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This paper presents an integrated microfluidic system for rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) by utilizing antibody-conjugated magnetic beads. By using immunomagnetic beads conjugated with specific antibodies and on-chip nucleic acid amplification, the developed microfluidic system can detect MRSA bacteria with a high sensitivity and specificity when compared with the bench-top diagnostic systems. The MRSA can be firstly bound onto the surface of the magnetic beads, followed by purifying the magnetic complexes with the incorporation of permanent magnet and the microfluidic control module. Finally, the specific genes of MRSA can be amplified by utilizing an on-chip polymerase chain reaction (PCR) module. Hence, the integrated microfluidic system can automatically perform isolation and detection of MRSA within a short period of time and can be used as a promising platform for biological and medical applications in the future.