S Bonilla et al. JPGN 2023; 77: 623-627. Helicobacter pylori Antimicrobial Resistance Using Next-Generation Sequencing in Stool Samples in a Pediatric Population

Background: Stool H pylori testing “has become available and is based on the detection of mutations in H pylori genome associated with antimicrobial resistance and corresponds well with resistance determined by culture”

Methods: The authors obtained stool susceptibility testing using a novel NGS-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 samples were sent to American Molecular Laboratories (description in supplemental material). Gastric samples were sent to Mayo Laboratories.

Key findings:

• Stool NGS-based antimicrobial susceptibility analysis was highly concordant with agar dilution (gastric biopsies) 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.
• 35% of patients had antibiotic resistance identified

• Link: American Molecular Laboratories stool H pylori testing
• Link: Mayo Laboratories for gastric H pylori resistance testing

My take: Since H pylori is difficult to treat, identifying susceptibility patterns can be very helpful. This study shows that stool specimens have good agreement with gastric biopsy testing. While the results for metronidazole are not as good, resistance to metronidazole can often be overcome as part of multidrug regimens.

Related blog posts:

• Understanding FDA Approval of Vonoprazan-Based Therapies for Helicobacter Pylori In this post, it is noted that metronidazole resistance is fairly common, but bismuth quadruple therapy can overcome much of the metronidazole resistance
• How To Achieve Helicobacter Pylori Cure Rates of >95%
• Antimicrobial Stewardship for Helicobacter Pylori
• Next-Generation Treatment for H Pylori
• Why Is There Low Adherence to H pylori Guidelines?
• AGA: Best Practice Advice for Refractory H pylori
• Brief Updates: H pylori Resistance Rates, VEDOKIDS, Increasing Bariatric Surgery in Kids

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