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A retrospective observational study was performed to determine the sensitivity and limitation of PCR test for the detection of  Mycobacterium tuberculosis  and  M. avium  complex. We obtained clinical specimens collected from the respiratory tract, cultured  M. tuberculosis  or  M. avium  complex, and performed PCR analysis. A total of 299 samples ( M. tuberculosis , 177;  M. avium , 35;  M. intracellulare , 87) were analyzed by COBAS TaqMan PCR from April 2007 to March 2011. The PCR positivity rates were 50–55%, 70–100%, 88–98%, and 100% in smear-negative, smear 1+, 2+, and 3+ groups, respectively. The PCR positivity of tuberculosis in smear 1+ was 80.6%, which was statistically significantly ( P  < 0.001) lower than that of smear 2+ (97.3%). From January 2005 to March 2007, we collected an additional 138 samples ( M. tuberculosis , 74;  M. avium , 21; M. intracellulare, 43), which were analyzed by COBAS Amplicor PCR. The PCR positivity rates obtained using COBAS TaqMan PCR and COBAS Amplicor PCR were not significantly different. The sensitivity of PCR test for mycobacteria is not sufficient in case of smear 1+. Careful consideration must be given to the interpretation of negative PCR test results in smear 1+, because smear-positive tuberculosis is the criterion for isolation.

Clinical Evaluation of COBAS TaqMan PCR for the Detection ofMycobacterium tuberculosisandM. aviumComplex