The TB Genomics group has its foundation in the molecular epidemiology of Mycobacterium tuberculosis in a high incidence setting, and has provided new insights into the epidemiology of both drug susceptible and drug resistant tuberculosis. Our group focuses on comparative genomics by whole genome sequencing (WGS), transcriptomics using RNA-seq, and proteomics, allowing us to investigate the epidemiology and evolution of M. tuberculosis. The group is supported by an outstanding microbiology core with expertise in mycobacterial culture, drug susceptibility testing, minimum inhibitory concentration determination and archiving of clinical isolates. The group has established one of the largest archives of both drug susceptible and drug resistant isolates of M. tuberculosis in the world. This archive includes samples from patients at baseline as well as serial isolates and more recently isolates from monthly culture positivity monitoring. This culture bank allows us to scrutinize the local epidemic in terms of outbreak investigations, within-patient evolution of drug-resistance, transmission and discovering novel drug-resistance causing mutations. By combining WGS with RNA-seq or proteomics we are able to determine the impact of drug resistance on the physiology of Mycobacterium tuberculosis. We are also involved in the development and evaluation of rapid molecular diagnostics for the detection of drug resistance that are based on information generated through molecular epidemiology studies/data, helping to tailor diagnostics to the local epidemic.
The TB Genomics groups is committed to and actively seeks to build capacity and train scientists in molecular techniques for tuberculosis characterization in African countries. We currently have collaborations with scientists or train, supervise and advise students from Zambia, Namibia, Botswana, Zimbabwe, Mozambique, Nigeria, Ethiopia and Kenya.