Molecular Detection of Drug-Resistant Mycobacterium tuberculosis with a Scanning-Frame Oligonucleotide Microarray

The increasing emergence of drug-resistant
Mycobacterium tuberculosis
poses significant threat to the treatment of tuberculosis (TB). Conventional drug susceptibility testing is time-consuming and takes several weeks because of the slow growth rate of
M. tuberculosis
and the requirement for the drugs to show antimycobacterial activity. Resistance to TB drugs in
M. tuberculosis
is caused by mutations in the corresponding drug resistance genes (e.g.,
katG, inhA, rpoB, pncA, embB, rrs, gyrA, gyrB
), and detection of these mutations can be a molecular indicator of drug resistance. In this chapter, we describe the utility of a microarray-based approach exploiting short overlapping oligonucleotides (sliding-frame array) to rapidly detect drug resistance–associated mutations (substitutions, deletions, and insertions) in the
pncA
gene responsible for resistance of
M. tuberculosis
to pyrazinamide (PZA) as an example for this approach. Hybridization of
pncA
-derived RNA or
DNA
with the microarray enables easy and simple screening of nucleotide changes in the
pncA
gene. Sliding-frame microarrays can be used to identify other drug-resistant TB strains that have mutations in relevant drug resistance genes.