Characteristics of Helicobacter pylori Heteroresistance in Gastric Biopsies and Its Clinical Relevance

The Accuracy of Melting Curve-Based Multiplex Real-Time PCR for Diagnosing Helicobacter pylori Resistance to Clarithromycin and Levofloxacin in Stool Specimens

AIMS

This study evaluates the accuracy of melting curve-based multiplex real-time PCR (multiplex rt-PCR) on stool samples for diagnosing antibiotic resistance in Helicobacter pylori (H. pylori) compared to E-test and sequencing.

METHODS

Gastric biopsies and stool samples were collected from 385 H. pylori-infected patients. A total of 325 strains were isolated, and genomic DNA was extracted from all 385 stool samples. E-tests were conducted to detect phenotypic resistance for clarithromycin and levofloxacin. Sanger sequencing and multiplex rt-PCR were employed to identify H. pylori 23S rRNA and GyrA mutations.

RESULTS

E-test results indicated that 203 (62.5%) were susceptible to both clarithromycin and levofloxacin, 33 (10.2%) exhibited mono-resistance to clarithromycin, 48 (14.8%) showed mono-resistance to levofloxacin, and 41 (12.6%) had dual resistance to both antibiotics. Compared to E-test results, the sensitivity and specificity of the multiplex rt-PCR method for detecting clarithromycin resistance mutation were 93.2 (95% CI 84.3-97.5) and 87.1% (95% CI 82.2-90.9), respectively. For levofloxacin resistance mutation, the multiplex rt-PCR method showed a sensitivity of 80.7 (95% CI 70.3-88.3) and a specificity of 93.0% (95% CI 88.7-95.8). Compared to Sanger sequencing, the sensitivity and specificity of the multiplex rt-PCR method for detecting clarithromycin resistance mutation were 95.8 (95% CI 90.0-98.4) and 96.0% (95% CI 92.6-98.0), respectively. For levofloxacin resistance mutation, the multiplex rt-PCR method showed a sensitivity of 91.3% (95% CI, 83.1-95.9) and a specificity of 96.1% (95% CI, 92.7-98.0).

CONCLUSION

Genotypic methods, including Sanger sequencing and multiplex rt-PCR, were rapid and reliable for diagnosing clarithromycin and levofloxacin resistance in the stool samples.

Pangenome Analysis of Helicobacter pylori Isolates from Selected Areas of Africa Indicated Diverse Antibiotic Resistance and Virulence Genes

The challenge facing Helicobacter pylori (H. pylori) infection management in some parts of Africa is the evolution of drug-resistant species, the lack of gold standard in diagnostic methods, and the ineffectiveness of current vaccines against the bacteria. It is being established that even though clinical consequences linked to the bacteria vary geographically, there is rather a generic approach to treatment. This situation has remained problematic in the successful fight against the bacteria in parts of Africa. As a result, this study compared the genomes of selected H. pylori isolates from selected areas of Africa and evaluated their virulence and antibiotic drug resistance, those that are highly pathogenic and are associated with specific clinical outcomes and those that are less virulent and rarely associated with clinical outcomes. 146 genomes of H. pylori isolated from selected locations of Africa were sampled, and bioinformatic tools such as Abricate, CARD RGI, MLST, Prokka, Roary, Phandango, Google Sheets, and iTOLS were used to compare the isolates and their antibiotic resistance or susceptibility. Over 20 k virulence and AMR genes were observed. About 95% of the isolates were genetically diverse, 90% of the isolates harbored shell genes, and 50% harbored cloud and core genes. Some isolates did not retain the cagA and vacA genes. Clarithromycin, metronidazole, amoxicillin, and tinidazole were resistant to most AMR genes (vacA, cagA, oip, and bab). Conclusion. This study found both virulence and AMR genes in all H. pylori strains in all the selected geographies around Africa with differing quantities. MLST, Pangenome, and ORF analyses showed disparities among the isolates. This in general could imply diversities in terms of genetics, evolution, and protein production. Therefore, generic administration of antibiotics such as clarithromycin, amoxicillin, and erythromycin as treatment methods in the African subregion could be contributing to the spread of the bacterium's antibiotic resistance.

Efficacy of genotypic susceptibility-guided tailored therapy for Helicobacter pylori infection: A systematic review and single arm meta-analysis

BACKGROUND AND AIM

The prevalence of antibiotic resistance for Helicobacter pylori (H. pylori) has been increasing over the year, making it more difficult for traditional empirical therapy to successfully eradicate H. pylori. Thus, tailored therapy (TT) guided by molecular-based antibiotic susceptibility testing (AST) has been frequently recommended. We conducted a single-arm meta-analysis to determine the efficacy of tailored therapy guided by molecular-based AST.

METHODS

A systematic literature review was performed on multiple databases, and studies on molecular-based TT were included. The eradication rates of TT by intention-to-treat (ITT) and per-protocol (PP) analyses were pooled respectively.

RESULTS

A total of 35 studies from 31 literature (4626 patients) were included in the single-arm meta-analysis. Overall, the pooled eradication rate of TT was 86.9% (95% CI:84.7%-89.1%) by the ITT analysis, and 91.5% (95% CI:89.8%-93.2%) by PP analysis. The pooled eradication rates of first-line TT and rescue TT were 86.6% and 85.1% by ITT analysis and 92.0% and 87.9% by PP analysis, respectively. When tailored rescue therapy was based on the genotypic resistance to at least four antibiotics, the pooled eradication rates reached 89.4% by ITT analysis and 92.1% by PP analysis. For genotype-susceptive strains, the pooled eradication rate of TT with targeted antibiotics was 93.1% (95% CI:91.3%-94.9%), among which the pooled eradication rate of tailored bismuth quadruple therapy was the highest (94.3%). Besides, the eradication rate of 7-day TT or tailored triple therapy without bismuth for genotype-susceptive strains could both reach more than 93.0%.

CONCLUSION

Tailored therapy guided by molecular-based AST can achieve somewhat ideal therapeutic outcomes. TT with a 7-day duration or without bismuth for genotype-susceptible strains can achieve good eradication efficacy. The effectiveness of TT can be improved to some extent by expanding the coverage of AST or by adding bismuth.

Helicobacter pylori infection: a dynamic process from diagnosis to treatment

Helicobacter pylori, a gram-negative microaerophilic pathogen, causes several upper gastrointestinal diseases, such as chronic gastritis, peptic ulcer disease, and gastric cancer. For the diseases listed above, H. pylori has different pathogenic mechanisms, including colonization and virulence factor expression. It is essential to make accurate diagnoses and provide patients with effective treatment to achieve positive clinical outcomes. Detection of H. pylori can be accomplished invasively and noninvasively, with both having advantages and limitations. To enhance therapeutic outcomes, novel therapeutic regimens, as well as adjunctive therapies with probiotics and traditional Chinese medicine, have been attempted along with traditional empiric treatments, such as triple and bismuth quadruple therapies. An H. pylori infection, however, is difficult to eradicate during treatment owing to bacterial resistance, and there is no commonly available preventive vaccine. The purpose of this review is to provide an overview of our understanding of H. pylori infections and to highlight current treatment and diagnostic options.

Whole Genome Sequencing for Studying Helicobacter pylori Antimicrobial Resistance

Antibiotic resistance (AMR) is an alarming concern worldwide and Helicobacter pylori, one of the most prevalent bacteria, is not an exception. With antibiotics being its primary therapy, increasing resistance leads to a higher rate of treatment failure. Understanding the genomic mechanisms of resistance to clarithromycin, levofloxacin, metronidazole, amoxicillin, tetracycline, and rifampicin through next-generation sequencing-based molecular tools, such as whole genome sequencing (WGS), can be of great value, not only to direct a patient's treatment, but also to establish and optimize treatment guidelines according to the local epidemiology and to avoid the use of inappropriate antibiotics. WGS approaches allow us to gain insight into the genomic determinants involved in AMR. To this end, different pipelines and platforms are continuously being developed. In this study, we take a more detailed view of the use and progression of WGS for in-depth study of H. pylori's AMR.

A comparative study of laboratory methods for detecting Helicobacter pylori antibiotic resistance

The rise of antibiotic resistance in H. pylori has led to a decrease in the effectiveness of eradication therapy. Treatment plans are now chosen based on local antibiotic resistance data, with a primary focus on clarithromycin. An approach tailored to individual patients for H. pylori eradication has been proposed, involving the assessment of antibiotic resistance before starting the initial treatment. The objective of this study is to compare and describe phenotypic and molecular-genetic methods for detecting antibiotic resistance in H. pylori, while also evaluating their diagnostic accuracy. Materials and methods. In this study, we examined 25 cultures of H. pylori with known phenotypic sensitivity and resistance to antibacterial agents. We determined resistance to clarithromycin and levofloxacin through a series of dilutions in Mueller-Hinton agar with added sheep blood, following the guidelines of the Clinical and Laboratory Standards Institute (CLSI). Molecular markers of resistance were analyzed using Sanger sequencing and real-time polymerase chain reaction (RT-PCR) with specific primers. To assess the diagnostic accuracy, we compared the results of these molecular methods with those of the phenotypic method. Results. We established a complete agreement between the results obtained through phenotypic and molecular methods when detecting H. pylori resistance to clarithromycin. When evaluating levofloxacin resistance, we observed that cultures displaying phenotypic resistance also harbored mutations in the gyrA gene associated with resistance. Interestingly, some cultures without phenotypic resistance still exhibited characteristic gyrA gene mutations. The molecular methods demonstrated 100% sensitivity in detecting clarithromycin resistance and 100% sensitivity in detecting levofloxacin resistance, with a specificity of 78.57%. Conclusion. This research highlights a strong correlation between phenotypic and molecular resistance assessments in H. pylori, particularly in the case of clarithromycin. Sanger sequencing and RT-PCR consistently yielded reliable results, underscoring the trustworthiness of these methods.

Helicobacter pylori infection

Helicobacter pylori infection causes chronic gastritis, which can progress to severe gastroduodenal pathologies, including peptic ulcer, gastric cancer and gastric mucosa-associated lymphoid tissue lymphoma. H. pylori is usually transmitted in childhood and persists for life if untreated. The infection affects around half of the population in the world but prevalence varies according to location and sanitation standards. H. pylori has unique properties to colonize gastric epithelium in an acidic environment. The pathophysiology of H. pylori infection is dependent on complex bacterial virulence mechanisms and their interaction with the host immune system and environmental factors, resulting in distinct gastritis phenotypes that determine possible progression to different gastroduodenal pathologies. The causative role of H. pylori infection in gastric cancer development presents the opportunity for preventive screen-and-treat strategies. Invasive, endoscopy-based and non-invasive methods, including breath, stool and serological tests, are used in the diagnosis of H. pylori infection. Their use depends on the specific individual patient history and local availability. H. pylori treatment consists of a strong acid suppressant in various combinations with antibiotics and/or bismuth. The dramatic increase in resistance to key antibiotics used in H. pylori eradication demands antibiotic susceptibility testing, surveillance of resistance and antibiotic stewardship.

Gastroprotective and anti-Helicobacter pylori potentials of essential oils from the oleoresins of Araucaria bidwillii and Araucaria heterophylla

Plant resins or oleoresins comprise a chemically complex mixture of different classes of compounds. Oleoresin of the genus Araucaria combines essential oil (EO) and resin. It possesses gastroprotective, cytotoxic, and timicrobial, antipyretic, and anti-inflammatory activities. The study aimed to investigate the EOs from the oleoresins of two Araucaria species, A. bidwillii and A. heterophylla, chemically and biologically for their gastroprotective, anti-inflammatory, antioxidant, and anti-Helicobacter pylori potentials. The chemical composition of both species cultivated in Egypt was analyzed with GC-MS and compared with those cultivated abroad using principal component analysis (PCA). There were 37 and 17 secondary metabolites identified in A. heterophylla and A. bidwillii, respectively. The EOs of both species showed a pronounced inhibitory effect on Helicobacter pylori activity in vitro. The gastroprotective effect was assessed in vivo using ethanol-induced gastric ulcer model in rats. Inflammatory cytokines, oxidative stress, and the nuclear factor-kappa B (NF-κB) biomarkers were assessed in the stomach tissues. The ulcer index and percentage of ulcer protection were determined. Stomach sections were examined histopathologically by staining with (H/E) and periodic acid Schiff (PAS). Moreover, the proliferative index was determined using the Ki-67 immunostaining. The treatment of rats with EOs (50, 100, and 200 mg/kg, orally) 1 hour prior to ethanol administration showed promising gastroprotective, anti-inflammatory, and antioxidant potentials. These findings declared the gastroprotective role played by both EOs with the superiority of A. bidwillii over A. heterophylla via modulation of oxidative stress/NF-κB/inflammatory cytokines. Their use can be recommended to protect against the recurrence of peptic ulcers.