Stool Tests Rapidly Predict H. pylori Antibiotic Resistance

Helicobacter pylori eradication rates have declined in concert with rising antimicrobial resistance worldwide. There is a need for rapid accurate, reliable antibiotic resistance testing, especially in refractory cases.

Culture-based susceptibility testing requires endoscopic gastric biopsy, with resultant inconvenience and costs. Molecular testing using next generation sequencing (NGS) of stool potentially allows rapid prediction of resistance to all six commonly used antimicrobials.


Clinical Scientists at the Rhode Island Hospital (Providence, RI, USA) and their colleagues compared the accuracy of NGS with gastric biopsy for identifying H. pylori antibiotic resistance in 262 patients scheduled for upper endoscopy at four clinical practices. Two gastric biopsies were taken for NGS and a spontaneously passed stool specimen was also obtained within two weeks of endoscopy, but before starting treatment for H. pylori. H. pylori was confirmed in biopsies by PCR followed by NGS. H pylori in stools was confirmed by fecal antigen test and PCR. Stool samples positive by at least two stool tests were also examined by NGS to predict resistance to amoxicillin, clarithromycin, metronidazole, tetracycline, levofloxacin, and rifabutin.

The investigators reported that 73 (29%) patients were H. pylori positive by stool testing; two had insufficient gastric DNA for analysis. Of the 71 evaluable cases identical results for stool and biopsy samples were obtained for all six antibiotics in 65 (91.5%). In six cases there was mismatch between gastric and stool results; in four cases this was due to one antibiotic-associated mutation difference. For 70.4% of gastric biopsies, there was at least one resistance-associated mutation. Only 21 (29.6%) had no mutations. Results for stool were similar: 50 cases (68.5%) had at least one resistance-associated mutation and 23 (31.5%) had no mutations. The concordance between stool and gastric biopsies for individual antibiotics ranged from 89% (metronidazole) to 100%.

Steven Moss, MD, a gastroenterologist and senior author of the study, said, “Culture-based susceptibility testing requires endoscopic gastric biopsy, with resultant inconvenience and costs. It is now possible to rapidly obtain susceptibility data without endoscopy.”

The authors concluded that profiling H. pylori antibiotic resistance by NGS from stool samples provides rapid results highly comparable to those obtained from gastric biopsies. Using NGS to determine H. pylori antibiotic resistance using stool obviates the cost, inconvenience and risks of endoscopy for patients in whom resistance profiling is needed. The study was presented at the 2021 Virtual Meeting of the American College of Gastroenterology (ACG) held October 22-27, 2021.

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