Data from: Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana

Cryptococcus neoformans var. grubii (Cng) is the most common cause of fungal meningitis in sub-Saharan Africa. Patients become infected by inhaling airborne spores or desiccated yeast cells from the environment, where the fungus thrives in avian droppings, trees, and soil. To investigate the prevalence and population structure of Cng in southern Africa, we analyzed isolates from 77 environmental samples and 64 patients. We detected significant genetic diversity among strains and strong evidence of geographic structure at the local level. High proportions of isolates with the rare MATa allele were observed in both clinical and environmental isolates; however, the mating type alleles were unevenly distributed among different subpopulations. Nearly equal proportions of the MATa and MATα mating types were observed among all clinical strains and in one environmental subpopulation from the eastern part of Botswana. As previously reported, there was evidence of both clonality and recombination in different geographic areas. These results provide a basic foundation for subsequent genome-wide association studies to identify genes and genotypes linked to pathogenicity in humans.