Dideoxy fingerprinting for rapid screening of rpoB gene mutations in clinical isolates of Mycobacterium tuberculosis

Rifampin is a key component of therapeutic regimens for tuberculosis control, and a marker for multidrug resistance of Mycobacterium tuberculosis. Mutations responsible for conferring rifampin in resistance in M. tuberculosis are known to occur in a 69-bp region of the rpoB gene. In this study, we assessed the accuracy of dideoxy fingerprinting (ddF), a hybrid technique employing elements of dideoxy sequencing and single-strand polymorphism analysis, for rapid screening of rifampin resistance in clinical isolates of M. tuberculosis. This technique was used to analyze 72 M. tuberculosis isolates. The results were compared with those of automated dideoxy sequencing and the antibiotic resistance profile (determined with the BACTEC system). Of the 72 isolates, 50 were rifampin resistant. The ddF findings were completely consistent with those of dideoxy sequencing in all isolates. In 68 (94%) isolates, the ddF findings were consistent with the rifampin resistance status determined with the BACTEC system; all four isolates with inconsistent results had no mutation in the 69-bp region, but were resistant to rifampin. Our findings suggest that ddF accurately detects mutations in the rifampin resistance-associated 69-bp region of the rpoB gene in clinical isolates of M. tuberculosis, and may be a valuable screening tool for rifampin resistance.