GeneXpert rapid TB diagnostic takes off in South Africa

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Dr. Wendy Stevens of the University of the Witwatersrand and the health ministry in South Africa reported on the first step in the national implementation of GeneXpert as a TB diagnostic tool in South Africa.  Stevens described Cepheid’s GeneXpert as a “remarkable contribution to the field of TB diagnostics.”

First some of the chilling news about South Africa and TB—20 percent of the world’s HIV associated tuberculosis cases and the second largest reported numbers of multi-drug resistant (MDR) TB in the world.  Seventy to 80 percent of South African TB suspects are HIV infected and at least 16 percent of all new TB cases are extra-pulmonary. Despite a strong TB control infrastructure – more than 4.7 million smears and 1 million cultures last year alone – TB diagnosis remains complete inadequate with poor results from smear microscopy and delay in culture results, frequently translating into patients lost to follow up.  The World Health Organization has issued a strong recommendation on the use of GeneXpert in settings with high rates of HIV/TB co-infection and drug-resistant tuberculosis.  According to Dr. Stevens, “This describes tuberculosis in South Africa.”

The Phase I rollout of GeneXpert is a limited pilot in nine provinces in the highest burden district in each province.  This effort is primarily funded by the health ministry but there is a contribution in the form of the purchase of some of the larger instruments by USAID.  These sites represent about 11 percent of the TB diagnoses in the country.  The goal is to replace two smears at diagnosis with one GeneXpert test.  An algorithm has been developed for the 25 sites that is likely too complex and will probably be modified. So far 80 lab technicians have been trained, most of them previous microscopists.

Since April 50,093 GeneXpert tests have been performed with a 17.15 percent positivity rate.  The rate of rifampicin resistance/potential MDR-TB was 7.33 percent.  There is substantial geographic variation in TB and MDR rates. KwaZulu-Natal provides an illustration of the impact of GeneXpert, where an historical average of eight to nine percent smear positivity had a 20 percent positive rate with GeneXpert.

Currently there are two possible scenarios for GeneXpert scale-up nationwide – a fast scenario with a goal of December 2012 and a slower scenario with a goal of September 2013.  The Bill & Melinda Gates Foundation is funding a study on the cost-effectiveness of the new diagnostic and patient outcomes.

The average cost of the test is $26 to $36, and there are significant hidden costs including recalibration of the instruments, waste management and others.  South Africa is developing a national TB cost model looking at the incremental cost of replacing the current diagnostic algorithm with this new algorithm.  Stevens reported that program costs could increase by 53 percent, with a 17 percent increase in the cost of diagnosis alone.  Nevertheless, South Africa will clearly diagnose many more cases and the pilot already shows a significant increase in early detection of TB and effective screening for MDR-TB.  The majority of patients were diagnosed within five days.

4 thoughts on “GeneXpert rapid TB diagnostic takes off in South Africa

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