Project Summary Resistance to anti-tuberculosis drugs complicates the care and worsens the outcomes of individuals with tuberculosis, the leading infectious cause of death worldwide. South Africa is using the new anti-tuberculosis drug bedaquiline as part of both shorter and longer all-oral treatment regimens for patients with rifampicin- resistant tuberculosis (RR-TB). While clinical trials and observational studies demonstrate improved treatment outcomes with bedaquiline-based treatment, the predictors of poor treatment response (defined as positive cultures two, four, or six months after diagnosis) and poor treatment outcomes are not well-characterized in programmatic settings. Alarmingly, resistance to bedaquiline has been detected in clinical Mycobacterium tuberculosis isolates. The background resistance to both new and old drugs that compose treatment regimens, combined with observed variation in pretreatment phenotypic susceptibility to bedaquiline, raise concerns that the risks of poor treatment response and outcomes may be higher than anticipated. To address these concerns, we will use the robust infrastructure of the South African National Health Laboratory system and the electronic drug-resistant tuberculosis register to assess programmatic poor treatment response among patients with RR-TB in South Africa. We will perform minimum inhibitory concentration testing of bedaquiline and companion drugs on routinely collected specimens in the Gauteng Province of South Africa to determine whether elevated minimum inhibitory concentrations of bedaquiline in phenotypically bedaquiline-susceptible pretreatment isolates are associated with poor treatment response or outcomes. Whole genome sequencing on routinely collected specimens will allow simultaneous characterization of the underlying molecular epidemiology of RR-TB. We will also use a novel approach of using the concentration of drugs with different half-lives determined programmatically and pharmacokinetic modeling to evaluate association with time to culture positivity and treatment outcomes. We will combine mycobacteriologic factors, drug concentration data, and clinical data to develop a prediction model for poor treatment response and outcomes. Our findings will guide targeted intervention strategies for individuals at high risk for poor treatment response, inform rapid drug susceptibility tests that incorporate genotypic data for bedaquiline and companion drugs in new treatment regimens of RR-TB, and explore the potential importance of measuring drug concentrations early in the course of RR-TB treatment. The insights gained about genotypic and phenotypic variation in relation to treatment outcomes of RR-TB will be highly valuable not only for South African tuberculosis programs, but also for high- burden and under-resourced settings worldwide. Our study team includes globally recognized content experts from South Africa and the US and will allow critical progress in drug-resistant TB r...