Host-Induced Genome Instability Rapidly Generates Phenotypic Variation across Candida albicans Strains and Ploidy States

Abstract

Candida albicans is an opportunistic fungal pathogen of humans that is typically diploid yet has a highly labile genome tolerant of large-scale perturbations including chromosomal aneuploidy and loss-of-heterozygosity events. The ability to rapidly generate genetic variation is crucial for C. albicans to adapt to changing or stressful environments, like those encountered in the host. Genetic variation occurs via stress-induced mutagenesis or can be generated through its parasexual cycle, in which tetraploids arise via diploid mating or stress-induced mitotic defects and undergo nonmeiotic ploidy reduction. However, it remains largely unknown how genetic background contributes to C. albicans genome instability in vitro or in the host environment. Here, we tested how genetic background, ploidy, and the host environment impacts C. albicans genome stability. We found that host association induced both loss-of-heterozygosity events and genome size changes, regardless of genetic background or ploidy. However, the magnitude and types of genome changes varied across C. albicans strain background and ploidy state. We then assessed if host-induced genomic changes resulted in fitness consequences on growth rate and nonlethal virulence phenotypes and found that many host-derived isolates significantly changed relative to their parental strain. Interestingly, diploid host-associated C. albicans predominantly decreased host reproductive fitness, whereas tetraploid host-associated C. albicans increased host reproductive fitness. Together, these results are important for understanding how host-induced genomic changes in C. albicans alter its relationship with the host. IMPORTANCE Candida albicans is an opportunistic fungal pathogen of humans. The ability to generate genetic variation is essential for adaptation and is a strategy that C. albicans and other fungal pathogens use to change their genome size. Stressful environments, including the host, induce C. albicans genome instability. Here, we investigated how C. albicans genetic background and ploidy state impact genome instability, both in vitro and in a host environment. We show that the host environment induces genome instability, but the magnitude depends on C. albicans genetic background. Furthermore, we show that tetraploid C. albicans is highly unstable in host environments and rapidly reduces in genome size. These reductions in genome size often resulted in reduced virulence. In contrast, diploid C. albicans displayed modest host-induced genome size changes, yet these frequently resulted in increased virulence. Such studies are essential for understanding how opportunistic pathogens respond and potentially adapt to the host environment.

Tetraploidy accelerates adaption under drug-selection in a fungal pathogen

“…In addition to higher mutation rates, tetraploid cells also frequently undergo random chromosome loss and reduce in genome size under a diverse set of growth conditions in vitro and in vivo (Bennett and Johnson 2003; Forche et al 2008; Hickman et al 2015; Gerstein et al 2017; Avramovska and Hickman 2019; Smith and Hickman 2020). Interestingly, we found that many of the tetraploid-evolved lines rapidly reduced in genome size by day 10, a timepoint prior to when we first observed any detectable caspofungin adaptation (Figure 2A).…”

Host defense mechanisms induce genome instability in an opportunistic fungal pathogen

“…We, and others, have shown that nematode and murine host environments induce C. albicans genome instability compared to in vitro [14][15][16][17][18] , but the specific host attributes driving genome instability have yet to be elucidated. Here, we tested whether components of host innate immune function contributed to host-associated genome instability by comparing the frequency of loss-of-heterozygosity (LOH) between C. albicans extracted from healthy and immunocompromised hosts (Fig.…”

“…This genetic variation may be a direct consequence of the stressors C. albicans encounters in the host which include immune stressors and other microbes. Recent work has demonstrated the host environment elevates genome instability in C. albicans similar to in vitro stressors [14][15][16][17][18] . However, the specific host components that generate this instability is largely unknown.…”

“…This suggests that the host environment rapidly generates genetic variation. Recent studies involving murine infection models have found that when exposed to different host niches, C. albicans has higher levels of genetic variation compared to in vitro [14][15][16][17] . Similar to clinical isolates, laboratory C. albicans often had large-scale genomic changes including aneuploidy and LOH following murine infection [14][15][16] .…”

“…Similar to clinical isolates, laboratory C. albicans often had large-scale genomic changes including aneuploidy and LOH following murine infection [14][15][16] . In addition to murine models, Caenorhabditis elegans has been used as a model to assess C. albicans genome stability and strains that differ in genetic background and ploidy have elevated host-associated genome instability 17 . It is clear that host environments perturbations may be a way in which C. albicans transitions from commensal to pathogenic in immunocompetent hosts.…”