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Nat Commun ; 10(1): 2035, 2019 05 02.
Article in English | MEDLINE | ID: mdl-31048698

ABSTRACT

Cryptococcus neoformans (C. neoformans var. grubii) is an environmentally acquired pathogen causing 181,000 HIV-associated deaths each year. We sequenced 699 isolates, primarily C. neoformans from HIV-infected patients, from 5 countries in Asia and Africa. The phylogeny of C. neoformans reveals a recent exponential population expansion, consistent with the increase in the number of susceptible hosts. In our study population, this expansion has been driven by three sub-clades of the C. neoformans VNIa lineage; VNIa-4, VNIa-5 and VNIa-93. These three sub-clades account for 91% of clinical isolates sequenced in our study. Combining the genome data with clinical information, we find that the VNIa-93 sub-clade, the most common sub-clade in Uganda and Malawi, was associated with better outcomes than VNIa-4 and VNIa-5, which predominate in Southeast Asia. This study lays the foundation for further work investigating the dominance of VNIa-4, VNIa-5 and VNIa-93 and the association between lineage and clinical phenotype.


Subject(s)
AIDS-Related Opportunistic Infections/microbiology , Cryptococcosis/microbiology , Cryptococcus neoformans/genetics , Genome, Fungal/genetics , Phylogeny , AIDS-Related Opportunistic Infections/epidemiology , Antifungal Agents/therapeutic use , Clinical Trials as Topic , Cryptococcosis/epidemiology , Cryptococcus neoformans/isolation & purification , Cryptococcus neoformans/pathogenicity , Humans , Incidence , Laos/epidemiology , Malawi/epidemiology , Thailand/epidemiology , Treatment Outcome , Uganda/epidemiology , Vietnam/epidemiology , Whole Genome Sequencing
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