Evaluation of the GeneXpert Mycobacterium tuberculosis/Rifampicin Assay for Early Detection of Extrapulmonary Tuberculosis and Rifampicin Resistance in Aligarh Region of Northern India

Purpose: Early diagnosis of extrapulmonary tuberculosis (TB) with simultaneous detection of rifampicin (RIF) resistance (RR) directly from the sample is a revolution brought by GeneXpert Mycobacterium TB (MTB/RIF) assay. Line probe assay (LPA) is not recommended for extrapulmonary/nonsputum specimens; GeneXpert MTB/RIF provides a diagnostic option for these. Hence, the following study aimed to evaluate the performance of GeneXpert MTB/RIF assay in nonsputum samples. Materials and Methods: A total number of 642 extrapulmonary and nonsputum respiratory samples were subjected to Ziehl–Neelsen (ZN) staining technique, fluorescent microscopy (FM), and GeneXpert MTB/RIF Assay. All samples were cultured on a solid Lowenstein–Jensen (LJ) medium and culture-positive samples were subjected to GenoType MTBDRplus LPA and drug susceptibility testing by 1% proportion method on a solid LJ medium. Results: GeneXpert MTB/RIF assay detected MTB in 25.9% (166/642) of the samples. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of ZN staining technique and FM were 21.52%, 99.35%, 91.89%, and 78.77% and 27.22%, 99.78%, 97.73%, and 80.07%, respectively. Sensitivity, specificity, PPV, and NPV of GeneXpert MTB/RIF in the detection of MTB were 93.75%, 96.53%, 90.36%, and 97.80%, and RIF RR was 92.0%, 97.74%, 88.46%, and 98.48%, respectively. LPA performed on positive culture growth showed 100% sensitivity and specificity in the detection of RIF and isoniazid resistance. Conclusion: GeneXpert MTB/RIF showed high sensitivity and specificity in detecting MTB and simultaneous RIF RR among the nonsputum samples which had a good concordance to LPA. It provides a judicious option for early detection of multidrug-resistant TB in extrapulmonary and nonsputum respiratory samples.