How to Cite
Abstract
Objective: This study evaluated the diagnostic performance of GeneXpert MTB/RIF in sputum samples from Pakistani patients with cavitary TB, using mycobacterial culture as the gold standard and comparing it to sputum smear microscopy.
Methods: In this cross-sectional study conducted at a tertiary hospital in Rawalpindi, 187 HIV-negative adults (18–60 years) with cavitary pulmonary TB were enrolled. Sputum samples were analyzed by smear microscopy, GeneXpert, and culture at baseline, 2, 5, and 6 months of therapy. Diagnostic accuracy indices (sensitivity, specificity, PPV, NPV) were compared with culture results.
Results: Among 187 patients (mean age 44.1 ± 17.1 years; 93.6% female), 32% had baseline culture-confirmed TB. GeneXpert detected 91.7% of culture-positive cases versus 28.3% by smear. After 2 months, 43.3% remained culture-positive, while GeneXpert and smear positivity were 35.3% and 32.6%, respectively. All patients achieved culture negativity by treatment completion; however, GeneXpert and smear remained positive in 49.2% and 41.7% due to non-viable bacilli.
Conclusion: GeneXpert MTB/RIF demonstrated superior sensitivity to smear microscopy in detecting cavitary TB and monitoring therapeutic response, but showed reduced specificity post-treatment due to residual DNA. Combining GeneXpert with culture improves reliability for therapy monitoring and outcome prediction.
Keywords: Tuberculosis, Mycobacterium tuberculosis; Polymerase Chain Reaction; Sputum; Sensitivity and Specificity; Treatment Outcome
References
World Health Organization. Global tuberculosis report 2023. Geneva: WHO; 2023.
Feng G, Jiang H, Chen Y. Efficacy of Xpert MTB/RIF assay in detecting Mycobacterium tuberculosis in samples with different results by smear and culture in a coastal city with high incidence of tuberculosis. BMC Infect Dis. 2025;25(1):55. https://doi.org/10.1186/s12879-025-10446-z
Comeche B, Pérez-Butragueño M, Ramos-Rincón JM, Tiziano G, Cuadros J, Górgolas M. Limitaciones del ensayo Xpert-MTB/RIF® en el diagnóstico inicial de tuberculosis en el contexto de un hospital rural en Etiopía. Rev Esp Quimioter. 2022;35(4):374–8. https://doi.org/10.37201/req/052.2022
Karuniawati A, Burhan E, Koendhori EB, Sari D, Haryanto B, Nuryastuti T, et al. Performance of Xpert MTB/RIF and sputum microscopy compared to culture in Indonesia. Front Med (Lausanne). 2022;9:909198. https://doi.org/10.3389/fmed.2022.909198
Barcellos RB, Macieira J, Bastos ML, de Souza B dos S, de Lemos ACM, Netto AR, et al. Xpert MTB/RIF Ultra for TB diagnosis and rifampicin resistance detection. Cochrane Database Syst Rev. 2021;3:CD009593. https://doi.org/10.1002/14651858.CD009593.pub3
Albert H, Nathavitharana RR, Isaacs C, Pai M, Denkinger CM, Boehme CC, et al. Development, roll-out, and impact of Xpert MTB/RIF for tuberculosis: what lessons have we learned and how can we do better? Eur Respir J. 2023;51(2):516–25. https://doi.org/10.1183/13993003.00345-2023
Horne DJ, Kohli M, Zifodya J, Schiller I, Dendukuri N, Tollefson D, et al. Sputum monitoring during TB treatment: observations from the REMoxTB trial revisited. Am J Respir Crit Care Med. 2024;200(4):486–88. https://doi.org/10.1164/rccm.2024-00127ED
Gill MJ, Costagliola D. Editorial commentary: Myocardial infarction in HIV-infected persons: time to focus on the silent elephant in the room? Clin Infect Dis. 2023;65(9):1424–25. https://doi.org/10.1093/cid/ciad123
Nguyen KV, Pham MPT, Nguyen NT, Nguyen VT, Duong QX, Vu HV. GeneXpert performance in HIV-infected smear-negative TB patients. PLoS One. 2021;16(7):e0253961. https://doi.org/10.1371/journal.pone.0253961
Terzić HA, Aydemir Ö, Karakeçe E, Demiray T, Köroğlu M. Evaluation of the Xpert MTB/RIF test performance in diagnosis of suspected M. tuberculosis in pulmonary and extrapulmonary specimens. Mediterr J Infect Microb Antimicrob Agents. 2024;13(1):13. https://doi.org/10.4274/mjima.galenos.2024.23055.13
Muthaura C, Githui W, Kiptoo M, Otiende C, Wanjala J, Gikunyi J, et al. Evaluation of MBLA and Xpert in monitoring TB treatment. J Infect. 2023;83(5):554–62. https://doi.org/10.1016/j.jinf.2023.03.001
Vasankari T, Holmström P, Ollgren J, Liippo K, Kokki M, Ruutu P. Risk factors for poor tuberculosis treatment outcome in Finland: a cohort study. BMC Public Health. 2024;24(1):291. https://doi.org/10.1186/s12889-024-01791-0
Ahmad N, Gessessew A, Asres K, Desalegn A, Basha F, Yitayal Z, et al. Xpert MTB/RIF assay in retreatment TB cases. Int J Tuberc Lung Dis. 2023;27(6):714–20. https://doi.org/10.5588/ijtld.22.0799
RNTCP India. Manual of Standard Operating Procedures (SOP) for Direct Microscopy, Culture and DST. New Delhi: Central TB Division, Ministry of Health & Family Welfare; 2024. [DOI Not Applicable]
Yuan J, Cai Y, Luo S, Hu Q, Wu J. Diagnostic accuracy of GeneXpert MTB/RIF assay for pulmonary tuberculosis in smear-negative patients: a systematic review and meta-analysis. Int J Infect Dis. 2023;131:1–8. https://doi.org/10.1016/j.ijid.2023.03.016
Meehan C, Torrea G, Wanjala J, Dlamini Z, Skhosana L, Oga C, et al. Xpert MTB/RIF Ultra trace call and TB recurrence. Clin Infect Dis. 2021;74(8):1982–1984. https://doi.org/10.1093/cid/ciab567
Chin DP, Juma R, Dlamini S, Tjituka F, Rusu R, Cattamanchi A, et al. Impact of Xpert MTB/RIF rollout on TB outcomes in three African countries. Int J Tuberc Lung Dis. 2022;26(3):239–47. https://doi.org/10.5588/ijtld.21.0461
Teo AS, Ong HT, Ong KW, Ho CL, Low JG. Novel biomarkers for TB treatment monitoring. J Clin Med. 2021;10(8):1626. https://doi.org/10.3390/jcm10081626
Nicholson TJ, Hoddinott G, Seddon JA, Claassens MM, van der Zalm MM, Lopez E, et al. A systematic review of risk factors for mortality among tuberculosis patients. Syst Rev. 2023;12(1):175. https://doi.org/10.1186/s13643-023-02175-8
Fibriani A, Tjandra K, Supriyanto Y, Budiman C. Chest X-ray versus microbiological clearance in tuberculosis. BMC Pulm Med. 2020;20(1):121. https://doi.org/10.1186/s12890-020-1159-2
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Copyright (c) 2025 Aisha Shafique, Eisha Arshad, Sara Daud