PCR test for Helicobcter pylori detection and clarithromycin resistance prediction on fecal samples: prediction power and correlation with eradication rate.

Background: Clarithromycin-based regimens are commonly used as a first line therapy in Helicobacter pylori positive patients, however treatment failures associate with resistance to clarithromycin are increasing worldwide. Objectives: to evaluate the use of stool samples to detect the presence of Helicobacter pylori DNA, while concurrently detecting mutations associated with the clarithromycin resistance. Methods: 292 Helicobacter pylori negative and positive patients were included. DNA was extracted from raw stools. TaqMan real-time PCR amplification was used to detect the presence of Helicobacter pylori as well as predict the genotype of the organism and the related outcome of patients treated with clarithromycin. Patients were also tested by Urea breath test and subjected to esophagogastroduodenoscopy followed by histology, culture and rapid urease test, to obtain a consensus patient infection status. Results: Out of 292 total stool samples, 228 were deemed true positives. The sensitivity and specificity for Helicobacter pylori detection by PCR was 92.8% and 77.6% respectively. Out of 239 samlples that resulted Hp positive with PCR, 213 were also sequenced, 36% showed point mutations associated with CLA resistance (A2142C, A2142G, A2143G). The final correlation of genotype and eradication was 83.5%. Conclusions: Helicobacter pylori DNA can be detected in human stool specimens with a high sensitivity, and therefore can be used to determine its presence without obtaining biopsy sample. Moreover, the genotypic resistance to clarithromycin can be detected without obtaining a biopsy sample in order to choose the right therapeutic approach.