Clinical utility of DNA amplification and sequencing to identify a strain of Mycobacterium avium in paraffin-embedded, formalin-fixed biopsies from an immunosuppressed child.

Nontuberculous mycobacterial (NTM) infections are serious, though rare, in patients with severe combined immunodeficiency who have received bone marrow transplants. A 5-year-old female patient underwent stem cell/bone marrow transplant with disseminated NTM. Real-time polymerase chain reaction (PCR) using a fluorescence resonance energy transfer (FRET) probe for detection and identification of NTM was performed. The FRET-based real-time PCR assay amplified mycobacterial DNA, and the postamplification melt curve analysis classified the organism as a NTM. The pyrosequence of the hypervariable region A definitively identified the infecting organism as Mycobacterium avium. Real-time PCR along with melt curve analysis and pyrosequencing provides faster, definitive identification of mycobacteria, as compared to bacterial culture. In this case report, we emphasize the importance of utilizing molecular means for fast and accurate diagnosis.