Evaluation of multiplex allele-specific PCR for rapid detection of isoniazid and fluoroquinolone resistance in Mycobacterium tuberculosis: A cross-sectional study in high-TB-burden settings in India.

INTRODUCTION: India accounts for 26 % of global tuberculosis (TB) cases, with delayed diagnosis of Mycobacterium tuberculosis (MTB) and drug resistance exacerbating disease transmission. Conventional drug susceptibility testing (DST) remains time-consuming, while molecular tools like the Xpert MTB/RIF assay-though rapid-are limited to detecting MTB and rifampicin (RIF) resistance. Testing for isoniazid (INH) and second-line drugs requires the costly Xpert MTB/XDR assay. Although line probe assays (LPAs) identifies first- and second-line drug resistance, their accessibility is restricted to specialized laboratories. This underscores the need for a rapid, cost-effective alternative to diagnose resistance to INH and fluoroquinolones (FQs).

METHODS: A cross-sectional study was performed at the Department of Microbiology, AIIMS Bhubaneswar, and the Intermediate Reference Laboratory (IRL), Cuttack, from March 2022 to April 2023. MTB isolates (n = 123) were analyzed using LPAs (Hain Lifescience's Genotype MTBDRplus and Genotype MTBDRsl) and multiplex allele-specific (MAS) PCR. The MAS-PCR targeted mutations in katG codon 315 and the inhA-15 promoter region for INH resistance, and gyrA codon 94 for FQ resistance.

RESULTS: MAS-PCR identified INH resistance in 28/123 (22.76 %) isolates. Compared to LPA, MAS-PCR demonstrated sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of 80.77 %, 93.81 %, 77.78 %, 94.79 %, and 91.06 %, respectively, for INH resistance. For FQ resistance, MAS-PCR identified 19/123 (15.44 %) resistant isolates, with sensitivity, specificity, PPV, NPV, and accuracy of 87.50 %, 95.33 %, 73.68 %, 98.08 %, and 94.31 %, respectively, relative to LPA.

CONCLUSION: MAS-PCR offers a rapid, technically feasible, and cost-effective method for detecting resistance to INH and FQs. Its high accuracy and affordability position it as a viable alternative in resource-limited settings, facilitating timely TB diagnosis and resistance management.