients. Resistance to one type of antibiotic was observed in 36.4% of the strains where mono-resistance to metronidazole was the most common. Resistance to ≥2 antibiotics was noted in 3.3% of isolates. High metronidazole MICs of ≥256 μg/mL were observed among the resistant strains.

CONCLUSIONS

The resistance rates of the antibiotics used in primary treatment of H. pylori infections in Malaysia are low, and multi-antibiotic-resistant strains are uncommon. Infections with mixed populations of metronidazole-sensitive and -resistant strains were also observed. However, the high metronidazole MIC values seen among the metronidazole-resistant strains are a cause for concern.

Transmission pathway of Helicobacter pylori: does food play a role in rural and urban areas?

Helicobacter pylori is a Gram-negative microaerophilic bacterium that has colonized the human gastric mucosa. This infection is very common and affects more than half of the human population. The prevalence is however unbalanced between rural developing areas (more than 80%) and urban developed areas (less than 40%). H. pylori is responsible for several pathologies, such as gastritis, peptic ulcer and gastric cancer but its transmission pathway is still not clear. The risk factors for H. pylori infection include poor social and economic development; poor hygienic practices; absence of hygienic drinking water; and unsanitary prepared food. There is evidence supporting a gastro-oral, oral-oral and faecal-oral transmission, but no predominant mechanism of transmission has been yet identified. Transmission may occur in a vertical mode (e.g. from parents to child) or in a horizontal mode (across individuals or from environmental contamination). In either case, the involvement of water and food cannot be excluded as vehicles or sources of infection. Indirect evidence of presence of H. pylori in water and food, namely the detection of its DNA and survival studies after artificial contamination of food and water has been described. This paper reviews data both favourable and against the role of water and food in the transmission of H. pylori, exploring their role as a potential transmission vehicle for person-to-person and food-chain transmission. The likelihood of the transmission pathway in developing rural and developed urban areas appears to be different. In developed areas, person-to-person transmission within families appears to be dominant, while in the rural developing areas the transmission pathway appears to be more complex. In this later case, the transmission by contaminated food, water, or via intensive contact between infants and non-parental caretakers may have a greater influence than within-family transmission.

Mixed infections of Helicobacter pylori: tissue tropism and histological significance

Mixed infections with Helicobacter pylori facilitate interstrain gene transfer and the maintenance of genetic diversity for adaptation to the gastric environment, but whether mixed infections with histological significance and tissue tropism occur in the human stomach is still unclear. Helicobacter pylori was isolated from the antrum and the corpus of 30 dyspeptic patients. Four to eight colonies were randomly collected from each site. The genetic diversity of each isolate was evaluated by comparing random amplified polymorphic DNA banding patterns. The prevalence of mixed infections was 23.3% (7/30), and different dominant strains were isolated from the antrum and the corpus specimens. In the 23 patients infected with a single strain, the acute inflammation (AI) score, chronic inflammation (CI) score, atrophy (AT) score and lymphoid follicle (LF) score of the antrum were usually higher than those of the corpus (p <or=0.002). However, in the seven patients with mixed infections, the CI, H. pylori density (HPD), AT and LF scores of the antrum and the corpus were similar (p >0.05). Moreover, the patients with mixed infections had marginally higher CI and HPD scores than those with single-strain infection (p 0.062 and p 0.095, respectively) in the corpus and had a significantly higher rate of appearance of intestinal metaplasia (IM) in the antrum (p 0.005). These data show that H. pylori tissue tropism was found in the human stomach, and suggest that mixed infections could change the histological features in the antrum and in the corpus, and that they could be associated with the appearance of IM in the antrum.

Lipopolysaccharide diversity evolving in Helicobacter pylori communities through genetic modifications in fucosyltransferases

Helicobacter pylori persistently colonizes the gastric mucosa of half the human population. It is one of the most genetically diverse bacterial organisms and subvariants are continuously emerging within an H. pylori population. In this study we characterized a number of single-colony isolates from H. pylori communities in various environmental settings, namely persistent human gastric infection, in vitro bacterial subcultures on agar medium, and experimental in vivo infection in mice. The lipopolysaccharide (LPS) O-antigen chain revealed considerable phenotypic diversity between individual cells in the studied bacterial communities, as demonstrated by size variable O-antigen chains and different levels of Lewis glycosylation. Absence of high-molecular-weight O-antigen chains was notable in a number of experimentally passaged isolates in vitro and in vivo. This phenotype was not evident in bacteria obtained from a human gastric biopsy, where all cells expressed high-molecular-weight O-antigen chains, which thus may be the preferred phenotype for H. pylori colonizing human gastric mucosa. Genotypic variability was monitored in the two genes encoding α1,3-fucosyltransferases, futA and futB, that are involved in Lewis antigen expression. Genetic modifications that could be attributable to recombination events within and between the two genes were commonly detected and created a diversity, which together with phase variation, contributed to divergent LPS expression. Our data suggest that the surrounding environment imposes a selective pressure on H. pylori to express certain LPS phenotypes. Thus, the milieu in a host will select for bacterial variants with particular characteristics that facilitate adaptation and survival in the gastric mucosa of that individual, and will shape the bacterial community structure.

A novel noninvasive genotyping method of Helicobacter pylori using stool specimens

BACKGROUND & AIMS

The source(s) of the infection and the route(s) of transmission of Helicobacter pylori have not yet been clarified. This is to introduce a noninvasive protocol allowing molecular typing of H pylori using stool specimens.

METHODS

The genotyping method is based on 2 H pylori-specific biprobe real-time polymerase chain reaction assays using fragments of the glmM and the recA genes as target sequences. Discrimination between strains results from differences in the melting temperature during melting curve analysis. In case of identical melting temperatures in both assays, sequence analysis of the glmM amplicon was performed to confirm strain identity. The method was validated using gastric biopsy specimens and stool specimens of 97 unrelated individuals suffering from abdominal pain and stool specimens of members of 10 families in Austria (infected index child and family members) and 8 African households.

RESULTS

Of the 97 patients, 27 were infected as shown by culture, histology, and rapid urease test. The sensitivity of each of the assays was 100% in gastric biopsy specimens and 92.2% in stool specimens; the specificity was 100%. The discriminatory capacity of the method was 100%. Clonal identities were found in 9 of 10 (90%) European and 7 of 8 (87.5%) African households. In 2 African households, 2 different clonal lineages each were found.

CONCLUSIONS

The genotyping protocol introduced allows for both accurate detection and discrimination of H pylori strains in stool samples. Large-scale studies using this protocol may contribute to the clarification of the transmission pathways of infection with H pylori.

Detection of mixed clarithromycin-resistant and -susceptible Helicobacter pylori using nested PCR and direct sequencing of DNA extracted from faeces

The major cause of chemotherapy failure in patients with chronic gastritis and peptic ulcers caused by Helicobacter pylori is clarithromycin (CAM) resistance due to a mutation in the 23S rRNA gene. This study describes a non-invasive and accurate method for the detection of mixed CAM-resistant and -susceptible H. pylori by sequencing of the H. pylori 23S rRNA gene. Faeces were crushed with beads and the 23S rRNA gene was amplified using a nested PCR on the extracted DNA. Mutation analysis of this gene using this method showed that 20.4 % of patients carried mixed CAM-susceptible (wild type) and -resistant (A2142G or A2143G mutant) H. pylori. Furthermore, it was found that 66.6 % of patients who had been treated unsuccessfully carried one of these mutations in the 23S rRNA gene (including the mixed type), whilst standard culture detected CAM-resistant isolates in only 22.2 % of patients with unsuccessful treatment. These data suggest that, for successful therapy, the diagnosis method described here would more accurately detect CAM-resistant H. pylori, including mixed infections.

Genomic methylation: a tool for typing Helicobacter pylori isolates

The genome sequences of three Helicobacter pylori strains revealed an abundant number of putative restriction and modification (R-M) systems within a small genome (1.60 to 1.67 Mb). Each R-M system includes an endonuclease that cleaves a specific DNA sequence and a DNA methyltransferase that methylates either adenosine or cytosine within the same DNA sequence. These are believed to be a defense mechanism, protecting bacteria from foreign DNA. They have been classified as selfish genetic elements; in some instances it has been shown that they are not easily lost from their host cell. Possibly because of this phenomenon, the H. pylori genome is very rich in R-M systems, with considerable variation in potential recognition sequences. For this reason the protective aspect of the methyltransferase gene has been proposed as a tool for typing H. pylori isolates. We studied the expression of H. pylori methyltransferases by digesting the genomic DNAs of 50 strains with 31 restriction endonucleases. We conclude that methyltransferase diversity is sufficiently high to enable the use of the genomic methylation status as a typing tool. The stability of methyltransferase expression was assessed by comparing the methylation status of genomic DNAs from strains that were isolated either from the same patient at different times or from different stomach locations (antrum and corpus). We found a group of five methyltransferases common to all tested strains. These five may be characteristic of the genetic pool analyzed, and their biological role may be important in the host/bacterium interaction.

Genetic analysis of Helicobacter pylori strain populations colonizing the stomach at different times postinfection

Genetic diversity of the human gastric pathogen Helicobacter pylori in an individual host has been observed; whether this diversity represents diversification of a founding strain or a mixed infection with distinct strain populations is not clear. To examine this issue, we analyzed multiple single-colony isolates from two to four separate stomach biopsies of eight adult and four pediatric patients from a high-incidence Mexican population. Eleven of the 12 patients contained isolates with identical random amplified polymorphic DNA, amplified fragment length polymorphism, and vacA allele molecular footprints, whereas a single adult patient had two distinct profiles. Comparative genomic hybridization using whole-genome microarrays (array CGH) revealed variation in 24 to 67 genes in isolates from patients with similar molecular footprints. The one patient with distinct profiles contained two strain populations differing at 113 gene loci, including the cag pathogenicity island virulence genes. The two strain populations in this single host had different spatial distributions in the stomach and exhibited very limited genetic exchange. The total genetic divergence and pairwise genetic divergence between isolates from adults and isolates from children were not statistically different. We also analyzed isolates obtained 15 and 90 days after experimental infection of humans and found no evidence of genetic divergence, indicating that transmission to a new host does not induce rapid genetic changes in the bacterial population in the human stomach. Our data suggest that humans are infected with a population of closely related strains that vary at a small number of gene loci, that this population of strains may already be present when an infection is acquired, and that even during superinfection genetic exchange among distinct strains is rare.

Analysis of genetic variability, antimicrobial susceptibility and virulence markers in Helicobacter pylori identified in Central Italy

OBJECTIVE

To assess the relationship between the presence of mixed infection of Helicobacter pylori and both antimicrobial susceptibility and virulence markers.

MATERIAL AND METHODS

Thirty-six patients with H. pylori infection were included in the study. Three colonies were selected from each positive biopsy sample collected from each host for a total of 108 H. pylori strains. The genetic variability was evaluated through the amplified fragment length polymorphism (AFLP) analysis; the antibiotic susceptibility to amoxicillin, clarithromycin, moxifloxacin, rifabutin and tinidazole was determined using the minimum inhibitory concentrations (MICs) with the agar dilution method. Moreover, the vacA, cagA, iceA and babA2 statuse were detected by polymerase chain reaction (PCR).

RESULTS

There was a strong connection between mixed H. pylori infection and antimicrobial resistance. In particular, H. pylori strains with genetic variability, in the same host, expressed more resistance to clarithromycin, moxifloxacin and tinidazole than that expressed in strains with a unique genetic host pattern. VacA s1m1/s1m2 genotypes were found in 70% of strains isolated in mixed infection, whereas the same allelic combinations were found in 42% of strains, isolated in single infection. The cagA(+) status prevailed both in patients with mixed (97%) and in those with single infection (85%) without significant differences. The iceA1 status was more commonly found in patients with mixed infection, whereas the babA2 status was significantly prevalent in single H. pylori infection.

CONCLUSIONS

Mixed H. pylori infection harbouring in one patient is significantly related to strains that are more resistant to antibiotics and with a more virulent genotype (vacA s1m1/s1m2, cagA, iceA1) than strains responsible for single infection.

An enzymatic ruler modulates Lewis antigen glycosylation of Helicobacter pylori LPS during persistent infection

Helicobacter pylori persistently colonizes about half the human population and contributes to the development of peptic ulcer disease and gastric cancer. This organism has evolved means to structurally alter its surface characteristics to evade innate and adaptive immune responses. H. pylori produces LPS O-antigen units that can be posttranslationally fucosylated to generate Lewis antigens, structures also found on human epithelial cells. We demonstrate an extensive diversity of Lewis x and Lewis y expression in LPS O-antigen units, occurring over time and in different regions of the human stomach. Lewis expression patterns were correlated with the on/off status of the three fucosyltransferases (FucT), FutA, FutB, and FutC, which are regulated via slipped-strand mispairing in intragenic polyC tract regions of the corresponding genes. The alpha1,3-FucT, FutA and FutB, each contain a C-terminal heptad repeat region, consisting of a variable number of DD/NLRV/INY tandem repeats. Variations in the number of heptad repeats correlated to the sizes of O-antigen polymers to become decorated by fucose residues. Our data support a molecular ruler mechanism for how H. pylori varies its LPS fucosylation pattern, where one heptad repeat in the enzyme corresponds to one N-acetyl-beta-lactosamine unit in the O-antigen polysaccharide.

Detection of non-pylori Helicobacter species in "Helicobacter heilmannii"-infected humans

BACKGROUND

A small proportion of patients suffering from chronic active gastritis are diagnosed with gastric Helicobacter species other than Helicobacter pylori. Circumstantial evidence has suggested that these bacteria, also referred to as "Helicobacter heilmannii"-like organisms (HHLO), may be transmitted through animals. The isolation of a Helicobacter bizzozeronii strain from a human patient confirmed this hypothesis. It was the aim of the present study to assess the presence of animal Helicobacter species and H. pylori in humans infected with HHLO, as diagnosed by histology.

METHODS

Paraffin-embedded gastric biopsy specimens of 108 HHLO-infected patients (42 women and 66 men) from three clinical centers were screened for the presence of animal gastric Helicobacter species by polymerase chain reaction (PCR), using assays targeting the 16S rDNA region of the three known canine and feline helicobacters (H. bizzozeronii, H. salomonis and H. felis), "Candidatus H. suis", and "Candidatus H. bovis". In addition, the presence of H. pylori was evaluated by multiplex PCR analysis.

RESULTS

In 63.4% of the stomachs (64/101) classification of the Helicobacter infection into the above mentioned groups was achieved. Non-pylori Helicobacter species commonly colonizing the stomachs of cats and dogs were found in 48.5% (49/101) of the patients. Fourteen (13.9%) samples tested positive for "Candidatus H. suis", and "Candidatus H. bovis" was demonstrated in 1 (0.9%) patient. The presence of H. pylori was established in 13 patients (12.9%). Eleven stomachs (10.9%) were infected with at least two different Helicobacter species.

CONCLUSIONS

This study identifies animal Helicobacter species in the stomach of a large series of HHLO-infected patients, which may have clinical implications in a subset of patients with gastric disease.

Susceptibilities to clarithromycin, amoxycillin and metronidazole of Helicobacter pylori isolates from the antrum and corpus in Tokyo, Japan, 1995-2001

The aim of this study was to determine the susceptibilities to clarithromycin, amoxycillin and metronidazole of Helicobacter pylori isolates from the antrum and corpus of Japanese patients examined during the period 1995-2001. There was an increase, from 6.2% in 1995 to 22.1% in 2000-2001, in the proportion of patients infected with clarithromycin-resistant H. pylori. Of patients infected with clarithromycin-resistant H. pylori, 39.1% were infected with both clarithromycin-susceptible and -resistant H. pylori. Furthermore, the MIC90 of clarithromycin for H. pylori rose from < 1 mg/L in 1995-1998 to 8 mg/L in 1999. In contrast, the MIC90s of amoxycillin and metronidazole were < or = 0.125 and 4 mg/L, respectively, throughout the study period. The results showed that, while most H. pylori isolates were susceptible to amoxycillin and metronidazole, resistance to clarithromycin among H. pylori isolates increased markedly in Japan during 1995-2001. The results also indicated a need to test the susceptibility of H. pylori isolates from more than two samples obtained from two different sites in the stomach of a single patient in order to diagnose the presence of clarithromycin-resistant H. pylori correctly.

Clinical evaluation of four one-week triple therapy regimens in eradicating Helicobacter pylori infection

AIM: To evaluate clinical efficacy of four one-week triple therapies in eradicating Helicobacter pylori infection.

METHODS: In this clinical trial, 132 patients with duodenal ulcer and chronic gastritis were randomly divided into four groups, and received treatment with OAC (omeprazole 20 mg + amoxicillin 1000 mg + clarithromycin 250 mg), OFC (omeprazole 20 mg + furazolidone 100 mg + clarithromycin 250 mg), OFA (omeprazole 20 mg + furazolidone 100 mg + amoxicillin 1000 mg) and OMC (omeprazole 20 mg + metronidazole 200 mg + clarithromycin 250 mg), respectively. Each drug was taken twice daily for one week. The ¹³C urea breath test was carried out 4-8 weeks after treatment to determine the success of H pylori eradication.

RESULTS: A total of 127 patients completed the treatment. The eradication rate for H pylori infection was 90.3%, 90.9%, 70.9% and 65.6%, respectively in OAC, OFC OMC and OFA groups.

CONCLUSION: A high eradication rate can be achieved with one-week OAC or OFC triple therapy. Thus, one-week triple therapies with OAC and OFC are recommended for Chinese patients with duodenal ulcers and chronic gastritis.

Concordance of Helicobacter pylori strains within families

Helicobacter pylori infection is typically acquired in early childhood, and a predominantly intrafamilial transmission has been postulated. To what extent family members share the same strains is poorly documented. Our aim was to explore patterns of shared strains within families by using molecular typing. Family members of H. pylori-infected 10- to 12-year-old index children identified in a school survey were invited to undergo gastroscopy. Bacterial isolates were typed with random amplified polymorphic DNA and PCR-restriction fragment length polymorphism of the genes ureA-B, glmM, or flaA. The presence or absence of the cag pathogenicity island, a bacterial virulence factor, was determined by PCR. GelCompar II software, supplemented with visual inspection, was used in the cluster analysis. In 39 families, 104 individuals contributed 208 bacterial isolates from the antrum and corpus. A large proportion, 29 of 36 (81%) of the offspring in a sibship, harbored the same strain as at least one sibling. Mother-offspring strain concordance was detected in 10 of 18 (56%) of the families. Of 17 investigated father-offspring relations in eight families, none were strain concordant. Spouses were infected with the same strains in 5 of 23 (22%) of the couples. Different strains in the antrum and corpus were found in 8 of 104 (8%) of the subjects. Our family-based fingerprinting study demonstrates a high proportion of shared strains among siblings. Transmission between spouses seems to be appreciable. The data support mother-child and sib-sib transmission as the primary transmission pathways of H. pylori.

Susceptibility of Helicobacter pylori to metronidazole

OBJECTIVES

The reliability of the Epsilometer-test (E-Test) and the disk diffusion (DD) method in the assessment of susceptibility of Helicobacter pylori (H. pylori) to metronidazole has recently been questioned, with possible clinical implications for the management of patients undergoing H. pylori eradication. The aims of this study were: 1) to compare the E-Test and disk diffusion methods to the agar dilution method for determining the susceptibility of H. pylori to metronidazole; and 2) to investigate whether potential discrepancies could be caused by the simultaneous presence of metronidazole susceptible and metronidazole resistant bacterial subpopulations.

METHODS

A total of 109 H. pylori strains from 121 consecutive patients were examined. All tests were carried out at the same time starting from primary plates. Agar dilution was performed according to National Committee for Clinical Laboratory Standard (NCCLS) standards, the E-Test according to the manufacturer's guidelines, and disk diffusion according to standard procedure using 5-mug metronidazole disks. Isolates were considered to be metronidazole resistant if the minimal inhibitory concentration was >8 mug/ml for the agar dilution and the E-Test, or if the inhibition zone around the disk was <20 mm for disk diffusion. Of 109 isolates, 43 were also investigated to detect mixed infection. Quantities of 100 mul of bacterial suspensions of each strain were seeded onto plain agar plates and plates containing 8 mug/ml of metronidazole. Cultures were considered to be mixed if the number of colonies on agar plates exceeded by at least 30% those on the metronidazole plates.

RESULTS

According to agar dilution, 57 strains (52.3%, 95% CI = 43-61.4) were metronidazole resistant. E-Test misdiagnosed two strains that were considered sensitive to metronidazole, but according to the agar dilution test they were resistant. Disk diffusion misdiagnosed three strains. Two of these strains (the same as the E-Test) were sensitive, but according to agar dilution they were metronidazole resistant; the third strain was resistant, but according to agar dilution it was sensitive. The percentages of discordance were 1.9 (95% CI = 0.5-6.6) and 2.8 (95% CI = 0.9-7.8), respectively, when the E-Test and disk diffusion were compared to agar dilution. Intertest variability among agar dilution and the E-Test showed that 39.4% (95% CI = 30.8-48.8) of minimal inhibitory concentrations were equivalent (within +/-1 log(2)), 60.6% (95% CI = 51.2-69.2) were major errors (more than +/-1 log(2)), and 3% (95% CI = 0.8-10.4) were very major errors (change in susceptibility pattern). Mixed infection was found in six of the 43 cases examined (13.9%). In four cases, metronidazole resistant strains were 1 log(10) less numerous than those that were metronidazole susceptible. In the remaining two cases, the metronidazole resistant strains were 2-3 log(10) less numerous, which caused the two misdiagnoses.

CONCLUSIONS

The E-Test and disk diffusion method are very good alternatives to agar dilution. Mixed infections are a possible cause of the discrepancies between these tests and the reference method.

Stability of randomly amplified polymorphic DNA fingerprinting in genotyping clinical isolates of Helicobacter pylori

AIM: H pylori genomes are highly diversified. This project was designed to genotype H pylori isolates by the polymerase chain reaction (PCR)-based randomly amplified polymorphic DNA (RAPD) fingerprinting technique and to verify its stability by Southern blotting and DNA sequencing.

METHODS: Clinical isolates of H pylori were cultured from gastric antra and cardia of 73 individuals, and genomic DNA was prepared for each isolate. RAPD was carried out under optimized conditions. 23S rDNA was regarded as an internal control, and a 361 bp rDNA fragment (RDF) was used as a probe to screen the RAPD products by Southern blotting. Ten RDFs from different clinical isolates and the flanking regions (both upstream and downstream) of four RDFs were amplified and sequenced.

RESULTS: H pylori isolates from different individuals had different RAPD profiles, but the profiles for isolates cultured from different gastric sites of a given individual were identical in all but one case. Isolates from 27 individuals were RDF positive by Southern blotting. Sequences of the RDFs and their flanking regions were almost the same between the RDF positive and negative isolates as determined by Southern blotting. There was no binding site for random PCR primer inside the sequences.

CONCLUSION: RAPD is very useful in genotyping H pylori grossly on a large scale. However, it seems unstable in amplification of low yield fragments, especially those that do not appear as visible bands on the agarose gel stained with EB, since the primer is partially matched to the template.

Analysis of the vacA, cagA, cagE, iceA, and babA2 genes in Helicobacter pylori from sixty-one pediatric patients from the Midwestern United States

This study was designed to characterize H. pylori from pediatric gastric biopsy specimens in terms of several genes (vacA, cagA, cagE, iceA1, iceA2, and babA2) proposed to be involved in the pathogenesis of this organism. Many of these genes have been studied in adult H. pylori isolates, however, these genes have not been well characterized in H. pylori from children. Using PCR we observed that 44% of the H. pylori in our biopsies shared two common genotypes (vacA s1b m1, cagA, cagE, iceA2 +/- babA2). While 26% of the H. pylori had unique genotypes. The cag pathogenicity island associated genes, cagA and cagE, were found together in 64% or our H. pylori, while 84% were iceA2 positive. The presence of the babA2 gene has been proposed to be associated with a higher risk of H. pylori related diseases, however, we found that only 36% of our H. pylori contained this gene.

Helicobacter pylori: resurrection of the cancer link

Helicobacter pylori is one of the most common pathogenic bacterial infections, colonizing an estimated half of all humans. In a subset of individuals, the infection leads to serious gastroduodenal disease such as peptic ulcers and gastric adenocarcinoma. The factors contributing to skewing this, in most cases benign, relationship into disease development are largely unknown. However, factors emanating from the bacterium, host and the environment have been shown to affect the risk for disease, although no factor can be singled out to be most important. The known factors are associated with affecting the risk of disease, and are not absolute. Virulence of H. pylori is affected by the existence and regulation of certain genes present in the bacterial population in a stomach. The effects of H. pylori on gastric cancer development have been challenged and the risk associated with infection with virulent (i.e. Cag PAI positive) H. pylori has likely been underestimated.

Evaluation of two stool antigen tests for the detection of Helicobacter pylori infection in the Chinese population

BACKGROUND AND AIM

The stool antigen test, the HpSA test, has been validated mainly in Western countries, but not properly in the Chinese population. Recently, another stool antigen test, the Apollo test, was developed, but its accuracy has rarely been validated. The aim of this study is to compare the accuracy of these two tests in the diagnosis of Helicobacter pylori infection in the Chinese population.

METHODS

Consecutive dyspeptic patients referred for upper endoscopy were recruited. During endoscopy, biopsies were taken for the rapid urease test and histological examination as the gold standard. Stool specimens were collected and used for the HpSA and Apollo tests.

RESULTS

Overall, 86 patients (39 males and 47 females, with a mean age of 55.8 years) were recruited. Helicobacter pylori infection was present in 44 (51%) patients as determined by the gold standard. The sensitivity, specificity and accuracy were 86.4, 100, and 93.0%, respectively, for the HpSA, and 90.9, 97.6, and 94.2%, respectively, for the Apollo test when cases with equivocal results were considered as positive. In addition, agreement was achieved in 81 (94.2%) cases between the two tests, with a Kappa value of 0.887.

CONCLUSION

Both the HpSA and Apollo tests achieve acceptable sensitivity and excellent specificity, with accuracies of over 90% for the detection of H. pylori infection in the Chinese population.

No association between Helicobacter pylori genotypes and antibiotic resistance phenotypes within families

BACKGROUND

Triple therapy combining a proton pump inhibitor with two antibiotics, e.g. clarythromycin (CLR), metronidazole (MTZ) or amoxicillin (AMX), represents the standard in Helicobacter pylori eradication regimens. Resistance to antimicrobial agents, particularly MTZ (up to 56% in Western countries) and CLR (up to 15% in southern Europe), is frequently observed and may be associated with treatment failure [1]. Recently, several studies indicated that individual H. pylori colonies from a single anatomic site may not always yield identical genotypes, or the identical patterns of susceptibility to antibiotics [2-5]. Representative for every single patient we analyzed 27 H. pylori antrum isolates for susceptibility to antimicrobial agents in order to test whether identical H. pylori genotypes exhibit a similar pattern of susceptibility to antibiotics.

METHODS

PCR, RELP, PFGE, antibiotic susceptibility testing.

RESULTS

H. pylori genotype and antibiotic susceptibility pattern in families do not segregrate.

CONCLUSION

Molecular typing of H. pylori from family members does not predict antibiotic susceptibility pattern.

Effect of lactoferrin on Helicobacter felis induced gastritis

Lactoferrin possesses antibiotic, antiinflammatory, and immune-modulating properties that may be active against the gastritis-, ulcer- and cancer-inducing bacterium Helicobacter pylori. In vitro testing of bovine and human lactoferrin by several laboratories has shown significant bacteriostatic and bactericidal activity. Subsequent in vivo testing of bovine lactoferrin in animal models of H. pylori infection has shown beneficial effects of this agent. Our laboratory has utilized a mouse model that is infected with the feline strain of this bacterium, H. felis. The resulting gastritis that develops in this model and the effects of bovine lactoferrin and recombinant human lactoferrin (from Aspergillus niger var. awamori, Agennix Inc., Houston, Tex.) treatment were assessed by various measures. Infected animals treated with orally administered lactoferrin showed reversals in all parameters. In addition, when recombinant human lactoferrin was used in combination with low doses of amoxicillin or tetracycline, there was an enhancement in gastritis-reducing activity. Possible mechanisms for these effects of lactoferrin are discussed. Lactoferrin has significant, orally active in vivo actions and should be further investigated for clinical situations involving Helicobacter infections where it may have utility when administered alone and also when given in combination with established antibiotic agents.

Potential of fumarate reductase as a novel therapeutic target in Helicobacter pylori infection

Approximately 50% of the world's population carries Helicobacter pylori, a gastric bacterial pathogen linked to diseases including gastritis, ulcers and gastric cancer. Chemotherapies are being routinely used to treat systemic H. pylori infection. The common regimens consist of proton pump inhibitors (PPIs) or ranitidine bismuth citrate (RBC) and two antibiotics. Although these regimens efficiently eradicate H. pylori, the emergence of antibiotic-resistant H. pylori strains, their severe side effects and high costs are major drawbacks of these treatments. More efficient, economic and friendly drugs need to be developed. Fumarate reductase (FRD) catalyses the reduction of fumarate to succinate in the Krebs cycle and is also a key enzyme in anaerobic respiration with fumarate as the terminal electron acceptor for many facultative bacteria. H. pylori FRD contains three subunits, FrdA, FrdB and FrdC. Genome analysis and experimental evidence indicate that this enzyme appears to play an important role in the energy metabolism of H. pylori. In addition, FRD is essential for the colonisation of H. pylori in the acidic stomach as demonstrated in the mouse model of infection. Furthermore, three FRD inhibitors used to cure helminthic infection in animals and humans have both inhibitory and bactericidal effects on H. pylori. These lines of evidence indicate that FRD may be a promising chemotherapeutic target. Given that FrdA is strongly immunogenic in the sera from H. pylori-positive patients, this protein may also be used as a candidate for the development of an anti-H. pylori vaccine.

Optimal serological tests for the detection of Helicobacter pylori infection in the Chinese population

BACKGROUND

Numerous serological tests for the detection of Helicobacter pylori infection have been developed. However, many perform poorly when evaluated in the Chinese population.

AIM

To search for optimal serological tests for the detection of H. pylori infection in Chinese patients.

METHODS

Consecutive dyspeptic patients referred for upper endoscopy were recruited. During endoscopy, gastric biopsies were taken for the CLOtest and histological examination. Patients were then given a 13C-urea breath test. Sera were used to test for H. pylori infection, employing three commercial enzyme-linked immunosorbent assay kits (pylori DTect, HP IgG and GAP IgG). Results were compared with the gold standard defined by the CLOtest, histology and 13C-urea breath test.

RESULTS

Among the 142 patients (47 male, 95 female; mean age, 49 years) recruited, 81 (57%) were H. pylori-positive, 57 (40%) were H. pylori-negative and four (3%) were defined to be indeterminate. Using a self-defined cut-off value after calculation, the best accuracies for the pylori DTect, HP IgG and GAP IgG tests were 97%, 91% and 80%, respectively.

CONCLUSIONS

The pylori DTect test is an optimal serological test for the detection of H. pylori infection in Hong Kong Chinese patients. The HP IgG test may be used as an alternative.

Review article: treatment of Helicobacter pylori infection and factors influencing eradication

Currently available Helicobacter pylori eradication therapies are considered very effective and safe. The most recent eradication guidelines proposed in the Maastricht 2-2000 Consensus Report recommend the use of proton pump inhibitors (standard b.d.) along with clarithromycin (500 mg b.d.) and amoxycillin (1000 mg b.d.) or metronidazole (500 mg b.d.) for a minimum of 7 days. The combination of amoxycillin and clarithromycin is preferred because it may favour best results with a second-line proton pump inhibitor quadruple therapy. The recommended second-line therapy includes a combination of a proton pump inhibitor (standard b.d.) with bismuth salt (subsalicylate/subcitrate 120 mg q.d.s.), metronidazole (500 mg t.d.s.), and tetracycline (500 mg q.d.s.) for a minimum of 7 days. Extended proton pump inhibitor-based triple therapy can be used if bismuth is not available. Specialists should manage subsequent failures. Based on direct and indirect evidence from well-designed studies and clinical experience, eradication is recommended in gastric and duodenal ulcers, MALToma, atrophic gastritis, postgastric cancer resection, and in first-degree relatives of gastric cancer patients. The most common reason for treatment failure is poor compliance with eradication guidelines. Antibiotic resistance may be a significant factor in certain geographical areas. Proton pump inhibitors are an integral part of the eradication regimens as proved by meta-analyses of clinical trials. Novel agents used in secondary failure are few and depend on the use of new antibiotics. The role of H. pylori-specific antibiotics, probiotics, and vaccines is not established as yet. Widespread acceptance of the eradication guidelines should be regarded as the single most important factor in eradication success.

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.