Comparison of polymerase chain reaction-based genotyping of Helicobacter pylori by direct polymerase chain reaction from biopsies and cultures from patients with dyspepsia in Nigeria

BACKGROUND: Helicobacter pylori infects 50% of humans worldwide. Since this bacterium is the main cause of gastritis and peptic ulcer disease, its accurate diagnosis and eradication are crucial steps in the management of these diseases. When endoscopy is required, there is an increasing interest in the real time diagnosis of H. pylori infection and its immediate treatment. Aim of this study was to determine the most accurate method for genotyping H. pylori in Nigeria, comparing results obtained from analysis of bacterial isolates versus those obtained from direct analysis on gastric biopsies. METHODS: Bioptic specimens, obtained during upper gastrointestinal endoscopy from 125 dyspeptic subjects, after informed consent, were analyzed to detect virulence genotyping of H. pylori, directly or on isolates obtained by culture. RESULTS: Out of 125 patients, 100 (80%) were positive for H. pylori by direct polymerase chain reaction (PCR) from bioptic specimens while culture was positive in 47 (37.6%). Results of amplified genes showed that comparing 47 samples, positive by culture and direct PCR, the agreement ranged from fair to good. In terms of age group and virulence genotypes, the age group 30-40 years was more common positive for cagA, vacA-s1b, vacA-m1 but not for dupA. However, this result was not statistically significant when compared to the other age-groups. CONCLUSIONS: The study of the virulence genotypes of H. pylori, using the two methods, direct PCR and PCR after culture, showed that the former was slightly superior to the latter. However, culture remains important for the treatment of patients after failure of antibiotic therapy.