Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex

Abstract

Phylogenetic analysis of 11 genetic loci and results from many genotyping studies revealed significant genetic diversity with the pathogenic Cryptococcus gattii/Cryptococcus neoformans species complex. Genealogical concordance, coalescence-based, and species tree approaches supported the presence of distinct and concordant lineages within the complex. Consequently, we propose to recognize the current C. neoformans var. grubii and C. neoformans var. neoformans as separate species, and five species within C. gattii. The type strain of C. neoformans CBS132 represents a serotype AD hybrid and is replaced. The newly delimited species differ in aspects of pathogenicity, prevalence for patient groups, as well as biochemical and physiological aspects, such as susceptibility to antifungals. MALDI-TOF mass spectrometry readily distinguishes the newly recognized species.

Name Changes for Fungi of Medical Importance, 2012 to 2015

“…Table 2 lists proposals for revisions to names associated with fungi of medical importance published between 2012 and 2015. The most controversial of these is the proposal to reorganize the Cryptococcus gattii-C. neoformans species complex into seven new species, two derived from C. neoformans and five from within C. gattii (16). This proposal is based on data from numerous phylogenetic analyses (including whole-genome analyses) and genotyping studies that have revealed significant genetic diversity within the species complex.…”

Cryptococcus neoformans isolates from Yaoundé human immunodeficiency virus-infected patients exhibited intra-individual genetic diversity and variation in antifungal susceptibility profiles between isolates from the same patient

“…grubii AFLP1/VNI Â C. gattii AFLP4/VGI (serotype AB, genotype AFLP9) and C. neoformans var. grubii AFLP1/VNI Â C. gattii AFLP6/VGII (serotype AB, genotype AFLP11) (Meyer et al, 2009;Trilles et al, 2012;Cogliati et al, 2013;Kaocharoen et al, 2013;Hagen et al, 2015). These major molecular types have subsequently been confirmed using RFLP analysis of the orotidine monophosphate pyrophosphorylase (URA5) or phospholipase B (PLB1) genes, amplified fragment-length polymorphism (AFLP) and multi-locus sequence typing (MLST) analysis.…”

“…The global incidence varies from 0.04 to 12 % and accounts for 13-40 % of the annual death rate among HIV-infected patients in areas of sub-Saharan Africa (Park et al, 2009). The fungal agent involved in the disease is the C. neoformans/Cryptococcus gattii species complex, belonging to the phylum Basidiomycota and subdivided into seven haploid and four hybrid genotypes (Trilles et al, 2008;Meyer et al, 2009;Cogliati et al, 2013;Hagen et al, 2015). C. neoformans var.…”

“…Differences in epidemiology, ecology and genetics have recently led to the taxonomic revision of the C. gattii/C. neoformans species complex (Hagen et al, 2015). C. neoformans isolates with genotype AFLP1/VNI are globally predominant, except in Australia where C. gattii genotype AFLP4/VGI seems to be more common (Cogliati, 2013).…”

Fungal DNA barcoding

“…Some of the ambiguities based on nonmolecular methods were caused by morphological diversity associated with different developmental stages of the same fungus (Singer 1986;Kurtzman et al 1998;O'Donnell 2000). On the other hand, multiple cryptic species are often found within previously described single morphological or physiological species, even for some "well-studied" species complexes (e.g., O'Donnell et al 2004;Short et al 2013;Hagen et al 2015). Furthermore, globally, the number of traditional taxonomists, including fungal taxonomists, is on the decline (Drew 2011).…”