Genomic and Phenotypic Variation in Morphogenetic Networks of Two Candida albicans Isolates Subtends Their Different Pathogenic Potential

Abstract

The transition from commensalism to pathogenicity of Candida albicans reflects both the host inability to mount specific immune responses and the microorganism’s dimorphic switch efficiency. In this study, we used whole genome sequencing and microarray analysis to investigate the genomic determinants of the phenotypic changes observed in two C. albicans clinical isolates (YL1 and YQ2). In vitro experiments employing epithelial, microglial, and peripheral blood mononuclear cells were thus used to evaluate C. albicans isolates interaction with first line host defenses, measuring adhesion, susceptibility to phagocytosis, and induction of secretory responses. Moreover, a murine model of peritoneal infection was used to compare the in vivo pathogenic potential of the two isolates. Genome sequence and gene expression analysis of C. albicans YL1 and YQ2 showed significant changes in cellular pathways involved in environmental stress response, adhesion, filamentous growth, invasiveness, and dimorphic transition. This was in accordance with the observed marked phenotypic differences in biofilm production, dimorphic switch efficiency, cell adhesion, invasion, and survival to phagocyte-mediated host defenses. The mutations in key regulators of the hyphal growth pathway in the more virulent strain corresponded to an overall greater number of budding yeast cells released. Compared to YQ2, YL1 consistently showed enhanced pathogenic potential, since in vitro, it was less susceptible to ingestion by phagocytic cells and more efficient in invading epithelial cells, while in vivo YL1 was more effective than YQ2 in recruiting inflammatory cells, eliciting IL-1β response and eluding phagocytic cells. Overall, these results indicate an unexpected isolate-specific variation in pathways important for host invasion and colonization, showing how the genetic background of C. albicans may greatly affect its behavior both in vitro and in vivo. Based on this approach, we propose that the co-occurrence of changes in sequence and expression in genes and pathways driving dimorphic transition and pathogenicity reflects a selective balance between traits favoring dissemination of the pathogen and traits involved in host defense evasion. This study highlights the importance of investigating strain-level, rather than species level, differences, when determining fungal–host interactions and defining commensal or pathogen behavior.

Population genomics reveals evolution and variation ofSaccharomyces cerevisiaein the human and insects gut

“…The standard Illumina protocol with minor modifications was followed for the creation of short‐insert paired‐end libraries (Illumina Inc., Cat. # PE‐930‐1001), as reported in Cavalieri and colleagues ().…”

“…Written informed consent was obtained for all the blood donors. Blood separation, cell culture and stimulation were performed as previously described (Cavalieri et al ., ). Challenges were carried out by culturing PBMCs (10 5 cells/ml) with or without (negative control) live yeasts (10 6 cells/ml) in RPMI 1640 medium supplemented with 10% heat‐inactivated foetal bovine serum, 2 mM l ‐glutamine, at 37 °C under 5% CO 2 .…”

“…Direct contact of immune cells with fungi leads to activation of antigen presenting cells and subsequent priming of adequate proinflammatory T helper (Th) response or regulatory T cells (Treg) response (Romani, 2011). Previous studies showed a fungal strain-dependent variation of immune recognition and consequent immune reactivity depending on strain features (Marakalala et al, 2013;Rizzetto et al, 2013;Smith et al, 2014;Cavalieri et al, 2018). Hence, to characterize the immune response elicited by human gut S. cerevisiae isolates, peripheral blood mononuclear cells (PBMCs) were challenged with HG isolates.…”

“…Differences among quantitative phenotypes were evaluated through Mann-Whitney U test. Additionally, cell wall sugar composition was assessed through cell wall extraction and sugar quantification (glucose for glucan content determination, mannose and glucosamine for chitin content) by using high-performance anion-exchange chromatography coupled with pulsed electrochemical detection (HPAEC-PAD), as previously described (Cavalieri et al, 2018). Aiming at the characterization of the immune response elicited by the human gut isolates, peripheral blood mononuclear cells (PBMCs) were challenged with S. cerevisiae cells.…”

Virulence phenotypes result from an interaction between pathogen ploidy and genetic background

“…These results indicate that virulence is not simply a binary 'avirulent/virulent' classification, but rather a complex trait and we need to start dissecting fungal virulence from this perspective. Recently, genome analysis of clinical isolates revealed genomic features that differ between clinical isolates and SC5314, the laboratory reference strain of C. albicans, and/or identify genetic determinants of antifungal drug resistance 21,37,[50][51][52][53] . Only a small number have attempted to identify the genetic loci underpinning virulence and only two genes were identified and validated, EFG1 20,51 and PHO100 46 .…”