M-PCR improved the detection of mecA gene in clinical samples. To compare the detection sensitivity of the M-PCR method with the conventional real-time PCR method, we analysed infectious tissues collected from patients. DNA was purified by conventional methods (A) or following centrifugation (B: M-PCR). A comparative Ct (ΔCt) analysis was performed to examine fold changes of the mecA gene. Only M-PCR, but not conventional real-time PCR, detected the mecA gene from three clinically infected samples, including one pseudoarthrosis (a). M-PCR improved the detection of the mecA gene 6.96 times higher than conventional real-time PCR methods (b). The experiment was performed in triplicate with similar results.