Sauters, T. J. C. | bioRxiv Science

bioRxiv2024

Pathogenicity is associated with population structure in a fungal pathogen of humans

Aspergillus flavus is a clinically and agriculturally important saprotrophic fungus responsible for severe human infections and extensive crop losses. We analyzed genomic data from 250 (95 clinical and 155 environmental) A. flavus isolates from 9 countries, including 70 newly sequenced clinical isolates, to examine population and pan-genome structure and their relationship to pathogenicity. We identified five A. flavus populations, including a new population, D, corresponding to distinct clades in the genome-wide phylogeny. Strikingly, > 75% of clinical isolates were from population D. Accessory genes, including genes within biosynthetic gene clusters, were significantly more common in some populations but rare in others. Population D was enriched for genes associated with zinc ion binding, lipid metabolism, and certain types of hydrolase activity. In contrast to the major human pathogen Aspergillus fumigatus, A. flavus pathogenicity in humans is strongly associated with population structure, making it a great system for investigating how population-specific genes contribute to pathogenicity.

evolutionary biology↗

bioRxiv2024

Strain heterogeneity in a non-pathogenic fungus highlights factors contributing to virulence

Fungal pathogens exhibit extensive strain heterogeneity, including variation in virulence. Whether closely related non-pathogenic species also exhibit strain heterogeneity remains unknown. Here, we comprehensively characterized the pathogenic potentials (i.e., the ability to cause morbidity and mortality) of 16 diverse strains of Aspergillus fischeri, a non-pathogenic close relative of the major pathogen Aspergillus fumigatus. In vitro immune response assays and in vivo virulence assays using a mouse model of pulmonary aspergillosis showed that A. fischeri strains varied widely in their pathogenic potential. Furthermore, pangenome analyses suggest that A. fischeri genomic and phenotypic diversity is even greater. Genomic, transcriptomic, and metabolomic profiling identified several pathways and secondary metabolites associated with variation in virulence. Notably, strain virulence was associated with the simultaneous presence of the secondary metabolites hexadehydroastechrome and gliotoxin. We submit that examining the pathogenic potentials of non-pathogenic close relatives is key for understanding the origins of fungal pathogenicity.

evolutionary biology↗

bioRxiv2022

Amoeba Predation of Cryptococcus: A Quantitative and Population Genomic Evaluation of the Accidental Pathogen Hypothesis

The "Amoeboid Predator-Fungal Animal Virulence Hypothesis" posits that interactions with environmental phagocytes shape the evolution of virulence traits in fungal pathogens. In this hypothesis, selection to avoid predation by amoeba inadvertently selects for traits that contribute to fungal escape from phagocytic immune cells. Here, we investigate this hypothesis in the human fungal pathogens Cryptococcus neoformans and Cryptococcus deneoformans. Applying quantitative trait locus (QTL) mapping and comparative genomics, we discovered a cross-species QTL region that is responsible for variation in resistance to amoeba predation. In C. neoformans, this same QTL was found to have pleiotropic effects on melanization, an established virulence factor. Through fine mapping and population genomic comparisons, we identified the gene encoding the transcription factor Bzp4 that underlies this pleiotropic QTL and we show that decreased expression of this gene reduces melanization and increases susceptibility to amoeba predation. Despite the joint effects of BZP4 on amoeba resistance and melanin production, we find no relationship between BZP4 genotype and escape from macrophages or virulence in murine models of disease. Our findings provide new perspectives on how microbial ecology shapes the genetic architecture of fungal virulence, and suggests the need for more nuanced models for the evolution of pathogenesis that account for the complexities of both microbe-microbe and microbe-host interactions. Author summaryA prominent hypothesis for the evolution of many environmental pathogens proposes that opportunistic pathogenesis is an "accidental" by-product of selection to survive encounters with microbial predators. Chief among the predators that have been suggested as relevant to the evolution of virulence are phagocytic amoebae. Amoebae share many characteristics with macrophages and other primary immune cells that microbial pathogens encounter during infection of animal hosts. This has led to the suggestion that amoebae may act as "training grounds" for both bacterial and fungal pathogens. In this study we test key tenets of the accidental pathogen hypothesis by examining two related questions: "Do alleles important for survival in the face of amoeba predation correspond to known virulence genes? And does genetic variation that increases resistance to amoeba predation increase virulence potential?" We carried out quantitative trait locus (QTL) mapping in two species of the human fungal pathogen Cryptococcus and identified an orthologous QTL, shared by the two species, where allelic variation is a key predictor of resistance to amoeba predation. In C. neoformans we show that this QTL corresponds to a deletion upstream of a transcription factor gene, BZP4. Variation at BZP4 also predicts melanin synthesis, another trait implicated in Cryptococcus virulence. Although BZP4 genotype is a strong predictor of resistance to amoeba predation, we find no correlation between genetic variation at this locus and the ability to proliferate in macrophages or to kill animal hosts. Our findings suggest that the evolutionary landscape of fungal virulence is complex, and highlights the importance of accounting for natural genetic variation when evaluating evolutionary hypotheses.

genomics↗