Molecular Evaluation of Rifampicin and Isoniazid Resistance in Pulmonary Tuberculosis Using Cartridge-Based Nucleic Acid Amplification Test and Line Probe Assay

Background Pulmonary tuberculosis (TB) continues to be a major public health problem, especially with the rising number of drug-resistant TB cases. Rapid molecular tests such as cartridge-based nucleic acid amplification test (CB-NAAT) and line probe assay (LPA) help in the early diagnosis of TB and detection of drug resistance, allowing timely treatment and better disease control. Methods This cross-sectional study included 3451 pulmonary samples collected from patients suspected of having pulmonary tuberculosis. All samples were tested by CB-NAAT for detection of Mycobacterium tuberculosis and rifampicin resistance. Samples showing drug resistance were further analyzed by first-line LPA to identify genetic mutations associated with rifampicin and isoniazid resistance. Results Among the 3451 pulmonary samples tested, M. tuberculosis was detected in 758 (21.9%) cases, while in 2682 (77.7%) samples, it was not detected. Invalid/error results were observed in only 11 (0.3%) samples. Rifampicin resistance was identified in 42 (5.5%) isolates. Sputum was the most common positive sample, accounting for 661 (87.2%) cases. Most patients were newly diagnosed TB cases (n=662, 87.3%), whereas previously treated cases, TB contacts, and HIV-positive patients constituted a smaller proportion. First-line LPA detected multidrug-resistant tuberculosis (MDR-TB) in 29 isolates. The most common mutation associated with rifampicin resistance was rpoB MUT3 (S531L/H531L), while katG MUT1 (S315T1) was the predominant mutation linked to isoniazid resistance. Conclusion CB-NAAT and LPA proved to be useful and reliable methods for rapid diagnosis of pulmonary tuberculosis and detection of drug resistance. Early identification of drug-resistant TB through molecular techniques can help in timely treatment initiation and improved tuberculosis control. The predominance of rpoB S531L/H531L and katG S315T1 mutations suggests their important role in the development of anti-tubercular drug resistance.