GeneXpert MTB/RIF

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The Xpert MTB/RIF is a cartridge-based nucleic acid amplification test (NAAT) for simultaneous rapid tuberculosis diagnosis and rapid antibiotic sensitivity test. It is an automated diagnostic test that can identify Mycobacterium tuberculosis (MTB) DNA and resistance to rifampicin (RIF). It was co-developed by the laboratory of Professor David Alland at the University of Medicine and Dentistry of New Jersey (UMDNJ).[1] Cepheid Inc. and Foundation for Innovative New Diagnostics, with additional financial support from the US National Institutes of Health (NIH).

In December 2010, the World Health Organization (WHO) endorsed the Xpert MTB/RIF for use in TB endemic countries.[2] This followed 18 months of assessment of its field effectiveness in TB, MDR-TB and TB/HIV co-infection.[3] This test, and others that are likely to follow, could have the potential to improve the diagnosis of TB in those that are likely to be missed by traditional tests.[3][4]

The CDC said in 2015[5] that the Xpert MTB/RIF test was "revolutionizing tuberculosis (TB) control by contributing to the rapid diagnosis of TB disease and drug resistance. The test simultaneously detects Mycobacterium tuberculosis complex (MTBC) and resistance to rifampin (RIF) in less than 2 hours. In comparison, standard cultures can take 2 to 6 weeks for MTBC to grow and conventional drug resistance tests can add 3 more weeks."[5]


Tuberculosis is one of the deadliest public health threats today. Traditionally, tuberculosis is mostly being diagnosed by a combination of chest X-rays, the staining of sputum with special dyes followed by microscopy, the growth of Mycobacterium tuberculosis in culture and the Mantoux test. The sputum smear microscopy is easy to do and is very cheap and combined with chest X-rays has been used for a long time by TB control agencies worldwide. However the sputum smear microscopy(sputum AFB ) test has some problems in HIV-positive patients and children, as well as patients with low bacterial load.The Xpert MTB/RIF test exhibits high sensitivity and specificity for detecting pulmonary TB disease. An in vitro study demonstrated a limit of detection of as few as 131 colony-forming units/mL of MTB, compared with approximately 10,000 colony-forming units/mL with conventional smear microscopy.[1][6] Drug susceptibility could only be diagnosed from the growth of Mycobacterium tuberculosis in culture which can take as long as six weeks and needs high bio safety labs and is costly. The determination of drug susceptibility is particularly relevant because Mycobacterium tuberculosis becomes increasingly resistant to two of the major anti-tuberculosis drugs, isoniazide and rifampicin. This form of tuberculosis is called multi-drug-resistant tuberculosis (MDR-TB) is rapidly on the rise globally. MDR-TB cases need different antibiotics and are more difficult to treat owing to higher costs of drugs and longer regimens .

How the test works[edit]

The Xpert MTB/RIF detects DNA sequences specific for Mycobacterium tuberculosis and rifampicin resistance by polymerase chain reaction[4][7] It is based on the Cepheid GeneXpert system, a rapid, simple-to-use nucleic acid amplification tests (NAAT). The Xpert® MTB/RIF purifies and concentrates Mycobacterium tuberculosis bacilli from sputum samples, isolates genomic material from the captured bacteria by sonication and subsequently amplifies the genomic DNA by PCR. The process identifies most of the clinically relevant Rifampicin resistance inducing mutations in the RNA polymerase beta (rpoB) gene in the Mycobacterium tuberculosis genome in a real time format using fluorescent probes called molecular beacons. Results are obtained from unprocessed sputum samples in 90 minutes, with minimal biohazard and very little technical training required to operate.[8] This test was developed as an on-demand near patient technology which could be performed even in a doctor's office if necessary.

A review to assess the diagnostic accuracy of Xpert TB found that when used as an initial test to replace smear microscopy it had pooled sensitivity of 89% and specificity of 99% . However, when Xpert TB was used as an add-on for cases of negative smear microscopy the sensitivity was only 67% and specificity 99%.[9][needs update] In a clinical study conducted the sensitivity of the MTB/RIF test on just 1 sputum sample was 92.2% for culture-positive TB; 98.2% for smear+ and culture-positive cases; and 72.5% for smear-negative, culture-positive cases, with a specificity of 99.2%. Sensitivity and higher specificity were slightly higher when 3 samples were tested[10]


Some concerns have been raised about the Xpert MTB/RIF, including minor operational issues and cost. The concessional price for a GeneXpert system is currently USD 32,000 for a four module instrument. As of 6 August 2012, the cost of a test cartridge in countries eligible for concessional pricing is USD 9.98.[11] As of 30 June 2013, 1,402 GeneXpert systems (comprising 7553 modules) and >3 million Xpert MTB/RIF cartridges had been procured in 88 of the 145 countries under concessional pricing.[12]


  1. ^ a b "Frequently asked questions on Xpert MTB/RIF assay" Retrieved on 12 June 2012
  2. ^ "WHO endorses new rapid tuberculosis test" 8 December 2010. Retrieved on 12 June 2012
  3. ^ a b Small, P. M., Pai, M. (2010) "Tuberculosis diagnosis - time for a game change" N. Engl. J. Med. 363: 1070-1071
  4. ^ a b Van Rie, A., Page-Shipp, L., Scott, L., Sanne, I., Stevens, W. (2010) "Xpert® MTB/RIF for point-of-care diagnosis of TB in high-HIV burden, resource-limited countries: hype or hope?" Expert Rev. Mol. Diagn. 10: 937-946
  5. ^ a b Centers for Disease Control and Prevention (2015), "A New Tool to Diagnose Tuberculosis: The Xpert MTB/RIF Assay" (PDF), CDC website, archived from the original (PDF) on 2017-12-17, retrieved 2018-05-25.
  6. ^ "A New Era: Molecular Tuberculosis Diagnosis".
  7. ^ Helb, D., et al (2010) "Rapid detection of Mycobacterium tuberculosis and Rifampin resistance by use of on-demand, near-patient technology. J. Clin. Microbiol. 48: 229-237
  8. ^ Boehme, C. C., et al. (2010) "Rapid molecular detection of tuberculosis and rifampin resistance" N. Engl. J. Med. 363: 1005-1015
  9. ^ Steingart, KR; Schiller, I; Horne, DJ; Pai, M; Boehme, CC; Dendukuri, N (21 January 2014). "Xpert® MTB/RIF assay for pulmonary tuberculosis and rifampicin resistance in adults". The Cochrane Database of Systematic Reviews. 1 (1): CD009593. doi:10.1002/14651858.CD009593.pub3. PMC 4470349. PMID 24448973.
  10. ^ Boehme CC, Nabeta P, Hillemann D, et al. (2010). "Rapid molecular detection of tuberculosis and rifampin resistance". N Engl J Med. 363 (11): 1005–1015. doi:10.1056/nejmoa0907847. PMC 2947799. PMID 20825313.
  11. ^ "Negotiated prices for Xpert® MTB/RIF and FIND country list". FIND Diagnostics. FIND. October 2013. Archived from the original on April 7, 2014. Retrieved 6 April 2014.
  12. ^ "WHO monitoring of Xpert MTB/RIF rollout" World Health Organisation. Retrieved on 1 Sept 2013

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