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Background/Aims: The validity of 13C-urea breath test (13C-UBT) for Helicobacter pylori detection is influenced by atrophic gastritis. The aim of this study was to evaluate the effect of citric acid on the accuracy of 13C-Urea breath test after H. pylori eradication therapy in a region where atrophic gastritis is common. Methods: In this prospective study, H. pylori-positive patients received 13C-UBT after H. pylori eradication regimen. They were classified into citric acid group and control group. To determine diagnostic accuracy of 13C-UBT, patients were offered invasive methods. Results: A total of 1,207 who successfully took H. pylori-eradication regimen received UBT. They were assigned into the citric acid group (n=562) and the control group (n=645). The mean 13C-UBT value of the citric acid group was 10.3±26.4‰, which was significantly (p<0.001) higher than that of that control group (5.1‰±12.6‰). Of these patients 122 patients were evaluated by endoscopic biopsy methods. Based on invasive tests, the accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of 13C-UBT for the citric acid group were 83.3%, 91.7%, 81.3%, 55.0%, and 97.5%, respectively. Those of the control group were 87.7%, 90.9%, 88.2%, 62.5%, and 97.8%, respectively. They were not significantly different between the two groups. Although the presence of gastric atrophy and intestinal metaplasia (IM) decreased the accuracy, the decrease was not significant. Conclusions: In a country with high prevalence of atrophic gastritis or IM, false positivity remained common despite the use of citric acid in 13C-UBT.