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

The status of cryptococcosis in Latin America

Cryptococcosis is a life-threatening fungal infection caused by the encapsulated yeasts Cryptococcus neoformans and C. gattii, acquired from the environment. In Latin America, as occurring worldwide, C. neoformans causes more than 90% of the cases of cryptococcosis, affecting predominantly patients with HIV, while C. gattii generally affects otherwise healthy individuals. In this region, cryptococcal meningitis is the most common presentation, with amphotericin B and fluconazole being the antifungal drugs of choice. Avian droppings are the predominant environmental reservoir of C. neoformans, while C. gattii is associated with several arboreal species. Importantly, C. gattii has a high prevalence in Latin America and has been proposed to be the likely origin of some C. gattii populations in North America. Thus, in the recent years, significant progress has been made with the study of the basic biology and laboratory identification of cryptococcal strains, in understanding their ecology, population genetics, host-pathogen interactions, and the clinical epidemiology of this important mycosis in Latin America.Fil: Firacative, Carolina. University of Sydney; AustraliaFil: Lizarazo, Jairo. Universidad de Pamplona; EspañaFil: Illnait Zaragozí, María Teresa. Tropical Medicine Institute Pedro Kourí; CubaFil: Castañeda, Maria Elizabeth. Instituto Nacional de Salud; Colombia. Latin American Cryptococcal Study Group; BrasilFil: Arechavala, Alicia. Gobierno de la Ciudad de Buenos Aires. Hospital de Infecciosas "Dr. Francisco Javier Muñiz"; Argentina. Latin American Cryptococcal Study Group; BrasilFil: Córdoba, Susana Beatríz. Latin American Cryptococcal Study Group; Brasil. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud “Dr. C. G. Malbrán”; ArgentinaFil: Mazza, Mariana. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud “Dr. C. G. Malbrán”; Argentina. Latin American Cryptococcal Study Group; BrasilFil: Taverna, Constanza Giselle. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud “Dr. C. G. Malbrán”; Argentina. Latin American Cryptococcal Study Group; BrasilFil: Isla, Guillermina. Latin American Cryptococcal Study Group; Brasil. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud “Dr. C. G. Malbrán”; ArgentinaFil: Chiapello, Laura Silvina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina. Latin American Cryptococcal Study Group; BrasilFil: Vergara, Mario León Silva. Universidade Federal do Triangulo Mineiro; Brasil. Latin American Cryptococcal Study Group; BrasilFil: Melhem, Marcia S. C.. Governo do Estado de São Paulo. Secretaria da Saúde. Instituto Adolfo Lutz; Brasil. Latin American Cryptococcal Study Group; BrasilFil: Szeszs, Maria Walderez. Governo do Estado de São Paulo. Secretaria da Saúde. Instituto Adolfo Lutz; Brasil. Latin American Cryptococcal Study Group; BrasilFil: Martins, Marilena dos Anjos. Latin American Cryptococcal Study Group; Brasil. Governo do Estado de São Paulo. Secretaria da Saúde. Instituto Adolfo Lutz; BrasilFil: Bonfietti, Lucas Xavier. Latin American Cryptococcal Study Group; Brasil. Governo do Estado de São Paulo. Secretaria da Saúde. Instituto Adolfo Lutz; BrasilFil: Oliveira, Rogério Antonio de. Governo do Estado de São Paulo. Secretaria da Saúde. Instituto Adolfo Lutz; Brasil. Latin American Cryptococcal Study Group; BrasilFil: Oliveira, Lidiane de. Governo do Estado de São Paulo. Secretaria da Saúde. Instituto Adolfo Lutz; Brasil. Latin American Cryptococcal Study Group; BrasilFil: Santos, Dayane Christine Silva. Latin American Cryptococcal Study Group; Brasil. Governo do Estado de São Paulo. Secretaria da Saúde. Instituto Adolfo Lutz; BrasilFil: Lazera, Marcia S.. Latin American Cryptococcal Study Group; Brasil. Fundación Oswaldo Cruz; BrasilFil: Wanke, Bodo. Fundación Oswaldo Cruz; Brasil. Latin American Cryptococcal Study Group; BrasilFil: Díaz, María Cristina. Latin American Cryptococcal Study Group; Brasil. Universidad de Chile; ChileFil: Escandón, Patricia. Instituto Nacional de Salud; Colombia. Latin American Cryptococcal Study Group; BrasilFil: Noguera, María Clara. Latin American Cryptococcal Study Group; Brasil. Universidad Metropolitana; ColombiaFil: Andreu, Carlos Manuel Fernández. Latin American Cryptococcal Study Group; BrasilFil: Castril­Lón, Laura. Universidad Nacional Autónoma de México; México. Latin American Cryptococcal Study Group; BrasilFil: Bustamante, Beatriz. Hospital Cayetano Heredia. Instituto de Medicina Tropical Alexander von Humboldt; Perú. Hospital Cayetano Heredia; Perú. Latin American Cryptococcal Study Group; BrasilFil: Dolande, Maribel. Universidad Central de Venezuela; Venezuela. Latin American Cryptococcal Study Group; BrasilFil: Ferrara, Giussepe. Universidad Central de Venezuela; Venezuela. Latin American Cryptococcal Study Group; Brasi

The Case for Adopting the "Species Complex" Nomenclature for the Etiologic Agents of Cryptococcosis.

Cryptococcosis is a potentially lethal disease of humans/animals caused by Cryptococcus neoformans and Cryptococcus gattii. Distinction between the two species is based on phenotypic and genotypic characteristics. Recently, it was proposed that C. neoformans be divided into two species and C. gattii into five species based on a phylogenetic analysis of 115 isolates. While this proposal adds to the knowledge about the genetic diversity and population structure of cryptococcosis agents, the published genotypes of 2,606 strains have already revealed more genetic diversity than is encompassed by seven species. Naming every clade as a separate species at this juncture will lead to continuing nomenclatural instability. In the absence of biological differences between clades and no consensus about how DNA sequence alone can delineate a species, we recommend using "Cryptococcus neoformans species complex" and "C. gattii species complex" as a practical intermediate step, rather than creating more species. This strategy recognizes genetic diversity without creating confusion

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