Mutations in the rpoB gene of Mycobacterium tuberculosis that interfere with PCR-single-strand conformation polymorphism analysis for rifampin susceptibility testing

Rifampin susceptibility of 32 rifampin-resistant and 26 rifampin-susceptible Mycobacterium tuberculosis strains was analyzed by PCR-single-strand conformation polymorphism (SSCP) and DNA sequencing within the 157-bp region of the rpoB gene (Ala(500) to Val(550)). Two false-positive PCR-SSCP results were observed among the susceptible strains due to the silent mutation Gln(513) (CAA-->CAG) and the deletion mutation Thr(508) and Ser(509). Another silent mutation [Leu(511) (CTG-->CTA)], combined with the mutation Ser(531)-->Leu, was observed in a resistant strain. These results suggest that to rule out false-positive PCR-SSCP results, sequencing of the target DNA is required.