Diagnostic accuracy of the MultNAT MTC/RIF assay for rapid detection of Mycobacterium tuberculosis and rifampicin resistance: a prospective comparative study

Purpose Tuberculosis (TB) remains a leading cause of morbidity and mortality worldwide, with diagnostic gaps most pronounced in extrapulmonary disease and resource-limited settings. Although the WHO-endorsed Xpert MTB/RIF assay revolutionized TB diagnostics, its cost, infrastructure requirements, and suboptimal sensitivity in paucibacillary specimens constrain accessibility. The MultNAT MTC/RIF assay is a newly developed dual-target, cartridge-based molecular platform designed to overcome these limitations and to support decentralized molecular testing in routine clinical laboratories. Methods We conducted a prospective diagnostic accuracy study among 414 patients with presumptive TB at a tertiary-care hospital serving both community and referral populations. Clinical specimens—including sputum, bronchoalveolar lavage fluid (BALF), pleural effusion, and pus—were analyzed using MultNAT MTC/RIF, Xpert MTB/RIF (reference comparator), ZEESAN, and CapitalBio assays. Diagnostic accuracy was evaluated by positive percent agreement (PPA), negative percent agreement (NPA), predictive values, overall percent agreement (OPA), and Cohen's κ, with subgroup analyses by specimen type. Rifampicin resistance detection was also assessed. Results Among the 414 specimens analyzed, 182 were sputum (43.9%), 182 bronchoalveolar lavage fluid (BALF, 43.9%), 27 pleural effusion (6.5%), and 23 pus (5.6%) samples. For MTC detection compared with Xpert, MultNAT achieved excellent PPA of 96.55% (95% CI 93.32–98.50) and NPA of 98.35% (95% CI 95.26–99.66), yielding an OPA of 97.34% and κ = 0.95. Critically, PPA remained high (≥ 91.7%) across all extrapulmonary samples. For rifampicin resistance, MultNAT demonstrated a PPA of 93.75% (95% CI 69.77–99.84) and an NPA of 99.50% (95% CI 97.26–99.99), surpassing CapitalBio. Conclusion MultNAT MTC/RIF assay combines high analytical accuracy with rapid (< 2 h) turnaround and ambient reagent stability, providing reliable detection of TB and rifampicin resistance across diverse specimen types. These features suggest strong potential for decentralized implementation in resource-constrained settings.