title: Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana.
abstract: Cryptococcus neoformans var. grubii (Cng) is the most common cause of fungal meningitis, and its prevalence is highest 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 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 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 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.
authors.affiliation: Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, 163 Hanes House, Trent Drive, Durham, NC, 27710, USA.|Department of Molecular Genetics and Microbiology, Duke University Medical Center, RM 214 Jones Building, Research Drive, Durham, NC, 27710, USA.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Department of Molecular Genetics and Microbiology, Duke University Medical Center, RM 214 Jones Building, Research Drive, Durham, NC, 27710, USA.
authors.forename: Anastasia P
authors.initials: AP
authors.lastname: Litvintseva
authors.affiliation: Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, 163 Hanes House, Trent Drive, Durham, NC, 27710, USA.
authors.forename: Aubrey E
authors.initials: AE
authors.lastname: Frazzitta
authors.affiliation: Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.|Botswana-UPenn Partnership, National Health Laboratory, PO Box AC 157 ACH, Plot 5353 Extension 10 Church Road, Gaborone, Botswana.
authors.forename: Miriam R
authors.initials: MR
authors.lastname: Haverkamp
authors.affiliation: Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, 163 Hanes House, Trent Drive, Durham, NC, 27710, USA.
authors.forename: Liuyang
authors.initials: L
authors.lastname: Wang
authors.affiliation: Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, 163 Hanes House, Trent Drive, Durham, NC, 27710, USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Fang
authors.affiliation: Botswana-UPenn Partnership, National Health Laboratory, PO Box AC 157 ACH, Plot 5353 Extension 10 Church Road, Gaborone, Botswana.
authors.forename: Charles
authors.initials: C
authors.lastname: Muthoga
authors.affiliation: Department of Molecular Genetics and Microbiology, Duke University Medical Center, RM 214 Jones Building, Research Drive, Durham, NC, 27710, USA.
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Mitchell
authors.affiliation: Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, 163 Hanes House, Trent Drive, Durham, NC, 27710, USA.
authors.forename: John R
authors.initials: JR
authors.lastname: Perfect
mesh_terms: D000483:Alleles; D001902:Botswana; D003453:Cryptococcosis / Q000382:microbiology; D003455:Cryptococcus neoformans / Q000235:genetics*; D004271:DNA, Fungal / Q000235:genetics; D004777:Environment; D049770:Genes, Mating Type, Fungal; D014644:Genetic Variation; D005828:Genetics, Population; D005843:Geography; D006801:Humans; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D017422:Sequence Analysis, DNA; D014197:Trees / Q000382:microbiology
chemical_list: D004271:DNA, Fungal
keywords: Cryptococcus neoformans; genotyping; population structure; recombination