RAPID IDENTIFICATION OF MYCOBACTERIA FROM AIDS PATIENTS BY CAPILLARY ELECTROPHORETIC PROFILING OF AMPLIFIED SOD GENE

Aim-Rapid differentiation of mycobacterial species at the genomic leve l. Methods-The manganese superoxide dismutase (SOD) gene (464 bp) and 16SrRNA (353 bp) from 104 isolates (18 species) of mycobacteria were a mplified using polymerase chain reaction (PCR). Products were sequence d and a phenogram of SOD sequences derived. PCR products of SOD gene w ere digested with HaeIII, and restriction fragment profiles visualised using capillary electrophoresis. Results-Novel SOD sequences were fou nd for M szulgai, M marinum, M phlei, M smegmatis, M chelonei, M parat uberculosis, M malmoense, M intracellulare serotype 7, M intracellular e serotype 18, and M celatum types 1, 2, and 3. Phylogenetic analysis indicated that 18 of 19 species studied had 8-29% interspecies and <6% intraspecies sequence diversity in the SOD gene. No consistent differ ences were detected between AIDS and non-AIDS isolates. M paratubercul osis showed a unique SOD sequence with a 1.1% (SD 0.5%) diversity from M avium. Capillary electrophoresis profiles were able to differentiat e 16 of 18 species within 24 hours. Conclusions-A phenogram of SOD seq uences clearly delineated all mycobacterial species and showed two dis tinct clusters, fast growing species, and the M avium complex (MAC). W ithin the MAC, M avium (five types), M intracellulare (five types), M scrofulaceum (two types), and M paratuberculosis (one type) could be d emonstrated. Phylogenetic diversity of M celatum from MAC, previously suggested by 16SrRNA data, was confirmed. This simple and rapid method for DNA extraction, in conjunction with capillary electrophoresis of SOD restriction fragments, allows rapid identification of mycobacteria l isolates.