Let me start by directly introducing you to this unassuming “grey box”!
It is a GeneXpert device located at the Stephen Robert and Pilar Crespi Robert Regional Reference Laboratory in Mirebalais, Haiti where I have spent the past five months on my PULSE assignment. I had already been aware about the GeneXpert technology for HIV Viral Load and TB / multi-drug resistant (MDR) diagnostic in developing countries. But only now, after I started to set up this cartridge based-PCR detection system for cancer diagnosis at the local pathology laboratory, I have realized how much this medium-sized bench top apparatus can really do!
For instance, GeneXpert MTB-RIF test results to confirm an active tuberculosis infection and to detect a multi-drug resistant TB strain are ready within 2 hours. Standards diagnostic procedures for multi-resistance are clearly more labor- and time-intensive and can take up to several months. The PCR-based Line Probe Assay test takes 2 – 3 days after sputum has been decontaminated and DNA is isolated, whereas the traditional culture-based method will take weeks for the primary isolate to grow followed by Drug Susceptibility Tests for first and second line drug resistance. Treating tuberculosis infection itself is an extremely long term and complex procedure. The so-called first line treatment for drug susceptible TB comprises of two antibiotics (isoniazid and rifampicin) for six months. Two additional antibiotics (pyrazinamide and ethambutol) must be taken for the first two months of this six-month treatment period. Multi-drug resistance is defined as TB strain resistant to isoniazid and rifampicin 1, with rifampicin resistance serving as a surrogate marker for MDR. The recommended second line treatment regimen for such a MDR case is a combination of at least four drugs. High-dose isoniazid, pyrazinamide, and ethambutol can be given in addition to these four 2.
After this already very medical start, we now venture deeper into the domain of science. I will try to keep it as short as possible – promise! Although, this is the interesting part! This is what the “grey box” does: All reagents for nucleic acid purification and amplification (nucleotides, enzymes, probes, buffers, washing solutions) are contained within the MTB-RIF cartridge. After mixing the collected sputum with lysis buffer, this has only to be added to the cartridge. Target detection is achieved by a six-colour laser system that collects the emission spectra of semi-nested molecular beacon probes which are located on the gene associated with rifampicin resistance. For all of us who are bench scientists compare it to the time needed to set up a comparable experiment from nucleic acid isolation to quantitative real-time PCR, not even speaking about establishing a multiplex reaction! Quite amazing, isn’t? And both sample preparation and running the test will really only take around 2 hours!
Now, I would like to put the “grey box” into the context of my PULSE assignment here at the laboratory in Mirebalais. Three of these GeneXpert devices have found a home on the second floor of the laboratory building. Two of them are used for TB diagnosis and, one is part of the local oncology program to detect the BCR-ABL gene translocation in Chronic Myeloid Leukemia (CML) patients and to determine success of kinase inhibitor treatment (i.e. Gleevec) in already diagnosed patients. When it comes to tuberculosis, Haiti has the highest rate of TB in the Western Hemisphere with an estimated incidence of 188 per 100.000 and 15.567 reported cases in 2016. The WHO estimates that 2.9% of new cases and 13% of previously treated cases have MDR-TB/ rifampicin resistant (RR)-TB 3. In the light of these numbers, state of the art TB detection seems an essential measure of infectious disease control and prevention. Yes, I am aware there is criticism regarding cost of GeneXpert cartridges and unaltered disease mortality despite use of the GeneXpert assay for diagnosis 4. But after having seen the “box in action”, I am convinced that it is an important part of reducing TB burden. Especially in a country as poor as Haiti where a TB infection is even more life-threatening due to HIV co-infection, drug accessibility issues, widespread spread malnutrition and poor housing conditions.
The 3 GeneXpert devices at HUM provide this state-of-the-art diagnostic technology in one of the poorest countries in the world. The HUM laboratory conducts a series of other essential diagnostic tests for the 185.000 people in the primary catchment area of the hospital. Around 200 external patients are seen at the laboratory each day. The clinical laboratory is equipped with automated hematology and biochemistry analyzers. Tests offered for instance are complete blood count, coagulation tests, lipid panel, liver and renal function and point of care test to diagnose HIV, HBV or syphilis. In addition, histology stainings are performed on biopsies to diagnosis cancer in the anatomic pathology laboratory. The microbiology and tuberculosis laboratories are currently in implementation phase to perform bacterial cultures for blood and cerebral spine fluid, automated liquid culture, and molecular detection for tuberculosis and drug susceptibility, which are part of further differential testing after the initial diagnosis using the GeneXpert MTB-RIF cartridges has been made.
My “GeneXpert” story is of course not entirely fitting, when I state, “What we ultimately work for at GSK!” considering that GSK develops drugs, not diagnostic equipment. Nevertheless, working with the “grey box” gave me back a strong feeling what science combined with the efforts of Partners In Health / Zanmi Lasante staff in building and contributing to the day-to-day operations of the hospital can do for a sick person particularly in a country with a public health care system that is still developing, where fast, technically unchallenging, robust diagnosis of TB and other diseases is even more crucial to initiate treatment.
2. “Best drug treatment for multidrug-resistant and extensively drug-resistant tuberculosis”: José A Caminero et al., Lancet Infect Dis. 2010 Sep.
3. WHO Global TB Report 2017
4. “Xpert MTB/RIF – why the lack of morbidity and mortality impact in intervention trials?”Auld AF et al., Trans R Soc Trop Med Hyg. 2016.