PCR-Based Detection and Genotyping of Helicobacter pylori in Endoscopic Biopsy Samples from Brazilian Patients. Gastroenterol Res Pract. 2013;2013:951034. [PMID: 23401678 PMCID: PMC3562691 DOI: 10.1155/2013/951034]

PCR-based RFLP and ERIC-PCR patterns of Helicobacter pylori strains linked to multidrug resistance in Egypt

H. pylori infects approximately 50% of the world's population that causes chronic gastritis, and may lead to peptic ulcer disease (PUD). H. pylori-induced chronic infections are associated with gastric adenocarcinoma and low-grade gastric lymphoma. In Egypt, H. pylori strains are widespread and became resistant to antimicrobial agents, thus advanced typing methods are needed to differentiate infectious strains that are resistant to antibiotics, and therefore earlier prognosis and infection control. The main objectives were (i) to determine susceptibility of infectious H. pylori strains to some antimicrobial agents that are currently used in eradication therapy in Egypt; (ii) to identify diverse strains commonly detected in the gastrointestinal (GIT) endoscopy units in Egypt through phenotypic and genotypic analyses. In this observational study we isolated 167 isolates from 232 gastric biopsies (antrum and corpus) of patients who were admitted to the upper GIT endoscopy units in five governmental Egyptian hospitals. Antimicrobial susceptibility patterns were investigated using Kirby Bauer disc diffusion and agar dilution Minimum Inhibitory Concentrations (MICs) methods. Phenotypic characterization was based on biotyping and antibiogram typing techniques. Genotypic characterization was carried out using PCR-based Restriction Fragment Length Polymorphism (RFLP) and Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR analyses. H. pylori isolates were highly resistant to diverse antimicrobial agents including Metronidazole, Fluoroquinolones, Macrolides, Amoxycillin, Tetracycline and Gentamicin. Two factors contributed to the increased resistance of H. pylori to the conventional therapy seen in Egypt: (i) Metronidazole and Amoxycillin are inexpensive and available drugs being abused by patients; (ii) the regional prescribing practice of Macrolids commonly used to treat upper respiratory and urinary tract infections. Five different biotypes were identified depending on the ability of the isolates to synthesize different enzymes. Nine antibiogram types were identified. PCR-RFLP analysis revealed fifteen different fingerprints while ERIC-PCR revealed 22 fingerprints. Biotyping alone or in combination with antibiogram typing are highly useful molecular tools in the prognosis of strain relatedness. PCR-RFLP and ERIC-PCR acquired good discriminatory power for identifying H. pylori infectious sub-types.

The Relation Between Host TLR9 -1486T/C, rs187084 Gene Polymorphisms and Helicobacter pylori cagA, sodB, hsp60, and vacA Virulence Genes among Gastric Cancer Patients

To identify the associations between different genotypes of TLR9 -1486T/C (rs187084) with gastric cancer patients and reveal their relation to Helicobacter pylori virulence genes (cagA, sodB, hsp60 and vacA). Patients with gastric cancer were recruited to our study, diagnosed both endoscopically and histopathologically. H. pylori were isolated from gastric samples by culture and PCR amplification of the glmM gene. Virulence genes cagA, sodB, hsp60, and vacA were detected by multiplex PCR. Blood samples were used for genotyping of TLR9 -1486T/C (rs187084) by PCR-RFLP. Out of 132 patients with gastric cancer, 106 (80.3%) were positive for H. pylori. A similar number of healthy participants was recruited as controls. The prevalence of cagA, sodB, hsp60, and vacA genes among H. pylori was 90.6%, 70.8%, 83.0%, and 95.3%, respectively. The vacA gene alleles had a prevalence of 95.3% for vacAs1/s2, 52.8% for vacAm1, and 42.5% for vacAm2. The CC genotype of TLR9 -1486T/C had a significantly higher frequency in gastric cancer patients when compared to healthy participants (p = 0.045). Furthermore, the CC genotype demonstrated a significant association with H. pylori strains carrying sodB, hsp60, and vacAm1 virulence genes (p = 0.021, p = 0.049, and p = 0.048 respectively). Patients with CC genotype of TLR9 -1486T/C (rs187084) might be at higher risk for the development of gastric cancer, and its co-existence with H. pylori strains carrying sodB, hsp60, or vacAm1 virulence genes might have a synergistic effect in the development of gastric cancer. Further studies on a wider scale are recommended.

Evolution of Diagnostic Methods for Helicobacter pylori Infections: From Traditional Tests to High Technology, Advanced Sensitivity and Discrimination Tools

Rapid diagnosis and treatment application in the early stages of H. pylori infection plays an important part in inhibiting the transmission of this infection as this bacterium is involved in various gastric pathologies such as gastritis, gastro-duodenal ulcer, and even gastric neoplasia. This review is devoted to a quick overview of conventional and advanced detection techniques successfully applied to the detection of H. pylori in the context of a compelling need to upgrade the standards of the diagnostic methods which are currently being used. Selecting the best diagnostic method implies evaluating different features, the use of one or another test depending on accessibility, laboratories equipment, and the clinical conditions of patients. This paper aims to expose the diagnosis methods for H. pylori that are currently available, highlighting their assets and limitations. The perspectives and the advantages of nanotechnology along with the concept of nano(bio)sensors and the development of lab-on-chip devices as advanced tools for H. pylori detection, differentiation, and discrimination is also presented, by emphasizing multiple advantages: simple, fast, cost-effective, portable, miniaturized, small volume of samples required, highly sensitive, and selective. It is generally accepted that the development of intelligent sensors will completely revolutionize the acquisition procedure and medical decision in the framework of smart healthcare monitoring systems.

Concurrent detection of cagA, vacA, sodB and hsp60 virulence genes and their relationship with clinical outcomes of disease in Helicobacter pylori isolated strains of southwest of Iran

BACKGROUND AND OBJECTIVES

Helicobacter pylori is a Gram-negative spiral-shaped bacterium that contaminates more than half of the world's inhabitants, and infection with this bacterium is associated with some gastric disorders. Also, 5% to 10% of H. pylori genes are specific to this bacterium and many bacterial virulence factors fall into this group. The cagA, vacA, sodB and hsp60 are among important virulence factors of H. pylori.

MATERIALS AND METHODS

A gastric biopsy specimen was taken from 341 gastric patients and cultivated on a Colombia agar plate, containing various antibiotics, such as vancomycin, amphotericin B, and trimethoprim & polymyxin B, and incubated for 3 to 10 days under microaerophilic conditions at 37°C. PCR was used to detect the ureC, cagA, vacA, sodB and hsp60 genes.

RESULTS

In this study, 131 isolates were identified as H. pylori. The prevalence of cagA, vacA, sodB and hsp60 were 74%, 100%, 92.4% and 96.2%, respectively. The correlation between the clinical forms of the disease and the virulence genes were analyzed by statistical tests and no significant correlation was found.

CONCLUSION

The obtained results are similar to some studies conducted in different parts of the world and is different in other cases. This discrepancy is due to the difference in the type of gastric disorders, sample size and methodology.

Prevalence of Specific Helicobacter PyloricagA, vacA, iceA, ureC Genotypes and its Clinical Relevance in the Patients with Acid-Peptic Diseases

INTRODUCTION

Virulent markers of H. pylori, the vacuolating cytotoxin (vacA), cytotoxin-associated gene A (cagA), induced by contact with epithelium factor antigen (iceA gene) and the urease C gene (ureC) may plays a major role in determining the clinical outcome of Helicobacter infections.

AIM

To detect the prevalence of the cagA, vacA, ureC and iceA genotypes of H. pylori from antral biopsy specimens of patients and to associate its role in specific disease.

MATERIALS AND METHODS

The study was conducted at Department of Microbiology of Shree P.M. Patel College of Paramedical Sciences, Anand, Gujarat, India. Seventy one antral biopsies of symptomatic patients referred for endoscopy from October 2012 to September 2013 were subjected to Multiplex PCR. DNA isolation from 71 biopsy samples was done by using "QIAamp DNA mini kit" from QIAGEN (GmbH, Hilden, Germany). Data was analysed using Chi square (χ²) test and p-value<0.05 was considered significant.

RESULTS

Out of the 71 biopsies screened, 22(31%) samples were positive for H. pylori by PCR, with high proportion of cagA positive (17/22 specimen; 77.27%), followed by ureC positive (4/22 specimen; 18.18%) and vacA positive (1/22 specimen; 4.54%) strains. Significant association was found between cagA and female gender (p-value=0.042). Out of 17 cagA positive strains, 9(52.94%) were found in patients with gastritis, 5(29.41%) in reflux oesophagitis and 3(17.64%) in patients with diodenal ulcer. We found 0% prevalence of iceA gene; conversely we had three peptic ulcer patients with only cagA positivity.

CONCLUSION

The cagA positive strain mainly affects the patients with gastritis specifically of female gender and iceA genotype is not a useful marker associated with peptic ulcer disease. Patients should be screened for cagA genotype when reported to be a case of gastritis for early treatment to prevent further complications such as cancer.

Multiplex PCR for detection of Helicobacter pylori infection in gastric biopsies with lower inflammatory score

BACKGROUND

No gold standard has yet been established for the diagnosis of H. pylori infection. A multiplex polymerase chain reaction (mPCR) was developed in this study for rapid, sensitive and specific detection of H. pylori from gastric biopsies.

METHODS

H. pylori infections were determined by in-house rapid urease test (iRUT), culture, histology and multiplex PCR.

RESULTS

A total of 140 (60.9%) from 230 patients were positive for H. pylori infection. H. pylori were detected in 9.6% (22/230), 17% (39/230), 12.6% (29/230) and 60% (138/230) of biopsy specimens by culture, iRUT, histology and mPCR, respectively. mPCR identified H. pylori infection in 100% of biopsies with positive histology and culture. All biopsies with positive iRUT yielded positive PCR except two cases. mPCR also detected H. pylori in additional 116, 101 and 109 biopsies that were negative by culture, iRUT and histology, respectively. Positive samples by mPCR showed lower average in H. pylori density, activity and inflammation scores. The Indians showed the highest prevalence of H. pylori infection compared to the Chinese and the Malays. In addition, Chinese patients with older age were significantly infected compared to other ethnicities.

CONCLUSION

PCR was able to detect the highest numbers of positive cases although the lowest average scores were recorded in the activity, inflammatory and H. pylori density.

Prevalence of Helicobacter pylori in children in eastern Turkey and molecular typing of isolates

The objectives of the present study were to determine Helicobacter pylori via culture, polymerase chain reaction and histopathological diagnosis in 101 children ranging in age from 4 to 18 years, to identify the association among restriction fragment length polymorphism types and clinical disease and to investigate the relationships among different isolates of H. pylori in different age groups. We observed a high prevalence of H. pylori infections in children between the ages of 13 and 18 (75.8%), while children aged 4 to 6 years had the lowest prevalence of infection (40%). H. pylori was detected in 30.7% (31 of 101), 66.3% (67 of 101) and 63.2% (60 of 95) of children as determined by culture methods, PCR and histological examination, respectively. H. pylori isolates with RFLP types I and III were the most common among children with antral nodularity, whereas RFLP types II and IV were the least detected types. Interestingly, all isolates from peptic ulcer patients were type III. Although our results show a high prevalence of H. pylori infections in the pediatric population in eastern Turkey, no association was identified between H. pylori infection with antral nodularity and recurring abdominal pain. In addition, we found low genetic variation among H. pylori isolates from children and no association between RFLP types and antral nodularity (p > 0.05). Additionally, we found that H. pylori isolates with specific RFLP types were predominant in different age groups.

Dual-priming oligonucleotide-based multiplex PCR using tissue samples in rapid urease test in the detection of Helicobacter pylori infection

AIM: To investigate whether tissue samples processed by the rapid urease test (RUT) kit are suitable for dual-priming oligonucleotide-based multiplex polymerase chain reaction (DPO-PCR) to detect Helicobacter pylori (H. pylori).

METHODS: A total of 54 patients with specific gastrointestinal symptom were enrolled in this study. During endoscopy, gastric biopsy specimens were taken for histology, RUT, and DPO-PCR. DPO-PCR was performed on gastric biopsy samples and tissue samples that were analyzed by RUT at 2 separate institutes. In detecting H. pylori, the concordance rate of the DPO-PCR tests between the tissue samples that had been submitted to RUT and the gastric biopsy samples was investigated.

RESULTS: H. pylori co-occurred with 76.0% (19/25) of gastric ulcers, 64.3% (9/14) of duodenal ulcers, and 33.3% (4/12) of gastritis cases. H. pylori infection was found in 100% (3/3) of the patients with both gastric and duodenal ulcers. Overall, H. pylori was detected in 35 of 54 (64.8%) patients. The diagnostic sensitivities of histology, RUT, and DPO-PCR were 85.7% (30/35), 74.3% (26/35), and 97.1% (34/35), respectively (P = 0.02). The positive predictive value (PPV) of DPO-PCR was 94.4%, whereas the negative predictive value (NPV) was 94.7%. In the rapid urease test (CLOtest)-negative cases, the frequency of positive DPO-PCR and histologic results was 20.0% (7/35). The concordance rate of the DPO-PCR tests between the tissue samples from the RUT kit and the gastric biopsy samples was 94.4% (51/54). The rate of DPO-PCR and silver stain positivity in the RUT-negative cases was 20.0% (7/35).

CONCLUSION: In diagnosing H. pylori infection, DPO-PCR can be performed on tissue samples that have been processed by the RUT kit. Particularly, in patients with RUT-negative results, DPO-PCR on these tissue samples could be helpful in detecting of H. pylori infection.