Genomics tools for the prediction of antifungal resistance in clinical samples
Fungal infections and resistance to antifungals are on the rise worldwide, with 14.9 million cases and 1.7 million deaths every year. Nearly 2% of Canadians have serious fungal infections and spikes in frequency have been associated with COVID-19, particularly in the most vulnerable patients. This project will develop faster and more accurate tools to identify fungal species and antifungal susceptibility from DNA sequencing directly from clinical samples. The deliverables will include a database of pre-validated resistance mutations, a procedure for generating multilocus sequencing from clinical samples, and a bioinformatic pipeline for species identification and prediction of antifungal resistance. The project will implement the diagnostic tools in Laboratoire de Santé Publique du Québec, Public Health Agency of Canada, Public Health Ontario and Alberta Precision Laboratories – Public Health Laboratory. These three organizations have vast experience in the development of diagnostic tests and play key roles in regulatory organizations and committees that set standards in the field. Implementing faster and more targeted and sensitive testing will reduce the number of deaths and morbidity of Canadians with invasive fungal infections.