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 must transition 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 much less virulent than CO2-tolerant strains. A microevolution experiment at elevated CO2 generated loss-of-function mutations in the nucleotide binding protein Avc1 that confer CO2 tolerance to CO2-intolerant environmental strains. Mechanistically, Avc1 positively regulates the expression of PDR9, a putative floppase that negatively modulates CO2 fitness. Deletion of AVC1 in five CO2-intolerant environmental strains increased competitive fitness in host CO2 and in a mouse infection model. Importantly, strains with similar AVC1 mutations have emerged 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.