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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 <jats:italic>Cng<\/jats:italic> in southern Africa, we analysed isolates from 77 environmental samples and 64 patients. We detected significant genetic diversity among isolates and strong evidence of geographic structure at the local level. High proportions of isolates with the rare <jats:italic><jats:styled-content style=\"fixed-case\">MAT<\/jats:styled-content><jats:bold>a<\/jats:bold><\/jats:italic> allele were observed in both clinical and environmental isolates; however, the mating\u2010type alleles were unevenly distributed among different subpopulations. Nearly equal proportions of the <jats:italic><jats:styled-content style=\"fixed-case\">MAT<\/jats:styled-content><jats:bold>a<\/jats:bold><\/jats:italic> and <jats:italic><jats:styled-content style=\"fixed-case\">MAT<\/jats:styled-content><\/jats:italic>\u03b1 mating types were observed among all clinical isolates 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 foundation for subsequent genomewide association studies to identify genes and genotypes linked to pathogenicity in humans.<\/jats:p>","DOI":"10.1111\/mec.13260","type":"journal-article","created":{"date-parts":[[2015,6,6]],"date-time":"2015-06-06T08:15:37Z","timestamp":1433578537000},"page":"3559-3571","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":61,"title":["Comparative analyses of clinical and environmental populations of <i><scp>C<\/scp>ryptococcus neoformans<\/i> in <scp>B<\/scp>otswana"],"prefix":"10.1111","volume":"24","author":[{"given":"Yuan","family":"Chen","sequence":"first","affiliation":[{"name":"Division of Infectious Diseases Department of Medicine Duke University Medical Center 163 Hanes House Trent Drive Durham NC 27710 USA"},{"name":"Department of Molecular Genetics and Microbiology Duke University Medical Center RM 214 Jones Building Research Drive Durham NC 27710 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