Drivers of diversification in fungal pathogen populations

Abstract

To manage and treat chronic fungal diseases effectively, we require an improved understanding of their complexity. There is an increasing appreciation that chronic infection populations are often heterogeneous due to diversification and drift, even within a single microbial species. Genetically diverse populations can contribute to persistence and resistance to treatment by maintaining cells with different phenotypes capable of thriving in these dynamic environments. In chronic infections, fungal pathogens undergo prolonged challenges that can drive trait selection to convergent adapted states through restricted access to critical nutrients, assault by immune effectors, competition with other species, and antifungal drugs. This review first highlights the various genetic and epigenetic mechanisms that promote diversity in pathogenic fungal populations and provide an additional barrier to assessing the actual heterogeneity of fungal infections. We then review existing studies of evolution and genetic heterogeneity in fungal populations from lung infections associated with the genetic disease cystic fibrosis. We conclude with a discussion of open research questions that, once answered, may aid in diagnosing and treating chronic fungal infections.

Fig 1. Genetic mechanisms leading to phenotype diversification in fungal pathogens.

Functional variation can arise through genome sequence changes such as (A) single nucleotide mutations, insertions, and deletions that occur during replication (in red). Hypermutators have an increased rate of mutation due to defects in mismatch repair, (B) loss of heterozygosity (LOH) in diploid species, (C) altered gene dosage of relevant alleles can occur through aneuploidy, and (D) copy number variation (CNV). (E) Fungi are also capable of parasexual recombination through the formation of a heterokaryon [1], the merging of nuclei to form a heterozygous diploid [2], followed by recombination and a return to haploidy [3]. (F) Mobile genetic elements and the presence of a mycophage can also alter phenotype. Figure prepared using BioRender.

Fig 2. Nongenetic mechanisms that diversify fungal populations: C. albicans as an example.

In C. albicans, morphological transitions (e.g., the yeast-to-hypha and hyphae-to-yeast transitions) and epigenetic phenotypic switches are driven by transcription factors Efg1 and Wor1. These transitions diversify cell types, such as white, opaque, and grey cell types, that have distinct properties. GlcNAc, N-acetyl-glucosamine; GUT, Gastrointestinally indUced Transition cells. Figure prepared using BioRender.

Fig 3. Factors contributing to genetic and phenotypic heterogeneity in fungal populations in CF-associated lung infections.

Initial colonizers generate genotypic and phenotypic diversity (variation) through the mechanisms described in Fig 1. Selective pressures include (1) hypoxia, (2) damaging toxic metabolites including hydrogen peroxide (H₂O₂) and methylglyoxal (MG), (3) products from other coinfecting microbes, (4) interactions with the immune effectors, (5) nutritional immunity factors that, for example, restrict access to transition metals such as iron (Fe) or zinc, and (6) antifungals or other therapeutic agents. Spatial separation across lungs and lobes of the lung and the dynamic infection environment with periods of disease stability and exacerbation increases the heterogeneity of the population. Figure prepared using BioRender.