Comparative evaluation of sputum microscopy and Xpert MTB/RIF assay for tuberculosis detection and rifampicin resistance surveillance in Biratnagar, Nepal

ABSTRACT Tuberculosis (TB) control in Nepal faces persistent challenges due to underdiagnosis and increasing drug resistance. This study assessed the diagnostic performance of the Xpert MTB/RIF assay compared with conventional smear microscopy and estimated the prevalence of rifampicin-resistant TB (RR-TB) in Biratnagar, a high-burden urban center. Between March and September 2023, 509 clinical specimens from TB suspects were analyzed by Ziehl-Neelsen (ZN) staining, fluorescence microscopy (FM), and Xpert MTB/RIF. Using Xpert as the operational reference, ZN and FM exhibited overall sensitivities of 55.9% (89/159) and 68.5% (109/159), respectively. In paired sputum-only analyses ( n = 446; sputum Xpert positives = 145), ZN and FM sensitivities were 60.0% (87/145) and 70.3% (102/145), respectively; sputum specificity was 100% for both methods. Xpert detected 31.2% (159/509) positive cases—78.7% more than ZN and 45.9% more than FM. Rifampicin resistance was identified in 5.03% (8/159) of Xpert-positive samples and was strongly associated with prior treatment ( P < 0.001); RR-TB occurred in 66.7% (6/9) of retreatment cases vs 1.3% (2/150) of new cases. Xpert increased detection in paucibacillary and extrapulmonary specimens. These findings support expanded use of rapid molecular testing, but results should be interpreted cautiously because culture/speciation was not performed. IMPORTANCE The spread of drug-resistant tuberculosis (TB) is a growing public health threat in Nepal. Using a rapid molecular test in Biratnagar, we simultaneously diagnosed TB and identified rifampicin resistance. We found rifampicin-resistant TB in >5% of Xpert-positive patients, higher than national averages for new cases, and a markedly elevated risk among previously treated patients. Rapid detection of resistance permits earlier initiation of appropriate therapy and can reduce onward transmission.