[The application of genotypic resistance testing for clarithromycin and levofloxacin in different types of Helicobacter pylori infected patients based on gastric mucosal samples].

Objective: To evaluate the utility of genotypic resistance testing for specific antibiotics in both treatment-naïve and rescue patients with Helicobacter pylori infection, providing a basis for the rational selection of patients suitable for individualized therapy. Methods: This was a single-center cross-sectional study performed between January 2024 and July 2025 involving 385 patients with active H. pylori infection. Participants were stratified into treatment-naïve or previously treated cohorts according to their eradication history. During endoscopy, paired biopsies were obtained from corresponding sites in the gastric antrum and body; one specimen was used for the qPCR-based detection of mutations in the 23S rRNA and gyrA genes, while the other was reserved for H. pylori culture with antimicrobial susceptibility testing to determine minimum inhibitory concentrations (MICs). Resistance was interpreted according to EUCAST (v.15.0) breakpoints. Categorical variables were compared using the χ2 test or Fisher's exact test. Agreement between genotypic and phenotypic resistance was assessed using the concordance rate and the Kappa statistic. Results: Genotypic resistance rates for clarithromycin and levofloxacin increased stepwise with previous treatment exposure. Clarithromycin genotypic resistance rates in the treatment-naïve, retreatment, and refractory groups were 50.7% (109/215), 75.7% (53/70), and 93.8% (91/97), respectively (χ2=59.01, P<0.001). For levofloxacin, the respective genotypic resistance rates were 35.3% (76/215), 58.6% (41/70), and 75.3% (73/97) (χ2=45.26, P<0.001). Meanwhile, the dual genotypic resistance rates reached 22.8% (49/215), 48.6% (34/70), and 70.1% (68/97) (χ2=65.53, P<0.001), respectively. High concordance (89%-94%) and agreement (Kappa=0.58-0.86) were observed between genotypic and phenotypic resistance. Conclusions: While the genotypic resistance rates of H. pylori to clarithromycin and levofloxacin were relatively low in treatment-naïve patients, they were significantly elevated in rescue patients. The high agreement with phenotypic resistance suggested that PCR-based genotypic resistance testing provides a viable alternative to bacterial culture and phenotypic susceptibility testing and is suitable for patients undergoing initial treatment.