Cartridge-based Nucleic Acid Amplification Test vs Conventional Methods in Diagnosis of Extra Pulmonary Tuberculosis at a Tertiary Healthcare Facility: A Diagnostic Cross-sectional Study

Aim and background: Extrapulmonary tuberculosis (EPTB) poses diagnostic challenges due to varied presentations and paucibacillary load.This study evaluates the role of cartridge-based nucleic acid amplification test (CBNAAT) in comparison with conventional methods for the diagnosis of EPTB at a tertiary healthcare facility.Materials and methods: A cross-sectional diagnostic study was conducted at UPUMS, Saifai, from January 2023 to March 2025, involving 104 clinically diagnosed EPTB patients.Specimens were tested using acid-fast bacillus (AFB) smear microscopy, mycobacteria growth indicator tube (MGIT) culture (gold standard), and CBNAAT.Diagnostic performance metrics were calculated, and statistical associations were analyzed using Chi-squared tests.Results: A total of 104 patients with EPTB were included, with a mean age of 30.48 ± 15.15 years.Among extrapulmonary TB, tubercular pleural effusion emerged as the most prevalent form, diagnosed in 52 patients (50.0%), followed by tubercular lymphadenopathy in 29 (27.9%) and tubercular meningitis in 15 (14.4%) cases.CBNAAT showed the highest diagnostic yield (69.2%), followed by MGIT culture (55.8%) and AFB smear (20.2%).CBNAAT and MGIT culture demonstrated statistically significant associations with EPTB types (p = 0.027 and p = 0.037, respectively), whereas AFB smear did not (p = 0.845).Compared to MGIT culture, CBNAAT showed high sensitivity (98.28%), good diagnostic accuracy (84.6%), and high negative predictive value (96.88%), though specificity was moderate (67.39%).CBNAAT also detected 62.7% of AFB smear-negative cases, indicating superior performance in paucibacillary disease.Conclusion: CBNAAT significantly outperforms AFB smear and closely aligns with MGIT culture in diagnosing EPTB.Its rapid turnaround and ability to detect rifampicin resistance support its integration into routine diagnostic protocols, especially in smear-negative and paucibacillary cases.