Molecular detection of antibiotic resistance in stool biopsy samples.

Aim: To compare (1) demographics in urea breath test (UBT) endoscopy patients; and (2) the molecular detection of antibiotic resistance in stool biopsy samples.

Methods: Six hundred and sixteen adult patients undergoing endoscopy or a UBT were prospectively recruited to the study. The GenoType HelicoDR assay was used to detect () and antibiotic resistance using biopsy and/or stool samples from CLO-positive endoscopy patients and stool samples from UBT-positive patients.

Results: Infection rates were significantly higher in patients referred for a UBT than endoscopy (overall rates: 33% 19%; treatment-naïve patients: 33% 14.7%, respectively). -infected UBT patients were younger than -infected endoscopy patients (41.4 48.4 years, respectively, < 0.005), with a higher percentage of -infected males in the endoscopy-compared to the UBT-cohort (52.6% 33.3%, = 0.03). The GenoType HelicoDR assay was more accurate at detecting infection using biopsy samples than stool samples [98.2% ( = 54/55) 80.3% ( =53/66), < 0.005]. Subset analysis using stool and biopsy samples from CLO-positive endoscopy patients revealed a higher detection rate of resistance-associated mutations using stool samples compared to biopsies. The concordance rates between stool and biopsy samples for the detection of DNA, clarithromycin and fluoroquinolone resistance were just 85%, 53% and 35%, respectively.

Conclusion: Differences between endoscopy and UBT patients provide a rationale for non-invasive detection of antibiotic resistance. However, the GenoType HelicoDR assay is an unsuitable approach.