Strain-specific variation in the dnaJ gene of mycobacteria

The polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique was evaluated for species identification among mycobacteria by analysis of the dnaJ gene. Nine clinical isolates of Mycobacterium tuberculosis with different fingerprint patterns all gave the same distinct SSCP banding pattern and could be distinguished from other mycobacteria, such as M. avium. In contrast, considerable strain-specific dnaJ gene variations were observed amongst 42 clinical isolates of M. avium and 13 other atypical mycobacterial strains. Only 62% of the M. avium isolates hybridised to an M. avium-specific probe and only 14% could be identified correctly as M. avium by both probe and restriction fragment length polymorphism analysis. This finding was supported by direct sequence analysis. Variations were also observed in M. gordonae and M. scrofulaceum isolates. Computerised analysis of M. avium samples broadly identified three clusters. Results suggest that although the SSCP procedure may be useful for distinguishing M. tuberculosis from other mycobacteria, this technique applied to the dnaJ gene may not be suitable for strain identification. The results stress the importance of testing a large collection of clinical isolates before new molecular procedures are introduced into routine laboratories.