Molecular characterization and prevalence of antibiotic resistance in Helicobacter pylori isolates in Kuala Lumpur, Malaysia

Role of high-dose amoxicillin dual therapy for Helicobacter pylori eradication in an Irish cohort: A prospective study

Helicobacter pylori (H. pylori) infections may cause chronic gastritis, peptic ulcer disease, gastric cancers, and other conditions outside of the gastrointestinal tract. Hence, it is important to diagnose and treat it early. H. pylori is resistant to certain drugs in traditional eradication therapy, so alternative therapy protocols are needed, such as high-dose amoxicillin dual therapy (HDADT). This article aims to comment on a recent paper by Costigan et al in the World Journal of Clinical Cases. In this study, the authors recruited 139 patients diagnosed with H. pylori, all treated with HDADT. Of these, 93 were treatment-naïve and 46 had received at least one alternative treatment in the past. Four weeks after the end of the treatment, the urea breath test was administered to estimate the eradication rate. The total eradication rate was 56% (78/139), 62% for the treatment-naïve arm and 43% for the previous treatment arm, thus indicating a lower success rate for the arm that had previously received a different treatment regimen. In conclusion, a therapeutic approach with first-line HDADT may potentially be a better treatment, but the results are not sufficient to recommend the use of this regimen in a country with high levels of dual resistance.

An eco-friendly liquid chromatographic analysis of the triple therapy protocol of amoxicillin, metronidazole and vonoprazan for H. Pylori eradication: application to combined dosage forms and simulated gastric fluid

Helicobacter pylori has a big sway when peptic ulcers are concerned. For its eradication, different protocols have been approved. Among which, the tripartite therapy protocol which embraces vonoprazan as potassium competitive acid blocker in combination with amoxicillin and metronidazole as antibiotics. An environmentally benign HPLC method is addressed in order to simultaneously determine amoxicillin (AMX), metronidazole (MET) and vonoprazan (VPZ) in bulk powder and combined tablet mixture. Full separation of AMX, MET and VPZ is accomplished using C8 column, and a gradient mobile phase system, composed of methanol and phosphate buffer of a pH value of 5. Fine linearity in the concentration ranges 50-600 µg mL-1 amoxicillin, 50-400 µg mL-1 metronidazole and 10-100 µg mL-1 vonoprazan was denoted by the high correlation coefficient (0.9999). The method accuracy and precision are confirmed upon analyzing AMX, MET and VPZ triple therapy not only in their synthetic mixtures and combined tablet mixtures but also in their combined tablet mixtures in simulated gastric fluid. AMX, MET and VPZ triple therapy could be routinely analyzed in QC labs, in case of being co-formulated, using the presented method. Three different assessment tools were adopted revealing the benign environmental impact of presented method.

Genetic variations of penicillin-binding protein 1A: insights into the current status of amoxicillin-based regimens for Helicobacter pylori eradication in Malaysia

Introduction. Resistance towards amoxicillin in Helicobacter pylori causes significant therapeutic impasse in healthcare settings worldwide. In Malaysia, the standard H. pylori treatment regimen includes a 14-day course of high-dose proton-pump inhibitor (rabeprazole, 20 mg) with amoxicillin (1000 mg) dual therapy.Hypothesis/Gap Statement. The high eradication rate with amoxicillin-based treatment could be attributed to the primary resistance rates of amoxicillin being relatively low at 0%, however, a low rate of secondary resistance has been documented in Malaysia recently.Aim. This study aims to investigate the amino acid mutations and related genetic variants in PBP1A of H. pylori, correlating with amoxicillin resistance in the Malaysian population.Methodology. The full-length pbp1A gene was amplified via PCR from 50 genomic DNA extracted from gastric biopsy samples of H. pylori-positive treatment-naïve Malaysian patients. The sequences were then compared with reference H. pylori strain ATCC 26695 for mutation and variant detection. A phylogenetic analysis of 50 sequences along with 43 additional sequences from the NCBI database was performed. These additional sequences included both amoxicillin-resistant strains (n=20) and amoxicillin-sensitive strains (n=23).Results. There was a total of 21 variants of amino acids, with three of them located in or near the PBP-motif (SKN402-404). The percentages of these three variants are as follows: K403X, 2%; S405I, 2% and E406K, 16%. Based on the genetic markers identified, the resistance rate for amoxicillin in our sample remained at 0%. The phylogenetic examination suggested that H. pylori might exhibit unique conserved pbp1A sequences within the Malaysian context.Conclusions. Overall, the molecular analysis of PBP1A supported the therapeutic superiority of amoxicillin-based regimens. Therefore, it is crucial to continue monitoring the amoxicillin resistance background of H. pylori with a larger sample size to ensure the sustained effectiveness of amoxicillin-based treatments in Malaysia.

Probiotic containing Lactobacillus reuteri DSM 17648 as an adjunct treatment for Helicobacter pylori infection: A randomized, double-blind, placebo-controlled trial

BACKGROUND

Despite multiple therapy regimens, the decline in the Helicobacter pylori eradication rate poses a significant challenge to the medical community. Adding Lactobacillus reuteri probiotic as an adjunct treatment has shown some promising results. This study aims to investigate the efficacy of Lactobacillus reuteri DSM 17648 in H. pylori eradication and its effect in ameliorating gastrointestinal symptoms and adverse treatment effects.

MATERIALS AND METHODS

This randomized, double-blinded, placebo-controlled trial involved treatment-naïve H. pylori-positive patients. Ninety patients received standard triple therapy for 2 weeks before receiving either a probiotic or placebo for 4 weeks. The posttreatment eradication rate was assessed via a 14 C urea breath test in Week 8. The Gastrointestinal Symptom Rating Scale (GSRS) questionnaire and an interview on treatment adverse effects were conducted during this study.

RESULTS

The eradication rate was higher in the probiotic group than in the placebo group, with a 22.2% difference in the intention-to-treat analysis (91.1% vs. 68.9%; p = 0.007) and 24.3% difference in the per-protocol analysis (93.2% vs. 68.9%; p = 0.007). The probiotic group showed significant pre- to post-treatment reductions in indigestion, constipation, abdominal pain, and total GSRS scores. The probiotic group showed significantly greater reductions in GSRS scores than the placebo group: indigestion (4.34 ± 5.00 vs. 1.78 ± 5.64; p = 0.026), abdominal pain (2.64 ± 2.88 vs. 0.89 ± 3.11; p = 0.007), constipation (2.34 ± 3.91 vs. 0.64 ± 2.92; p = 0.023), and total score (12.41 ± 12.19 vs. 4.24 ± 13.72; p = 0.004). The probiotic group reported significantly fewer adverse headache (0% vs. 15.6%; p = 0.012) and abdominal pain (0% vs. 13.3%; p = 0.026) effects.

CONCLUSIONS

There was a significant increase in H. pylori eradication rate and attenuation of symptoms and adverse treatment effects when L. reuteri was given as an adjunct treatment.

Management of Helicobacter pylori treatment failures: A large population-based study (HP treatment failures trial)

BACKGROUND

Helicobacter pylori treatment failure remains a challenging problem. This study aimed to identify predictive factors for successful eradication in patients following treatment failures.

METHODS

This was a retrospective cohort study. This study included 1,050 dyspeptic patients diagnosed with H. pylori infection at tertiary care center in Thailand between March 2014 and October 2021. Patients' demographic data, endoscopic findings, H. pylori culture, antimicrobial susceptibility testing (AST), treatment regimens and outcomes were analysed.

RESULTS

Of 1,050 patients with H. pylori infections, 302 (28.7%) experienced treatment failure (mean age 58.4 years; 44.7% males). AST was performed in 192. Resistance was observed for metronidazole (43.2%), levofloxacin (33.9%), clarithromycin (24%), and amoxicillin (2.1%). There was no tetracycline resistance. Multidrug-resistance (MDR) was significantly more common following treatment failure (45.5% vs. 15.7%, p<0.001). Baseline characteristics were similar between treatment successes and failures. Eradication rates after first-line and second-line regimens were 71.2% and 54.5%, respectively. Medication nonadherence [OR 36.6 (95%CI 8.65-155.03, p<0.001)] and MDR [OR 4.49 (95%CI 2.29-8.81, p<0.001)] were associated with treatment failure. Over time, resistance increased for metronidazole, levofloxacin, and clarithromycin, while eradication rates with triple therapy declined. Tailored antibiotic therapy [OR 4.92 (95%CI 1.61-14.99, p = 0.005)] and a regimen including 4-times-daily dosing of amoxicillin (2 grams/day) [OR 3.05 (95%CI 1.10-8.41, p = 0.032)] were significantly associated with treatment success after first-line failure. Eradication rates when using tailored therapy and 4-times-daily dosing of amoxicillin (2 grams/day) were 91.1% and 89.4%, respectively. Performing AST before first-line therapy resulted in the highest cure rates. AST performed after multiple treatment failures was also associated with higher eradication rates compared with the group without AST (94.4% vs. 50%,p = 0.008).

CONCLUSIONS

AST either before or after treatment failure correlated with a higher proportion of successful eradication. Nonadherence and the MDR infections predicted treatment failure. Tailored therapy and 4-times-daily dosing of amoxicillin after treatment failure were likely to be successful.

Polymorphism of virulence genes and biofilm associated with in vitro induced resistance to clarithromycin in Helicobacter pylori

BACKGROUND

Clarithromycin-containing triple therapy is commonly used to treat Helicobacter pylori infections. Clarithromycin resistance is the leading cause of H. pylori treatment failure. Understanding the specific mutations that occur in H. pylori strains that have evolved antibiotic resistance can help create a more effective and individualised antibiotic treatment plan. However, little is understood about the genetic reprogramming linked to clarithromycin exposure and the emergence of antibiotic resistance in H. pylori. Therefore, this study aims to identify compensatory mutations and biofilm formation associated with the development of clarithromycin resistance in H. pylori. Clarithromycin-sensitive H. pylori clinical isolates were induced to develop clarithromycin resistance through in vitro exposure to incrementally increasing concentration of the antibiotic. The genomes of the origin sensitive isolates (S), isogenic breakpoint (B), and resistant isolates (R) were sequenced. Single nucleotide variations (SNVs), and insertions or deletions (InDels) associated with the development of clarithromycin resistance were identified. Growth and biofilm production were also assessed.

RESULTS

The S isolates with A2143G mutation in the 23S rRNA gene were successfully induced to be resistant. According to the data, antibiotic exposure may alter the expression of certain genes, including those that code for the Cag4/Cag protein, the vacuolating cytotoxin domain-containing protein, the sel1 repeat family protein, and the rsmh gene, which may increase the risk of developing and enhances virulence in H. pylori. Enhanced biofilm formation was detected among R isolates compared to B and S isolates. Furthermore, high polymorphism was also detected among the genes associated with biofilm production.

CONCLUSIONS

Therefore, this study suggests that H. pylori may acquire virulence factors while also developing antibiotic resistance due to clarithromycin exposure.

A Malaysian consensus report on the diagnosis and treatment of Helicobacter pylori infection

Helicobacter pylori is one of the most common chronic bacterial infections in humans and responsible for 90% of duodenal ulcers and 70-90% of gastric ulcers. Despite this, many misconceptions regarding the appropriate diagnostic method and treatment strategies still exist in the Malaysian clinical practice. Under the initiative of the steering committee, an expert panel consisting of nine key opinion leaders in the field of gastroenterology convened to develop a set of consensus statements that are relevant to the Malaysian healthcare practice. The panel members reviewed the current evidence on the management of H. pylori infection, focusing on the best practices that are relevant to the Malaysian population based on clinical experience and published clinical evidence. Using the modified Delphi method, the panel achieved consensus in three areas of H. pylori infection management: indications for testing, diagnosis, and treatment. The panel proposed a set of 19 consensus statements, which were synthesized via two rounds of blinded voting and group discussions. The recommendations provided are relevant to the Malaysian population and can be used as a guide by physicians across various healthcare settings to facilitate appropriate diagnostic testing and treatment of H. pylori infection.

Mutations Related to Antibiotics Resistance in Helicobacter pylori Clinical Isolates from Bangladesh

Current management of gastric inflammation involves the eradication of Helicobacter pylori. However, the effectiveness of commonly used antibiotics against H. pylori infection has decreased due to antibiotic resistance. Phenotypic-based diagnostics are laborious and finding the cause of resistance can be difficult. Therefore, early detection and understanding of the underlying mechanism of this resistance are necessary. This study evaluated the mutations in the genes related to the Antimicrobial Resistance (AMR) of the clinical isolates from Bangladeshi subjects. Whole-genome sequencing was performed on 56 isolates and the genes (such as pbp1a, rdxA, ribF, fur, gyrA, gyrB, 23S rRNA, and infB) were extracted. The reads were assembled, and the SNPs were extracted by the latest pipeline for antibiotic mutation analysis, ARIBA. The mutations and the association with the antibiotic phenotypes were evaluated using Fisher's exact test. In this study, the clarithromycin resistance rate was high, 39.3% (22/56), with the median MIC 24 mg/L ranging from 2 to 128 mg/L. The mutation of A2147G was significantly associated with resistance (p = 0.000018) but not in locus A2146G (p = 0.056). Levofloxacin also posed a high resistance. We observed that the mutation of D91N (but not D91Y) (p = 0.002) and N87K (p = 0.002) of gyrA was associated with levofloxacin resistance. Mutations in locus A343V (p = 0.041) of gyrB also showed a significant association. Meanwhile, in the pbp1a gene, several mutations might explain the resistance; they were G594fs (p = 0.036), K306R (p = 0.036), N562Y (p = 0.0006), and V45I (p = 0.018). The prevalence of metronidazole was exceptionally high (96.4%), and numerous mutations occurred in rdxA genes, including the truncation of genes. These results imply that the mutation in genes encoding the target protein of antibiotics remains the critical resistance mechanism in H. pylori.

A Comparison of Doxycycline and Amoxicillin Containing Quadruple Eradication Therapy for Treating Helicobacter pylori-Infected Duodenal Ulcers: A Multicenter, Opened, Randomized Controlled Trial in China

Background: Increased antibiotic resistance is one of the major factors contributing to the failure of H. pylori eradication. This study aimed to compare the efficacy and safety of doxycycline and amoxicillin, both critical components for bismuth-based quadruple therapy, for the first-line treatment of H. pylori-infected duodenal ulcers. Methods: An open, randomized case-controlled, multicenter trial was conducted in seven hospitals in China. A total of 184 eligible participants were divided into an IDFB (ilaprazole 5 mg, doxycycline 100 mg, furazolidone 100 mg, and bismuth 220 mg bid) or IAFB (ilaprazole 5 mg, amoxicillin 1000 mg, furazolidone 100 mg, and bismuth 220 mg bid) group for 14 days. Both groups were administrated with ilaprazole 5 mg qd for another 14 days. The main outcome was an H. pylori eradication rate; secondary outcomes were ulcer healing, relief of symptoms, and incidence of adverse effects. Results: The H. pylori eradication rates were 85.9% (95% CI 78.6−93.9) in the IDFB vs. 84.8% (95% CI 77.3−92.3) in the IAFB group in ITT analysis (p > 0.05), and 92.9% (95% CI 87.4−98.5) vs. and 91.8% (95% CI 85.8−97.7) in PP analysis (p > 0.05). The overall ulcer healing rates of IDFB and IAFB were 79.1% and 84.7% (p > 0.05), both effective in relieving symptoms. Only nine participants had adverse reactions in this trial (4/92 in IDFB and 5/92 in IAFB). Conclusion: A bismuth quadruple regimen containing doxycycline or amoxicillin could be an effective and safe treatment for H. pylori eradication, while doxycycline replacement is an alternative for participants with penicillin allergy.

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.

Next-Generation Sequencing-Based Study of Helicobacter pylori Isolates from Myanmar and Their Susceptibility to Antibiotics

Evaluation of Helicobacter pylori resistance to antibiotics is crucial for treatment strategy in Myanmar. Moreover, the genetic mechanisms involved remain unknown. We aimed to investigate the prevalence of H. pylori infection, antibiotic resistance, and genetic mechanisms in Myanmar. One hundred fifty patients from two cities, Mawlamyine (n = 99) and Yangon (n = 51), were recruited. The prevalence of H. pylori infection was 43.3% (65/150). The successfully cultured H. pylori isolates (n = 65) were tested for antibiotic susceptibility to metronidazole, levofloxacin, clarithromycin, amoxicillin, and tetracycline by Etest, and the resistance rates were 80%, 33.8%, 7.7%, 4.6%, and 0%, respectively. In the multidrug resistance pattern, the metronidazole–levofloxacin resistance was highest for double-drug resistance (16/19; 84.2%), and all triple-drug resistance (3/3) was clarithromycin–metronidazole–levofloxacin resistance. Twenty-three strains were subjected to next-generation sequencing to study their genetic mechanisms. Interestingly, none of the strains resistant to clarithromycin had well-known mutations in 23S rRNA (e.g., A2142G, A2142C, and A2143G). New type mutation genotypes such as pbp1-A (e.g., V45I, S/R414R), 23S rRNA (e.g., T248C), gyrA (e.g., D210N, K230Q), gyrB (e.g., A584V, N679H), rdxA (e.g., V175I, S91P), and frxA (e.g., L33M) were also detected. In conclusion, the prevalence of H. pylori infection and its antibiotic resistance to metronidazole was high in Myanmar. The H. pylori eradication regimen with classical triple therapy, including amoxicillin and clarithromycin, can be used as the first-line therapy in Myanmar. In addition, next-generation sequencing is a powerful high-throughput method for identifying mutations within antibiotic resistance genes and monitoring the spread of H. pylori antibiotic-resistant strains.

Development and Validation of Multiplex Quantitative PCR Assay for Detection of Helicobacter pylori and Mutations Conferring Resistance to Clarithromycin and Levofloxacin in Gastric Biopsy

Aims and Objectives

More than half of the world's population is infected with Helicobacter pylori, which can cause chronic gastritis. WHO has regarded clarithromycin-resistant H. pylori as a high priority pathogen. Hence, accurate diagnosis and detection of clarithromycin- and levofloxacin-resistant H. pylori strains is essential for proper management of infection. The objective of this study was to develop and optimize multiplex quantitative PCR assay for detection of mutations associated with clarithromycin and levofloxacin resistance in H. pylori directly from the gastric biopsies.

Materials and Methods

Specific primers and probes were designed to amplify ureA and mutations in 23S rRNA and gyrA genes. Singleplex and triplex qPCR assays were optimized and the assay's sensitivities and specificities were determined. The optimized multiplex qPCR assay was performed on 571 gastric biopsies.

Results

In this study, 14.7% (84/571) of the gastric biopsies were positive for H. pylori by conventional methods and 23.8% (136/571) were positive by the ureA-qPCR with 96.4% sensitivity and 88.5% specificity, while the +LR and -LR were 8.72 and 0.04, respectively. The ureA-positive samples (n=136) were subjected to multiplex qPCR which detected A2142G and A2143G mutations in the 23S rRNA gene (20.6%, 28/136) conferring clarithromycin resistance and gyrA mutations N87K, N87I, D91N, and D91Y (11.8%, 16/136) leading to levofloxacin resistance. The sensitivity and specificity of qPCR of 23S rRNA gene were 100% and 98.7%, respectively, while 100% and 99.8% for qPCR of gyrA, respectively.

Conclusion

The effectiveness of this qPCR is that it is sensitive in detecting low bacterial load and will help in timely detection of clarithromycin- and levofloxacin-resistant strains, especially in case of mixed infections. Since it is culture independent, it can inform clinicians about antibiotics to be included in the first-line therapy, thereby improving the management of H. pylori infection at a much greater pace.

The Emergence of Multidrug-Resistant Helicobacter pylori in Southeast Asia: A Systematic Review on the Trends and Intervention Strategies Using Antimicrobial Peptides

The emergence of multidrug-resistant H. pylori poses a public healthcare threat, particularly in low- and middle-income countries. Recently, the World Health Organization has classified clarithromycin-resistant H. pylori as high priority in the research and discovery of novel antibiotics. This study was aimed to systematically review the prevalence of primary antibiotic resistance in H. pylori in Southeast Asian countries (SEAC) and to review current studies of antimicrobial peptides against H. pylori. We systematically searched through electronic databases of studies conducted on antimicrobial resistance of H. pylori in SEA countries. Furthermore, we searched articles that conducted studies on antimicrobial peptides, naturally occurring host’s defense molecules, against H. pylori. After a series of screening processes, 15 studies were included in our systematic review. Our analysis revealed that primary resistance of H. pylori to metronidazole, clarithromycin, and levofloxacin were high in SEAC, although the primary resistance to amoxicillin and tetracycline remains low. Multidrug-resistant H. pylori are emerging in SE Asian countries. The antimicrobial peptides show promising antibacterial and antibiofilm activity against drug-resistant H. pylori. The research and discovery of antimicrobial peptides against H. pylori in SEAC will help in limiting the spread of antimicrobial resistance of H. pylori.

Pepsinogen and Serum IgG Detection Is a Valuable Diagnostic Method for Helicobacter pylori Infection in a Low-Prevalence Country: A Report from Sri Lanka

The use of serum anti-Helicobacter pylori IgG and pepsinogen (PG) detection as a diagnostic method was evaluated in Sri Lanka. Gastric biopsies were performed (353 patients), and the prevalence of H. pylori infection was 1.7% (culture) and 2.0% (histology). IgG serology testing showed an area under the curve (AUC) of 0.922 (cut-off, 2.95 U/mL; specificity, 91.56%; sensitivity, 88.89%). Histological evaluation showed mild atrophy (34.3%), moderate atrophy (1.7%), metaplasia (1.7%), chronic gastritis (6.2%), and normal tissue (56%). The PGI/PGII ratio was significantly higher in H. pylori-negative patients (p < 0.01). PGII and PGI/PGII levels were lower in patients with metaplasia than in those with normal mucosa (p = 0.049 and p < 0.001, respectively). The PGI/PGII ratio best discriminated metaplasia and moderate atrophy (AUC 0.88 and 0.76, respectively). PGI and PGII alone showed poor discriminative ability, especially in mild atrophy (0.55 and 0.53, respectively) and chronic gastritis (0.55 and 0.53, respectively). The best cut-off to discriminate metaplasia was 3.25 U/mL (95.19% specificity, 83.33% sensitivity). Anti-H. pylori IgG and PG assessment (ABC method) was performed (group B, 2.0%; group A, 92.1%). The new cut-off more accurately identified patients with metaplasia requiring follow-up (group B, 5.4%). Assessment of anti-H. pylori IgG and PG is valuable in countries with a low prevalence of H. pylori infection.

Current status of Helicobacter pylori resistance to Clarithromycin and Levofloxacin in Malaysia-findings from a molecular based study

Background

Resistance to clarithromycin and levofloxacin in Helicobacter pylori which resulted in treatment failures has become a major challenge for physicians worldwide. The resistance is mainly mediated by mutations in a specific domain of the 23S rRNA, gyrA and gyrB genes for clarithromycin and levofloxacin respectively. Hence in this study, we aimed to investigate the current status of H. pylori resistance in our hospital to these two antibiotics based on the molecular approach.

Materials and Methods

Gastric biopsy samples were obtained from treatment-naïve patients. Bacterial genomic DNA was extracted using a commercial kit and continued with DNA amplification using polymerase chain reaction (PCR) with specific primers. The PCR amplicons were subjected to sequencing on 23S rRNA gene targeting nucleotide positions at 2,146, 2,147, 2,186 and amino acids at gyrA positions 87 and 91 and gyrB positions 436, 438, 481, 484 to investigate the possible mutations or polymorphisms of genes that lead to clarithromycin and levofloxacin resistance respectively.

Results

Sixty-one urease-positive gastric biopsy samples were studied. The findings revealed the primary resistance rates to clarithromycin was 14.8% and to levofloxacin was 3.3% in our current scenario based on detection of reported resistance-related mutations of A2147G and D91N in 23S rRNA and gyrA genes, respectively. Interestingly, we found a high rate of silent mutations of the gyrA codon 87Asn (32.8%, 20/61) and two polymorphisms of the gyrB D481E (16.4%, 10/61) and R484K (21.3%, 13/61). The role of these polymorphisms in gyrB remained to be elucidated whether the levels of levofloxacin resistance are related to the position/amino acid.

Conclusion

The primary resistance rate of H. pylori to clarithromycin has increased compared to the previous report in Malaysia. Therefore, molecular screening could aid and is important for the selection of antibiotics for H. pylori eradication therapies.

Phenotypic and Genotypic Antibiotic Resistance Patterns in Helicobacter pylori Strains From Ethnically Diverse Population in México

Helicobacter pylori strains carry a range of mutations in genes that confer antimicrobial resistance and restrict the available options to treat the infection. Latin America is a region that conserve a large number of indigenous communities relatively isolated that practice a traditional medicine without consumption of drugs. We hypothesized that rates of antibiotic resistance are lower in these communities. Recent progress in whole-genome sequencing has allowed the study of drug susceptibility by searching for the known mutations associated with antibiotic resistance. The aim of this work was to study trends of antibiotic resistance over a 20-year period in Mexican H. pylori strains and to compare susceptibility between strains from Mexican mestizos and from indigenous population; we also aimed to learn the prevalence of mutational patterns in genes gyrA, gyrB, rdxA, frxA, rpsU, omp11, dppA, and 23S rRNA and its association with phenotypic tests. Resistance to clarithromycin, metronidazole, amoxicillin and levofloxacin was determined in167 H. pylori isolates by E-test, and the occurrence of mutational patterns in specific genes was determined by whole genome sequencing (WGS). The trend of resistance over 20 years in mestizo isolates showed significant resistant increase for clarithromycin and levofloxacin to frequencies that banned its clinical use. Resistance in H. pylori isolates of native communities was lower for all antibiotics tested. Phenotypic resistance showed good to moderate correlation with genotypic tests. Genetic methods for characterizing antibiotic resistance require further validation in each population.

Enzyme Inhibitory Kinetics and Molecular Docking Studies of Halo-Substituted Mixed Ester/Amide-Based Derivatives as Jack Bean Urease Inhibitors

A series of halo-substituted mixed ester/amide-based analogues 4a-l have been prepared as jack bean urease inhibitor, which showed good to excellent inhibition of enzyme activity. The role of halo-substituted benzoyl moieties and alkyl substituted anilines in urease inhibitory kinetics was also investigated. The alkyl-substituted anilines 1a-b reacted with chloroacetyl chloride to afford intermediates 2a-b, which were then reacted with different halo-substituted benzoic acids 3a-f to prepare the title compounds 4a-l. The chemical structures of final products 4a-l were ascertained by FTIR, 1H NMR, 13C NMR, and mass spectra. The compound 4b showed remarkable activity with IC501.6 ± 0.2 nM, better than the standard thiourea having IC50472.1 ± 135.1 nM. The 2-chloro-substituted phenyl ring on one side of compound 4b and 4-isopropyl-substituted benzene on the other side play an essential role in inhibition of urease activity. Lineweaver-Burk plots (kinetics study) indicated about 4b derivative as a mixed type of inhibitor. The virtual screening performed against urease enzyme (PDBID 4H9M) showed that compounds 4b and 4e have binding energies of -7.8 and -7.9 Kcal/mol, respectively. Based upon our results, it was found that derivative 4b is a highly potent urease inhibitor, better than the standard thiourea.

The outward shift of clarithromycin binding to the ribosome in mutant Helicobacter pylori strains

OBJECTIVES

Disruption of protein synthesis, by drug-mediated restriction of the ribosomal nascent peptide exit tunnel (NPET), may inhibit bacterial growth. Here, we have studied the secondary and tertiary structures of domain V of the 23S rRNA in the wild-type and mutant (resistant) H. pylori strains and their mechanisms of interaction with clarithromycin (CLA).

METHODS

H pylori strains, isolated from cultured gastric biopsies, underwent CLA susceptibility testing by E test, followed by PCR amplification and sequencing of domain V of 23S rRNA. The homology model of this domain in H pylori, in complex with L4 and L22 accessory proteins, was determined based on the E. coli ribosome 3D structure. The interactions between CLA and 23S rRNA complex were determined by molecular docking studies.

RESULTS

Of the 70 H pylori strains, isolated from 200 dyspeptic patients, 11 (16%) were CLA-resistant. DNA sequencing identified categories with no (A), A2142G (B), and A2143G (C) mutations. Docking studies of our homology model of 23S rRNA complex with CLA showed deviated positions for categories B and C, in reference to category A, with 12.19 Å and 7.92 Å RMSD values, respectively. In both mutant categories, CLA lost its interactions at positions 2142 and 2587 and gained two new bonds with the L4 accessory protein.

CONCLUSION

Our data suggest that, in mutant H pylori strains, once the nucleotides at positions 2142 and 2587 are detached from the drug, CLA interacts with and is peeled back by the L4 accessory protein, removing the drug-imposed spatial restriction of the NPET.

Sequencing-based detection of 23S rRNA domain V mutations in treatment-naïve Helicobacter pylori patients from Malaysia

OBJECTIVES

In Malaysia, the prevalence of Helicobacter pylori resistance to clarithromycin is increasing. This study aimed to determine mutations in the 23S rRNA domain V directly using bacterial DNA extracted from gastric biopsy specimens with a urease-positive result.

METHODS

A 1085-bp fragment of 23S rRNA domain V from samples of 62 treatment-naïve patients with H. pylori infection was amplified by PCR with newly designed primers, followed by sequencing.

RESULTS

Of the 62 cases, 42 patients were treated with clarithromycin-based triple therapy and 20 patients were treated with amoxicillin and proton pump inhibitor only; both therapies showed successful eradication rates of 70-73.8%. Sequencing analysis detected 37 point mutations (6 known and 31 novel) with prevalences ranging from 1.6% (1/62) to 72.6% (45/62). A2147G (aka A2143G) appears to be associated with a low eradication rate [40% (2/5) failure rate and 13.3% (6/45) treatment success rate], supporting its role as a clinically significant point mutation. T2186C (aka T2182C) was found in 71.1% (32/45) and 80% (4/5) of treatment success and failure cases, respectively, suggesting that the mutation is clinically insignificant. The eradication success rate in patients with the novel T2929C mutation was decreased three-fold (6.7%; 3/45) compared with the failure rate (20%; 1/5), suggesting that it may play an important role in clarithromycin resistance, thus warranting further study.

CONCLUSION

This study identified multiple known and novel mutations in 23S rRNA domain V through direct sequencing. Molecular detection of clarithromycin resistance directly on biopsies offers an alternative to conventional susceptibility testing.

Searching for an optimal therapy for H pylori eradication: High-dose proton-pump inhibitor dual therapy with amoxicillin vs. standard triple therapy for 14 days

BACKGROUND & AIMS

We compared a high-dose dual therapy (HDDT) with rabeprazole and amoxicillin and compared it with a standard triple therapy (STT) with rabeprazole, amoxicillin, and clarithromycin for 2 weeks for H pylori eradication in treatment naïve patients.

METHODS

H pylori-positive patients were randomly assigned to either a rabeparzole (Pariet) 20 mg b.i.d., amoxicillin (Ospamox) 1 g b.i.d. and clarithromycin (Klacid) 500 mg b.i.d. for 14 days or rabeprazole (Pariet) 20 mg q.i.d., amoxicillin (Ospamox) 1 g q.i.d. also for 14 days. Eradication was tested for by the C¹³ -UBT at least 4 weeks after the completion of therapy.

RESULTS

H pylori was eradicated in 86.2% of patients (81/94) (95% CI: 77.8-91.7) in the STT group compared with 92.8% (90/97) (95% CI: 85.9-96.5) in the HDDT group on ITT analysis. On PP analysis, H pylori was eradicated in 91.0% of patients (81/89) (95% CI: 83.3-95.4) in the STT group compared with 93.8% (90/96) (95% CI: 87.0-97.1) in the HDDT group. Side effects were few although many patients in the STT arm complained of bitter taste. The HDDT arm was well tolerated by patients.

CONCLUSIONS

The HDDT gave a high eradication rate comparable to the STT for 2 weeks and was a well-tolerated regimen for H pylori eradication.

Review - Treatment of Helicobacter pylori infection 2020

This review summarizes important studies regarding Helicobacter pylori therapy published from April 2019 to April 2020. The main themes that emerge involve studies assessing antibiotic resistance, and there is also growing momentum behind the utility of vonoprazan as an alternative to proton pump inhibitor (PPI) therapy and also bismuth-based regimens as a first-line regimen. Antibiotic resistance is rising wherever it is being assessed, and clarithromycin resistance in particular has reached a point where it may no longer be a viable therapy without previous testing in many regions of the world. The evidence for the efficacy of a bismuth-based quadruple therapy as a first-line therapy is now very clearly established, and there is substantial evidence that it is the best performing first-line therapy. The utility of vonoprazan as an alternative to PPI therapy, especially in resistant and difficult-to-treat groups, has also been considered in great detail this year, and it may offer an opportunity in the near future to reduce the problem of antibiotic resistance.

Update on quinolone-containing rescue therapies for Helicobacter pylori infection

Third generation of quinolones, such as levofloxacin and moxifloxacin, -containing regimens are often used in second-line or rescue treatment of Helicobacter pylori infection. However, the increasing antibiotic resistance to quinolones affects the efficacies of quinolones-containing therapies in recent years. Therefore, there is a need to enhance the effectiveness of quinolones-containing therapies. Sitafloxacin, a fourth-generation quinolone, and vonoprazan, a novel potassium-competitive acid blocker, are now available as more effective treatment options. The aim of this paper is to summarize the current evidence of quinolone-containing therapies in rescue treatments, and to discuss the importance of drug sensitivity tests or analysis of gyrA mutation before treatments.

Molecular Assessment of Resistance to Clarithromycin in Helicobacter pylori Strains Isolated from Patients with Dyspepsia by Fluorescent In Situ Hybridization in the Center of Iran

Background and Aims

Helicobacter pylori is a common infectious bacterium mostly found in gastroduodenal diseases. The increased prevalence of clarithromycin-resistant H. pylori strains is a major challenge in the successful treatment of infections caused by this organism. The present study is aimed at detecting the clarithromycin resistance pattern of H. pylori strains isolated from gastric biopsies and evaluating point mutations of the 23S rRNA gene. Patients and methods. In the present descriptive cross-sectional study, 165 patients with gastrointestinal disorders, who were referred to the Endoscopy Center of Dr. Shariati Hospital of Isfahan, Iran, were enrolled from April to July 2018. H. pylori infection was diagnosed by culture, and susceptibility of the isolates to clarithromycin was assessed by the E-test. Minimum inhibitory concentration (MIC) values were obtained based on EUCAST recommendations. Also, fluorescence in situ hybridization (FISH) was used to determine point mutations associated with clarithromycin resistance.

Results

By using culturing, H. pylori was isolated from 50.3% (83/165) gastric biopsy specimens. The overall frequency of resistance to clarithromycin was 25.3% (21/83) by the E-test. In the resistance genotypic analysis, 19 isolates had mutations. The prevalence of A2143G and A2144G mutations was 68.4% (13/19) and 31.5% (6/19), respectively. A2143C mutation was not tracked in any isolate. Two isolates with MIC > 0.5 μg/mL had no mutations that could be related to other mechanisms of resistance.

Conclusion

As presented in the study, the high prevalence of clarithromycin-resistant H. pylori due to point mutations of the 23S rRNA gene indicates the necessity of revising the standard treatment regimen based on antibiotic susceptibility pattern of each region.

Eradication Treatment of Helicobacter pylori Infection Based on Molecular Pathologic Antibiotic Resistance

Background

Unfortunately, the eradication rate of Helicobacter pylori (H. pylori) treatment is markedly decreasing in recent years and the major reason is antibiotic resistance. Our study was designed to determine the effect and safety of H. pylori eradication treatment based on the molecular pathologic antibiotic resistance.

Methods

261 patients were analyzed retrospectively, including 111 patients who were treated for the first time (one group as First-treated) and 150 patients who failed at least once in bismuth quadruple therapy (another group as Re-treatment). Antibiotic resistance was examined by Real-time PCR detection and conventional PCR and sequencing method. The eradication rate (ER) was compared per intention to treat (ITT) and per protocol (PP) between the two groups.

Results

The resistance rates to amoxicillin, clarithromycin, fluoroquinolone and tetracycline were 5.5%, 42.1%, 41.7% and 12.9% in the 111 first-treated patients, and 11.7%, 79.7%, 70.7% and 30.0% in the 150 re-treatment patients. The ERs in the ITT and PP analyses were 92.79% (95% CI, 87.98–97.60%, n=111) and 98.10% (95% CI, 95.48–100%, n=105), respectively, in the first-treated patients and 90.67% (95% CI, 86.01–95.32%, n=150) and 95.10% (95% CI, 91.57–98.64%, n=143), respectively, in the re-treatment patients. No significant differences were shown in the ERs between two group patients, and no serious adverse events were found.

Conclusion

H. pylori eradication treatment based on molecular pathologic antibiotic resistance showed good effect and safety in both first and re-treated patients.