Identification of mycobacterial species by PCR sequencing of quinolone resistance-determining regions of DNA gyrase genes

Abstract

The determination of the amino acid sequence of quinolone resistance-determining regions (QRDRs) in the A and B subunits of DNA gyrase is the molecular test for the detection of fluoroquinolone resistance in mycobacteria. We looked to see if the assignment of mycobacterial species could be obtained simultaneously by analysis of the corresponding nucleotide sequences. PCR sequencing of gyrA and gyrB QRDRs was performed for 133 reference and clinical strains of 21 mycobacterial species commonly isolated in clinical laboratories. Nucleotide sequences of gyrA and gyrB QRDRs were species specific, regardless of fluoroquinolone susceptibility.

FIG. 1.

Alignment of the nucleotide sequences of the gyrA and gyrB QRDRs from the 21 mycobacterial species. Sequences of M. tuberculosis were taken as the reference sequences, and dashes represent identical nucleotides. The nucleotide polymorphisms, i.e., a nucleotide difference that has been observed between strains within the same species, were indicated by a letter in boldface type, and their meaning is the following: the letter R when A or G was observed, Y for C or T, M for A or C, K for G or T, S for G or C, and W for A or T.