Immune-based detection of rifampicin-resistance in HIV/TB

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DESCRIPTION (provided by applicant): Nearly 2 billion people, one third of the World's population, are at risk of active tuberculosis (TB) because they are latently infected with the causative agent Mycobacterium tuberculosis (Mtb), and almost 2 million TB- related deaths occur annually. HIV increases the risk of TB, and multi-drug resistant TB (MDR-TB), defined as TB resistant to both isoniazid (INH) and rifampicin, has become a public health emergency in some parts of sub-Saharan Africa, where the HIV prevalence and TB incidence rates are the highest in the world. A major barrier to TB control is that detection of Mtb drug resistance requires collection of microbiological samples, which are not available in many cases of active disease in HIV and in all cases of latent infection. Indeed, treatment of latent infection, a necessary approach to global TB elimination, cannot be properly targeted if drug resistance is suspected and, importantly, the scope of drug-resistant latent Mtb infection is unknown. A central tenet of microbiology and infectious diseases holds that identification of antibiotic resistance in human pathogens requires direct access to the organism. Our overarching hypothesis challenges this paradigm by hypothesizing that the changes in the proteome of pathogens that specifically occur as a result of genetic mutation(s) conferring drug resistance can be immunologically detected by the host adaptive immune system. This hypothesis has two parts - 1) that certain genes are specifically upregulated by drug resistant strains, and 2) that te products of these genes can be recognized by the host adaptive immune system. Our recently published proteomics experiments have identified numerous specific proteins that are either upregulated in or specifically expressed by Mtb strains that have single nucleotide polymorphisms (SNPs) in rpoB conferring resistance to rifampicin, which, if present in clinical disease, usually indicates MDR-TB. Furthermore, specific gene activation by rifampicin-resistant, rpoB-mutant Mtb is consistent with data from model organisms, including Bacillus subtilis and Streptomyces lividans, in that rpoB mutation can dramatically activate dormant gene networks not expressed by wild-type strains. In this proposal, we will analyze cellular immune responses to previously identified candidate "rifampicin-resistance antigens" in HIV- infected and uninfected adults in Botswana, where the prevalence of HIV is nearly 20%. Specifically, we will prospectively compare memory immune responses to a panel of novel antigens in individuals with rifampicin- resistant versus rifampicin-susceptible pulmonary TB, as the underlying drug-susceptibility of the infecting Mtb isolates can be determined in active disease. This proof-of-concept study represents an important first step to evaluating an innovative, indirect method to determine drug susceptibility in Mtb, particularly during latent infection, wher drug resistance currently cannot be assessed. By so doing, this proposal has the potential to improve TB clinical care by allowing, for the first time, study of the epidemiology of drug-resistant latent infection and, most importantly, radically transforming public health approaches to global TB control.