Isogenic variation of Helicobacter pylori strain resulting in heteroresistant antibacterial phenotypes in a single host in vivo

Prevalence of antibiotic heteroresistance associated with Helicobacter pylori infection: A systematic review and meta-analysis

BACKGROUND

Heteroresistance is a general term to describe diverse responses to specific antibiotics that can occur due to infection with either multiple bacterial strains or microevolution of a single strain during chronic infection. Due to limited information regarding heteroresistance Helicobacter pylori (H. pylori) infection, the current study was carried out to evaluate the prevalence of this phenomenon.

METHODS

For this study, all potential relevant studies were collected by searching international databases such as ISI Web of Science, PubMed, Scopus, ScienceDirect, ProQuest, Embase, DOAJ, China National Knowledge Infrastructure (CNKI), and Google Scholar. Finally, the frequency of heteroresistance H. pylori infection was measured using the event rate corresponding to 95% confidence intervals.

RESULTS

A total of 26 studies met our criteria; the eligible studies were related to the years 2001-2022. Our results showed that the prevalence of heteroresistance H. pylori strains was 60.1% to clarithromycin, 61.1% to metronidazole, 46.1% to levofloxacin, 3.8% to amoxicillin, and 21.1% to tetracycline. Our literature review also showed discrepancy of antimicrobial susceptibility test in strains isolated from different anatomical sites of the stomach. Heteroresistance H. pylori infection in developing countries is mostly due to infection with multiple H. pylori strains, while in developed countries it is due to microevolution of a single H. pylori strain in response to antibiotic pressure.

CONCLUSIONS

Heteroresistance H. pylori infection interferes with successful therapy and eventually can lead to the treatment failure. If a biopsy is taken from only one gastric site, resistant strains of H. pylori may be underestimated. Considering the role of heteroresistance H. pylori infection in treatment failure, it is very important for gastroenterologists to improve their knowledge about this fact. Regardingly, new guidelines should be developed and designed for the management and treatment of heteroresistance H. pylori infection.

Heteroresistance to clarithromycin and metronidazole in patients with a Helicobacter pylori infection: a systematic review and meta-analysis

BACKGROUND

Antimicrobial resistance of H. pylori can lead to treatment failure. Importantly, several studies have reported on heteroresistance, i.e. the presence of resistant and susceptible H. pylori populations in the same sample and/or a difference in the susceptibility patterns between biopsy samples. This meta-analysis aims to provide comprehensive data on the prevalence of metronidazole and clarithromycin heteroresistance and the approaches to their detection.

MATERIAL AND METHODS

A systematic review was performed after the search of MEDLINE, Scopus and Web of Science. The study outcomes were the weighted pooled prevalence of heteroresistance to clarithromycin and metronidazole in H. pylori positive samples and/or isolates with a subanalysis by continent.

RESULTS

A total of 22 studies that had investigated 3852 H. pylori positive patients were included in the meta-analysis. Heteroresistance to clarithromycin was reported in 20 studies, with a weighted pooled prevalence of 6.8% (95% CI 5.1-8.6; 3654 H. pylori positive patients; the substantial heterogeneity I² = 55.6%). Heteroresistance to metronidazole was reported in 12 studies, with a weighted pooled prevalence of 13.8% (95% CI 8.9-18.6; 1670 H. pylori positive patients; the substantial heterogeneity I² = 60.9%). The weighted pooled prevalence of clarithromycin heteroresistance was similar in Asia and Europe (p = 0.174584), however, metronidazole heteroresistance was detected more often in Europe (p < 0.00001). Clarithromycin heteroresistance was detected more often by phenotype rather than by using genotyping methods (12 vs 8 studies), whereas heteroresistance to metronidazole was detected only by phenotype.

CONCLUSION

The prevalence of heteroresistance to clarithromycin and/or metronidazole is not negligible and can be detected in approximately 7 and 14% of H. pylori positive samples, respectively. These findings highlight the need to raise the awareness of gastroenterologists and microbiologists to the heteroresistance to clarithromycin and metronidazole in patients with a H. pylori infection.

Efficacy of Seven-Day Potassium-Competitive Acid Blocker-Based First-Line Helicobacter Pylori Eradication Therapy Administered with Bismuth

PURPOSE

To determine the efficacy of a potassium-competitive acid blocker (P-CAB)-based first-line eradication therapy with bismuth compared with that of proton pump inhibitor-based first-line therapy with bismuth.

MATERIALS AND METHODS

Eradication-naive H. pylori-infected patients were consecutively enrolled from January to November 2020. Before approval of the P-CAB-based eradication therapy, twice daily administration of a regimen containing lansoprazole 30 mg, amoxicillin 1 g, clarithromycin 500 mg, and bismuth potassium citrate 300 mg was prescribed for 7 days. After approval, lansoprazole was replaced with tegoprazan (50 mg). Clarithromycin resistance was examined in patients who underwent gastroscopic biopsy at our center. Efficacy was assessed via the ¹³C-urea breath test.

RESULTS

Of the 381 eradication-naive patients, eradication was successful in 88.3% (151/171) treated with tegoprazan and 82.8% (140/169) treated with lansoprazole in per-protocol analysis (p=0.151). In intention-to-treat analysis, eradication rates were 78.8% (152/193) in the tegoprazan and 74.5% (140/188) in the lansoprazole group (p=0.323). Clarithromycin resistance was observed in 30 (20.1%) of the 148 patients (74 from each group), and only four of the 16 clarithromycin-resistant patients in the tegoprazan group achieved successful eradication. Clarithromycin resistance [odds ratio (OR)=42.1, 95% confidence intervals (CIs)=12.6-141.0] and poor patient compliance (OR=17.1, 95% CIs=1.6-189.1) were independent risk factors for eradication failure.

CONCLUSION

In eradication-naive patients, eradication success rates for 7-day first-line triple therapy regimen exceeded 82% with bismuth administration. In clarithromycin-resistant patients, neither tegoprazan 50 mg nor lansoprazole 30 mg achieved acceptable eradication rates when administered twice daily for 7 days.

Clinical Evaluation of a Real-Time PCR Assay for Simultaneous Detection of Helicobacter pylori and Genotypic Markers of Clarithromycin Resistance Directly from Stool

Helicobacter pylori infection is mainly diagnosed noninvasively, with susceptibility testing traditionally requiring endoscopy. Treatment is empirical, with clarithromycin-based triple therapy recommended where resistance rates are below 15%. Rising rates of clarithromycin resistance, resulting in high clarithromycin-based therapy failure rates, are seen worldwide, but U.S. data are limited. We developed a real-time PCR assay for simultaneous detection of H. pylori and genotypic markers of clarithromycin resistance directly from stool specimens. The assay was validated by testing 524 stool samples using an H. pylori stool antigen test as the reference method for detection accuracy and Sanger sequencing to confirm genotypic susceptibility results. A separate set of 223 antigen-positive stool samples was tested and retrospective medical record review conducted to define clinical utility. PCR resulted in 88.6% and 92.8% sensitivity in the validation and clinical study sets, respectively. Sequencing confirmed correct detection of clarithromycin resistance-associated mutations in all positive validation samples. The PCR-predicted clarithromycin resistance rate was 39% in the clinical data set overall and 31% in treatment-naive patients; the clarithromycin-based triple therapy eradication rate in treatment-naive patients was 62%. The clarithromycin-based triple therapy success was lower when resistance was predicted by PCR (41%) than when no resistance was predicted (70%; P = 0.03). PCR results were positive in 98% of antigen-positive stools from patients tested for eradication. The described PCR assay can accurately and noninvasively diagnose H. pylori, provide genotypic susceptibility, and test for eradication. Our findings support the need for susceptibility-guided therapy in our region if a clarithromycin-based regimen is considered.

Discovery of a Novel Mutation in DNA Gyrase and Changes in the Fluoroquinolone Resistance of Helicobacter pylori over a 14-Year Period: A Single Center Study in Korea

The efficacy of fluoroquinolone-based eradication therapy largely depends on the fluoroquinolone resistance of H. pylori. The aim of this study was to investigate the changes in the primary resistance rate of H. pylori to fluoroquinolone and the mechanism of resistance in Korea. A total of 153 strains and 48 strains of H. pylori were isolated at a tertiary hospital in 2005/2006 and 2017/2018, respectively. The minimum inhibitory concentrations (MICs) of fluoroquinolone were determined by the serial 2-fold agar dilution method. DNA sequences in the quinolone resistance-determining regions of gyrA/gyrB were analyzed in resistant strains. Subsequent natural transformation study was performed to determine the association between gyrase mutation and resistance. The resistance rates increased from 19.0% (29/153) to 43.8% (21/48) both for levofloxacin and moxifloxacin. The MIC values for resistant strains increased from 2–8 µg/mL to 4–16 µg/mL over time. Mutation of gyrA was detected in 93.1% (27/29) and 100% (21/21) among the resistant strains in both periods, respectively. A novel Gly-85 mutation of gyrA was found and confirmed to be associated with fluoroquinolone resistance. Fluoroquinolone resistance rate of H. pylori has markedly increased over time in Korea. The resistance is mostly due to the point mutation of gyrA. Fluoroquinolone-containing regimens should be carefully selected in Korea, considering the increasing fluoroquinolone resistance.

The analysis of virulence factors and antibiotic resistance between Helicobacter pylori strains isolated from gastric antrum and body

Background

Individuals can be infected with multiple strains of Helicobacter pylori. However, the differences among co-infecting strains have not been well analyzed yet. This study aimed to investigate whether the virulence factors and antibiotic resistance patterns of H. pylori differ between strains isolated from different locations of the stomach in the same patient.

Methods

H. pylori isolates were obtained from the antrum and body of the stomach. Genetic differences were examined by random amplified polymorphic DNA (RAPD) fingerprinting. Antibiotic resistance was assessed using the agar dilution method. Virulence factors were identified by polymerase chain reaction and DNA sequencing.

Results

Among 80 patients, co-infection by two H. pylori strains was detected in 10 patients. Among the 10 pairs of H. pylori strains, differences in antibiotic resistance patterns were detected in 7 pairs (clarithromycin, 1 patient; quinolone, 3 patients; metronidazole, 4 patients) and differences in virulence factors were detected in 5 pairs. The cagA virulence gene was detected in all 10 patients, and 2 patients had H. pylori strains with different EPIYA motifs. Differences in vacA genotypes were detected in 4 patients.

Conclusions

Co-infection by two H. pylori strains was confirmed by RAPD fingerprinting. Frequently, two H. pylori strains obtained from a single host differed in their virulence factors and antibiotic resistance patterns. Co-infection by multiple H. pylori strains could undermine the success of eradication therapy and should be considered when interpreting the results of antimicrobial susceptibility tests.

Electronic supplementary material

The online version of this article (10.1186/s12876-019-1062-5) contains supplementary material, which is available to authorized users.

Appropriateness of Repeating Helicobacter pylori Culture and Susceptibility Testing Following Failure of Individualized Antibiotic Therapy

BACKGROUND

Current guidelines recommend direct Helicobacter pylori culture and antibiotic susceptibility testing following 2 failed eradication attempts. If this process is followed and yet subsequent treatment is unsuccessful, it is unclear whether susceptibility testing should be repeated. This is the first study to examine the appropriateness of repeated H. pylori culture and susceptibility testing following failure of individualized treatment.

METHODS

Between 2007 and 2014, consecutive patients who underwent at least 2 upper gastrointestinal endoscopies with H. pylori culture and susceptibility testing at our institution following several treatment failures were retrospectively identified. Antibiotic susceptibility was recorded and linked to demographic data.

RESULTS

A total of 68 cultures from 34 patients were included (12 (35.3%) men, 41.4 ± 16.6 years), and 20 (58.8%) cultures had a different antibiotic susceptibility profile on repeat testing (8 (23.5%) with new susceptibility and 13 (38.2%) with new resistance). Acquired resistance to clarithromycin, levofloxacin and metronidazole was observed in 9 (26.5%), 2 (5.9%) and 10 (29.4%) cultures, respectively. Subjects with resistance to ≤1 antibiotic at baseline were more likely to develop resistance to at least 1 antibiotic on subsequent culture, compared to subjects with resistance to ≥2 antibiotics at baseline (13 (100%) vs. 5 (23.8%), p < 0.01).

CONCLUSION

Repeating H. pylori culture and susceptibility testing usually yields new antimicrobial susceptibility data. However, the clinical usefulness of this approach remains unclear.

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.

[Guidelines for the diagnosis and treatment of Helicobacter pylori infection in Korea, 2013 revised edition]

Since the Korean College of Helicobacter and Upper Gastrointestinal Research has first developed the guideline for the diagnosis and treatment of Helicobacter pylori infection in 1998, the revised guideline was proposed in 2009 by the same group. Although the revised guideline was made by comprehensive review of previous articles and consensus of authoritative expert opinions, the evidence-based developmental process was not applied in the revision of the guideline. This new guideline has been revised especially in terms of changes in the indication and treatment of H. pylori infection in Korea, and developed by the adaptation process as evidence-based method; 6 guidelines were retrieved by systematic review and the Appraisal of Guidelines for Research and Evaluation (AGREE) II process, 21 statements were made with grading system and revised by modified Delphi method. After revision, 11 statements for the indication of test and treatment, 4 statements for the diagnosis and 4 statements for the treatment have been developed, respectively. The revised guideline has been reviewed by external experts before the official endorsement, and will be disseminated for usual clinical practice in Korea. Also, the scheduled update and revision of the guideline will be made periodically.

Guidelines for the diagnosis and treatment of Helicobacter pylori infection in Korea, 2013 revised edition

The Korean College of Helicobacter and Upper Gastrointestinal Research first developed guidelines for the diagnosis and treatment of Helicobacter pylori (H. pylori) infection in 1998, and revised guidelines were proposed in 2009 by the same group. Although the revised guidelines were based on a comprehensive review of published articles and the consensus of expert opinions, the revised guidelines were not developed using an evidence-based process. The new guidelines presented in this study include specific changes regarding indication and treatment of H. pylori infection in Korea, and were developed through the adaptation process using an evidence-based approach. After systematic review of the literature, six guidelines were selected using the Appraisal of Guidelines for Research and Evaluation (AGREE) II process. A total of 21 statements were proposed with the grading system and revised using the modified Delphi method. After the guideline revisions, 11 statements about indication of test and treatment, four statements about diagnosis, and four statements about treatment of H. pylori infection were developed. The revised guidelines were reviewed by external experts before receiving official endorsement from the Korean College of Helicobacter and Upper Gastrointestinal Research, and disseminated to physicians and other medical professionals for use in clinical practice in Korea. The guidelines will continue to be updated and revised periodically.

Heteroresistance of Helicobacter pylori from the same patient prior to antibiotic treatment

Antibiotic resistance among Helicobacter pylori strains has been increasing worldwide and has affected the efficacy of current treatments. The aim of this study was to evaluate whether treatment failure was due to the presence of antibiotic-susceptible and -resistant H. pylori simultaneously within the same host before eradication. In order to discover H. pylori with antibiotic heteroresistance in the same patient, we examined the antibiotic susceptibility of H. pylori isolated from 412 patients without H. pylori eradication. The E-test was used to determine the minimal inhibitory concentration of these strains. The results showed 19 (4.6%) of patients harbored antibiotic heteroresistant H. pylori, resistant to levofloxacin (5/19), clarithromycin (1/19) and metronidazole (16/19). Among them, three patients' isolates showed heteroresistance to two antibiotics. The genetic diversity of each isolate was evaluated by random amplified polymorphic DNA PCR and the results showed that only 1 patient' isolate (5.3%) had a different pattern while the others showed identical or similar fingerprinting patterns. Mutations in the genes responsible for antibiotic resistance were investigated by direct sequencing and compared between strains within each pair. All 5 levofloxacin-resistant isolates had mutations in GyrA at the QRDR region (N87 or D91). Strain 1571R with clarithromycin resistance had a A2042G substitution in its 23S rRNA. There were 15 metronidazole-resistant strains (100%) with isogenic variation of RdxA, and 6 strains (40%) contained FrxA variation (excluded pair 1159). These results suggest that the treatment failure of heteroresistant H. pylori mostly develops from high genomic variation of pre-existing strains through long term evolution rather than mixed infection with different strains.

Current progress toward eradicating Helicobacter pylori in East Asian countries: Differences in the 2013 revised guidelines between China, Japan, and South Korea

New 2013 guidelines on Helicobacter pylori (H. pylori) infection have been published in China, Japan, and South Korea. Like the previous ones, these new guidelines differ between the three countries with regard to the indications for H. pylori eradication, diagnostic methods, and treatment regimens. The most profound change among all of the guidelines is that the Japanese national health insurance system now covers the expenses for all infected subjects up to second-line treatment. This makes the Japanese indications for eradication much wider than those in China and South Korea. With regard to the diagnosis, a serum H. pylori antibody test is not recommended in China, whereas it is considered to be the most reliable method in Japan. A decrease relative to the initial antibody titer of more than 50% after 6-12 mo is considered to be the most accurate method for determining successful eradication in Japan. In contrast, only the urea breath test is recommended after eradication in China, while either noninvasive or invasive methods (except the bacterial culture) are recommended in South Korea. Due to the increased rate of antibiotics resistance, first-line treatment is omitted in China and South Korea in cases of clarithromycin resistance. Notably, the Japanese regimen consists of a lower dose of antibiotics for a shorter duration (7 d) than in the other countries. There is neither 14 d nor bismuth-based regimen in the first-line and second-line treatment in Japan. Such differences among countries might be due to differences in the approvals granted by the governments and national health insurance system in each country. Further studies are required to achieve the best results in the diagnosis and treatment of H. pylori infection based on cost-effectiveness in East Asian countries.

Clonality Analysis of Helicobacter pylori in Patients Isolated from Several Biopsy Specimens and Gastric Juice in a Japanese Urban Population by Random Amplified Polymorphic DNA Fingerprinting

Background. The number of Helicobacter pylori clones infecting a single host has been discussed in numerous reports. The number has been suggested to vary depending on the regions in the world. Aim. The purpose of this study was to examine the number of clones infecting a single host in a Japanese urban population. Materials and Methods. Thirty-one Japanese patients undergoing upper gastrointestinal endoscopy were enrolled in this study. H. pylori isolates (total 104 strains) were obtained from biopsy specimens (antrum, corpus, and duodenum) and gastric juice. Clonal diversity was examined by the random amplified polymorphic DNA (RAPD) fingerprinting method. Results. The RAPD fingerprinting patterns of isolates from each patient were identical or very similar. And the isolates obtained from several patients with 5- to 9-year intervals showed identical or very similar RAPD patterns. Conclusion. Each Japanese individual of an urban population is predominantly infected with a single H. pylori clone.

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.

Comparison of primary and secondary antimicrobial minimum inhibitory concentrations for Helicobacter pylori isolated from Korean patients

In this study we assessed minimum inhibitory concentration (MIC) values and resistance rates of several antibiotics in 65 primary and 324 secondary Helicobacter pylori isolates from Korean patients. Primary resistance to amoxicillin, clarithromycin, metronidazole, tetracycline, azithromycin, ciprofloxacin, levofloxacin and moxifloxacin was 18.5%, 13.8%, 66.2%, 12.3%, 32.3%, 33.8%, 21.5% and 21.5%, respectively. Secondary resistance was 31.3%, 85.1%, 70.1%, 0%, 89.6%, 35.8%, 32.8% and 32.8%, respectively. Sequence analysis of pbp1A in H. pylori strains with an amoxicillin MIC >or=2 microg/mL revealed C206T (Asp69-->Val), C1667G (Thr556-->Ser), A1684T (Asn562-->Tyr), A1777G (Thr593-->Ala) and C1798A (Pro600-->Thr) substitutions. Eleven (16.4%) of 67 treatment failures showed mixed infections with antibiotic-susceptible and -resistant H. pylori. The most common multidrug resistance profile was to clarithromycin, metronidazole and azithromycin. These results indicate that MIC values of secondary isolates were higher than those of primary isolates and that resistance to amoxicillin is probably mediated through mutations in pbp1A.