GeneXpert

From Tuberculosis Wiki

GeneXpert is a molecular testing platform used to diagnose tuberculosis, drug resistant tuberculosis, and other infectious diseases. GeneXpert is a polymerase chain reaction (PCR) device, which means it is a Nucleic Acid Amplification Test (NAAT).[1] GeneXpert is produced by Cepheid, which is a subsidiary of Danaher. GeneXpert is endorsed by WHO as a rapid diagnostic to replace sputum smear microscopy. Because GeneXpert can produce an accurate diagnosis of tuberculosis and drug resistance within 2 hours, it can enable faster and more appropriate treatment than cell culture and sputum smear microscopy.

History[edit | edit source]

In the early 1990s, the technology underlying GeneXpert was developed at Lawrence Livermore National Laboratory (LLNL) in Livermore, California. One of the LLNL researchers who worked on the technology, Allen Northrup, co-founded Cepheid in 1996.[2] Cepheid paid LLNL a one-time fee of $150,000 for the exclusive license on related patents and agreed to pay royalties on sales of the device.[2] In 2006, the first GeneXpert test was approved for clinical use, a group B Streptococcus test.[2] In 2006, Cepheid signed a Cooperative Research and Development Agreement (CRADA) with FIND to develop the Xpert MTB/RIF test.[2] In 2010, WHO endorsed Xpert MTB/RIF as a replacement for sputum smear microscopy.[3] Over the following years, various governmental and non-governmental organizations formed agreements with Cepheid, and testing volumes increased amid pricing controversies.

Technology[edit | edit source]

GeneXpert is a quantitative real-time polymerase chain reaction (qPCR) platform. qPCR is commonly used in many research and clinical settings to identify the presence of specific genetic sequences in a sample. GeneXpert is the machine that runs the tests, and Xpert is the test itself.

Operation[edit | edit source]

GeneXpert requires a limited number of user steps. First, sputum (phlegm or mucus from the lung) is collected from the patient and mixed with a sample reagent, then incubated at 20-30°C for 15 minutes. Then, the operator uses a disposable plastic transfer pipette to transfer the sample to a test cartridge. After the sample is transferred into the cartridge, there is no risk of contact between the operator and the sample, reducing chances of exposure.[4] The cartridge is then placed inside of a GeneXpert device.

All of the chemicals needed for the qPCR process are inside of the cartridge, and the process is fully automated after the cartridge is inserted into the device.[5] First, the bacteria are separated from the sputum. Next, the bacteria are broken up to extract the DNA. Then, primers are added. Primers are single-stranded nucleic acids that match specific genetic sequences that the test is trying to find. Through a reaction with an enzyme and several cycles of heating and cooling, any genetic sequences that match the primers get multiplied. Every time this happens the matching sequences emit light of a specific color that demonstrates which sequence is present. The GeneXpert device measures the intensity of this light in order to quantify how much of each genetic sequence is present.[5] Because M. tuberculosis strains have different genetic sequences that indicate resistance to different drugs, qPCR tests can use primers for those genetic sequences to look for resistance to specific drugs. A single MTB/RIF or MTB/XDR test produces a diagnosis within 2 hours.

Variations[edit | edit source]

GeneXpert originally came with 6 colors, but in 2022, Cepheid expanded the GeneXpert modules to 10 colors, allowing for detection of more genetic sequences at once.[6] The 10-channel modules were still compatible with the original 6-color tests.[6] To use the new 10-color tests such as MTB/XDR, customers needed to purchase a whole new system, purchase a new satellite instrument that connects to an existing system, or replace the 6-color modules with 10-color modules.[7]

GeneXpert systems come in multiple sizes. GeneXpert II can run 2 tests at a time, GeneXpert IV can run 4 tests at a time, and GeneXpert XVI can run 16 tests at a time.[8] While the standard systems require an external computer, GeneXpert Infinity and GeneXpert Xpress have a touchscreen interface. GeneXpert Xpress IV-2 can run 2 tests at a time, and GeneXpert Xpress IV-4 can run 4 tests at a time. However, GeneXpert Xpress cannot run MTB/RIF Ultra and MTB/XDR tests.[9] GeneXpert Infinity allows for larger test volumes, where the GeneXpert Infinity-48s can run 16, 24, 32, 40, or 48 tests at once, and the GeneXpert Infinity-80 can run 16, 24, 32, 40, 48, 56, 64, 72, or 80 tests at once.[10] However, GeneXpert Infinity is not compatible with Xpert MTB/XDR tests.[11]

The standard GeneXpert systems plug into the wall and require a stable source of electricity and temperature control. Some users hack the instruments with power converters to allow them to run on car batteries.[12] In 2015, Cepheid announced that they were planning a new platform, GeneXpert Omni, designed for point-of-care diagnostics. However, GeneXpert Omni was cancelled in 2021.[13] In 2018, Cepheid announced another battery-powered platform, GeneXpert Edge, which is less portable than Omni.[12] GeneXpert Edge is compatible with Xpert MTB/RIF Ultra tests but is not compatible with Xpert MTB/XDR tests.[11]

Tests[edit | edit source]

There are two tests available for tuberculosis: MTB/RIF Ultra (Mycobacterium tuberculosis/Resistance to Rifampin), and MTB/XDR (Mycobacterium tuberculosis/Extensively Drug Resistant Tuberculosis). MTB/RIF Ultra tests for presence of the bacterium and specific sequences that indicate resistance to rifampin, and MTB/XDR tests for specific sequences that indicate resistance to isoniazid, fluoroquinolones, amikacin, kanamycin, capreomycin, and ethionamide.[14] The MTB/XDR test requires the 10-color GeneXpert module.[14] MTB/RIF Ultra was introduced in 2017 and eventually replaced an older test, MTB/RIF.[15][16]

GeneXpert machines can be used to test for other diseases by using different reagents. The GeneXpert machines are used to test combination COVID-19/Flu/RSV swabs in at least the United States,[17] U.S. territories,[18] and Canada.[19] Cepheid also sells Xpert tests for respiratory bacteria (Strep A), healthcare-related bacteria (MRSA, S. aureus, Carba-R, Norovirus, C. diff, vanA/vanB), Ebola, blood virology/women’s health/sexual health (chlamydia/gonorrhea, HPV, Group B Strep, trichomonas vaginalis, M. genitalium and macrolide resistance, Hepatitis B, Hepatitis C, HIV), oncology and human genetics (BCR-ABL, NMP1, bladder cancer, breast cancer, risk factors for thrombosis Fil/FV). Detection times vary between 18 minutes and 3 hours for different tests.[20]

Efficacy[edit | edit source]

The pathway recommended by Cepheid is to first run the MTB/RIF Ultra test, then if that comes back positive run the MTB/XDR test using a new sputum sample, then initiate treatment and run cell culture for 4-6 weeks to confirm the level of drug resistance.[14] Studies have shown the test is more prone to false positives than false negatives,[21] so Cepheid states that no culture confirmation is required if the MTB/RIF Ultra comes up negative.[22]

Pricing[edit | edit source]

Main article: GeneXpert Pricing

In the United States, Xpert tests cost US $30-60.[23] In low-to-middle income countries (LMICs) which are part of the Global Fund, MTB/RIF Ultra costs $8, which Danaher claims is the cost to produce the test.[24] MTB/XDR costs $15. Other tests vary by cost, including $20 for COVID tests.[25] GeneXpert 4-module systems cost $17,000.[26]

Patents[edit | edit source]

The technology behind GeneXpert is protected by several patents.

Patents on GeneXpert technology
Patent number Holder Filed Expiration Title
US6440725B1 Cepheid (expired) 1998 December 24 2017 December 24 Integrated fluid manipulation cartridge
US9057674B2 Cepheid 2014 May 15 2026 July 13 Reagent reservoir system for analytical instruments
US8592157B2 Cepheid (expired) 2012 July 19 2018 December 24 Method for separating an analyte from a sample
US8728765B2 Cepheid 2012 February 15 2025 December 27 Closed-system multi-stage nucleic acid amplification reactions
US20220226809A1 Cepheid (pending) 27 January 2022 Pending Integrated purification and measurement of dna methylation and co-measurement of mutations and/or mrna expression levels in an automated reaction cartridge
US9446409B2 Cepheid 2014 May 2 2025 June 6 Method and apparatus for storing and dispensing reagent beads
US20180163270A1 Cepheid (abandoned) 2017 December 11 Abandoned Integrated immuno-pcr and nucleic acid analysis in an automated reaction cartridge

See also[edit | edit source]

References[edit | edit source]

  1. ^ "Nucleic Acid Amplification Tests (NAATs)". Centers for Disease Control and Prevention. 12 May 2023.
  2. ^ a b c d Gotham D, McKenna L, Deborggraeve S, Madoori S, Branigan D (2021). "Public investments in the development of GeneXpert molecular diagnostic technology". PLoS One. 16 (8): e0256883. doi:10.1371/journal.pone.0256883. PMC 8407584. PMID 34464413.
  3. ^ "WHO Endorses New Rapid Tuberculosis Test". World Health Organization. 8 December 2010.
  4. ^ Xpert MTB/RIF Assay: Reference GXMTB/RIF-US-10 (PDF) (Report). Cepheid. 2020.
  5. ^ a b Journey Inside the Cepheid GeneXpert® Cartridge - 3D Animation. Cepheid. 24 April 2019.
  6. ^ a b Cepheid Regulatory Team (November 2022). "GeneXpert® Systems with 10-Color Technology and Compatibility with Xpert® Tests" (PDF). Letter to Cepheid Customer. Retrieved 10 November 2023.
  7. ^ Xpert MTB/XDR Brochure (PDF) (Report). Cepheid. 2022.
  8. ^ "GeneXpert Systems". Cepheid.
  9. ^ "GeneXpert Xpress". Cepheid. Retrieved 15 January 2024.
  10. ^ "GeneXpert Infinity Systems". Cepheid. Retrieved 15 January 2024.
  11. ^ a b "Increasing Access to TB Testing Around the World". Cepheid. Retrieved 15 January 2024.
  12. ^ a b Johnson, Madeleine (19 July 2018). "Cepheid to Launch GeneXpert Edge for Decentralized Testing While Omni Remains Delayed". 360Dx.
  13. ^ Johnson, Madeleine (25 July 2022). "Highly Anticipated Cepheid Omni Point-of-Care System Falls Off Radar". 360Dx.
  14. ^ a b c "Xpert MTB/XDR". Cepheid. Retrieved 8 October 2023.
  15. ^ "Xpert MTB/RIF Ultra". Cepheid. Retrieved 8 October 2023.
  16. ^ "2017 launch of new TB test ultra backed by WHO recommendation". Find. 24 March 2017.
  17. ^ "Introducing Xpert® Xpress CoV-2/Flu/RSV plus* and Xpert® Xpress CoV-2 plus*". Cepheid. Retrieved 8 October 2023.
  18. ^ "Interior Provides $858,924 to Procure GeneXpert COVID-19 Testing Kits and Machine for the U.S. Pacific Territories and Freely Associated States". U.S. Department of the Interior. 26 March 2020.
  19. ^ Ranadheera, C; Antonation, K; Corbett, C (2023). "Comparison of fifteen SARS-CoV-2 nucleic acid amplification test assays used during the Canadian Laboratory Response Network's National SARS-CoV-2 Proficiency Program, May 2020 to June 2021". Can Commun Dis Rep. 49 (5): 180–189. doi:10.14745/ccdr.v49i05a03.
  20. ^ "CE-IVD Xpert Test Menu" (PDF). Cepheid. 2023.
  21. ^ World Health Organization (2017). WHO Meeting Report of a Technical Expert Consultation: Non-inferiority analysis of Xpert MTB/RIF Ultra compared to Xpert MTB/RIF (PDF) (Report). Geneva: World Health Organization.
  22. ^ Xpert MTB/RIF Ultra CE Brochure (PDF) (Report). Cepheid. 2023.
  23. ^ Branigan, David (September 2021). Realizing Returns on U.S. Government Investments in GeneXpert Diagnostic Technologies (PDF) (Report). Treatment Action Group.
  24. ^ "Danaher to Provide Cepheid's Tuberculosis Test to the Global Fund at Cost". Danaher Corporation. 19 September 2023.
  25. ^ "Diagnostic company Cepheid charging four times more than it should for COVID-19 tests". Médecins Sans Frontières. 28 July 2020.
  26. ^ "TB REACH Xpert Budget Estimation Tool". Stop TB Partnership.