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Background  Human cryptococcal infections have been associated with bird droppings as a likely source of infection. Studies toward the local and global epidemiology of  Cryptococcus  spp. have been hampered by the lack of rapid, discriminatory, and exchangeable molecular typing methods.    Methodology/Principal Findings  We selected nine microsatellite markers for high-resolution fingerprinting from the genome of  C. neoformans  var.  grubii . This panel of markers was applied to a collection of clinical (n = 122) and environmental (n = 68; from pigeon guano)  C. neoformans  var.  grubii  isolates from Cuba. All markers proved to be polymorphic. The average number of alleles per marker was 9 (range 5–51). A total of 104 genotypes could be distinguished. The discriminatory power of this panel of markers was 0.993. Multiple clusters of related genotypes could be discriminated that differed in only one or two microsatellite markers. These clusters were assigned as microsatellite complexes. The majority of environmental isolates (>70%) fell into 1 microsatellite complex containing only few clinical isolates (49 environmental versus 2 clinical). Clinical isolates were segregated over multiple microsatellite complexes.    Conclusions/Significance  A large genotypic variation exists in  C. neoformans  var.  grubii . The genotypic segregation between clinical and environmental isolates from pigeon guano suggests additional source(s) of human cryptococcal infections. The selected panel of microsatellite markers is an excellent tool to study the epidemiology of  C. neoformans  var.  grubii.

Microsatellite Typing of Clinical and Environmental Cryptococcus neoformans var. grubii Isolates from Cuba Shows Multiple Genetic Lineages