Rapid characterization of mycobacteria and drug resistance in paucibacillary TB

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DESCRIPTION (provided by applicant): Global challenges to tuberculosis (TB) control are multidrug-resistance (MDR-TB; a NIAID Category C Priority Pathogen under Biodefense Agenda) and the increased susceptibility of populations such as elderely, HIV infection, type 2 diabetes and other immunosuppressive chronic diseases. We propose to exploit our established study sites both sides of the south Texas/Mexico border and in Medellin, Colombia, where rates of MDR-TB and type 2 diabetes are high. We will use our recently developed extraction/real time PCR (qPCR) techniques to study the pathogenesis of TB and evolution of MDR-TB in these populations. Our initial emphasis will be on paucibacillary disease such as extrapulmonary TB (EPTB) and smear negative pulmonary TB (PTB). In aim 1 we examine the potential of our highly sensitive and specific qPCR for TB DNA to improve the detection of MTB as well as to quantitate its distribution in several different cellular and physiologic compartments. This non-invasive technique has the ability to determine the number of gene copies, cellular location and nature (intact or lysed) of mycobacteria in pulmonary and extra- pulmonary specimens. It is also sufficiently sensitive to detect mycobacterial DNA in specimens from paucibacillary TB, including MDR-TB, where diagnosis and pathogenesis are major challenges. In Aim 2 we adapt our qPCR method using molecular beacon probes for detection of mutations to rifampicin (RIF) as the first step in developing a rapid direct indicator of MDR-TB in pulmonary and extrapulmonary specimens. Finally we will explore the feasibility of refining the detection of resistance mutations by qPCR from the current qualitative "presence" or "absence" of resistance, to quantification of the ratio of RIF-resistant to sensitive bacteria. This approach will provide a means to study the evolution of resistance in patients who may be infected with mixed populations of resistant and sensitive MTB. We are particularly interested in this respect in patients with diabetes who we have shown to be particularly susceptible to recurrent disease with MDR-TB. The PI is an Assistant Professor working in a medically underserved community, characterized by low rates of HIV-co-infection, but high rates of type 2 diabetes. Funding of this R21 is critical to generate preliminary data that will strengthen future, more complex studies of the pathogenesis and evolution of MDR- TB in high-risk populations.