Helicobacter pylori Antimicrobial Resistance Using Next-Generation Sequencing in stool samples in a pediatric population.

Abstract

Helicobacter pylori (H. pylori) eradication rates have declined globally, stressing the importance of antimicrobial susceptibility testing to inform treatment. Molecular tests such as next-generation sequencing provide susceptibility data for the antibiotics used in the treatment of H. pylori in a non-invasive, effective, and rapid manner. We obtained stool susceptibility testing using a novel -next-generation sequencing-based analysis and compared results with the current "gold standard" of gastric biopsy culture via agar dilution in 20 pediatric patients with evidence of H. pylori in gastric biopsies. Stool next-generation sequencing-based antimicrobial susceptibility analysis was highly concordant with agar dilution for no resistance (100% agreement), as well as clarithromycin, levofloxacin, and amoxicillin resistance (100%, 67%, and 100% agreement respectively) but not concordant for metronidazole in our cohort of patients. Future studies involving a larger number of patients and geographical regions are needed to further validate this analysis.