Molecular Epidemiology Reveals Low Genetic Diversity among Cryptococcus neoformans Isolates from People Living with HIV in Lima, Peru, during the Pre-HAART Era.

Cryptococcosis, a mycosis presenting mostly as meningoencephalitis, affecting predominantly human immunodeficiency virus (HIV)-infected people, is mainly caused by Cryptococcus neoformans. The genetic variation of 48 C. neoformans isolates, recovered from 20 HIV-positive people in Lima, Peru, during the pre-highly active antiretroviral therapy (HAART) era, was studied retrospectively. The mating type of the isolates was determined by PCR, and the serotype by agglutination and CAP59-restriction fragment length polymorphism (RFLP). Genetic diversity was assessed by URA5-RFLP, PCR-fingerprinting, amplified fragment length polymorphism (AFLP), and multilocus sequence typing (MLST). All isolates were mating type alpha, with 39 molecular type VNI, seven VNII, corresponding to C. neoformans var. grubii serotype A, and two VNIII AD hybrids. Overall, the cryptococcal population from HIV-positive people in Lima shows a low degree of genetic diversity. In most patients with persistent cryptococcal infection, the same genotype was recovered during the follow-up. In four patients with relapse and one with therapy failure, different genotypes were found in isolates from the re-infection and from the isolate recovered at the end of the treatment. In one patient, two genotypes were found in the first cryptococcosis episode. This study contributes data from Peru to the ongoing worldwide population genetic analysis of Cryptococcus.

Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal.

The emergence of distinct populations of Cryptococcus gattii in the temperate North American Pacific Northwest (PNW) was surprising, as this species was previously thought to be confined to tropical and semitropical regions. Beyond a new habitat niche, the dominant emergent population displayed increased virulence and caused primary pulmonary disease, as opposed to the predominantly neurologic disease seen previously elsewhere. Whole-genome sequencing was performed on 118 C. gattii isolates, including the PNW subtypes and the global diversity of molecular type VGII, to better ascertain the natural source and genomic adaptations leading to the emergence of infection in the PNW. Overall, the VGII population was highly diverse, demonstrating large numbers of mutational and recombinational events; however, the three dominant subtypes from the PNW were of low diversity and were completely clonal. Although strains of VGII were found on at least five continents, all genetic subpopulations were represented or were most closely related to strains from South America. The phylogenetic data are consistent with multiple dispersal events from South America to North America and elsewhere. Numerous gene content differences were identified between the emergent clones and other VGII lineages, including genes potentially related to habitat adaptation, virulence, and pathology. Evidence was also found for possible gene introgression from Cryptococcus neoformans var. grubii that is rarely seen in global C. gattii but that was present in all PNW populations. These findings provide greater understanding of C. gattii evolution in North America and support extensive evolution in, and dispersal from, South America. Importance: Cryptococcus gattii emerged in the temperate North American Pacific Northwest (PNW) in the late 1990s. Beyond a new environmental niche, these emergent populations displayed increased virulence and resulted in a different pattern of clinical disease. In particular, severe pulmonary infections predominated in contrast to presentation with neurologic disease as seen previously elsewhere. We employed population-level whole-genome sequencing and analysis to explore the genetic relationships and gene content of the PNW C. gattii populations. We provide evidence that the PNW strains originated from South America and identified numerous genes potentially related to habitat adaptation, virulence expression, and clinical presentation. Characterization of these genetic features may lead to improved diagnostics and therapies for such fungal infections. The data indicate that there were multiple recent introductions of C. gattii into the PNW. Public health vigilance is warranted for emergence in regions where C. gattii is not thought to be endemic.

Reclassification of Graphium tectonae as Parascedosporium tectonae gen. nov., comb. nov., Pseudallescheria africana as Petriellopsis africana gen. nov., comb. nov. and Pseudallescheria fimeti as Lophotrichus fimeti comb. nov.

During a biodiversity survey of Argentinian soil fungi, we recovered a rare Scedosporium-like fungus which was proven to be genetically and morphologically different from known species of Scedosporium (anamorph of Pseudallescheria) and relatives and is proposed here as representing a new genus. This genus is mainly characterized by producing sympodial conidia from denticulate conidiogenous cells. This isolate was morphologically identical to Graphium tectonae and thus the new combination Parascedosporium tectonae gen. nov., comb. nov. is proposed. Sequence analysis of four regions of three genes, i.e. beta-tubulin (two loci), calmodulin and the internal transcribed spacer region of the 5.8S rRNA, confirmed our proposal. Both the phylogenetic analysis and morphological studies excluded Pseudallescheria africana and Pseudallescheria fimeti from the genus Pseudallescheria. The former is proposed as a member of the new genus Petriellopsis, and the latter has been accommodated in Lophotrichus. The type strains of Parascedosporium tectonae gen. nov., comb. nov., Petriellopsis africana gen. nov., comb. nov. and Lophotrichus fimeti comb. nov. are respectively CBS 127.84(T), CBS 311.72(T) and CBS 129.78(T).