Microevolution of Cryptococcus neoformans in high CO2 converges on mutations isolated from patients with relapsed cryptococcosis

Cryptococcus neoformans is an environmental fungus that causes an estimated 180,000 deaths annually and transitions from the external environment to the host environment to cause disease. CO₂ concentrations in the atmosphere (0.04%) are dramatically lower than in mammalian tissues (5%). Environmental C. neoformans strains that cannot tolerate 5% CO₂ are less virulent than CO₂-tolerant strains. Microevolution at elevated CO₂ generates loss-of-function mutations in the nucleotide binding protein Avc1 that confer CO₂ tolerance to CO₂-intolerant strains. Mechanistically, Avc1 positively regulates the expression of plasma membrane transporters, including PDR9, a phospholipid floppase that negatively modulates CO₂ fitness. Deletion of AVC1 in five CO₂-intolerant environmental strains increases competitive fitness in host CO₂ and in a mouse infection model. Importantly, strains with similar AVC1 mutations emerge in patients with relapsed cryptococcosis. Therefore, this microevolutionary convergence strongly suggests that adaptation to host CO₂ is a significant driver of C. neoformans fitness during infection.