Application of polymerase chain reaction-based assays for rapid identification and antibiotic resistance screening of Helicobacter pylori in gastric biopsies. Diagn Microbiol Infect Dis. 2008;61:67-71. [PMID: 18248939 DOI: 10.1016/j.diagmicrobio.2007.12.005]

The second Irish Helicobacter pylori Working Group consensus for the diagnosis and treatment of Helicobacter pylori infection in adult patients in Ireland

BACKGROUND

There has been an increase in resistance to many of the antimicrobials used to treat Helicobacter pylori ( H. pylori ) nationally and internationally. Primary clarithromycin resistance and dual clarithromycin and metronidazole resistance are high in Ireland. These trends call for an evaluation of best-practice management strategies.

OBJECTIVE

The objective of this study was to revise the recommendations for the management of H. pylori infection in adult patients in the Irish healthcare setting.

METHODS

The Irish H. pylori working group (IHPWG) was established in 2016 and reconvened in 2023 to evaluate the most up-to-date literature on H. pylori diagnosis, eradication rates and antimicrobial resistance. The 'GRADE' approach was then used to rate the quality of available evidence and grade the resulting recommendations.

RESULTS

The Irish H. pylori working group agreed on 14 consensus statements. Key recommendations include (1) routine antimicrobial susceptibility testing to guide therapy is no longer recommended other than for clarithromycin susceptibility testing for first-line treatment (statements 6 and 9), (2) clarithromycin triple therapy should only be prescribed as first-line therapy in cases where clarithromycin susceptibility has been confirmed (statement 9), (3) bismuth quadruple therapy (proton pump inhibitor, bismuth, metronidazole, tetracycline) is the recommended first-line therapy if clarithromycin resistance is unknown or confirmed (statement 10), (4) bismuth quadruple therapy with a proton pump inhibitor, levofloxacin and amoxicillin is the recommended second-line treatment (statement 11) and (5) rifabutin amoxicillin triple therapy is the recommend rescue therapy (statement 12).

CONCLUSION

These recommendations are intended to provide the most relevant current best-practice guidelines for the management of H. pylori infection in adults in Ireland.

Practice guidelines for the management of Helicobacter pylori infection: The Saudi H. pylori Working Group recommendations

The eradication rates for Helicobacter pylori globally are decreasing with a dramatic increase in the prevalence of antibiotic resistant bacteria all over the world, including Saudi Arabia. There is no current consensus on the management of H. pylori in Saudi Arabia. The Saudi Gastroenterology Association developed these practice guidelines after reviewing the local and regional studies on the management of H. pylori. The aim was to establish recommendations to guide healthcare providers in managing H. pylori in Saudi Arabia. Experts in the areas of H. pylori management and microbiology were invited to write these guidelines. A literature search was performed, and all authors participated in writing and reviewing the guidelines. In addition, international guidelines and consensus reports were reviewed to bridge the gap in knowledge when local and regional data were unavailable. There is limited local data on treatment of H. pylori. The rate of clarithromycin and metronidazole resistance is high; therefore, standard triple therapy for 10-14 days is no longer recommended in the treatment of H. pylori unless antimicrobial susceptibility testing was performed. Based on the available data, bismuth quadruple therapy for 10-14 days is considered the best first-line and second-line therapy. Culture and antimicrobial susceptibility testing should be considered following two treatment failures. These recommendations are intended to provide the most relevant evidence-based guidelines for the management of H. pylori infection in Saudi Arabia. The working group recommends further studies to explore more therapeutic options to eradicate H. pylori.

Genotypic detection of metronidazole and clarithromycin resistance in dyspeptic patients with helicobacter pylori

In Egypt, antibiotic sensitivity analysis for Helicobacter pylori is not routinely performed. We aimed to identify the clarithromycin and metronidazole resistance directly from gastric biopsies for better guide treatment regimens. This cross-sectional descriptive study included 75 adult dyspeptic patients referred to the upper endoscopy unit in Suez Canal University Hospital, Ismailia, Egypt. Gastric biopsies were taken for rapid urease test (RUT) and cultured on brucella agar with antibiotic supplements. Genomic DNA was extracted directly from the specimen, and PCR was performed for direct detection of H. pylori. Also, to explore clarithromycin and metronidazole resistance, mutations in the 23S rRNA gene and the rdxA gene were investigated. We found that 60 samples were positive to RUT (80%), and only 4 samples were positive by culture. UreC gene was detected in 45 specimens. Meanwhile, 26 isolates were contained mutations at positions 2142 and 2143. Amplification of the metronidazole rdx gene was performed by conventional PCR. Out of 45 isolates, DNA sequence analysis of PCR product showed the wild type (ACA) in 9 isolates, while the mutant type (ATA) was detected in 28 isolates. We found a significant proportion of clarithromycin and metronidazole resistance among H. pylori infected patients in our region.

Resistance mechanisms of Helicobacter pylori and its dual target precise therapy

Helicobacter pylori drug resistance presents a significant challenge to the successful eradication of this pathogen. To find strategies to improve the eradication efficacy of H. pylori, it is necessary to clarify the resistance mechanisms involved. The mechanisms of H. pylori drug resistance can be investigated from two angles: the pathogen and the host. A comprehensive understanding of the molecular mechanisms of H. pylori resistance based on both pathogen and host would aid the implementation of precise therapy, or ideally "dual target precise therapy" (bacteria and host-specific target therapy). In recent years, with increased understanding of the mechanisms of H. pylori resistance, the focus of eradication has shifted from disease-specific to patient-specific treatment. The implementation of "precision medicine" has also provided a new perspective on the treatment of infectious diseases. In this article, we systematically review current research on H. pylori drug resistance from the perspective of both the pathogen and the host. We also review therapeutic strategies targeted to pathogen and host factors that are aimed at achieving precise treatment of H. pylori.

A novel RT-PCR for the detection of Helicobacter pylori and identification of clarithromycin resistance mediated by mutations in the 23S rRNA gene

In this study we evaluated the commercially available LightMix® RT-PCR assay for Helicobacter pylori detection and identification of clarithromycin (CLR) resistance in culture and clinical specimens (gastric biopsies and stool). The H. pylori LightMix® RT-PCR detects a 97bp long fragment of the 23S rRNA gene and allows the identification of 3 distinct point mutations conferring CLR resistance via melting curve analysis. The performance of the H. pylori LightMix® RT-PCR was evaluated using a set of 60 H. pylori strains showing phenotypical CLR susceptibility or CLR resistance (Minimum inhibitory concentrations from 0.016 to 256mg/L). We found high concordance (95%) between phenotypical CLR resistance screening by E-Test® and the Lightmix® RT-PCR. Discrepant results were verified by sequencing of the 23S rRNA gene that always confirmed the results obtained by Lightmix® RT-PCR. Furthermore, H. pylori was detected in clinical biopsy and stool specimens by Lightmix® RT-PCR that identified the correct H. pylori genotype. The LightMix® RT-PCR is an accurate, sensitive and easy to use test for H. pylori and CLR resistance detection and can therefore be readily implemented in any diagnostic laboratory.

Gastrointestinal Infections

Establishing a specific etiology for gastrointestinal infections can be challenging because of the common clinical features and wide variety of causative microorganisms. In many cases, the etiologic agent cannot be determined using traditional diagnostic methods and may result in unnecessary antibiotic use or prolonged periods of illness. Molecular tests provide many advantages over traditional laboratory methods but, with the exception of a few analytes, are still largely in the developmental phase for gastrointestinal pathogens and are not widely used. The main advantages of molecular tests include increased sensitivity and the ability to detect agents which will not grow in culture. To test for all possible gastrointestinal pathogens at one time would require a large panel that would include a variety of bacterial, viral and parasitic agents. Challenges inherent in developing diagnostic molecular panels include ensuring that all variants of a particular microorganism can be detected as well as the rapid evolution of pathogens. In this chapter, the diagnostic merit of molecular tests as well as available tests will be presented for the major groups of gastrointestinal pathogens.

Management of Helicobacter pylori infection in Latin America: a Delphi technique-based consensus

AIM

To optimize diagnosis and treatment guidelines for this geographic region, a panel of gastroenterologists, epidemiologists, and basic scientists carried out a structured evaluation of available literature.

METHODS

Relevant questions were distributed among the experts, who generated draft statements for consideration by the entire panel. A modified three-round Delphi technique method was used to reach consensus. Critical input was also obtained from representatives of the concerned medical community. The quality of the evidence and level of recommendation supporting each statement was graded according to United States Preventive Services Task Force criteria.

RESULTS

A group of ten experts was established. The survey included 15 open-ended questions that were distributed among the experts, who assessed the articles associated with each question. The levels of agreement achieved by the panel were 50% in the first round, 73.3% in the second round and 100% in the third round. Main consensus recommendations included: (1) when available, urea breath and stool antigen test (HpSA) should be used for non-invasive diagnosis; (2) detect and eradicate Helicobacter pylori (H. pylori) in all gastroscopy patients to decrease risk of peptic ulcer disease, prevent o retard progression in patients with preneoplastic lesions, and to prevent recurrence in patients treated for gastric cancer; (3) further investigate implementation issues and health outcomes of H. pylori eradication for primary prevention of gastric cancer in high-risk populations; (4) prescribe standard 14-d triple therapy or sequential therapy for first-line treatment; (5) routinely assess eradication success post-treatment in clinical settings; and (6) select second- and third-line therapies according to antibiotic susceptibility testing.

CONCLUSION

These achievable steps toward better region-specific management can be expected to improve clinical health outcomes.

Antimicrobial susceptibility testing for Helicobacter pylori in times of increasing antibiotic resistance

The gram-negative bacterium Helicobacter pylori (H. pylori) causes chronic gastritis, gastric and duodenal ulcers, gastric cancer and mucosa-associated lymphoid tissue lymphoma. Treatment is recommended in all symptomatic patients. The current treatment options for H. pylori infection are outlined in this review in light of the recent challenges in eradication success, largely due to the rapid emergence of antibiotic resistant strains of H. pylori. Antibiotic resistance is a constantly evolving process and numerous studies have shown that the prevalence of H. pylori antibiotic resistance varies significantly from country to country, and even between regions within the same country. In addition, recent data has shown that previous antibiotic use is associated with harbouring antibiotic resistant H. pylori. Local surveillance of antibiotic resistance is warranted to guide clinicians in their choice of therapy. Antimicrobial resistance is assessed by H. pylori culture and antimicrobial susceptibility testing. Recently developed molecular tests offer an attractive alternative to culture and allow for the rapid molecular genetic identification of H. pylori and resistance-associated mutations directly from biopsy samples or bacterial culture material. Accumulating evidence indicates that surveillance of antimicrobial resistance by susceptibility testing is feasible and necessary to inform clinicians in their choice of therapy for management of H. pylori infection.

Antigenic proteins of Helicobacter pylori of potential diagnostic value

Helicobacter pylori antigen was prepared from an isolate from a patient with a duodenal ulcer. Serum samples were obtained from culture-positive H. pylori infected patients with duodenal ulcers, gastric ulcers and gastritis (n=30). As controls, three kinds of sera without detectable H. pylori IgG antibodies were used: 30 from healthy individuals without history of gastric disorders, 30 from patients who were seen in the endoscopy clinic but were H. pylori culture negative and 30 from people with other diseases. OFF-GEL electrophoresis, SDS-PAGE and Western blots of individual serum samples were used to identify protein bands with good sensitivity and specificity when probed with the above sera and HRP-conjugated anti-human IgG. Four H. pylori protein bands showed good (≥ 70%) sensitivity and high specificity (98-100%) towards anti-Helicobacter IgG antibody in culture- positive patients sera and control sera, respectively. The identities of the antigenic proteins were elucidated by mass spectrometry. The relative molecular weights and the identities of the proteins, based on MALDI TOF/ TOF, were as follows: CagI (25 kDa), urease G accessory protein (25 kDa), UreB (63 kDa) and proline/pyrroline- 5-carboxylate dehydrogenase (118 KDa). These identified proteins, singly and/or in combinations, may be useful for diagnosis of H. pylori infection in patients.

Change of point mutations in Helicobacter pylori rRNA associated with clarithromycin resistance in Italy

Primary clarithromycin resistance is the main factor affecting the efficacy of Helicobacter pylori therapy. This study aimed: (i) to assess the concordance between phenotypic (culture) and genotypic (real-time PCR) tests in resistant strains; (ii) to search, in the case of disagreement between the methods, for point mutations other than those reported as the most frequent in Europe; and (iii) to compare the MICs associated with the single point mutations. In order to perform real-time PCR, we retrieved biopsies from patients in whom H. pylori infection was successful diagnosed by bacterial culture and clarithromycin resistance was assessed using the Etest. Only patients who had never been previously treated, and with H. pylori strains that were either resistant exclusively to clarithromycin or without any resistance, were included. Biopsies from 82 infected patients were analysed, including 42 strains that were clarithromycin resistant and 40 that were clarithromycin susceptible on culture. On genotypic analysis, at least one of the three most frequently reported point mutations (A2142C, A2142G and A2143G) was detected in only 23 cases (54.8%), with a concordance between the two methods of 0.67. Novel point mutations (A2115G, G2141A and A2144T) were detected in a further 14 out of 19 discordant cases, increasing the resistance detection rate of PCR to 88% (P<0.001; odds ratio 6.1, 95% confidence interval 2-18.6) and the concordance to 0.81. No significant differences in MIC values among different point mutations were observed. This study suggests that: (i) the prevalence of the usually reported point mutations may be decreasing, with a concomitant emergence of new mutations; (ii) PCR-based methods should search for at least six point mutations to achieve good accuracy in detecting clarithromycin resistance; and (iii) none of the tested point mutations is associated with significantly higher MIC values than the others.

Detection of Helicobacter pylori DNA in preliminary stage gastric cancer cells

AIMS

Helicobacter pylori (HP) DNA was assayed using a newly fabricated voltammetric handheld circuit equipped with an interfaced graphite pencil electrode (PE) sensor.

METHODS

Under optimum analytical parameters, the square-wave (SW) stripping detection range attained was 0.1-0.7 mg/L.

RESULTS

A relative standard deviation of 1.68% (RSD, n = 5) was observed at a 3.2 mg/L HP DNA within a 90 s accumulation time. Under these conditions, the analytical detection limit approached 0.07 mg/L.

CONCLUSIONS

The developed methods can be applied to HP assays of preliminary stage gastric cancer patient tissues.

Evaluation for Helicobacter pylori in Meckel's diverticulum by using real-time PCR

BACKGROUND

Although Helicobacter pylori (H. pylori) has been identified in heterotopic gastric mucosa of Meckel's diverticulum, controversial results are reported in the pertinent literature.

AIMS

The aim of this study was to evaluate for the presence of H. pylori histologically using hematoxylin-eosin and Toluidine Blue in Meckel's diverticulum and by real-time TaqMan polymerase chain reaction (PCR) in those with heterotopic gastric mucosa.

METHODS

The study included 21 consecutive patients who had undergone resection of Meckel's diverticulum at our hospital between 1995 and 2007. The paraffin-embedded tissues were retrieved and reviewed for the presence of histological abnormalities and H. pylori-like organisms and for the presence or absence of heterotopic mucosa. H. pylori was sought in those cases that contained heterotopic gastric mucosa using real-time TaqMan PCR to amplify a fragment of the 23S ribosomal RNA (rRNA) gene of H. pylori.

RESULTS

Upon histological examination, heterotopic gastric mucosa was found to be present in 12 cases. H. pylori was not identified in any of the sections examined. A genomic PCR product was also not obtained in real-time PCR study.

CONCLUSIONS

We have confirmed that colonization of H. pylori, if it occurs at all, is exceedingly rare in heterotopic gastric mucosa of Meckel's diverticulum.

Detection, cloning and sequence analysis of the urea channel protein gene ureI of Helicobacter pylori

AIM: To detect, clone and sequence the urea channel protein gene ureI of Helicobacter pylori (H. pylori) strains isolated from Zhenjiang area.

METHODS: Sixty H. pylori strains were isolated from gastric mucosa of patients with chronic gastritis, peptic ulcer or gastric cancer, and cultured on solid agar medium. The gene encoding UreI protein was amplified from H. pylori genomic DNA by polymerase chain reaction (PCR). The amplified ureI genes from some strains derived from different patients were cloned into T vector, sequenced and analyzed using bioinformatic methods.

RESULTS: The ureI gene was detected in 100% (60/60) of H. pylori strains. The ureI genes of eight H. pylori strains derived from patients with chronic gastritis, peptic ulcer and gastric cancer were cloned and sequenced. The nucleotide and amino acid sequence homology among the ureI genes derived from different H. pylori strains is more than 95.6%.

CONCLUSION: The ureI gene is conserved among H. pylori strains and can be used as a good molecular marker for identification of H. pylori.

Phenotypic and genotypic Helicobacter pylori clarithromycin resistance and therapeutic outcome: benefits and limits

INTRODUCTION

Primary clarithromycin resistance is increasing worldwide, and it has been regarded as the main factor reducing the efficacy of Helicobacter pylori therapy. However, the clinical consequence of either phenotypic or genotypic resistance still remains unclear. This study aimed to evaluate: (i) the concordance between phenotypic (culture) and genotypic (real-time PCR) tests in assessing primary clarithromycin resistance; and (ii) the role of both in therapeutic outcome.

METHODS

A post hoc subgroup study was selected from a double-blind, placebo-controlled trial, enrolling 146 patients with dyspepsia or peptic ulcers never previously treated. Real-time PCR and Etest on bacterial culture for assessing clarithromycin resistance were performed. [(13)C]urea breath test (UBT), histology and rapid urease tests at entry and UBT after 4-8 weeks were used to assess infection and eradication. All patients received a 10 day therapy.

RESULTS

Prevalence of clarithromycin phenotypic resistance was significantly lower as compared with genotypic resistance (18.4% versus 37.6%, P < 0.001). A concordance between the two methods was present in 71.2% of cases. A significant difference in the eradication rate was seen between clarithromycin-susceptible and -resistant strains, when assessed with either Etest (92.4% versus 55.5%, P < 0.001) or a PCR-based method (94.5% versus 70.9%; P < 0.001). Of note, the eradication rate showed the lowest value (30.7%) when phenotypic bacterial resistance was genetically linked to the A2143G point mutation.

CONCLUSIONS

This study showed that: (i) there is a relevant discordance between the two methods; and (ii) phenotypic clarithromycin resistance markedly reduces H. pylori eradication when it is linked to a specific point mutation.

Diagnosis of Helicobacter pylori infection

The articles published this last year in the field of Helicobacter pylori diagnosis reported the development of in vivo histology, small improvements in some invasive methods (urease test, culture, and histology) and new kits for the stool antigen tests. They also contributed to increasing our knowledge, by further exploration into specific conditions for the urea breath test and into the significance of cagA antibodies. The role of serum markers of atrophy was also confirmed. Molecular methods are still being developed for direct genotyping, detection of H. pylori and its clarithromycin resistance, either by polymerase chain reaction or fluorescent in-situ hybridization. For the first time, there was a report on a possible interest of magnetic resonance spectroscopy.

Frequency and molecular characteristics of ciprofloxacin- and rifampicin-resistant Helicobacter pylori from gastric infections in the UK

Treatment failure with standard Helicobacter pylori eradication regimes may require the use of 'rescue' therapies containing fluoroquinolones or rifamycins. The susceptibilities of H. pylori in the UK to such antimicrobials are unknown; therefore, this study aimed to determine the frequencies and molecular markers of resistance. Ciprofloxacin and rifampicin susceptibilities were determined by Etest and/or disc diffusion for 255 isolates of H. pylori, including 171 isolates from adult dyspeptic patients with refractive infections. Mutations in known resistance-determining regions of gyrA and rpoB were determined. The ciprofloxacin resistance rate was 7.5 %, and gyrA mutations, predominantly at codon position 91, were identified in most resistant isolates. One isolate (<1 %) had an unequivocal rifampicin-resistant phenotype by Etest yet had no associated mutations in the rpoB gene. As resistance rates were low in H. pylori isolates, including those from patients with refractive infections, it was concluded that fluoroquinolones or rifamycins might be considered in the UK for inclusion in 'rescue' therapies.

Dual-priming oligonucleotide-based multiplex PCR for the detection of Helicobacter pylori and determination of clarithromycin resistance with gastric biopsy specimens

BACKGROUND

Assessment of Helicobacter pylori (H. pylori) clarithromycin resistance has rarely been performed routinely despite an increasing resistance rate. Our aim was to develop and evaluate the use of dual-priming oligonucleotide (DPO)-based multiplex polymerase chain reaction (PCR) to detect point mutations in the 23S rRNA gene responsible for clarithromycin resistance of H. pylori.

MATERIALS AND METHODS

Gastric biopsy specimens from 212 untreated patients with dyspepsia were examined by culture, histology, and DPO-based multiplex PCR. A disk diffusion test and E-test were used for performing phenotypic antibiotic susceptibility tests.

RESULTS

Among the biopsy specimens tested, 22.2% (47/212), 42.5% (90/212), and 41.5% (88/212) of the specimens were classified as H. pylori positive by culture, histology, and DPO-based multiplex PCR, respectively. Among 96 strains identified by either culture or DPO-based multiplex PCR, 80 strains were clarithromycin-susceptible and 16 strains (16.7%) were clarithromycin-resistant. There was 94.1% (32/34) concordance between phenotypic susceptibility tests and DPO-based multiplex PCR. In two patients with discrepant results, only DPO-based multiplex PCR detected clarithromycin-resistant strains. DPO-based multiplex PCR identified additional 49 clarithromycin-resistant or clarithromycin-susceptible H. pylori among 165 culture-negative specimens.

CONCLUSIONS

DPO-based multiplex PCR can be used as a practical method for the detection of H. pylori infection and the determination of clarithromycin susceptibility in addition to phenotypic antimicrobial susceptibility tests.

Diagnosis of Helicobacter pylori

The different invasive and noninvasive diagnostic tests for Helicobacter pylori have been applied mainly in emerging countries. Molecular methods have been developed, especially a test for detection of H. pylori and its clarithromycin resistance directly from stools. The long-term effects of eradication on histologic lesions have been studied in a meta-analysis and the prognostic value of post-treatment in gastric mucosa-associated lymphoid tissue lymphoma has been assessed. An operating link for gastritis assessment (the OLGA staging) has also been published. Attempts to simplify the urea breath test protocol have been made, and new stool antigen tests have been proposed and compared to those previously available.