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Despite advances in the molecular epidemiology of<jats:italic>C. neoformans<\/jats:italic>, its population structure and mode of reproduction are not well understood. In the environment, it is associated with avian guano or vegetation. We collected nearly 800 environmental isolates from three locations in the United States (viz., North Carolina, California, and Texas) and compared them with one another and with clinical isolates from North Carolina. As expected, they consisted of the most prevalent serotypes, serotypes A and D, as well as serotype AD hybrids. The majority of environmental isolates were obtained from pigeon excreta. All environmental and clinical isolates of serotype A or D had the<jats:italic>MAT<\/jats:italic>\u03b1 mating-type allele. However, the AD hybrids included<jats:italic>MAT<\/jats:italic><jats:bold>a<\/jats:bold>alleles typical of serotypes A and D. Using an amplified fragment length polymorphism fingerprinting technique with two primer pairs, we identified 12 genotypes among the isolates of serotype A. Six of these genotypes were present in both the clinical and the environmental populations. However, one of the most prevalent environmental genotypes was absent from the clinical samples, and two other genotypes were isolated only from patients. The combined molecular data suggest that this environmental population of<jats:italic>C. neoformans<\/jats:italic>is predominantly clonal, although there was evidence for recent or past recombination.<\/jats:p>","DOI":"10.1128\/jcm.43.2.556-564.2005","type":"journal-article","created":{"date-parts":[[2005,2,4]],"date-time":"2005-02-04T21:42:56Z","timestamp":1107553376000},"page":"556-564","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":128,"title":["Comparative Analysis of Environmental and Clinical Populations of<i>Cryptococcus neoformans<\/i>"],"prefix":"10.1128","volume":"43","author":[{"given":"Anastasia P.","family":"Litvintseva","sequence":"first","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University Medical Center"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lori","family":"Kestenbaum","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University Medical Center"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rytas","family":"Vilgalys","sequence":"additional","affiliation":[{"name":"Department of Biology, Duke University, Durham, North Carolina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas G.","family":"Mitchell","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University Medical Center"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1471-8278.2000.00014.x"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.2307\/2992285"},{"key":"e_1_3_2_4_2","first-page":"15","volume":"4","year":"1999","unstructured":"Benham, J., J.-U. 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