Cryptococcus genetic diversity and mixed infections in Ivorian HIV patients: A follow up study

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 93% being VNI and 7% 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.

Population Genetic Analysis Reveals a High Genetic Diversity in the Brazilian Cryptococcus gattii VGII Population and Shifts the Global Origin from the Amazon Rainforest to the Semi-arid Desert in the Northeast of Brazil

Cryptococcus neoformans and Cryptococcus gattii are responsible globally for almost one million cryptococcosis cases yearly, mostly in immunocompromised patients, such as those living with HIV. Infections due to C. gattii have mainly been described in tropical and subtropical regions, but its adaptation to temperate regions was crucial in the species evolution and highlighted the importance of this pathogenic yeast in the context of disease. Cryptococcus gattii molecular type VGII has come to the forefront in connection with an on-going emergence in the Pacific North West of North America. Taking into account that previous work pointed towards South America as an origin of this species, the present work aimed to assess the genetic diversity within the Brazilian C. gattii VGII population in order to gain new insights into its origin and global dispersal from the South American continent using the ISHAM consensus MLST typing scheme. Our results corroborate the finding that the Brazilian C. gattii VGII population is highly diverse. The diversity is likely due to recombination generated from sexual reproduction, as evidenced by the presence of both mating types in clinical and environmental samples. The data presented herein strongly supports the emergence of highly virulent strains from ancestors in the Northern regions of Brazil, Amazonia and the Northeast. Numerous genotypes represent a link between Brazil and other parts of the world reinforcing South America as the most likely origin of the C. gattii VGII subtypes and their subsequent global spread, including their dispersal into North America, where they caused a major emergence.

Cryptococcus neoformans and Cryptococcus gattii are fungal agents responsible globally for almost one million cryptococcosis cases yearly, mostly in immunocompromised patients, such as those living with HIV. Cryptococcosis is a life-threatening mycosis, frequently causing meningoencephalitis. Infections due to C. gattii were originally described in tropical and subtropical regions, but its adaptation to temperate regions was highlighted by the emergence in the Pacific North West of North America by C. gattii molecular type VGII. The present work aimed to assess the genetic diversity within the Brazilian C. gattii VGII population to gain new insights into its origin and global dispersal from the South American continent using the ISHAM MLST consensus typing scheme. Our results corroborate that the Brazilian C. gattii VGII population is highly diverse, and strongly supports the emergence of highly virulent strains from ancestors in the Northern regions of Brazil. Numerous genotypes represent a link between Brazil and other parts of the world, and the isolates from the transitional ecological area in Northeast Brazil are the most likely ancestor lineages, translocating from caatinga/cerrado by adapting progressively throughout Amazonia in South America, and spread to the North American Pacific Northwest region and other parts of the world on multiple occasions.

Cryptococcus gattii in the Age of Whole-Genome Sequencing

Cryptococcus gattii, the sister species of Cryptococcus neoformans, is an emerging pathogen which gained importance in connection with the ongoing cryptococcosis outbreak on Vancouver Island. Many molecular studies have divided this species into for major lineages: VGI, VGII, VGIII, and VGIV. This commentary summarizes the whole-genome sequencing (WGS) studies that have been carried out with this species, re-emphasizing the phylogenetic relationships, showing chromosomal rearrangements between those four groups, and identifying VGII as ancestral population within C. gattii. In addition, WGS specific to VGII, containing the Vancouver Island outbreak genotypes and those from the Pacific Northwest region of the United States, has placed the origin of this lineage within South America and identified specific genes responsible for either brain or lung infection. It also showed, that many genotypes are spread across a number of different continents, as has been previously shown by multilocus sequence typing (MLST). In addition, it showed that recombination occurs more frequently between mitochondrial than nuclear genomes.