Abstract
Opportunistic microbial pathogens that infect humans must adapt to radically different fitness landscapes as they transition from the external environment to the host niche. The nature, frequency, and magnitude of genomic changes that accompany adaptation to the human host niche are not well understood for many eukaryotic pathogens because of the logistical challenges of obtaining longitudinal samples of pathogen populations in individual patients. Drawing on a set of case studies, we characterize in-host genomic and phenotypic evolution of the opportunistic human fungal pathogen Cryptococcus neoformans during chronic infections. We find that fungal genome evolution during chronic infection is characterized by large-scale genome restructuring and increasing genomic heterogeneity within hosts. Phenotypic changes include diversification in virulence traits and antifungal susceptibility. Genotypically and phenotypically distinct sublineages arise and co-persist within the same host tissues, consistent with a model of strong and/or diversifying selection in the complex environment of human hosts.