An expanded toolkit of drug resistance cassettes for Candida glabrata, Candida auris, and Candida albicans leads to new insights into the ergosterol pathway

In Vitro and In Vivo Anti-Candida albicans Activity of a Scorpion-Derived Peptide

The increasing infection and drug resistance frequency has encouraged the exploration of new and effective anti-Candida albicans agents. In this study, CT-K3K7, a scorpion antimicrobial peptide derivative, effectively inhibit the growth of C. albicans. CT-K3K7 killed C. albicans cells in a dose-dependent manner, mainly by damaging the plasma membrane. CT-K3K7 could also disrupt the nucleus and interact with nucleic acid. Moreover, CT-K3K7 induced C. albicans cells necrosis via a reactive oxygen species (ROS)-related pathway. Furthermore, CT-K3K7 inhibited the hyphal and biofilm formation of C. albicans. In the mouse skin subcutaneous infection model, CT-K3K7 significantly prevented skin abscess formation and reduced the number of C. albicans cells recovered from the infection area. Taken together, CT-K3K7 has the potential to be a therapeutic for C. albicans skin infections.

Targeting fungal lipid synthesis for antifungal drug development and potentiation of contemporary antifungals

Two of the three most commonly used classes of antifungal drugs target the fungal membrane through perturbation of sterol biosynthesis or function. In addition to these triazole and polyene antifungals, recent research is identifying new antifungal molecules that perturb lipid biosynthesis and function. Here, we review fungal lipid biosynthesis pathways and their potential as targets for antifungal drug development. An emerging goal is discovering new molecules that potentiate contemporary antifungal drugs in part through perturbation of lipid form and function.

The multidrug-resistant Candida auris, Candida haemulonii complex and phylogenetic related species: Insights into antifungal resistance mechanisms

The rise of multidrug-resistant (MDR) fungal pathogens poses a serious global threat to human health. Of particular concern are Candida auris, the Candida haemulonii complex (which includes C. haemulonii sensu stricto, C. duobushaemulonii and C. haemulonii var. vulnera), and phylogenetically related species, including C. pseudohaemulonii and C. vulturna. These emerging, widespread, and opportunistic pathogens have drawn significant attention due to their reduced susceptibility to commonly used antifungal agents, particularly azoles and polyenes, and, in some cases, therapy-induced resistance to echinocandins. Notably, C. auris is classified in the critical priority group on the World Health Organization's fungal priority pathogens list, which highlights fungal species capable of causing systemic infections with significant mortality and morbidity risks as well as the challenges posed by their MDR profiles, limited treatment and management options. The mechanisms underlying antifungal resistance within these emerging fungal species is still being explored, but some advances have been achieved in the past few years. In this review, we compile current literature on the distribution of susceptible and resistant clinical strains of C. auris, C. haemulonii complex, C. pseudohaemulonii and C. vulturna across various antifungal classes, including azoles (fluconazole, voriconazole, itraconazole), polyenes (amphotericin B), echinocandins (caspofungin, micafungin, anidulafungin), and pyrimidine analogues (flucytosine). We also outline the main antifungal resistance mechanisms identified in planktonic cells of these yeast species. Finally, we explore the impact of biofilm formation, a classical virulence attribute of fungi, on antifungal resistance, highlighting the resistance mechanisms associated with this complex microbial structure that have been uncovered to date.

The evolution of antifungal therapy: Traditional agents, current challenges and future perspectives

Fungal infections kill more than 3 million people every year. This high number reflects the significant challenges that treating these diseases worldwide presents. The current arsenal of antifungal drugs is limited and often accompanied by high toxicity to patients, elevated treatment costs, increased frequency of resistance rates, and the emergence of naturally resistant species. These treatment challenges highlight the urgency of developing new antifungal therapies, which could positively impact millions of lives each year globally. Our review offers an overview of the antifungal drugs currently available for treatment, presents the status of new antifungal drugs under clinical study, and explores ahead to future candidates that aim to help address this important global health issue.

Candida glabrata: A Tale of Stealth and Endurance

Candida (Nakaseomyces) glabrata, an opportunistic human fungal pathogen, causes mucosal and deep-seated infections in immunocompromised individuals. Recently designated as a high-priority fungal pathogen by the World Health Organization (WHO), C. glabrata exhibits low inherent susceptibility to azole antifungals. In addition, about 10% clinical isolates of C. glabrata display co-resistance to both azole and echinocandin drugs. Molecular mechanisms of antifungal resistance and virulence in C. glabrata are currently being delineated in-depth. This Review provides an overview of the epidemiology, biology, drug resistance, tools and host model systems for C. glabrata. Additionally, we discuss the immune evasion strategies that aid C. glabrata in establishing infections in the host. Overall, this Review aims to contribute to ongoing efforts to raise awareness of human pathogenic fungi, the growing threat of antifungal drug resistance and the unmet need for novel antifungal therapies, with an ultimate goal of improving clinical outcomes of affected individuals.

Unraveling the secrets: Evolution of resistance mediated by membrane proteins

Membrane protein-mediated resistance is a multidisciplinary challenge that spans fields such as medicine, agriculture, and environmental science. Understanding its complexity and devising innovative strategies are crucial for treating diseases like cancer and managing resistant pests in agriculture. This paper explores the dual nature of resistance mechanisms across different organisms: On one hand, animals, bacteria, fungi, plants, and insects exhibit convergent evolution, leading to the development of similar resistance mechanisms. On the other hand, influenced by diverse environmental pressures and structural differences among organisms, they also demonstrate divergent resistance characteristics. Membrane protein-mediated resistance mechanisms are prevalent across animals, bacteria, fungi, plants, and insects, reflecting their shared survival strategies evolved through convergent evolution to address similar survival challenges. However, variations in ecological environments and biological characteristics result in differing responses to resistance. Therefore, examining these differences not only enhances our understanding of adaptive resistance mechanisms but also provides crucial theoretical support and insights for addressing drug resistance and advancing pharmaceutical development.

Probing gene function in Candida albicans wild-type strains by Cas9-facilitated one-step integration of two dominant selection markers: a systematic analysis of recombination events at the target locus

The adaptation of gene deletion methods based on the CRISPR-Cas9 system has facilitated the genetic manipulation of the pathogenic yeast Candida albicans, because homozygous mutants of this diploid fungus can now be generated in a single step, allowing the rapid screening of candidate genes for their involvement in a phenotype of interest. However, the Cas9-mediated double-strand breaks at the target site may result in an undesired loss of heterozygosity (LOH) on the affected chromosome and cause phenotypic alterations that are not related to the function of the investigated gene. In our present study, we harnessed Cas9-facilitated gene deletion to probe a set of genes that are constitutively overexpressed in strains containing hyperactive forms of the transcription factor Mrr1 for a possible contribution to the fluconazole resistance of such strains. To this aim, we used gene deletion cassettes containing two different dominant selection markers, caSAT1 and HygB, which confer resistance to nourseothricin and hygromycin, respectively, for simultaneous genomic integration in a single step, hypothesizing that this would minimize undesired LOH events at the target locus. We found that selection for resistance to both nourseothricin and hygromycin strongly increased the proportion of homozygous deletion mutants among the transformants compared with selection on media containing only one of the antibiotics, but it did not avoid undesired LOH events. Our results demonstrate that LOH on the target chromosome is a significant problem when using Cas9 for the generation of C. albicans gene deletion mutants, which demands a thorough examination of recombination events at the target site.

IMPORTANCE

Candida albicans is one of the medically most important fungi and a model organism to study fungal pathogenicity. Investigating gene function in this diploid yeast has been facilitated by the adaptation of gene deletion methods based on the bacterial CRISPR-Cas9 system, because they enable the generation of homozygous mutants in a single step. We found that, in addition to increasing the efficiency of gene replacement by selection markers, the Cas9-mediated double-strand breaks also result in frequent loss of heterozygosity on the same chromosome, even when two different selection markers were independently integrated into the two alleles of the target gene. Since loss of heterozygosity for other genes can result in phenotypic alterations that are not caused by the absence of the target gene, these findings show that it is important to thoroughly analyze recombination events at the target locus when using Cas9 to generate gene deletion mutants in C. albicans.

Development of a Shuttle Vector That Transforms at High Frequency for the Emerging Human Fungal Pathogen: Candida auris

Routine molecular manipulation of any organism is inefficient and difficult without the existence of a plasmid. Although transformation is possible in C. auris, no plasmids are available that can serve as cloning or shuttle vectors. C. auris centromeres have been well characterized but have not been explored further as molecular tools. We tested C. auris centromeric sequences to identify which, if any, could be used to create a plasmid that was stably maintained after transformation. We cloned all seven C. auris centromeric sequences and tested them for transformation frequency and stability. Transformation frequency varied significantly; however, one was found to transform at a very high frequency. A 1.7 Kb subclone of this sequence was used to construct a shuttle vector. The vector was stable with selection and maintained at ~1 copy per cell but could be easily lost when selection was removed, which suggested that the properties of the centromeric sequence were more Autonomously Replicating Sequence (ARS)-like than centromere-like when part of a plasmid. Rescue of this plasmid from transformed C. auris cells into E. coli revealed that it remained intact after the initial C. auris transformation, even when carrying large inserts. The plasmid was found to be able to transform all four clades of C. auris, with varying frequencies. This plasmid is an important new reagent in the C. auris molecular toolbox, which will enhance the investigation of this human fungal pathogen.

A CUG codon-adapted anchor-away toolkit for functional analysis of genes in Candida albicans

Promoter shutoff of essential genes in the diploid Candida albicans has often been insufficient to create tight, conditional null alleles due to leaky expression and has been a stumbling block in pathogenesis research. Moreover, homozygous deletion of non-essential genes has often been problematic due to the frequent aneuploidy in the mutant strains. Rapid, conditional depletion of essential genes by the anchor-away strategy has been successfully employed in Saccharomyces cerevisiae and other model organisms. Here, rapamycin mediates the dimerization of human FK506-binding protein (FKBP12) and FKBP12-rapamycin-binding (FRB) domain-containing target protein, resulting in relocalization to altered sub-cellular locations. In this work, we used the ribosomal protein Rpl13 as the anchor and took two nuclear proteins as targets to construct a set of mutants in a proof-of-principle approach. We first constructed a rapamycin-resistant C. albicans strain by introducing a dominant mutation in the CaTOR1 gene and a homozygous deletion of RBP1, the ortholog of FKBP12, a primary target of rapamycin. The FKBP12 and the FRB coding sequences were then CUG codon-adapted for C. albicans by site-directed mutagenesis. Anchor-away strains expressing the essential TBP1 gene or the non-essential SPT8 gene as FRB fusions were constructed. We found that rapamycin caused rapid cessation of growth of the TBP-AA strain within 15 minutes and the SPT8-AA strain phenocopied the constitutive filamentous phenotype of the spt8Δ/spt8Δ mutant. Thus, the anchor-away toolbox for C. albicans developed here can be employed for genome-wide analysis to identify gene function in a rapid and reliable manner, further accelerating anti-fungal drug development in C. albicans.

IMPORTANCE

Molecular genetic studies thus far have identified ~27% open-reading frames as being essential for the vegetative growth of Candida albicans in rich medium out of a total 6,198 haploid set of open reading frames. However, a major limitation has been to construct rapid conditional alleles of essential C. albicans genes with near quantitative depletion of encoded proteins. Here, we have developed a toolbox for rapid and conditional depletion of genes that would aid studies of gene function of both essential and non-essential genes.