GeneXpert MTB-RIF assay as a rapid and effective molecular method for the diagnosis of tuberculosis in Erbil City

  • Salah Tofik Balaky Department of Medical Microbiology, College of Health Sciences, Hawler Medical University, Erbil, Iraq.
Keywords: Mycobacterium tuberculosis, Diagnosis, Pulmonary, Extrapulmonary, GeneXpert, AFB


Background and objective: Tuberculosis is a major public health problem worldwide, especially in developing countries. The disease poses a massive threat to public health, causing increased morbidity and mortality. Therefore, early detection is essential to reduce the death rate and interrupt transmission. In this study, GeneXpert assay was used for the rapid identification of bacteria, and its sensitivity and specificity were compared with acid fast bacilli staining in both pulmonary and extrapulmonary clinical specimens.

Methods: A total of 115 pulmonary and extrapulmonary samples were collected and diagnosed for tuberculosis detection. Acid fastbacilli, culture, and GeneXpert methods were used for the diagnosis of tuberculosis.

Results: Out of 115 tuberculosis specimens, 70 were acid fast bacilli smear positive, while 97 samples were positive for Mycobacterium tuberculosis by GeneXpert assay. The results indicated a higher sensitivity of GeneXpert assay compared to the acid fastbacillistaining method. The sensitivity of GeneXpert was 91.6%, specificity 50%; positive and negative predictive values were 89.7% and 55.6%, respectively. No significant differences were detected between the Gene Xpert test results and the culture results (P = 0.815), and the total agreement between the tests was 84.3%.

Conclusion: We concluded that the GeneXpert test results is sensitive as culture results for both pulmonary and extrapulmonary specimens. Although culture remains the gold standard for laboratory confirmation of tuberculosis disease, GeneXpert should become standard practice for patients suspected of tuberculosis, and all clinicians and public health tuberculosis programs should have access to molecular testing for tuberculosis to shorten the time of diagnosis.


World Health Organization. Global tuberculosis report 2017. World Health Organization; 2017. (Accessed February 12, 2018, at

Huang SY, Chang JR, Liao YC, Dou HY, Chuang MC. Simultaneous detections of genetic fragment and single nucleotide mutation with a three-tiered output for tuberculosis diagnosis. Analytica Chimica Acta 2018; 1007:1–9.

Houben RM, Dodd PJ. The global burden of latent tuberculosis infection: a re-estimation using mathematical modelling. PLoS Medicine 2016; 13(10):e1002152.

Munir MK, Rehman S, Iqbal R, Saeed MS, Aasim M. Comparison of Gene Xpert MTB/RIF Assays with Conventional Standard Proportion Method for Determination of Drug Susceptibility In multidrug resistant TB suspects. AKEMU 2018; 24(1):570–6.

Ahmed ST. Genexpert MTB/RIF assay: A major milestone for diagnosing mycobacterium tuberculosis and rifampicin-resistant cases in pulmonary and extra pulmonary specimens. Infect Dis Prev Control 2018; 1:1.

Van Rie A, Enarson D. XDR tuberculosis: an indicator of public-health negligence. The Lancet 2006; 368(9547):1554–6.

Mohapatra D, Bhatia V. Gene Xpertmtb/rif: the evidence based path breaking diagnostic tool fortuberculosis diagnosis. Int J Scie Res 2018; 7(8).

Iram S, Zeenat A, Hussain S, Yusuf NW, Aslam M. Rapid diagnosis of tuberculosis using Xpert MTB/RIF assay-Report from a developing country. Pak J Med Sci 2015; 31:105.

Zhang Q, Sun BQ, Liu C, Su AN, Wang XH, et al. GeneXpert MTB/RIF for rapid diagnosis and rifampin resistance detection of endobronchial tuberculosis. Respirology 2018; 23:950–5.

Centers for Disease Control and Prevention (CDC). Updated guidelines for the use of nucleic acid amplification tests in the diagnosis of tuberculosis. MMWR. Morb Mortal Wkly Rep 2009; 58(1):7.

Palomino JC. Molecular detection, identification and drug resistance detection in Mycobacterium tuberculosis. FEMS Immunol Med Microbiol 2009; 56(2):103–11.

El-Hajj HH, Marras SA, Tyagi S, Kramer FR, Alland D. Detection of Rifampin Resistance in Mycobacterium tuberculosis in a Single Tube with Molecular Beacons. J Clin Microbiol 2001; 39(11):4131–7.

Lawn SD, Nicol MP. Xpert MTB/RIF assay: development, evaluation and implementation of a new rapid molecular diagnostic for tuberculosis and rifampicin resistance. Future Microbiol 2011; 6(9):1067–82.

Amin B. Diagnostic Assessment of XPERT MTB/RIF in a sample of mycobacterium tuberculosis in Iraqi Kurdistan patients. Int J Tech Res App 2015; 3(5):255–9.

Zeka AN, Tasbakan S, Cavusoglu C. Evaluation of the GeneXpert MTB/RIF assay for the rapid diagnosis of tuberculosis and detection of RIF-resistance in pulmonary and extrapulmonary specimens. J Clin Microbiol 2011; 28:5434.

Helb D, Jones M, Story E, Boehme C, Wallace E, Ho K, et al. Rapid detection of Mycobacterium tuberculosis and rifampin resistance by use of on-demand, near-patient technology. J Clin Microbiol 2010; 48(1):229–37.

Banada PP, Sivasubramani SK, Blakemore R, Boehme C, Perkins MD, Fennelly K, et al. Containment of bioaerosol infection risk by the Xpert MTB/RIF assay and its applicability to point-of-care settings. J Clin Microbiol 2010; 48(10):3551–7.

Riello FN, Brígido RT, Araújo S, Moreira TA, Goulart LR, Goulart IM. Diagnosis of mycobacterial infections based on acid-fast bacilli test and bacterial growth time and implications on treatment and disease outcome. BMC Inf Dis 2016; 16(1):142.

García-Rodríguez JF, Álvarez-Díaz H, Lorenzo-García MV, Marino-Callejo A, Fernández-Rial Á, Sesma-Sánchez P. Extrapulmonary tuberculosis: epidemiology and risk factors. EnfermInfecc Microbiol Clin 2011; 29(7):502–9.

Rani P, Bilolikar AK, Sarma VC, Udayasri B, Reddy SG, Kakarla PL, et al. A comparative study of AFB smear and GeneXpert MTB/ RIF assay in pulmonary and extrapulmonary specimens and detection of rifampicin resistance in a tertiary care hospital. J Med Sci Res 2017; 4:115–20.

Shi J, Dong W, Ma Y, Liang Q, Shang Y, Wang F, et al. GeneXpert MTB/RIF Outperforms Mycobacterial Culture in Detecting Mycobacterium tuberculosis from Salivary Sputum. Bio Med Res Int 2018; 2018:1514381.

Pantoja A, Fitzpatrick C, Vassall A, Weyer K, Floyd K. Xpert MTB/RIF for diagnosis of TB and drug-resistant TB: a cost and affordability analysis. Eur Respir J 2013; 42(3):708–20.

Laserson KF, Yen NT, Thornton CG, Mai VT, Jones W, An DQ, et al. Improved sensitivity of sputum smear microscopy after processing specimens with C18-carboxypropylbetaine to detect acid-fast bacilli: a study of United States-bound immigrants from Vietnam. J Clin Microbiol 2005; 43(7):3460–2.

Kanaujia GV, Lam PK, Perry S, Brusasca PN, Catanzaro A, Gennaro ML. Integration of microscopy and serodiagnostic tests to screen for active tuberculosis. Int J Tuberc Lung Dis 2005; 9(10):1120–6.

Frimpong EH, Adukpo R, Owusu-Darko K. Evaluation of two novel Ziehl-Neelsen methods for tuberculosis diagnosis. West Afr J Med 2005; 24(4):316–20.

Lee JS, Kim EC, Joo SI, Lee SM, Yoo CG, Kim YW, et al. The incidence and clinical implication of sputum with positive acid-fast bacilli smear but negative in mycobacterial culture in a tertiary referral hospital in South Korea. J Korean Med Sci 2008; 23(5):767–71.

Boehme CC, Nabeta P, Hillemann D, Nicol MP, Shenai S, Krapp F, et al. Rapid molecular detection of tuberculosis and rifampin resistance. New Eng J Med 2010; 363(11):1005–15.

Hillemann D, Rüsch-Gerdes S, Boehme C, Richter E. Rapid molecular detection of extrapulmonary tuberculosis by automated GeneXpert MTB/RIF system. J Clin Microbiol 2011; 49(4):1202–5.

Moure R, Muñoz L, Torres M, Santin M, Martín R, Alcaide F. Rapid detection of Mycobacterium tuberculosis complex and rifampin resistance in smear-negative clinical samples by use of an integrated real-time PCR method. J Clin Microbiol 2011; 49(3):1137–9.

Salina EG, Vostroknutova GN, Shleeva MO, Kaprelyants AS. Cell-cell interactions during the formation and reactivation of “nonculturable” mycobacteria. Microbiology 2006; 75(4):432–7.

Zumla A, Nahid P, Cole ST. Advances in the development of new tuberculosis drugs and treatment regimens. Nat Rev Drug Discov 2013; 12(5):388.

Nikolayevskyy V, Miotto P, Pimkina E, Balabanova Y, Kontsevaya, Ignatyeva O, et al. Utility of propidiummonoazide viability assay as a biomarker for a tuberculosis disease. Tuberculosis 2015; 95(2):179–85.

Ali AA, Razzaq MA, AL-Saadi MA. Incidence of tuberculosis in Babylon Province-Iraq. Int J Curr Microbiol App Sci 2013; 2(9):1–4.

How to Cite
Balaky, S. (2019). GeneXpert MTB-RIF assay as a rapid and effective molecular method for the diagnosis of tuberculosis in Erbil City. Zanco Journal of Medical Sciences (Zanco J Med Sci), 23(3), 412-420.
Original Articles