A new oligonucleotide array for the detection of multidrug and extensively drug-resistance tuberculosis

Abstract

Drug-resistant tuberculosis (TB) is a global crisis and a threat to health security. Since conventional drug susceptibility testing (DST) takes several weeks, we herein described a molecular assay to rapidly identify multidrug-resistant (MDR) and extensively drug-resistant (XDR) and reveal transmission associated-mutations of Mycobacterium tuberculosis complex (MTBC) isolates in 6 to 7 hours. An array was designed with 12 pairs of primers and 60 single nucleotide polymorphisms of 9 genes: rpoB, katG, inhA, ahpC, embB, rpsL, gyrA, rrs and eis. We assessed the performance of the array using 176 clinical MTBC isolates. The results of culture-based DST were used as the gold standard, the GenoType MTBDRplus and MTBDRsl tests were used for parallel comparison, and gene sequencing was performed to resolve the discordance. The sensitivities and specificities of the array are comparable to those of the MTBDRplus test for resistance to isoniazid (INH) (100.0%, 96.7%) and rifampicin (RIF) (99.4%, 96.7%) and of the MTBDRsl test for resistance to fluoroquinolones (FQs) (100%, 100%) and second-line injectable drugs (SLIDs) (98.3%, 100%). The sensitivities of the array for detecting resistance to ethambutol and streptomycin were 79.3% and 64.9%, respectively. The array has potential as a powerful tool for clinical diagnosis and epidemiological investigations.

Diagnosis of Multidrug-Resistant Pathogens of Pneumonia

“…For example, the Genotype MTBDRplus assay (Hain Lifescience, GmbH, Germany) detects rpoB , katG , and inhA genes of both rifampicin and isoniazid resistance on isolates from solid and liquid culture as well as directly on smear-positive pulmonary specimens, whereas the INNO-LiPA Rif.TB (Innogenetics, Zwijndrecht, Belgium) detects the rpoB gene conferring rifampicin resistance on M. tuberculosis complex isolates grown on solid culture only [ 68 ]. Many microarray assays were developed that detect mutations conferring resistance to rifampin, isoniazid, ethambutol, streptomycin, ofloxacin, kanamycin, amikacin, and capreomycin simultaneously in six to seven hours [ 71 ].…”

Multiplex PCR via Microarray a Surrogate for Rapid Molecular Detection of Mycobacterial and Fungal Species Along with Anti-Microbial Resistant Genes, Directly from Clinical Specimens’

“…He designed 12 pairs of primers and 60 single nucleotide polymorphisms of 9 genes i.e isoniazid (inhA), rifampicin (rpoB), pyrazinamide (pncA), ethambutol (embB), kanamycin (katG), streptomycin (rpsL & rrs), flouroquinolones (gyrA & gyrB), and amikacin (eis). The successful results had given a ray of hope for early identification of resistant genes of ATT [5]. Another study concluded the utility of microarray for rapid genomic detection of fungal isolates.…”

Pediatric Tuberculosis: The Impact of “Omics” on Diagnostics Development

“…These outcomes present excellent suitability for reliable use in a clinical setting for the identification and monitoring of resistant strains. Development of such methods could have a large impact not only on diagnosis of MTB, but also on disease prognosis [ 83 ].…”