Comparative Evaluation of GeneXpert With Ziehl-Neelsen (ZN) Stain in Samples of Suspected Tuberculosis Cases at a Tertiary Care Teaching Hospital in Central India

Background Tuberculosis (TB) remains a significant public health challenge, particularly in developing countries, where delayed diagnosis contributes to ongoing transmission. Ziehl-Neelsen (ZN) smear microscopy, commonly used for TB diagnosis, has limitations in sensitivity, especially in cases of extrapulmonary tuberculosis (ETB). The GeneXpert <i>Mycobacterium tuberculosis</i> (MTB)/rifampicin (RIF) assay, a molecular diagnostic tool, offers rapid and accurate detection of MTB and RIF resistance. This study aimed to compare the diagnostic efficacy of GeneXpert MTB/RIF with ZN staining in detecting pulmonary tuberculosis (PTB) and ETB. Methods A prospective study was conducted over two years (April 2022 to April 2024) at a tertiary care teaching hospital in India. A total of 319 clinical samples from patients with suspected PTB and ETB were analyzed. Samples underwent ZN staining and GeneXpert MTB/RIF assay. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated using mycobacterial culture as the gold standard. The chi-square test was employed to compare diagnostic accuracy, with a p-value of <0.05 considered statistically significant. Results Of the 319 samples, ZN staining was positive in 18.2% of cases, while GeneXpert was positive in 21.6%. GeneXpert demonstrated a perfect sensitivity of 100% and a specificity of 98.81%, compared to ZN staining's sensitivity of 84.85% and specificity of 99.21%. GeneXpert showed superior performance in detecting TB in both pulmonary and extrapulmonary samples, with a statistically significant difference (p<0.001). Additionally, GeneXpert identified six cases of RIF resistance. Conclusion The GeneXpert MTB/RIF assay outperforms ZN staining in diagnosing TB, offering higher sensitivity and comparable specificity. Its ability to detect RIF resistance adds significant clinical value. Despite its cost, the integration of GeneXpert into routine diagnostic workflows, particularly in high TB prevalence areas, is recommended to enhance early detection and treatment, thereby reducing TB transmission.