Agreement between TrueNat MTB/RIF and Microscopy for detection of Pulmonary and Extrapulmonary Tuberculosis at a Tertiary Care Hospital of Eastern Uttar Pradesh, India.

Background: Tuberculosis (TB) remains a significant public health problem in India, with both pulmonary and extra-pulmonary forms contributing substantially to disease burden. Smear microscopy, though inexpensive and rapid, has limited sensitivity, particularly in paucibacillary cases. TrueNat MTB/RIF, a chip-based real-time PCR endorsed by WHO, provides rapid molecular detection and rifampicin resistance profiling. Objective: To evaluate the diagnostic performance and agreement between Ziehl–Neelsen (ZN) smear microscopy and TrueNat MTB/RIF for pulmonary and extra-pulmonary TB at a tertiary care hospital in Eastern Uttar Pradesh. Methods: A retrospective study was conducted on 4,249 clinical specimens (65% pulmonary, 35% extra-pulmonary). All samples were tested by both ZN microscopy and TrueNat MTB/RIF. Diagnostic positivity rates, rifampicin resistance, and agreement across sample categories and patient subgroups (HIV, diabetes) were analyzed using Cohen’s kappa. Results: The majority of patients were aged 18–40 years (37.6%) and were males (55.4%). Cough (71.5%) and fever (40.8 %) were the most frequent symptoms. Smear microscopy detected acid-fast bacilli in 4.3% (185/4249) of samples, while TrueNat MTB/RIF identified Mycobacterium tuberculosis in 13.7% (583/4249). Rifampicin resistance was observed in 5.6% of TrueNat-positive cases, with 26.4% indeterminate results. The overall agreement between microscopy and TrueNat was 42.2%. Agreement was higher in pulmonary (57%) than extra-pulmonary samples (6.1%), with the highest concordance in sputum (60.5%). Agreement was also higher among HIV-positive (78.4%) and diabetic patients (58.3%) compared to their counterparts.