Methodological evaluation of Helicobacter pylori infection and clarithromycin resistance detection via gastric fluid PCR

Objective To evaluate the clinical feasibility of using PCR testing based on gastric juice samples as an alternative to gastric mucosa samples for determining Helicobacter pylori ( H. pylori ) infection and clarithromycin resistance. Methods A total of 470 patients who underwent upper gastrointestinal endoscopy and a rapid urease test (RUT) at our hospital between January 2025 and April 2025 were selected. Both gastric juice and gastric mucosa samples were collected from each patient. Fluorescent PCR melting curve analysis was used to detect H. pylori DNA and mutations at the 2142 or 2143 sites of the 23S rRNA gene in both sample types in order to assess H. pylori infection status and clarithromycin resistance. Results Compared to RUT, PCR testing of gastric juice samples for determining H. pylori infection showed a sensitivity of 92.86% (95% CI: 89.6–95.3), specificity of 95.0% (95% CI: 89.5–97.9), positive predictive value (PPV) of 98.19% (95% CI: 96.1–99.3), negative predictive value (NPV) of 82.01% (95% CI: 74.6–87.8), and good agreement (Kappa = 0.835, P < 0.001). Using gastric mucosa PCR as the “gold standard,” PCR testing of gastric juice samples for H. pylori infection demonstrated a sensitivity of 93.90% (95% CI: 90.8–96.1), specificity of 93.65% (95% CI:87.9–97.0), PPV of 97.58% (95% CI: 95.2–98.9), NPV of 84.89% (95% CI: 77.7–90.3), and good agreement (Kappa = 0.848, P < 0.001). Using culture-based drug susceptibility testing as the “gold standard,” the resistance detection rate of gastric juice PCR was 86.42% (70/81), with moderate agreement (Kappa = 0.684, P < 0.001). The resistance detection rate of gastric mucosa PCR was 88.89% (72/81), with good agreement (Kappa = 0.788, P < 0.001). Using first-generation sequencing gene detection as the “gold standard,” the resistance detection rate of gastric juice PCR was 84.27% (75/89), with moderate agreement (Kappa = 0.694, P < 0.001). The resistance detection rate of gastric mucosa PCR was 87.64% (78/89), with good agreement (Kappa = 0.805, P < 0.001). Conclusion Compared to gastric mucosa samples, PCR testing using gastric juice samples enables relatively non-invasive, rapid, efficient, and reliable diagnosis of H. pylori infection and clarithromycin resistance.