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Genetic diversity analyses were performed by sero-genotyping and multi-locus sequence typing on 252 cryptococcal isolates from 13 HIV-positive Ivorian patients followed-up for cryptococcal meningitis. Antifungal susceptibility analyses were performed according to the CLSI M27A3 method. The majority (67.8%) of the isolates belonged to the Cryptococcus neoformans (serotype A) species complex, with 91.9% being VNI and 7.1% being VNII. Cryptococcus deuterogattii VGII (serotype B) represented 16.7% of the strains, while C. neoformans/C. deneoformans VNIII (serotype AD) hybrids accounted for 15.1% of the strains. One strain (0.4%) was not identifiable. Nine different sequence types (STs 5, 6, 23, 40, 93, 207, 311, and a new ST; 555) were identified in the C. neoformans population, while the C. deuterogattii population comprised the single ST 173. The distribution of the strains showed that, while the majority of patients (9/13) harboured a single sequence type, 4 patients showed mixed infections. These patients experienced up to 4 shifts in strain content either at the species and/or ST level during their follow-up. This evolution of diversity over time led to the co-existence of up to 3 different Cryptococcus species and 4 different ST within the same individual during the course of infection. Susceptibility testing showed that all strains were susceptible to amphotericin B while 3.6% of them had a none-wild type phenotype to 5-flucytosine. Concerning fluconazole, 2.9% of C.neoformans serotype A strains and 2.4% of C. deuterogattii had also respectively a none-wild type phenotype to this molecule. All C. neoformans x C. deneoformans serotype AD hybrids had however a wild type phenotype to fluconazole. The present study showed that mixed infections exist and could be of particular importance for care outcomes. Indeed, (i) the different Cryptococcus species are known to exhibit different virulence and different susceptibility patterns to antifungal drugs and (ii) the strains genetic diversity within the samples may influence the susceptibility to antifungal treatment. Author summary: Cryptococcal meningitis is a neglected fungal disease responsible for 181 000 deaths worldwide in 2014, with 75% of deaths occurring in sub-Saharan Africa. Cryptococcal meningitis is caused by environmental yeasts belonging to the Cryptococcus neoformans/Cryptococcus gattii species complexes. The evolution of the diversity of the yeast populations within the patients and during the course of treatment is poorly understood. Indeed, it was believed for a long time that infections were of a single strain type. It was only recently that the complexity of the yeast diversity during infection began to be assessed. Here, the researchers evaluated the diversity of the Cryptococcus population within Ivoirian patients. The purpose was to generate data about the overall diversity of such yeast in Western Africa where the data are scarce and to better understand the evolution of the pathogen populations during patient follow-up. This last point is particularly important because some species are more virulent or naturally more resistant to antifungal treatments and could be an issue in the case of relapses during care protocols. [ABSTRACT FROM AUTHOR]