Development of biomarkers for efficient identification of human fungal pathogens

为了有效治疗对人类健康的最大威胁之一：真菌病原体，迫切需要快速和准确诊断的创新方法。真菌感染猖獗，耐药性问题日益严重。然而，目前用于诊断真菌感染和确定其对抗真菌药物敏感性的方法还很初级，为患者提供最佳治疗方案存在明显的时间滞后，通常是几天，有时是几周。我们将开发快速准确的分子诊断方法，不仅可以识别广泛的真菌病原体，还可以检测临床上重要的耐药机制。为了实现这一目标，我们将采取综合的方法，系统地分析分类学、种群遗传学和基因组学文献，以确定真菌病原菌物种、种群和菌株内部和之间的DNA序列变异模式。通过这些比较，我们将为物种、种群以及在某些情况下的菌株开发出高度敏感和特定的DNA签名序列。由于临床微生物学实验室在运行基于DNA的分子诊断方面的设置和能力不同，我们将尽可能与行业合作伙伴一起测试和开发适用于不同平台的生物标记物，包括荧光原位杂交(FISH)、经典PCR、实时PCR和等温扩增。这里开发的生物标志物和方法将由我们的行业合作伙伴进一步评估，以评估它们作为分子诊断试剂盒和/或作为医疗保健提供者服务平台的商业潜力。目前，在商业医学真菌诊断或用于快速准确诊断人类真菌病原体的分子生物标记物的开发中，几乎没有加拿大的存在。

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.