|Eamon Duffy, K-RITH Research
Intern reading TB culture plates
On World Tuberculosis Day, IBM and the KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH) have announced plans to research new treatment approaches to fight tuberculosis (TB) in South Africa. IBM’s Big Data analytics technologies will be put to work on bacterial genetics and drug susceptibility tests to better understand the genomic mechanisms that cause resistance to antibiotics. The ultimate goal is to find new treatments and diagnostic approaches to fight TB.
The scale of the TB problem in Southern Africa is largely a result of HIV infection, lack of integration between HIV and TB treatments and historic challenges in healthcare delivery. Currently South Africa has the world’s third highest burden of TB, with the province of KwaZulu-Natal being the most affected by both drug-susceptible and drug-resistant tuberculosis. Over 100,000 cases of TB are reported every year from this province alone and over 60% are also infected with HIV.
The KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), which is based at the University of Kwazulu-Natal’s Nelson R. Mandela School of Medicine, is an independent research institute established in 2009 to conduct basic science research into TB and HIV, and translate the scientific findings into new tools to control these deadly diseases. The Institute’s work has boosted the TB and HIV research capabilities of scientists in South Africa. The work with IBM involving its Big Data and deep data analytics technology– will enable K-RITH to understand bacteria genomes from drug-resistant strains of M. tuberculosis— the bacteria that causes TB.
According to Associate Investigator at K-RITH, Dr. Alex Pym, the agreement with IBM is “a significant collaboration” that gives South African scientists access to IBM’s computational expertise in bioinformatics and machine learning. “This will allow us to analyze data in new and imaginative ways and it holds the promise of giving us better insight into the mechanisms of drug resistance, leading to better diagnostic tests,” said Dr. Pym.
The science has benefitted from IBM’s global network of research labs and world leading expertise in computational biology. Researchers from the Haifa, Melbourne, and Africa labs are working together to analyze over 200 TB genomes, each with 4.4 million base pairs, to better understand the complex clinical picture of African tuberculosis infections.
|The classic mycobacterial stain is an acid fast
stain, in which TB appears red with a blue counterstain.
Michal Rosen-Zvi, senior manager of analytics at IBM’s Research Lab in Haifa, Israel said, “TB drug resistance is a far more complex genome by comparison to something like the HIV virus. The bioinformatics or computational tools needed to extract information on the disease are very new, yet cracking the code of this genomic information will help define which treatment combinations work best for different patients and how they work on different strains of TB.”
“For HIV, technology can look at the difference in viral load before and after treatment, and use that to understand whether the treatment was a success. But in TB, there is no single measure that defines the status of the disease. We will need to develop multiple ways to label the treatment outcomes and new methods to indicate whether a treatment was effective,” said Rosen-Zvi.
IBM’s work on other solutions, including the well known EuResist programme, developed to help physicians select the optimal treatments for HIV patients, have paved the way for the use of bioinformatics in disease treatment. EuResist combines large databases and new prediction engines to provide predictive modeling of how HIV would react in a particular person treated with specific combination of drugs. This system, available since 2008, is the world’s largest database containing clinical and genomic information on HIV.
Dr. Pym said, “What we believe is that through the partnership between K-RITH and IBM we can combine and enable TB analytics from IBM to map which antibiotic treatments are successful for which TB strains. And then, by finding the associations between the genetic markers and the correct antibiotic treatment, we can improve treatment protocols. This can make a significant difference to many lives across the globe, let alone Africa.”
Sequencing of the KRITH strains was performed by the Broad Institute, a world leader in genomics, with funding from the National Institute of Allergy and Infectious Diseases of the U.S. National In
stitutes of Health. Analysis of sequencing data from the K-RITH strains and other organizations in South Africa was given first priority due to the magnitude of TB drug resistance in that country.
The research work at IBM and K-RITH can interact with global initiatives like TBresist, and with leadership and collaboration from organizations such as the CDC Foundation. The intent is to add data from different parts of the world, from different strains of TB, to culture a global database that researchers and physicians can use to determine the best treatment to combat a particular strain of tuberculosis. The impact of this would be more effective treatments for patients and a reduction of the cost of treating tuberculosis in Africa and potentially around the world.
In similar news, last week the New York Genome Center and IBM announced that they will test a unique IBM Watson prototype designed specifically for genomic research as a tool to help oncologists deliver more personalized care to cancer patients.
IBM is making a long term, strategic investment in the future of Africa and the company’s new Africa research lab is at the heart of its operations. IBM has been present in Africa for over 70 years and today has a presence in over 20 African countries, including Tanzania, Senegal, South Africa, Morocco, Egypt, Tunisia, Algeria, Ghana, Nigeria, Kenya, and Mauritius