Early Diagnostic Utility of Genexpert for the Detection of Mycobacterium tuberculosis

Usman Aslam; Muhammad Shams ul Haq; Muhammad Yousuf; Aleena Batool; Usman Ali; Komal Zaman; Syed Muhammad Asif Shah

doi:10.62497/irabcs.158

Authors

Dr. Usman Aslam Medical Officer, Department of General Surgery, SUM, THQ Hospital Jand, District Attock, Pakistan; Medical Officer, Department of General Surgery, The Health Service Executive (HSE), Ireland Author https://orcid.org/0009-0000-6592-1052
Dr. Muhammad Shams ul Haq Senior House Officer, General Medicine, The Health Service Executive (HSE), Ireland Author https://orcid.org/0009-0007-2116-4126
Dr. Muhammad Yousuf Medical Officer, General Medicine, Allama Iqbal Teaching Hospital, D.G. Khan, Pakistan Author https://orcid.org/0009-0000-7388-6277
Dr. Aleena Batool Senior House Officer, General Medicine, The Health Service Executive (HSE), Ireland Author https://orcid.org/0009-0002-2444-1516
Dr. Usman Ali Medical Officer, General Medicine, SUM, THQ Hospital Jand, District Attock, Pakistan Author https://orcid.org/0009-0002-4312-3230
Dr. Komal Zaman WMO, Department of Emergency Medicine, Allied Hospital, Faisalabad, Pakistan Author https://orcid.org/0009-0006-9184-9043
Dr. Syed Muhammad Asif Shah Medical Officer, General Surgery, DHQ Hospital Bahawalnagar, Pakistan Author https://orcid.org/0009-0007-7389-2010

DOI:

https://doi.org/10.62497/irabcs.158

Keywords:

Tuberculosis, TB, diagnostic accuracy, rifampicin resistance, smear microscopy, GeneXpert MTB/RIF

Abstract

Background: Tuberculosis (TB) remains a leading cause of morbidity and mortality worldwide, necessitating accurate and rapid diagnostic methods to improve early detection and treatment outcomes.

Objective: To evaluate the diagnostic performance of the GeneXpert MTB/RIF assay compared with sputum smear microscopy in suspected pulmonary TB patients.

Methodology: This was a descriptive, cross-sectional study conducted over a period of six months (January to June 2024) at THQ Hospital Jand, District Attock. This cross-sectional study was conducted on 150 patients with suspected pulmonary TB. Demographic and clinical data were recorded, and all participants underwent sputum smear microscopy and GeneXpert MTB/RIF testing. Smear microscopy was used as the reference standard to evaluate diagnostic performance in terms of sensitivity, specificity, predictive values, likelihood ratios, and accuracy. SPSS version 20 was used to analyze the data. Relationships between continuous variables were ascertained using the Pearson correlation coefficient. P-values less than 0.05 were deemed statistically significant.

Results: The mean age of participants was 36.40 ± 17.12 years, with 74 (49.33%) males and 76 (50.67%) females. Most patients resided in rural areas (111; 74.0%) and were married (107; 71.33%), with farmers constituting the largest occupational group (94; 62.67%). Common symptoms included fatigue (140; 93.33%), chest pain (139; 92.67%), unintentional weight loss (137; 91.33%), and coughing up mucus or blood (117; 78.0%). GeneXpert detected TB in 123 (82.0%) patients compared to 85 (56.67%) by smear microscopy. Among smear-negative patients, GeneXpert identified 43 additional cases. The assay showed moderate diagnostic performance with strong agreement with smear microscopy.

Conclusion: GeneXpert MTB/RIF assay offers a rapid and more sensitive alternative to smear microscopy, particularly beneficial for detecting smear-negative TB cases, thereby improving case detection in high-burden settings.

Downloads

Download data is not yet available.

References

Silva S, Arinaminpathy N, Atun R, Goosby E, Reid M. Economic impact of tuberculosis mortality in 120 countries and the cost of not achieving the Sustainable Development Goals tuberculosis targets: a full-income analysis. The Lancet Global Health. 2021 Oct 1;9(10):e1372-9. DOI: 10.1016/S2214-109X(21)00299-0 .

Pezzella AT. History of pulmonary tuberculosis. Thoracic surgery clinics. 2019 Feb 1;29(1):1-7. DOI: 10.1016/j.thorsurg.2018.09.002.

Verma A, Singh V, Singh Chouhan AP, Dutt PK. TUBERCULOSIS: SYMPTOMS, DIAGNOSIS AND THE FIGHT AGAINST DRUG RESISTANCE. Biochemical & Cellular Archives. 2024 Oct 2. DOI: 10.51470/bca.2024.24.1-S.3337

Swaminathan N, Perloff SR, Zuckerman JM. Prevention of Mycobacterium tuberculosis transmission in health care settings. Infectious Disease Clinics. 2021 Dec 1;35(4):1013-25. DOI: 10.1016/j.idc.2021.07.003 External Link.

Harries AD, Kumar AM, Satyanarayana S, Takarinda KC, Timire C, Dlodlo RA. Treatment for latent tuberculosis infection in low-and middle-income countries: progress and challenges with implementation and scale-up. Expert review of respiratory medicine. 2020 Feb 1;14(2):195-208. https://doi.org/10.1080/17476348.2020.1694907

Arif S, Mehboob Q, Arif W. Prevalence and Analysis of Drug Resistance Pattern of MDR-TB in Retreatment Cases at Allied Hospital, Faisalabad, Pakistan. Annals of Punjab Medical College. 2020 Dec 31;14(4):331-5. DOI: https://doi.org/10.29054/apmc/2020.994.

Garg SK, Tiwari RP, Tiwari D, Singh R, Malhotra D, Ramnani VK, Prasad GB, Chandra R, Fraziano M, Colizzi V, Bisen PS. Diagnosis of tuberculosis: available technologies, limitations, and possibilities. Journal of clinical laboratory analysis. 2003;17(5):155-63. https://doi.org/10.1002/jcla.10086

Che-Engku-Chik CE, Yusof NA, Abdullah J, Othman SS, Said MH, Wasoh H. Detection of tuberculosis (TB) using gold standard method, direct sputum smears microscopy, PCR, qPCR and electrochemical DNA sensor: A mini review. Journal of Biochemistry, Microbiology and Biotechnology. 2016 Dec 30;4(2):16-21. DOI: https://doi.org/10.54987/jobimb.v4i2.305

Chopra KK, Singh S. Newer diagnostic tests for tuberculosis, their utility, and their limitations. Current Medicine Research and Practice. 2020 Jan 1;10(1):8-11. https://doi.org/10.1016/j.cmrp.2020.01.004

Shah HD, Nazli Khatib M, Syed ZQ, Gaidhane AM, Yasobant S, Narkhede K, Bhavsar P, Patel J, Sinha A, Puwar T, Saha S. Gaps and interventions across the diagnostic care cascade of TB patients at the level of patient, community and health system: a qualitative review of the literature. Tropical Medicine and Infectious Disease. 2022 Jul 15;7(7):136. https://doi.org/10.3390/tropicalmed7070136

Yadav S, Rawal G, Jeyaraman M, Jeyaraman N. Advancements in tuberculosis Diagnostics: a comprehensive review of the critical role and future prospects of Xpert MTB/RIF Ultra technology. Cureus. 2024 Mar 31;16(3). DOI: 10.7759/cureus.57311.

Sahana KS, Prabhu AS, Saldanha PR. Usage of cartridge based nucleic acid amplification test (CB-NAAT/GeneXpert) test as diagnostic modality for pediatric tuberculosis; case series from Mangalore, South India. Journal of Clinical Tuberculosis and Other Mycobacterial Diseases. 2018 May 1;11:7-9. https://doi.org/10.1016/j.jctube.2017.12.002.

Bartolomeu-Gonçalves G, Souza JM, Fernandes BT, Spoladori LFA, Correia GF, Castro IM, Borges PHG, Silva-Rodrigues G, Tavares ER, Yamauchi LM, Pelisson M, Perugini MRE, Yamada-Ogatta SF. Tuberculosis Diagnosis: Current, Ongoing, and Future Approaches. Diseases. 2024 Sep 3;12(9):202. doi: 10.3390/diseases12090202.

Williams V, Calnan M, Edem B, Onwuchekwa C, Okoro C, Candari C, Cruz R, Otwombe K. GeneXpert rollout in three high-burden tuberculosis countries in Africa: A review of pulmonary tuberculosis diagnosis and outcomes from 2001 to 2019. African Journal of Laboratory Medicine. 2022 Aug 30;11(1):1811. https://hdl.handle.net/10520/ejc-ajlab_v11_i1_a1811

Sasikumar C, Utpat K, Desai U, Joshi J. Role of GeneXpert in the diagnosis of mycobacterium tuberculosis. Advances in Respiratory Medicine. 2020;88(3):183-8. DOI: 10.5603/ARM.2020.0102

van den Boom M, Bennani K, Sismanidis C, Gunneberg C, Khawaja L, Safdar MA, Muhwa C, Heldal E, Cirillo DM, Khan AW, Fatima R. 2022 TB programme review in Pakistan: strengthening governance, with better patient diagnosis and treatment. IJTLD open. 2024 Mar 1;1(3):136-43. DOI: https://doi.org/10.5588/ijtldopen.23.0587.

Patel S, Dadheech M, Maurya AK, Singh J, Purwar S, Rai N, Sarawagi R, Joshi A, Khadanga S, Patel Jr S, Rai NK. Assessment of the diagnostic utility of GeneXpert Mycobacterium tuberculosis/Rifampicin (MTB/RIF) assay in the suspected cases of tuberculous meningitis. Cureus. 2023 Apr 18;15(4). doi: 10.7759/cureus.37761.

Arora D, Dhanashree B. Utility of smear microscopy and GeneXpert for the detection of Mycobacterium tuberculosis in clinical samples. Germs. 2020 Jun 2;10(2):81. doi: 10.18683/germs.2020.1188.

Walusimbi S, Bwanga F, De Costa A, Haile M, Joloba M, Hoffner S. Meta-analysis to compare the accuracy of GeneXpert, MODS and the WHO 2007 algorithm for diagnosis of smear-negative pulmonary tuberculosis. BMC infectious diseases. 2013 Oct 30;13(1):507. https://doi.org/10.1186/1471-2334-13-507.

Li H, Li Z, Cui X, Liu X, Zhao J, Zhang Y, Wang C, Li B, Fan Y, Han J, Xia Y, Xiong Z, Zou X, Zhu Y, Li M, Lu B, Cao B. Mycobacterium tuberculosis Detection in Diverse Clinical Specimens by GeneXpert MTB/RIF: A Large-Scale Retrospective Study. Infect Drug Resist. 2025 May 8;18:2401-2413. doi: 10.2147/IDR.S514220. PMID: 40357422; PMCID: PMC12068387.

Jain J, Jadhao P, Banait S, Salunkhe P. Diagnostic accuracy of GeneXpert MTB/RIF assay for detection of tubercular pleural effusion. PLoS One. 2021 Jun 14;16(6):e0251618. https://doi.org/10.1371/journal.pone.0251618

Li A, Yuan SY, Li QG, Li JX, Yin XY, Liu NN. Prevalence and risk factors of malnutrition in patients with pulmonary tuberculosis: a systematic review and meta-analysis. Frontiers in Medicine. 2023 Aug 10;10:1173619. https://doi.org/10.3389/fmed.2023.1173619

Luies L, Du Preez I. The echo of pulmonary tuberculosis: mechanisms of clinical symptoms and other disease-induced systemic complications. Clinical microbiology reviews. 2020 Sep 16;33(4):10-128. https://doi.org/10.1128/cmr.00036-20.