Association of Resistance-Associated 23S rRNA and gyrA Mutations with Antimicrobial Resistance and Eradication Outcomes in Helicobacter pylori

Background/Objectives: The increasing prevalence of antimicrobial resistance has become a major challenge in the management of Helicobacter pylori infection and is a leading cause of eradication failure. Resistance to clarithromycin and fluoroquinolones is primarily mediated by mutations in the 23S rRNA and gyrA genes, respectively. This study aimed to evaluate the prevalence of resistance-associated mutations in the 23S rRNA and gyrA genes, investigate their relationship with phenotypic antimicrobial resistance, assess their impact on eradication outcomes, and develop a prediction model for treatment failure. Methods: This retrospective real-world cohort study included 294 adult patients with confirmed H. pylori infection evaluated at the Oradea County Emergency Clinical Hospital, Romania, between November 2022 and November 2025. Clinical, endoscopic, histopathological, microbiological, molecular, and treatment outcome data were collected from medical records. Resistance-associated mutations in the 23S rRNA (A2143G, A2142G, and A2142C) and gyrA (N87K, D91G, and D91N) genes were analyzed and correlated with phenotypic antimicrobial resistance and eradication outcomes. Independent predictors of eradication failure were identified using multivariable logistic regression, and a prediction model was subsequently developed. Results: Overall, 101 patients (34.4%) harbored 23S rRNA mutations and 64 (21.8%) carried gyrA mutations, while 27 patients (9.2%) exhibited mutations in both genes. A2143G was the most frequent mutation (25.2%). Resistance-associated mutations showed strong concordance with phenotypic antimicrobial resistance. Patients with wild-type strains achieved eradication rates exceeding 90%, whereas significantly lower success rates were observed among patients carrying A2143G, A2142G, or gyrA mutations. Multivariable analysis identified previous eradication attempts (aOR 3.12, 95% CI 1.71–5.68), A2143G mutation (aOR 4.86, 95% CI 2.43–9.72), gyrA mutation (aOR 2.91, 95% CI 1.45–5.84), increasing age (aOR 1.03, 95% CI 1.01–1.05), and treatment with clarithromycin-based triple therapy (aOR 2.18, 95% CI 1.02–4.63) as independent predictors of eradication failure. The prediction model demonstrated excellent discriminatory performance (AUC 0.88, 95% CI 0.84–0.92), with a sensitivity of 82.5%, specificity of 80.1%, and satisfactory calibration (Hosmer–Lemeshow p = 0.68). Conclusions: Resistance-associated mutations in the 23S rRNA and gyrA genes are strongly associated with phenotypic antimicrobial resistance and reduced H. pylori eradication success. Molecular resistance testing may facilitate individualized treatment selection and improve clinical outcomes. The proposed prediction model, integrating clinical characteristics, treatment regimen, and molecular resistance markers, demonstrated excellent performance and may represent a useful tool for identifying patients at increased risk of eradication failure.