Comparative accuracy of molecular assays for detecting methicillin-resistant Staphylococcus aureus: Evidence from 32 studies

Methicillin-resistant Staphylococcus aureus (MRSA) remains a major global health concern due to its multidrug resistance and associated morbidity. Conventional culture-based antimicrobial susceptibility testing is time-consuming and may delay optimal treatment. Molecular assays have emerged as rapid alternatives, but their diagnostic performance across clinical settings has not been comprehensively synthesized. To evaluate the diagnostic accuracy of molecular assays for MRSA detection and explore potential sources of variability related to assay type, specimen type, and study setting. Following the PRISMA-DTA statement, we systematically searched PubMed, Embase, Web of Science, and the Cochrane Library from database inception to March 2026. Studies evaluating molecular assays against culture-based antimicrobial susceptibility testing were included. Pooled sensitivity, specificity, and summary area under the curve (AUC) were estimated using a bivariate random-effects model. Subgroup analyses were performed based on assay modality, specimen type, and country income level. Thirty-two studies involving 5342 clinical specimens were included. Molecular assays demonstrated high diagnostic accuracy, with a pooled sensitivity of 0.92 (95% CI: 0.91–0.93) and specificity of 0.95 (95% CI: 0.92–0.96). The summary AUC was 0.98 (95% CI: 0.96–0.99). Subgroup analyses showed that real-time PCR outperformed conventional PCR, and nasal swabs yielded the highest diagnostic performance among specimen types. Diagnostic accuracy was slightly higher in high-income countries than in low- and middle-income settings. Deeks' test indicated no significant publication bias ( P = 0.22). Molecular assays demonstrate excellent diagnostic accuracy for MRSA detection and can substantially reduce diagnostic turnaround time. Their integration into clinical workflows may support earlier infection control and antimicrobial decision-making. Further standardization and validation are warranted to optimize their use across diverse healthcare settings. • Molecular assays demonstrate excellent diagnostic accuracy for MRSA detection, with a pooled sensitivity of 0.92, specificity of 0.95, and an AUC of 0.98. • Real-time PCR shows superior performance compared to conventional PCR, with higher sensitivity (0.95 vs. 0.89) and specificity (0.96 vs. 0.94). • Diagnostic accuracy is highest with nasal swabs (sensitivity: 0.96; specificity: 0.97), outperforming wound and blood specimens. • Studies conducted in high-income countries report significantly higher diagnostic accuracy (AUC = 0.98) than those in low- and middle-income countries (AUC = 0.96). • The analysis found no significant publication bias, strengthening the reliability of the pooled estimates despite moderate heterogeneity.