Christian Landry - Understanding the evolution of antifungal resistance using genome editing and experimental evolution

The mechanisms of action of most antifungal drugs are well known. However, we still do not know many of the resistance mechanisms. Still to be discovered are the set of potential resistance mutations, the conditions that affect their likelihood of occurrence, and the fitness benefits and tradeoff they incur. I will present our most recent attempts to fill these knowledge gaps using budding yeast as a model and one of the oldest antifungals, flucytosine. We performed experiments at two levels of resolution. At high resolution, we used genome editing to examine all possible mutations in one of the drug targets.  We identified the properties of resistance mutations and uncovered the existence of a very strong tradeoff between resistance and fitness. These results show that the spread of resistance mutations could be limited in certain growth conditions due to a strong tradeoff.  At low resolution, we evolved hundreds of independent resistant mutants to narrow down on the most likely resistance genes and mutations. We identified one major resistance hub for this drug but failed to discover other known resistance genes. Through further experiments, we showed that although functionally equivalent in isolation, some gene loss of function mutations failed to evolve in populations because of cooperative interactions among cells. Altogether, these projects bring new light on the conditions that will influence the routes taken by evolution during antifungal drug treatment.