Rapid screening of mutations for second-line-drug-resistant genes in Mycobacterium tuberculosis culture isolates by in-house developed DNA bio-chip

The rate of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) has been steadily increasing and is a major setback to TB control in India. The availability of quick and reliable methods for detecting second-line drug resistance (SLDR) is vital to managing patients satisfactorily. A rapid molecular technique to detect SLDR in Mycobacterium tuberculosis (M. tuberculosis) has been developed using DNA biochip. Specific probes containing wild-type region or specific mutations were designed for immobilization on DNA bio-chip. DNA bio-chip was developed in-house on polycarbonate track-etched membranes (PC-TEM). DNA bio-chip allows the identification of mutations in gyrA gene for fluoroquinolone (FQ) resistance, in rrs gene and the eis promoter region for resistance to second-line injectable drugs (SLID). An asymmetric multiplex PCR was standardized for gyrA, rrs and eis genes. A chemiluminescence based biochip assay was optimized. Bio-chip was tested on 112 M. tuberculosis clinical isolates with different resistance spectra. Isolates analyzed using bio-chip shows that 61 (61%) samples were wild-type. Twelve samples show mutations in gyrA gene, 11 samples in rrs gene, 12 samples in eis gene and 4 samples show double mutation in rrs and eis genes. The sensitivity and specificity of bio-chip for detection of FQ resistance ranged from 75 to 100% and 96.7%-100%, respectively. The sensitivity and specificity of SLID detection ranged from 90.9 to 100% and 96.7-100% respectively. The analytical sensitivity of the bio-chip was ~ 250 genome copies per assay. The biochip has high sensitivity and specificity and could be useful for clinical microbiology studies and epidemiological surveillance of drug resistant (DR) M. tuberculosis. It is a highly accurate tool for screening for SLDR, significantly reducing the time for phenotypic drug susceptibility test (DST) results from weeks to a single day.