Despite the availability of curative therapy, tuberculosis continues to be the leading cause of death from a bacterial pathogen worldwide. Effective TB control requires the early diagnosis and treatment of infectious cases to prevent further transmission of the disease. The World Health Organization reports that the global TB case detection rate in 2011 was only 66%; thus, over 30% of the 8 million incident TB cases estimated to have occurred that year were neither diagnosed nor started on effective therapy.

Much of the problem stems from the failure of traditional TB diagnostic tools which rely on sputum smear microscopy and to a lesser extent culture confirmation of disease and drug resistance phenotypes. While smear microscopy is inexpensive and readily available, its poor sensitivity has meant that many TB patients go undiagnosed. The sensitivity of smear is particularly low in two groups: HIV infected patients, especially those with low Cd4 counts, and young children. Not only are sputum smears of low diagnostic yield, cultures for Mycobacteria tuberculosis (MTB) grow notoriously slowly. Since drug resistance is traditionally assessed by growth inhibition by antibiotics, drug resistant TB is often detected months after the initiation of empirical drug regimens. These delays not only lead to the acquisition of further resistance in patients receiving inadequate regimens but also to the prolonged infectiousness of those with resistant organisms and the consequent spread of drug resistant strains.

The recent development of rapid molecular diagnostics promises to revolutionize TB control. Such tests can be performed directly on sputum or other clinical samples and rely on the rapid detection of MTB genetic signatures as well as resistance-associated mutations. Clinical studies demonstrate that they perform better than sputum smear microscopy and reliably identify resistance to the first line drug, rifampicin. However, these tools suffer from two important limitations. First, current platforms are substantially less sensitive than culture and often miss smear negative TB. And secondly, gaps in our knowledge of the genetic determinants of phenotypic resistance limit the spectrum of drugs to which resistance can be detected. Here, we propose to address these gaps through a multi-disciplinary collaboration emphasizing discovery of new biomarkers of resistance, the identification of optimal clinical sampling strategies directed toward detection of MTB DNA and the development of a sensitive micro-array based rapid diagnostic. Our long-term goal is to develop a diagnostic strategy that will improve the diagnosis of childhood and DR TB and stem the further spread of the disease. Our specific aims are to:

1. Discover and characterize novel biomarkers of TB drug resistance
2. Develop the most promising clinical sampling strategies with which to detect MTB DNA
3. Develop and optimize a micro-array based POC diagnostic designed to detect MTB and its DR