Clinical Utility of Cartridge-Based Nucleic Acid Amplification Test for Tuberculosis and Rifampicin Resistance...

Background Early diagnosis of tuberculosis (TB) and prompt detection of rifampicin resistance are essential to reduce transmission of TB and improve its treatment outcomes. The cartridge-based nucleic acid amplification test (CBNAAT) simultaneously detects the Mycobacterium tuberculosis complex and rifampicin resistance within a short turnaround time. This study evaluated the clinical utility of CBNAAT for rifampicin resistance identification and quick microbiological confirmation of extrapulmonary and pulmonary TB in standard clinical practice at a tertiary care center in Central India. Methods In this retrospective observational study, records of 2,640 patients with clinically suspected TB who underwent CBNAAT and subsequent line probe assay (LPA) analysis of rifampicin-resistant specimens between June 2024 and May 2025 were analyzed. Demographic characteristics, clinical variables, specimen type, and drug resistance profile were retrieved from laboratory records. Categorical associations were assessed by the chi-square or Fisher's exact test, and independent associations with CBNAAT positivity were identified by multivariable logistic regression. p < 0.05 was considered significant. Results CBNAAT detected Mycobacterium tuberculosis in 590 of 2,640 patients (22.35%). Positivity was significantly higher among patients aged 41-60 years, males, rural residents, individuals with diabetes or human immunodeficiency virus (HIV) infection, and those with a history of TB contact or of previous antituberculosis treatment (ATT). Pulmonary specimens showed a substantially higher detection rate (524/1900; 27.58%) than extrapulmonary specimens (66/740; 8.92%). Among confirmed cases, 556 (94.24%) were rifampicin-sensitive, 34 (5.76%) were rifampicin-resistant, and among these rifampicin-resistant cases, 12 (2.03%) were multidrug-resistant (MDR) on LPA. Independent associates of positivity were male sex (adjusted odds ratio (AOR) 1.58, 95% confidence interval (CI) 1.18-2.11), rural residence (AOR 1.42, 95% CI 1.06-1.91), diabetes mellitus (AOR 4.25, 95% CI 3.38-5.34), HIV infection (AOR 5.14, 95% CI 3.57-7.40), pulmonary specimen type (AOR 3.52, 95% CI 2.35-5.27), and previous TB treatment (AOR 2.18, 95% CI 1.61-2.95). Conclusions CBNAAT offers rapid microbiological confirmation and thus allows early start of treatment, which is critical in decreasing community transmission of Mycobacterium tuberculosis. The significant finding of rifampicin resistance further highlights the utility of this molecular tool to address the challenge of drug-resistant TB (DR-TB) in a tertiary care setting. These findings confirm that the test remains an important part of diagnostic protocols, mainly for pulmonary specimens where the detection rate was substantially higher. Expansion of molecular diagnostic services and their prioritization as the primary screening tool at all levels of clinical care is recommended to achieve the goals of the National Tuberculosis Elimination Program (NTEP) of India. Higher positivity rates in rural populations indicate the need for policy efforts to improve access to diagnostic facilities in rural areas. Longitudinal studies should be performed in the future to understand the effect of rapid diagnosis by CBNAAT on the long-term outcomes of therapy and mortality rates. Continuous monitoring of drug resistance patterns and integration of molecular testing in routine clinical pathways is important to guide regional TB control strategies.