Enabling Metagenomics To Be Applied for Diagnostics of Mycoses in Crtically Ill Patients

Despite the unique opportunity unlocked by the steady maturation of long read nucleotide sequencing to unambiguously inform the front-lines of clinical practice, clinical applications are not widespread due to prohibitive data analytic requirements in expertise and infrastructure that Infectious Disease departments cannot easily integrate. We aim to develop a significantly less burdensome diagnostic metagenomic solution using Oxford Nanopore sequencing for the reliable identification of mycotic agents from complex clinical samples (e.g. BAL, Sputum, blood, tissue). This will necessitate integration of DNA extraction, sequence aggregation, data algorithms, and novel bioinformatic tools to identify relevant mycotic agents with greater accuracy and expediecy in guiding diagnostics. We will compare the metagenomics-based identification workflows we build against traditional mycological diagnostics to assess the translational viability and ultimately, to promote the adoption of untargeted sequencing.

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Juan Monroy - Nieto