Evaluation of real-time PCR compared to culture for the detection of clarithromycin resistant Helicobacter pylori in the Irish healthcare setting

Abstract

Objective: Molecular methods offer a more rapid alternative for the detection of H. pylori resistance to antibiotics than traditional culture-based methods. The aim of the study was to evaluate the RIDAGENE H. pylori real-time PCR assay compared to culture-based methods for the detection of H. pylori and clarithromycin resistance using gastric biopsies. Patients and Methods: Following ethical approval and informed consent, adults were recruited prospectively from Tallaght University Hospital and Letterkenny University Hospital, Ireland, regardless of H. pylori treatment history. During routine gastroscopy, subjects had 1 antrum and 1 corpus biopsy taken for H. pylori culture and DNA extraction. Clarithromycin susceptibility testing on cultures was performed by ETEST (Biomerieux, UK). The RIDAGENE H. pylori assay (R-Biopharm AG, Germany) was used for detection of H. pylori DNA and clarithromycin resistance-associated point mutations. Results: In all, samples from 191 culture-positive patients (mean age 48.4 ± 15.3 years; 45.0% (N=86) female) were analysed. The RIDAGENE assay detected H. pylori in 100% of biopsy samples from which H. pylori was cultured. The clarithromycin resistance rate by culture was significantly higher than by real-time PCR (49.2% (N=94/191) and 38.7% (N=74/191, respectively; p=0.04; χ2 test). Results agreed between both methods in 84.3% (N=161/191) of cases. The sensitivity and specificity of the RIDAGENE assay compared to culture for the detection of clarithromycin resistance were 74.0% (95% CI: 64.0-82.4%) and 94.7% (95% CI: 88.1-98.3%), respectively. The positive predictive value was 93.4% (95% CI: 85.7-97.1%) and the negative predictive value was 78.3% (95% CI: 71.9-83.5%). Conclusions: The RIDAGENE assay detected H. pylori in all culture-positive samples. However, the low sensitivity compared to culture for clarithromycin susceptibility testing in our cohort may limit its use to cases where culture-based methods are unsuccessful. Further studies are required to fully characterise H. pylori clarithromycin resistance mechanisms in our study population.

Keywords

• helicobacter pylori
• clarithromycin
• antimicrobial resistance
• antimicrobial susceptibility testing
• molecular methods
• real-time pcr.