Ancient Dispersal of the Human Fungal Pathogen Cryptococcus gattii from the Amazon Rainforest

Ferry Hagen,Leszek P Pryszcz,Elizabeth Castañeda,Hansong Ma,Itzhack Polacheck,Robin C May,Hans L Hoogveld,Dieter Deforce,Kerstin Voelz,E Rhiannon Pursall,Sarah Kagan,Jacques F Meis,Leen Stougie,Karen H Bartlett,Gunnar W Klau,Corné H W Klaassen,Wieland Meyer,Filip Van Nieuwerburgh,Teun Boekhout,Toni Gabaldón,Paulo Cézar Ceresini ,Márcia Dos Santos Lazéra ,Steven Kelk ,Leo Van Iersel

doi:10.1371/journal.pone.0071148

Abstract

Over the past two decades, several fungal outbreaks have occurred, including the high-profile ‘Vancouver Island’ and ‘Pacific Northwest’ outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy humans and animals. Over the same time period, C. gattii was the cause of several additional case clusters at localities outside of the tropical and subtropical climate zones where the species normally occurs. In every case, the causative agent belongs to a previously rare genotype of C. gattii called AFLP6/VGII, but the origin of the outbreak clades remains enigmatic. Here we used phylogenetic and recombination analyses, based on AFLP and multiple MLST datasets, and coalescence gene genealogy to demonstrate that these outbreaks have arisen from a highly-recombining C. gattii population in the native rainforest of Northern Brazil. Thus the modern virulent C. gattii AFLP6/VGII outbreak lineages derived from mating events in South America and then dispersed to temperate regions where they cause serious infections in humans and animals.

Highlights

During the past two decades, fungal outbreaks caused by previously rare genotypes or even novel species have emerged that affect humans, mammals and amphibians
We performed additional sequencing and re-analyzed recently published MLST data [3,8] by expanding the geographic range through the inclusion of more strains from South America. These analyses revealed that South American C. gattii AFLP6/VGII strains represent the ancestral lineages within the global population, which is in agreement with the observed high genetic diversity at that locality
The historical population structure of C. gattii AFLP6/VGII was assessed by application of coalescence gene genealogy analysis using the SCAR-MLST dataset which was analyzed after removing 59 homoplasious sites in the 3,357 nucleotides alignment which resulted in 32 haplotypes compared to 49 sequence types (STs) when all recombination breakpoints remained intact

Summary

Introduction

During the past two decades, fungal outbreaks caused by previously rare genotypes or even novel species have emerged that affect humans, mammals and amphibians. With the Vancouver Island outbreak, there have been clusters of AFLP6/VGII C. gattii-related disease reported from captive psittacine birds in Sao Paulo, Brazil (this study; [8]), a higher incidence of C. gattii AFLP6/VGII infections among immunocompetent children in Northern Brazil [11,12,13] and a case cluster among sheep in Western Australia [4,14] All these outbreaks and case clusters are caused by genotype AFLP6/VGII strains, one of the five known genotypes within the C. gattii complex [6,7,15,16,17]. We performed additional sequencing and re-analyzed recently published MLST data [3,8] by expanding the geographic range through the inclusion of more strains from South America These analyses revealed that South American C. gattii AFLP6/VGII strains represent the ancestral lineages within the global population, which is in agreement with the observed high genetic diversity at that locality. We provide strong evidence that South America is the cradle for the global population, including the expanding C. gattii AFLP6/VGII outbreaks in British Columbia (Canada) and in the Pacific Northwest of the USA [3,6,7]

Results

Discussion

Materials and Methods