Detection of rifampin-resistant Mycobacterium tuberculosis strains by using a specialized oligonucleotide microarray

DNA microarray represents one of the major advances in diagnostic sequencing of polymerase chain reaction (PCR) products. Until now, arrays have been relatively expensive, complex to perform, and difficult to interpret, limiting their wide application in the clinical laboratory. A moderate-density oligonucleotide microarray that can rapidly identify Mycobacterium tuberculosis rifampin-resistant strains was developed. The method is based on the detection of point mutations and other rearrangements in the rpoB gene region determining rifampin resistance. Rifampin resistance was determined by hybridizing fluorescently labeled, amplified genetic material generated from bacterial colonies to the array. Fifty-three rifampin-resistant M. tuberculosis and 15 rifampin-susceptible M. tuberculosis were tested and results were concordant with those based on culture drug susceptibility testing and sequencing. Rifampin-resistant clinical isolates were detected in as little as 1.5 hours after PCR amplification with visual results. It is demonstrated that oligonucleotide microarray is an efficient, specialized technique to implement and can be used as a rapid method for detecting rifampin resistance to complement standard culture-based method.