His main research activity is in the area of tuberculosis drug development. For the last thirty years Stephen Gillespie has been involved in various aspects of tuberculosis diagnosis and drug development. This has included the evaluation of new candidate antituberculosis agents in vitro. This work has expanded into studies of the molecular mechanisms of resistance and the development of model systems to measure the fitness deficits found in resistant strains. He has been involved in the development of fluoroquinolones for tuberculosis having performed early bacterial activity studies and clinical trials of ciprofloxacin. More recently he has led the group working on the clinical development of moxifloxacin in collaboration with the Global Alliance for TB Drug Development as Chief Investigator of the REMox TB study. He later went on to be the coordinating investigator for the TB Alliance STAND trial (Shortening Treatment by Advancing New Drugs) and currently the SimpliciTB project. He is also one of the Chief Investigators of the PanACEA consortium that links European and African research groups in enhancing anti-tuberculosis therapy.
He has an extensive record of developing novel mirobiological diagnostics. Most recently, he has developed SLIC (Scattered Light Integrating Collector), which performs phenotypic antibiotic susceptibility testing in less than 30 minutes. This innovation recently won a Longitude Prize Discovery Award. In addition he has developed the Molecular Bacterial Load Assay, an innovative way of detecting, quantifiying and determining the viability of bacteria in a single test that allows both diagnosis and the monitoring of treatment response.