Diagnostic Accuracy of Sputum Microscopy in Comparison With GeneXpert in Pulmonary Tuberculosis.

Background Tuberculosis (TB) is a major health problem. In Pakistan, the diagnosis of pulmonary tuberculosis mainly relies on acid-fast bacilli (AFB) smear microscopy and Xpert® MTB/RIF assay (Cepheid Inc., Sunnyvale, CA) - a nucleic acid amplification test - where available. There is a wide variation in the reported sensitivity of Ziehl-Neelsen (ZN) smear microscopy across previous studies. This study aimed to determine the accuracy of sputum ZN smear microscopy in diagnosing pulmonary tuberculosis as compared with the sputum GeneXpert (Xpert MTB/RIF assay) as the reference test. Materials and methods This is a retrospective cross-sectional study conducted in the outpatient department of the Pakistan Institute of Medical Sciences. This study included 326 patients, aged 12 years and above, who had their sputum samples tested for ZN smear microscopy and GeneXpert during the period January to June 2019. Patients' demographic details, sputum ZN smear microscopy, and GeneXpert test results were collected for data analysis. A case of pulmonary tuberculosis was defined as a patient with positive sputum GeneXpert test result. Results Out of the 326 patients, GeneXpert detected MTB deoxyribonucleic acid (DNA) in 50 patients and ZN smear microscopy detected AFB in 30 patients. There was a marginal male predominance among GeneXpert positive cases. Adolescents were the least affected age group. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of ZN smear microscopy were 60%, 100%, 100%, 93.24%, and 93.87%, respectively. The positive likelihood ratio was infinite whereas the negative likelihood ratio was 0.4. The area under curve (AUC) for ZN smear microscopy was 0.800 and receiver operating characteristic (ROC) curve analysis revealed a diagonal straight line closer to the left upper corner. Conclusion Sputum ZN smear microscopy is a highly specific but moderately sensitive test for the diagnosis of pulmonary tuberculosis. This study recommends the sputum GeneXpert MTB/RIF test to avoid a missed diagnosis of smear-negative pulmonary TB.