Development of biomarkers for efficient identification of human fungal pathogens

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Innovative methods for rapid and accurate diagnosis are urgently needed for the effective treatment of one of the biggest threats to human health: fungal pathogens. Fungal infections are rampant and drug resistance is increasingly problematic. However, the current methods used in the diagnosis of fungal infections and the determination their susceptibilities to antifungal drugs are rudimentary and there is a significant time lag, usually days and sometimes weeks, in providing the best treatment options to patients.We will develop rapid and accurate molecular diagnosis methods that can identify not only a wide range of fungal pathogens but also detect clinically significant resistance mechanisms. To achieve this goal, we will take an integrative approach to systematically analyze the taxonomy, population genetics and genomics literature to identify the patterns of DNA sequence variation within and between fungal pathogen species, populations, and strains. From these comparisons, we will develop highly sensitive and specific DNA signature sequences for species, populations, and in certain cases, strains. Because clinical microbiology laboratories differ in their setup and capabilities in running DNA-based molecular diagnosis, whenever possible, together with our industrial partners, we will test and develop the biomarkers for different platforms, including fluorescent in situ hybridization (FISH), classical PCR, real-time PCR, and isothermal amplifications. The biomarkers and methods developed here will be further evaluated by our industrial partner to assess their commercial potential as molecular diagnosis kits and/or as service platforms to healthcare providers. At present, there is almost no Canadian presence in commercial medical fungi diagnosis or in the development of molecular biomarkers for rapid and accurate diagnosis of human fungal pathogens.