Comparison of GeneXpert and line probe assay for the detection of Mycobacterium tuberculosis in direct sputum samples
Abstract
Tuberculosis (TB) remains a major global health issue, particularly in low-and- middle-income countries (LMICs) like Indonesia. Diagnostic methods for TB and multidrug-resistant TB (MDR-TB) such as Lowenstein-Jensen (LJ) solid media and Mycobacterium Growth Indicator Tube (MGIT), are time-consuming, causing delays in patient management. Rapid molecular diagnostics, like the GeneXpert MTB/RIF ultra assay and line probe assay (LPA), offer faster and more accurate detection of Mycobacterium tuberculosis and drug resistance. This study aimed to compare the efficacy of GeneXpert and LPA in detecting M. tuberculosis and assessing drug resistance in sputum samples from 20 patients with confirmed TB. The samples were categorized into four groups based on GeneXpert results: very low, low, medium, and high DNA concentration. GeneXpert identified 20% of samples as rifampicin-resistant, while LPA identified 35%. Additionally, LPA detected isoniazid resistance in 10% of samples. The five discordance results between GeneXpert and LPA, from samples with very low DNA concentrations, were confirmed using MGIT 960 culture DST as the gold standard. The LPA successfully identified 2 (10%) Hr-TB among TB cases detected by the GeneXpert TB/ RIF. While LPA demonstrates superior performance characteristics, particularly in detecting isoniazid, GeneXpert demonstrated better sensitivity and specificity, making it a more reliable diagnostic tool under suboptimal conditions, followed by culture-based DST to assure accuracy and examine resistance to other drugs.
References
World Health Organization Global Tuberculosis Report. Geneva: World Health Organization; 2022. PMID: 36521512
Zhou X, Wu H, Ruan Q, Jiang N, Chen X, Shen Y, et al. Clinical evaluation of diagnosis efficacy of active Mycobacterium tuberculosis complex infection via metagenomic next-generation sequencing of direct clinical samples. Front Cell Infect Microbiol 2019; 9:351.
https://doi.org/10.3389/fcimb.2019.00351
World Health Organization. Global tuberculosis report. Geneva: World Health Organization: 2023.
Lawson L, Emenyonu N, Abdurrahman ST, Lawson JO, Uzoewulu GN, Sogaolu OM, et al. Comparison of Mycobacterium tuberculosis drug susceptibility using solid and liquid culture in Nigeria. BMC Res Notes 2013; 6:1-5.
https://doi.org/10.1186/1756-0500-6-215
Pai M, Nicol MP, Boehme CC. Tuberculosis diagnostics: state of the art and future directions. Microbiol Spectr 2016; 4(5):361-78.
https://doi.org/10.1128/microbiolspec.tbtb2-0019-2016
Leylabadlo HE, Kafil HS, Yousefi M, Aghazadeh M, Asgharzadeh M. Pulmonary tuberculosis diagnosis: where we are. Tuberc Respir Dis 2016; 79(3):134-42.
https://doi.org/10.4046/trd.2016.79.3.134
Eloi P, Nascimento GA, Córdula C, Visani V, Castelletti H, Bezerra G, et al. Toward a point-of-care diagnostic for specific detection of Mycobacterium tuberculosis from sputum samples. Tuberculosis 2020; 121:101919.
https://doi.org/10.1016/j.tube.2020.101919
Rimal R, Shrestha D, Pyakurel S, Poudel R, Shrestha P, Rai KR, et al. Diagnostic performance of GeneXpert MTB/RIF in detecting MTB in smear-negative presumptive TB patients. BMC Infect Dis 2022; 22(1):321.
https://doi.org/10.1186/s12879-022-07287-5
Massou F, Fandohan M, Wachinou AP, Agbla SC, Agodokpessi G, Rigouts L, et al. Spot specimen testing with GeneXpert MTB/RIF results compared to morning specimen in a programmatic setting in Cotonou, Benin. BMC Infect Dis 2021; 21(1):979.
https://doi.org/10.1186/s12879-021-06676-6
Berhanu RH, Schnippel K, Kularatne R, Firnhaber C, Jacobson KR, Horsburgh CR, et al. Discordant rifampicin susceptibility results are associated with Xpert® MTB/RIF probe B and probe binding delay. Int J Tuberc Lung Dis 2019; 23(3):358-62.
https://doi.org/10.5588/ijtld.16.0837
Mchaki BR, Mgaya FX, Kunambi PP, Hang’ombe B, Matee MI, Munyeme M. Comparative performance of line probe assay and GeneXpert in the detection of rifampicin monoresistance in a TB-endemic African Country. Antibiotics 2022; 11(11):1489.
https://doi.org/10.3390/antibiotics11111489
Ocheretina O, Byrt E, Mabou MM, Royal-Mardi G, Merveille YM, Rouzier V, et al. False-positive rifampin resistant results with Xpert MTB/RIF version 4 assay in clinical samples with a low bacterial load. Diagnostic microbiology and infectious disease. 2016; 85(1):53-5.
https://doi.org/10.1016/j.diagmicrobio.2016.01.009
Getahun M, Ameni G, Mollalign H, Diriba G, Beyene D. Genotypic and phenotypic drug-resistance detection and prevalence of heteroresistance in patients with isoniazid-and multidrug-resistant tuberculosis in Ethiopia. IJID Reg 2022; 2:149-53.
https://doi.org/10.1016/j.ijregi.2021.12.007
Global Laboratory Initiative. Line probe assays for drug-resistant tuberculosis detection. Interpretation and reporting guide for laboratory staff and clinicians. Geneva: World Health Organization. 2018.
World Health Organization recommendations on Xpert MTB/RIF Ultra. World Health Organization: consolidated guidelines on tuberculosis: Module 3: diagnosis – rapid diagnostics for tuberculosis detection. Geneva: 2022. p160.
