Mucosal polymerase chain reaction for diagnosing Helicobacter pylori infection in patients with bleeding peptic ulcers

Helicobacter pylori Infection, Its Laboratory Diagnosis, and Antimicrobial Resistance: a Perspective of Clinical Relevance

Despite the recent decrease in overall prevalence of Helicobacter pylori infection, morbidity and mortality rates associated with gastric cancer remain high. The antimicrobial resistance developments and treatment failure are fueling the global burden of H. pylori-associated gastric complications. Accurate diagnosis remains the opening move for treatment and eradication of infections caused by microorganisms. Although several reports have been published on diagnostic approaches for H. pylori infection, most lack the data regarding diagnosis from a clinical perspective. Therefore, we provide an intensive, comprehensive, and updated description of the currently available diagnostic methods that can help clinicians, infection diagnosis professionals, and H. pylori researchers working on infection epidemiology to broaden their understanding and to select appropriate diagnostic methods. We also emphasize appropriate diagnostic approaches based on clinical settings (either clinical diagnosis or mass screening), patient factors (either age or other predisposing factors), and clinical factors (either upper gastrointestinal bleeding or partial gastrectomy) and appropriate methods to be considered for evaluating eradication efficacy. Furthermore, to cope with the increasing trend of antimicrobial resistance, a better understanding of its emergence and current diagnostic approaches for resistance detection remain inevitable.

Molecular detection of Helicobacter pylori and clarithromycin resistance in gastric biopsies: a prospective evaluation of RIDA®GENE Helicobacter pylori assay

Background: Empirical treatment of Helicobacter pylori (HP) depends on the local prevalence of clarithromycin resistance but data are lacking and culturing of HP is time-consuming. We evaluated RIDA®GENE Helicobacter pylori assay (r-biopharm), a quantitative PCR assay for detecting HP and clarithromycin resistance mutations in gastric biopsies.Material/methods: Gastric biopsies were obtained from each of 436 consecutive patients referred for gastroscopic investigation and results of qPCR were compared to culture and immunohistochemical staining (IHCS).Results: Of 436 samples, 47 were positive for HP by PCR (11%), 42 by culture (9.7%) and 44 by IHCS (10%). Compared to culture, sensitivity and specificity of the qPCR were 100% and 99%, respectively, and 96% and 99% compared to IHCS. The sensitivity and specificity for clarithromycin resistance detection were 92% and 97%, respectively.Conclusions: RIDA®GENE Helicobacter pylori assay reliably and rapidly detects HP and its resistance to clarithromycin in human gastric biopsies.

Accuracy of the Helicobacter pylori diagnostic tests in patients with peptic ulcer bleeding: a systematic review and network meta-analysis

INTRODUCTION

Some studies suggest that the accuracy of Helicobacter pylori diagnostic tests is decreased in peptic ulcer bleeding (PUB). We aimed to assess the accuracy of diagnostic tests for H. pylori in patients with PUB in a diagnostic test accuracy (DTA) network meta-analysis.

METHODS

A systematic search was carried out in seven databases until November 2019. We collected or calculated true and false positive and negative values, and constructed 2×2 diagnostic contingency tables with reference standards including histology, rapid urease test, urea breath test, serology, stool antigen test, culture, and polymerase chain reaction. We ranked the index tests by the superiority indices (SI) and calculated pooled sensitivity and specificity of each test.

DISCUSSION

Our search yielded 40 eligible studies with 27 different diagnostic strategies for H. pylori. In 32 articles, the reference standard was a combination of multiple tests. In 12 studies, the index tests were compared with a single testing method. We analyzed seven networks with the reference standards against a single or a combination of diagnostic index tests. None of the index tests had better diagnostic accuracy (SI between 9.94 and 2.17) compared with the individual index tests as all the confidence intervals included 1. Combined testing strategies had higher sensitivities (0.92-0.62) and lower specificities (0.85-0.46) while single tests proved to have higher specificities (0.83-0.77) and lower sensitivities (0.73-0.42).

CONCLUSION

Use of combined tests may have a rationale in clinical practice due to their higher sensitivities. The differences between the included DTA studies limited the comparison of the testing strategies.

Droplet Digital PCR Detects Low-Density Infection in a Significant Proportion of Helicobacter Pylori-Negative Gastric Biopsies of Dyspeptic Patients

INTRODUCTION

Helicobacter pylori-infected individuals may present low-density infection, undetectable by conventional tests such as histology, rapid urease test, or urea breath test. Droplet digital polymerase chain reaction (ddPCR) is more sensitive than other polymerase chain reaction methods. We aimed to evaluate the ability of ddPCR to detect H. pylori infection in patients diagnosed as negative by conventional tests.

METHODS

Dyspeptic patients (n = 236) were tested for H. pylori by histology, urea breath test, and rapid urease test. Patients were classified as having 3 positive (n = 25, control group), 2 positive (n = 12), one positive (n = 41), or zero positive (n = 158) diagnostic tests. DNA was extracted from gastric biopsies. Triplicate ddPCR testing for each of the 16S rDNA, ureA, and vacA(s) genes was performed using a QX200 ddPCR system (Bio-Rad). A gene was considered positive when detected by at least 2 of 3 repeated ddPCRs. H. pylori positivity was defined as having 2 or more positive genes.

RESULTS

All the biopsies of the control patients were positive for all 3 16S rDNA, ureA, and vacA(s) genes. H. pylori infection was detected in 57 (36%), 22 (54%), and 9 (75%) patients with zero, 1, and 2 positive diagnostic tests, respectively. The density of infection was 5, 121, 599, and 3,133 copies of H. pylori genome equivalents for patients with zero, 1, and 2 of 3 positive test results and for the control group, respectively.

DISCUSSION

ddPCR detected low-density "occult" H. pylori infection in a significant proportion (36%) of patients diagnosed as negative by conventional methods. The number of conventional positive tests was related to the density of infection.

IVTH BRAZILIAN CONSENSUS CONFERENCE ON HELICOBACTER PYLORI INFECTION

ABSTRACT Significant progress has been obtained since the III Brazilian Consensus Conference on H. pylori infection held in 2012, in Bento Gonçalves, Brazil, and justify a fourth meeting to establish updated guidelines on the current management of H. pylori infection. Therefore, the Núcleo Brasileiro para Estudo do Helicobacter pylori e Microbiota (NBEHPM), association linked to Brazilian Federation of Gastroenterology (FBG) held its fourth meeting again in Bento Gonçalves, RS, Brazil, on August 25-27, 2017. Twenty-six delegates, including gastroenterologists, endoscopists, and pathologists from the five regions of Brazil as well as one international guest from the United States, participated in the meeting. The participants were invited based on their knowledge and contribution to the study of H. pylori infection. The meeting sought to review different aspects of treatment for infection; establish a correlation between infection, dyspepsia, intestinal microbiota changes, and other disorders with a special emphasis on gastric cancer; and reassess the epidemiological and diagnostic aspects of H. pylori infection. Participants were allocated into four groups as follows: 1) Epidemiology and Diagnosis, 2) Dyspepsia, intestinal microbiota and other afections, 3) Gastric Cancer, and, 4) Treatment. Before the consensus meeting, participants received a topic to be discussed and prepared a document containing a recent literature review and statements that should be discussed and eventually modified during the face-to-face meeting. All statements were evaluated in two rounds of voting. Initially, each participant discussed the document and statements with his group for possible modifications and voting. Subsequently, during a second voting in a plenary session in the presence of all participants, the statements were voted upon and eventually modified. The participants could vote using five alternatives: 1) strongly agree; 2) partially agree; 3) undecided; 4) disagree; and 5) strongly disagree. The adopted consensus index was that 80% of the participants responded that they strongly or partially agreed with each statement. The recommendations reported are intended to provide the most current and relevant evidences to management of H. pylori infection in adult population in Brazil.

Mixed Infections of Helicobacter pylori Isolated from Patients with Gastrointestinal Diseases in Taiwan

Background. Persistent Helicobacter pylori infection may induce several upper gastrointestinal diseases. Two major virulence factors of H. pylori, vacuolating cytotoxin A (VacA) and cytotoxin-associated gene A (CagA), are thought to be associated with the severity of disease progression. The distribution of vacA and cag-pathogenicity island (cag-PAI) alleles varies in H. pylori isolated from patients in different geographic regions. Aim. To assess the association between mixed infection of H. pylori clinical isolates from Taiwanese patients and the severity of gastrointestinal diseases. Methods. A total of 70 patients were enrolled in this study. Six distinct and well-separated colonies were isolated from each patient and 420 colonies were analyzed to determine the genotypes of virulence genes. Results. The prevalence of mixed infections of all H. pylori-infected patients was 28.6% (20/70). The rate of mixed infections in patients with duodenal ulcer (47.6%) was much higher than that with other gastrointestinal diseases (P < 0.05). Conclusions. H. pylori mixed infections show high genetic diversity that may enhance bacterial adaptation to the hostile environment of the stomach and contribute to disease development.

Diagnosis, treatment, and outcome in patients with bleeding peptic ulcers and Helicobacter pylori infections

Upper gastrointestinal (UGI) bleeding is the most frequently encountered complication of peptic ulcer disease. Helicobacter pylori (Hp) infection and nonsteroidal anti-inflammatory drug (NSAID) administration are two independent risk factors for UGI bleeding. Therefore, testing for and diagnosing Hp infection are essential for every patient with UGI hemorrhage. The presence of the infection is usually underestimated in cases of bleeding peptic ulcers. A rapid urease test (RUT), with or without histology, is usually the first test performed during endoscopy. If the initial diagnostic test is negative, a delayed ¹³C-urea breath test (UBT) or serology should be performed. Once an infection is diagnosed, antibiotic treatment is advocated. Sufficient evidence supports the concept that Hp infection eradication can heal the ulcer and reduce the likelihood of rebleeding. With increased awareness of the effects of Hp infection, the etiologies of bleeding peptic ulcers have shifted to NSAID use, old age, and disease comorbidity.

Association of IS605 and cag-PAI of Helicobacter pylori Isolated from Patients with Gastrointestinal Diseases in Taiwan

Background. The cag pathogenicity island (cag-PAI) is one of the most important virulent determinants of Helicobacter pylori. An insertion sequence (IS) element of cag-PAI (IS605) has been found to generate H. pylori strains with varying virulence. Aim. To evaluate the impact of IS605 and cag-PAI on H. pylori strains isolated from Taiwanese patients with severity of gastric diseases. Methods. H. pylori isolates were cultured from gastric biopsies from 99 patients with peptic ulcer, chronic gastritis, and gastric carcinoma. Six distinct, well-separated colonies were isolated from each patient and analyzed by genotyping. Results. cagA, cagE, cagM, cagT, orf10, and orf13 were found to be present in 90.0%–100.0% of the H. pylori isolates. A total deletion of cagA, cagE, cagM, cagT, orf10, and orf13 was found in 1 isolate (1.0%). The IS605 element was found to be positive in 15.2% of the isolates. The presence of IS605 was higher in H. pylori isolated from patients with gastric carcinoma (25.0%) than in patients with duodenal ulcer (6.5%) or chronic gastritis (6.3%) (P < 0.001). Conclusions. The majority of the patients examined had intact cag-PAI. IS605 was present in 15.2% and was higher in H. pylori isolated from patients with gastric carcinoma than in those with peptic ulcer.

Real-time PCR for diagnosing Helicobacter pylori infection in patients with upper gastrointestinal bleeding: comparison with other classical diagnostic methods

The aim of this study was to determine the diagnostic usefulness of quantification of the H. pylori genome in detection of infection in patients with upper gastrointestinal bleeding (UGB). A total of 158 consecutive patients with digestive disorders, 80 of whom had clinical presentation of UGB, were studied. The number of microorganisms was quantified using a real-time PCR system which amplifies the urease gene with an internal control for eliminating the false negatives. A biopsy sample from the antrum and corpus of each patient was processed. The rapid urease test, culture, histological study, stool antigen test, and breath test were done. The gold standard was a positive culture or positive results in at least two of the other techniques. When a positive result was defined as any number of microorganisms/human cell, the sensitivity of real-time PCR was greater in bleeding patients, especially in the gastric corpus: 68.4% (95% confidence interval [CI], 52.3 to 84.5%) in non-UGB patients versus 91.5% (95% CI, 79.6 to 97.6%) in UGB patients. When a positive result was defined as a number of microorganisms/human cell above the optimal value that maximizes the Youden index (>3.56 microorganisms/human cell in the antrum and >2.69 in the corpus), the sensitivity and specificity in UGB patients were over 80% in both antrum and corpus. Our findings suggest that some bleeding patients with infection caused by H. pylori may not be correctly diagnosed by classical methods, and such patients could benefit from the improved diagnosis provided by real-time PCR. However, the clinical significance of a small number of microorganisms in patients with negative results in classical tests should be evaluated.

Real-time PCR improves Helicobacter pylori detection in patients with peptic ulcer bleeding

BACKGROUND AND AIMS

Histological and rapid urease tests to detect H. pylori in biopsy specimens obtained during peptic ulcer bleeding episodes (PUB) often produce false-negative results. We aimed to examine whether immunohistochemistry and real-time PCR can improve the sensitivity of these biopsies.

PATIENTS AND METHODS

We selected 52 histology-negative formalin-fixed paraffin-embedded biopsy specimens obtained during PUB episodes. Additional tests showed 10 were true negatives and 42 were false negatives. We also selected 17 histology-positive biopsy specimens obtained during PUB to use as controls. We performed immunohistochemistry staining and real-time PCR for 16S rRNA, ureA, and 23S rRNA for H. pylori genes on all specimens.

RESULTS

All controls were positive for H. pylori on all PCR assays and immunohistochemical staining. Regarding the 52 initially negative biopsies, all PCR tests were significantly more sensitive than immunohistochemical staining (p<0.01). Sensitivity and specificity were 55% and 80% for 16S rRNA PCR, 43% and 90% for ureA PCR, 41% and 80% for 23S rRNA PCR, and 7% and 100% for immunohistochemical staining, respectively. Combined analysis of PCR assays for two genes were significantly more sensitive than ureA or 23S rRNA PCR tests alone (p<0.05) and marginally better than 16S rRNA PCR alone. The best combination was 16S rRNA+ureA, with a sensitivity of 64% and a specificity of 80%.

CONCLUSIONS

Real-time PCR improves the detection of H. pylori infection in histology-negative formalin-fixed paraffin-embedded biopsy samples obtained during PUB episodes. The low reported prevalence of H. pylori in PUB may be due to the failure of conventional tests to detect infection.

Has H. pylori prevalence in bleeding peptic ulcer been underestimated? A meta-regression

OBJECTIVES

It has been suggested that prevalence of Helicobacter pylori (Hp) in peptic ulcer bleeding (PUB) is lower than that in non-complicated ulcers. As Hp infection is elusive in PUB, we hypothesized that this low prevalence could be related to an insufficiently intensive search for the bacteria. The aim of the study was to evaluate whether the prevalence of Hp in PUB depends on the diagnostic methods used in a given study.

METHODS

A systematic review was performed of studies assessing the prevalence of Hp infection in patients with PUB. Data were extracted in duplicate. Univariate and multivariate random-effects meta-regression analyses were performed to determine the factors that explained the differences in Hp prevalence between studies.

RESULTS

The review retrieved 71 articles, including 8,496 patients. The mean prevalence of Hp infection in PUB was 72%. The meta-regression analysis showed that the most significant variables associated with a high prevalence of Hp infection were the use of a diagnostic test delayed until at least 4 weeks after the PUB episode-odds ratio: 2.08, 95% confidence interval: 1.10-3.93, P=0.024-and a lower mean age of patients-odds ratio: 0.95 per additional year, 95% confidence interval: 0.92-0.99, P=0.008.

CONCLUSIONS

Studies that performed a delayed test and those including younger patients found a higher prevalence of Hp, approaching that recorded in cases of non-bleeding ulcers. These results suggest that the low prevalence of Hp infection described in PUB may be related to the methodology of the studies and to patients' characteristics, and that the true prevalence of Hp in PUB is still to be determined. Our data also support the recent recommendations of the International Consensus on Non-Variceal Upper Gastrointestinal Bleeding regarding the performance of a delayed diagnostic test when Hp tests carried out during the acute PUB episode are negative.

Irritable bowel syndrome and chronic gastritis, hemorrhoid, urolithiasis

OBJECTIVE

Approximately 10-20% of the general population has irritable bowel syndrome (IBS), and IBS patients usually suffer from chronic gastritis (CG), hemorrhoids (H), and urolithiasis (U).

MATERIAL AND METHODS

We randomly chose consecutive patients with upper abdominal discomfort. All possible causes of IBS including celiac sprue, giardiasis, lactose intolerance, and cholelithiasis were investigated. U was diagnosed either by medical history or as a result of laboratory findings.

RESULTS

IBS patients (51) and patients without IBS (70) were studied. CG was diagnosed in 78.4% (40) of IBS cases, whereas this ratio was 50.0% (35) in cases without IBS (p<0.001). Similarly, H was detected in 33.3% (17) of IBS cases, but it was only detected in 15.7% (11) of cases without IBS (p<0.05). Additionally, U was detected in 17.6% (9) of IBS cases and in 5.7% (4) of cases without IBS (p<0.05).

CONCLUSION

Relationships between IBS and CG, H, and U are significant. IBS is a cascade of many physiologic events that is initiated by infection, inflammation, and psychological disturbances like many stresses, and this eventually terminates with gut dysfunction. Gastric acid is probably not involved in the etiology of IBS, but psychological factors also seem to be important in CG. The significant association between CG and IBS also support this hypothesis. Therefore, we believe CG is one of terminating points of the physiologic cascade of events in IBS. Bearing these associations in mind will be helpful during prevention, treatment, and follow up of these disorders, especially in internal medicine, urology, and general surgery polyclinics and primary health centers.

Endoscopic diagnosis of Helicobacter pylori infection by rapid urease test in bleeding peptic ulcers: a prospective case-control study

GOAL

To assess the efficacy of rapid urease test (RUT) in patients with bleeding ulcers, as well as the effects of visible blood in the stomach and short-term (<24 h) use of standard-dose proton pump inhibitor (PPI) on RUT sensitivity.

BACKGROUND

The sensitivity of RUT in the diagnosis of Helicobacter pylori in upper gastrointestinal bleeding has been reported with conflicting results.

STUDY

This was a prospective case-control study evaluating 324 consecutive patients with bleeding peptic ulcers (study group) and 164 with uncomplicated ulcers (control group). The presence of H. pylori infection was determined by both RUT and histology. Prevalence of H. pylori infection and the RUT sensitivity in diagnosing the bacteria between study and control groups were conducted.

RESULTS

The prevalence of H. pylori infection in those with bleeding ulcers was significantly lower than that of controls (53.7% vs. 65.2%, P=0.015). The false-negative rate of RUT in the study group was significantly greater than that of the control group (16.7% vs. 5.6%, P=0.006), whereas the sensitivity rates in the study group with or without gastric blood were significantly lower than those of the controls (79.6% vs. 94.4%, P=0.005; 84.8% vs. 94.4%, P=0.019). There was no significant difference in RUT sensitivity between study group with or without visible gastric blood (P=0.41). The RUT sensitivity rate was also not significantly different between those treated with PPI and those without in patients with bleeding ulcers (82.7% vs. 85.7%, P=0.67).

CONCLUSIONS

This study shows that the sensitivity of RUT in patients with bleeding ulcers is reduced. The presence of blood in the stomach and the short-term use of standard-dose PPI do not affect the RUT sensitivity in bleeding ulcers.

Significantly elevated Helicobacter pylori density and different genotype distribution in erosions as compared with normal gastric biopsy specimen detected by quantitative real-time PCR

BACKGROUND AND AIM

Determination of the local densities of Helicobacter pylori and its genotypic variations in gastric biopsy specimens by using novel real-time PCR-based methods could support the precise diagnosis and understanding of H. pylori infections.

METHODS

Serial dilutions of H. pylori (0.016-16 microg/microl), control, bacterial, and human DNA samples were prepared. Fresh-frozen gastric biopsy specimens were taken from 103 patients, and the DNA was isolated. Quantitative determination of the ureaseA gene using hybridization probes with parallel evaluation of an internal human control gene (beta-globin) was performed by real-time PCR. CagA and VacA s1 genotypic characterizations were also performed. The data were compared with urea breath test (UBT), histology, and serological testing.

RESULTS

The presence of H. pylori could be detected by ureaseA-fluorescence energy transfer (53%), UBT (51%), serological testing (48%), and histology (52%) when compared with the gold standard (54%). A significant correlation was found between the quantitative real-time ureaseA/beta-globin ratio-based H. pylori frequency and the UBT results (P<0.01). Significantly increased bacterial density was found in the erosions when compared with the healthy part of the antrum and corpus (P<0.01). Real-time PCR VacA s1 results were in significant correlation (P<0.01) with those of serological tests, but CagA results were not. The genomic profiles (VAC/GAC) were different in 13.7% of the cases, which involved three different locations in the stomach.

CONCLUSION

Real-time PCR was the most reliable method for H. pylori diagnosis. Furthermore, quantification and genotyping could also be performed using this technique. The density of H. pylori was significantly increased in macroscopic erosions.

Surgical perspectives in peptic ulcer disease and gastritis

For much of the twentieth century, surgery was frequently the solution for peptic ulcer disease. Our understanding of the pathophysiology of ulcers paralleled the development of potent pharmaceutical therapy. As the surgical world developed parietal cell vagotomy which would minimize the complications of surgery, patients failing medical therapy became rare. Emergent surgery for complicated peptic ulcers has not declined however. The development of proton pump inhibitors and the full understanding of the impact of H pylori has led to a trend towards minimalism in surgical therapy for complicated peptic ulcer disease. In addition to the changes in patient care, these developments have had an impact on the training of surgeons. This article outlines these trends and developments.

Accuracy of Helicobacter pylori diagnostic tests in patients with bleeding peptic ulcer: a systematic review and meta-analysis

OBJECTIVE

To perform a systematic review and a meta-analysis of diagnostic accuracy of the different tests aimed to detect Helicobacter pylori infection in patients with upper gastrointestinal bleeding (UGIB).

SELECTION OF STUDIES

assessing the accuracy of H. pylori diagnostic methods in patients with UGIB.

SEARCH STRATEGY

electronic bibliographical searches.

DATA EXTRACTION

independently done by two reviewers.

DATA SYNTHESIS

meta-analyses of the different tests were performed combining the sensitivities, specificities, and likelihood ratios (LRs) of the individual studies.

RESULTS

Studies showed a high degree of heterogeneity. Pooled sensitivity, specificity, LR+ and LR- (95% confidence interval (CI)) for the different methods were: Rapid urease test (16 studies/1,417 patients): 0.67 (0.64-0.70), 0.93 (0.90-0.96), 9.6 (5.1-18.1), and 0.31 (0.22-0.44). Histology (10 studies/827 patients): 0.70 (0.66-0.74), 0.90 (0.85-0.94), 6.7 (2.5-18.4), and 0.23 (0.12-0.46). Culture (3 studies/314 patients): 0.45 (0.39-0.51), 0.98 (0.92-1.00), 19.6 (4-96), and 0.31 (0.05-1.9). Urea breath test (8 studies/520 patients): 0.93 (0.90-0.95), 0.92 (0.87-0.96), 9.5 (3.9-23.3), and 0.11 (0.07-0.16). Stool antigen test (6 studies/377 patients): 0.87 (0.82-0.91), 0.70 (0.62-0.78), 2.3 (1.4-4), and 0.2 (0.13-0.3). Serology (9 studies/803 patients): 0.88 (0.85-0.90), 0.69 (0.62-0.75), 2.5 (1.6-4.1), and 0.25 (0.19-0.33).

CONCLUSION

Biopsy-based methods, such as rapid urease test, histology, and culture, have a low sensitivity, but a high specificity, in patients with UGIB. The accuracy of 13C-urea breath test remains very high in these patients. Stool antigen test is less accurate in UGIB. Although serology seems not to be influenced by UGIB, it cannot be recommended as the first diagnostic test for H. pylori infection in this setting.

Diagnosis of Helicobacter pylori Infection

A large number of studies on diagnostic tests have been published this year. New tests were proposed for the detection of Helicobacter pylori antigens in stools and new molecular methods (real-time polymerase chain reaction) to look for antimicrobial susceptibility. The other standard tests have been applied in different situations to improve the diagnosis of the infection.