Utility of smear microscopy and GeneXpert for the detection of Mycobacterium tuberculosis in clinical samples

Abstract

Rapid identification of Mycobacterium tuberculosis (MTB), its resistance to rifampicin and differentiation of MTB from nontuberculous mycobacteria (NTM) is necessary in the management of mycobacterial diseases. Culture, the "gold standard" for the detection of MTB, is time consuming. In spite of its rapidity and low cost, smear microscopy has poor sensitivity for the detection of acid-fast bacilli (AFB). A real-time PCR based rapid diagnostic method like GeneXpert MTB/RIF assay can simultaneously detect M. tuberculosis and rifampicin (RIF) resistance. Hence, we aim to compare the performance of GeneXpert MTB/RIF assay with smear microscopy and culture. In this descriptive cross-sectional study, we compared the performance of GeneXpert in pulmonary (N=127) and extrapulmonary (N=48) clinical specimens with other diagnostic methods like culture, Auramine O (AO), and Ziehl Neelsen (ZN) staining. Rifampicin resistance was detected only by GeneXpert. Demographic data and clinical history of the subjects were collected from the patient's hospital records. AO and ZN staining when compared with mycobacterial growth indicator (MGIT) culture showed the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy of 68.6, 95.7, 80, 92.4, 90.3% and 65.7, 95.7, 79.3, 91.8, 89.7%, respectively. The sensitivity, specificity, PPV, NPV and accuracy of GeneXpert was 88.6, 93.6, 77.5, 97.0 and 92.6%, respectively. GeneXpert is the best available rapid diagnostic method as it can detect MTB and rifampicin resistance gene simultaneously. Accuracy and negative predictive value of GeneXpert was found to be better than AFB staining. Thus, a negative GeneXpert test can rule out TB. Further, a negative GeneXpert and a positive smear microscopy results indicate the presence of NTM. However, GeneXpert is expensive and needs sophisticated instrument when compared to smear microscopy.