PCR and RFLP Analysis for Identification and Typing of Helicobacter pylori Strains from Gastric Biopsy Specimens

Helicobacter pylori is the causative agent of chronic gastritis and peptic ulcer diseases and is also a risk factor for gastric cancer. Since culture of Helicobacter pylori is relatively insensitive and cumbersome, PCR-based molecular detection and typing of this organism is gaining importance for strain differentiation. The aim of present study was to apply molecular methods for detection and genotyping of H. pylori directly on gastrointestinal biopsy. For this purpose 79 samples were tested by bacteriological methods including Gram stain, urease test and culture in a selective medium. Genomic DNA was directly extracted from gastric biopsy specimens followed by PCR amplification using ureC primers. PCR products from positive samples were purified and digested using three different restriction endonucleases, AluI, MboI and CfoI. The numbers of positive samples detected by bacteriological methods were 71, 40 and 73 using Gram stain, culture and urease test respectively. Through PCR assay 64 samples were positive with sensitivity of about 92 and specificity of 100%. The specificity and sensitivity of the PCR assay was higher than that of all bacteriological methods applied. RFLP performed on the positive samples and five patterns for AluI, five patterns for MboI and four patterns for CfoI detected. The patterns were classified based on the number of produced bands in gel electrophoresis. From our study it is concluded that the PCR-based RFLP technique would be an useful approach for identification and genotyping of specific H. pylori strains directly in gastric biopsy specimens without culture.