A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands.

Rhys A Farrer,Matthew C Fisher,Duncan Chanda,Lucy Van Dorp,Yun C Chang,Hannah M Edwards,Thomas R Sewell,Kyung J Kwon-Chung,Terrance Shea,Geoffrey Kwenda,Michael J Davis,Christina A Cuomo,Mathieu Vanhove,Wieland Meyer,Francois Balloux,Miwha Chang,Dong-Hoon Yang

doi:10.1128/mbio.02306-19

Abstract

We discovered a new lineage of the globally important fungal pathogen Cryptococcus gattii on the basis of analysis of six isolates collected from three locations spanning the Central Miombo Woodlands of Zambia, Africa. All isolates were from environments (middens and tree holes) that are associated with a small mammal, the African hyrax. Phylogenetic and population genetic analyses confirmed that these isolates form a distinct, deeply divergent lineage, which we name VGV. VGV comprises two subclades (A and B) that are capable of causing mild lung infection with negligible neurotropism in mice. Comparing the VGV genome to previously identified lineages of C. gattii revealed a unique suite of genes together with gene loss and inversion events. However, standard URA5 restriction fragment length polymorphism (RFLP) analysis could not distinguish between VGV and VGIV isolates. We therefore developed a new URA5 RFLP method that can reliably identify the newly described lineage. Our work highlights how sampling understudied ecological regions alongside genomic and functional characterization can broaden our understanding of the evolution and ecology of major global pathogens.IMPORTANCECryptococcus gattii is an environmental pathogen that causes severe systemic infection in immunocompetent individuals more often than in immunocompromised humans. Over the past 2 decades, researchers have shown that C. gattii falls within four genetically distinct major lineages. By combining field work from an understudied ecological region (the Central Miombo Woodlands of Zambia, Africa), genome sequencing and assemblies, phylogenetic and population genetic analyses, and phenotypic characterization (morphology, histopathological, drug-sensitivity, survival experiments), we discovered a hitherto unknown lineage, which we name VGV (variety gattii five). The discovery of a new lineage from an understudied ecological region has far-reaching implications for the study and understanding of fungal pathogens and diseases they cause.

Highlights

We discovered a new lineage of the globally important fungal pathogen Cryptococcus gattii on the basis of analysis of six isolates collected from three locations spanning the Central Miombo Woodlands of Zambia, Africa
We discovered a new lineage of Cryptococcus gattii from a panel of 32 genomesequenced isolates recovered from Southern tree hyrax (Dendrohyrax arboreus) middens, midden soil, or tree holes from the Central Zambezian Miombo Woodland ecoregion, a densely forested ecoregion that covers much of Central and East Africa (Fig. 1) (Table 1; see Table S1 in the supplemental material)
All VGV isolates were identified as serotype B, which encompasses strains from VGI, VGII, the VGIIIa subgroup, and rare isolates among VGIV strains

Summary

Introduction

We discovered a new lineage of the globally important fungal pathogen Cryptococcus gattii on the basis of analysis of six isolates collected from three locations spanning the Central Miombo Woodlands of Zambia, Africa. By combining field work from an understudied ecological region (the Central Miombo Woodlands of Zambia, Africa), genome sequencing and assemblies, phylogenetic and population genetic analyses, and phenotypic characterization (morphology, histopathological, drugsensitivity, survival experiments), we discovered a hitherto unknown lineage, which we name VGV (variety gattii five). Subsequent discovery of two distinct sexual cycles produced by the isolates of serotypes A and D versus serotypes B and C [7, 8] and phylogenetic analysis using various gene sequences [9,10,11] confirmed these complexes to be genetically divergent enough to be considered separate species. A fifth genotype was described on the basis of a single strain but with several different designations, including clade B (based on multilocus sequence typing [MLST]), VGIIIc/VGIV, and C. decagattii [17, 18] Elevation of these five lineages to separate species has been proposed previously [17]. We present a new, improved genome assembly and gene sets for C. decagattii [17] which we confirmed for the first time to represent a separate lineage and which we name “VGVI” for consistency with the other lineages

Methods

Results

Conclusion