Rapid identification of Helicobacter pylori and assessment of clarithromycin susceptibility from clinical specimens using FISH

Advances on diagnosis of Helicobacter pylori infections

The association of Helicobacter pylori to several gastric diseases, such as chronic gastritis, peptic ulcer disease, and gastric cancer, and its high prevalence worldwide, raised the necessity to use methods for a proper and fast diagnosis and monitoring the pathogen eradication. Available diagnostic methods can be classified as invasive or non-invasive, and the selection of the best relies on the clinical condition of the patient, as well as on the sensitivity, specificity, and accessibility of the diagnostic test. This review summarises all diagnostic methods currently available, including the invasive methods: endoscopy, histology, culture, and molecular methods, and the rapid urease test (RUT), as well as the non-invasive methods urea breath test (UBT), serological assays, biosensors, and microfluidic devices and the stool antigen test (SAT). Moreover, it lists the diagnostic advantages and limitations, as well as the main advances for each methodology. In the end, research on the development of new diagnostic methods, such as bacteriophage-based H. pylori diagnostic tools, is also discussed.

Optical detection using CRISPR-Cas12a of Helicobacter pylori for veterinary applications

Helicobacter pylori (H. pylori) is a zoonotic gastric microorganism capable of efficient interspecies transmission. Domesticated companion animals, particularly dogs and cats, serve as natural reservoirs for H. pylori. This phenomenon facilitates the extensive dissemination of H. pylori among households with pets. Hence, the prompt and precise identification of H. pylori in companion animals holds paramount importance for the well-being of both animals and their owners. With the assistance of Multienzyme Isothermal Rapid Amplification (MIRA) and CRISPR-Cas12a system, we successfully crafted a highly adaptable optical detection platform for H. pylori. Three sensor systems with corresponding visual interpretations were proposed. This study demonstrated a rapid turnaround time of approximately 45 min from DNA extraction to the result display. Moreover, this platform topped germiculture and real-time PCR in terms of sensitivity or efficiency in clinical diagnoses of 66 samples. This platform possesses significant potential as a versatile approach and represents the premiere application of CRISPR for the non-invasive detection of H. pylori in companion animals, thereby mitigating the dissemination of H. pylori among household members.

Approaches for detection of antibiotic resistance of Helicobacter pylori: Recent research advances

Helicobacter pylori (H. pylori) infection, a contagious disease, has affected approximately half of the global population. It is associated with the occurrence and development of many diseases, which seriously endangers human public health. Antibiotics play an important role in H. pylori eradication therapy, and the common regimens for H. pylori eradication contain one to three antibiotics. Antibiotic resistance is one of the main reasons for the failure of H. pylori eradication. Detection of antibiotic resistance can be helpful for individualized management, reduction of drug resistance, and improvement of H. pylori eradication. Methods to detect antibiotic resistance of H. pylori primarily consist of traditional drug sensitivity tests and molecular biology methods, such as polymerase chain reaction and its related techniques, DNA sequencing, fluorescence in situ hybridization, and gene chip. This paper reviews the recent advances in approaches for detection of antibiotic resistance of H. pylori.

Effectiveness of 7-day triple therapy with half-dose clarithromycin for the eradication of Helicobacter pylori without the A2143G and A2142G point mutations of the 23S rRNA gene in a high clarithromycin resistance area

Background

Tailored therapy has been widely used for patients with Helicobacter pylori (H. pylori) infection in South Korea. Herein, we evaluated the treatment outcomes of tailored clarithromycin-based triple therapy (TT) in patients infected with H. pylori.

Methods

We enrolled 460 patients without A2142G and A2143G point mutations by dual priming oligonucleotide-based polymerase chain reaction who had taken TT and undergone the urease breath test to evaluate eradication in clinical practice. Eradication rates according to the treatment duration and dose of clarithromycin were analyzed.

Results

Among 460 patients (164 women, median age 63.0 years), 250 patients underwent TT with full-dose clarithromycin (TT-full CLA), and 216 patients underwent TT with half-dose clarithromycin (TT-half CLA). The eradication rates were 88.0% (220/250) in patients with TT-full CLA and 85.2% (179/210) in patients with TT-half CLA. In 250 patients with TT-full CLA, the eradication rates were 86.8% (33/38) in patients with 7-day TT-full CLA and 88.2% (187/212) in patients with 10-day or 14-day TT-full CLA (P = 0.788). In 210 patients with TT-half CLA, the eradication rates were 84.2% (139/165) in those with a 7-day TT-half CLA and 88.9% (40/45) in those with a 10-day or 14-day TT-half CLA (P = 0.436).

Conclusion

For patients with H. pylori infection without A2142G and A2143G point mutations by DPO-PCR in clinical practice, treatment extension above 7-day TT with full CLA did not improve the eradication rates. Future studies on the treatment outcomes of TT-half CLA considering effectiveness and compliance are warranted.

The prevalence of clarithromycin-resistant Helicobacter pylori isolates: a systematic review and meta-analysis

Background

Knowledge of global clarithromycin (CLA)-resistant rates of Helicobacter pylori (H. pylori) is crucial for decision of the most appropriate eradication therapies with good clinical outcomes. Therefore, this review and meta-analysis aimed to evaluate the global prevalence of the CLA resistance in H. pylori to provide some guidance for selecting the first-line antibiotics.

Method

A comprehensive search was performed for relevant literature until April 2021 in PubMed, Embase, and Web of Science databases. Freeman-Tukey double arcsine transformation was performed to estimate the weighted pooled prevalence of resistance.

Results

The meta-analysis included 248 articles. The prevalence of CLA-resistant H. pylori was 27.53% (95% CI [25.41-29.69]). The heterogeneity between reports was significant (I² = 97.80%, P < 0.01). The resistance rate increased from 24.28% in 2010-2017 to 32.14% in 2018-2021 (P < 0.01). Iran, with 38 articles, has the most report. Nevertheless, Switzerland, Portugal, and Israel had the highest resistance rates (67.16%, 48.11%, and 46.12%, respectively). The heterogeneity between the continents and the antimicrobial susceptibility methods also interpreted standard guidelines and breakpoints was insignificant (P > 0.05).

Conclusion

Overall CLA resistance rate was 27.53%, worldwide. The difference in CLA resistance rate among the included studies can be due to several reasons such as differences in antibiotic prescription rates in various geographic areas, use of different breakpoints or inaccurate criteria in performed studies, and the emergence of multidrug-resistant (MDR) strains.

Antibacterial and antibiofilm activity of mannose-modified chitosan/PMLA nanoparticles against multidrug-resistant Helicobacter pylori

Because of the apparent stasis in antibiotic discoveries and the growth of multidrug resistance, Helicobacter pylori-associated gastric infections are difficult to eradicate. In the search for alternative therapy, the reductive amination of chitosan with mannose, followed by ionic gelation, produced mannose functionalized chitosan nanoparticles. Then, molecular docking and molecular dynamics (MD) simulations were conducted with H. pylori lectin (HPLectin) as a target protein involved in bacterium adherence to host cells, biofilm formation, and cytotoxicity. Changes in zeta potential and FTIR spectroscopy revealed that chitosan was functionalized with mannose. Time-kill, polystyrene adherence, and antibiofilm studies were utilized to assess nanoparticles as an alternative antibacterial treatment against a resistant gastric pathogen. Man-CS-Nps were discovered to have effective anti-adherence and biofilm disruption characteristics in suppressing the development of resistant H. pylori. In addition, bioimaging studies with CLSM, TEM, and SEM illustrated that Man-CS-Nps interacted with bacterial cells and induced membrane disruption by creating holes in the outer membranes of the bacterial cells, resulting in the leakage of amino acids. Importantly, molecular docking and 20 ns MD simulations revealed that Man-CS-Nps inhibited the target protein through slow-binding inhibition and hydrogen bond interactions with active site residues. As a consequence of the findings of this study, the Man-CS-Nps is an excellent candidate for developing alternative therapies for the increasing incidences of resistant gastric infections.

Exploring the potential of Cinnamomum zeylanicum oil against drug resistant Helicobacter pylori-producing cytotoxic genes

Thirty-one of sixty dyspeptic patients tested positive for Helicobacter pylori colonization in this study, as determined by histopathology and 16S rRNA. The cytotoxin-associated gene A (cagA) and vacuolating cytotoxin A (vacA) genes were found in 67.7 and 93.5% of H. pylori patients, respectively. The cagA gene was found to be associated with 100% of patients with duodenal erosion and ulceration identified via endoscopy examination. In addition, 86.7% of patients with cancerous and precancerous lesions, glandular atrophy, and intestinal metaplasia identified via histopathology examination. The vacA s1m1 mutation was associated with more severe forms of gastric erosion and ulceration, as well as the presence of precancerous and cancerous lesions. Eighteen (64.3%) of the twenty-eight isolates were classified as multi-drug resistant (MDR) or pan-drug resistant (PDR) H. pylori. Due to a resurgence of interest in alternative therapies derived from plants as a result of H. pylori resistance to the majority of commonly used antibiotics, the inhibitory activity of five essential oils extracted from some commonly used medicinal plants was evaluated in vitro against drug-resistant H. pylori clinical isolates. Cinnamomum zeylanicum essential oil demonstrated the highest anti-H. pylori activity when compared to the other essential oils tested. Cinnamaldehyde was the most abundant compound in C. zeylanicum (65.91%). The toxicological evaluation established the safety of C. zeylanicum oil for human use. As a result, C. zeylanicum essential oil may represent a novel antibacterial agent capable of combating drug-resistant H. pylori carrying cytotoxin genes.

Genetic Diversity of Helicobacter pylori Isolates from Patients with Gastric Diseases in Isfahan

Background

Helicobacter pylori (H. pylori), a spiral-shaped bacterium colonizing the human stomach, is generally acquired in childhood. This pathogen is highly diverse and can be used as genetic markers for predict the history of human migrations. This study aimed to determine the genetic diversity of H. pylori isolates from patients with dyspepsia by the multi-locus sequence typing (MLST) and update data on the prevalence of H. pylori among Iranian dyspeptic patients.

Materials and Methods

In this descriptive cross-sectional study, 165 gastric biopsy specimens were obtained from patients with dyspepsia referred to Dr. Shariati Hospital of Isfahan, Iran, from April to July 2018. The status of H. pylori infection was determined by FISH in paraffin-embedded biopsy specimens. MLST of seven housekeeping genes was performed for 20 H. pylori isolates. The phylogenetic tree was plotted using CLC v8 and iTol software.

Results

The overall prevalence of H. pylori infection was 53.3%. In the results of the analysis of MLST, a total of 14 new STs were recorded. The results of the global analysis showed that all the isolates, with a wide diversity, have a genetic affinity with members of the European population, such as Italy and Russia, and are in the hpEurope haplotype.

Conclusion

Given the high prevalence of H. pylori infection in this region, early and accurate identification of patients seems necessary. Sequence analysis and determination of the origin of the phylogeny of strains can be effective in clinical management and monitoring of risk factors for chronic and recurrence of infection.

Primary and secondary clarithromycin resistance in Helicobacter pylori and mathematical modeling of the role of macrolides

Clarithromycin is a macrolide antibiotic widely used for eradication of Helicobacter pylori infection, and thus resistance to this antibiotic is a major cause of treatment failure. Here, we present the results of a retrospective observational study of clarithromycin resistance (Cla-res) in 4744 H. pylori-infected patients from Central Hungary. We use immunohistochemistry and fluorescence in situ hybridization on fixed gastric tissue samples to determine H. pylori infection and to infer Cla-res status, respectively. We correlate this information with macrolide dispensing data for the same patients (available through a prescription database) and develop a mathematical model of the population dynamics of Cla-res H. pylori infections. Cla-res is found in 5.5% of macrolide-naive patients (primary Cla-res), with no significant sex difference. The model predicts that this primary Cla-res originates from transmission of resistant bacteria in 98.7% of cases, and derives from spontaneous mutations in the other 1.3%. We find an age-dependent preponderance of female patients among secondary (macrolide-exposed) clarithromycin-resistant infections, predominantly associated with prior use of macrolides for non-eradication purposes. Our results shed light into the sources of primary resistant cases, and indicate that the growth rate of Cla-res prevalence would likely decrease if macrolides were no longer used for purposes other than H. pylori eradication.

Clarithromycin is a macrolide antibiotic widely used for eradication of Helicobacter pylori infection. Here, Kocsmár et al. study clarithromycin resistance and previous macrolide consumption in 4,744 H. pylori-infected patients, shedding light into the sources of primary resistant cases and the role played by prior consumption of macrolides for non-eradication purposes.

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.

Antibiotic resistance in Helicobacter pylori

PURPOSE OF REVIEW

Treatment of Helicobacter pylori is difficult nowadays because of its high resistance. The prevalence and mechanism of resistance, the different methods to detect it and the clinical implication of resistance were addressed in several research papers last year.

RECENT FINDINGS

Clarithromycin-resistant H. pylori has been recognized by the WHO as 'high priority', for which new antibiotics are needed. Moreover, the Maastricht consensus recommended, in areas with high resistance, that susceptibility tests should be performed, at least after a treatment failure.

SUMMARY

Metronidazole and clarithromycin resistance rates are alarming although they vary among populations. Tetracycline and amoxicillin-resistance are very low in most countries. H. pylori resistance can be detected by phenotypic or by molecular methods. Different break points may be used when performing an antimicrobial susceptibility test, so comparing resistance among different populations is challenging. Genomic techniques open new possibilities in the diagnosis of H. pylori, and the detection of H. pylori and its antimicrobial resistance in faeces is an interesting approach. Eradication rates are dependent on the susceptibility of the strain to metronidazole and clarithromycin, being lower in patients infected with a resistant strain.

Diagnosis of Helicobacter pylori infection

Important progress is being made in endoscopic methods which allow clinicians to predict the presence of Helicobacter pylori based on characteristics of gastric mucosa and to obtain targeted biopsies. There are also important developments in molecular methods with various techniques derived from standard PCR, applied both on gastric biopsies and stool specimens. Progress is being made in microfluidic systems to get a reliable diagnosis in a very short time. The interest of the ¹³ C urea breath test has been confirmed as well as stool antigen tests. Attempts are being made to find biological markers of premalignant conditions by serology, other than pepsinogens.