Comparative Evaluation of Smear Microscopy, Xpert MTB/RIF, Löwenstein-Jensen Culture, and MGIT 960 for the Diagnosis of Pulmonary and Extrapulmonary Tuberculosis in Tangier, Morocco

Introduction Tuberculosis (TB) remains a major public health concern, requiring rapid and accurate diagnostic tools to improve patient management and limit transmission. The aim of this study was to assess the diagnostic performance of smear microscopy, Xpert MTB/RIF, and Löwenstein-Jensen culture compared with liquid culture using the Mycobacterial Growth Indicator Tube (MGIT) 960 liquid culture system as the reference standard. A secondary objective was to evaluate rifampicin resistance and compare its detection by Xpert MTB/RIF with phenotypic methods. Materials and methods A retrospective diagnostic performance study was conducted over nine months (July 2025 to March 2026), including both pulmonary and extrapulmonary samples. All specimens were processed under biosafety level 3 laboratory conditions and tested in parallel using smear microscopy, Xpert MTB/RIF, and culture on Löwenstein-Jensen medium and in the MGIT 960 liquid culture system. Diagnostic performance parameters, including sensitivity, specificity, positive predictive value, and negative predictive value, were calculated using the MGIT 960 liquid culture system as the reference standard. The corresponding 95% confidence intervals (95% CIs) were calculated using the exact Clopper-Pearson method. Results A total of 386 specimens were included in the analysis, comprising 233 pulmonary samples (60.4%) and 153 extrapulmonary samples (39.6%). Overall, Mycobacterium tuberculosis complex was detected in 46 cases (11.9%) by liquid culture using the MGIT 960 system. The positivity rate of Xpert MTB/RIF was 49 cases (12.7%), while smear microscopy detected 31 cases (8.0%) and Löwenstein-Jensen culture identified 36 cases (9.3%). Among culture-negative specimens (340/386, 88.1%), 19/340 cases (5.6%) were positive by Xpert MTB/RIF, of which 3/19 (15.8%) were also smear-positive. Compared with liquid culture using the MGIT 960 system as the reference standard, Xpert MTB/RIF demonstrated higher sensitivity than smear microscopy in both pulmonary specimens (63.3% vs 53.3%) and extrapulmonary specimens (68.8% vs 62.5%), while both tests maintained high specificity. Löwenstein-Jensen culture showed a sensitivity of 76.1% and a specificity of 99.7%. High concordance was observed between Xpert MTB/RIF and phenotypic drug susceptibility testing for rifampicin resistance. Conclusion An integrated diagnostic approach combining molecular testing, smear microscopy, and complementary culture methods remains essential for optimal TB diagnosis. Xpert MTB/RIF provides rapid and reliable detection, particularly in smear-negative and extrapulmonary specimens, although culture remains indispensable for confirmation and drug susceptibility testing.