Mutations in TAC1 and ERG11 are major drivers of triazole antifungal resistance in clinical isolates of Candida parapsilosis

Unravelling fungal genome editing revolution: pathological and biotechnological application aspects

Fungi represent a broad and evolutionarily unique group within the eukaryotic domain, characterized by extensive ecological adaptability and metabolic versatility. Their inherent biological intricacy is evident in the diverse and dynamic relationships they establish with various hosts and environmental niches. Notably, fungi are integral to disease processes and a wide array of biotechnological innovations, highlighting their significance in medical, agricultural, and industrial domains. Recent advances in genetic engineering have revolutionized fungal research, with CRISPR/Cas emerging as the most potent and versatile genome editing platform. This technology enables precise manipulation of fungal genomes, from silencing efflux pump genes in Candida albicans (enhancing antifungal susceptibility) to targeting virulence-associated sirtuins in Aspergillus fumigatus (attenuating pathogenicity). Its applications span gene overexpression, multiplexed mutagenesis, and secondary metabolite induction, proving transformative for disease management and biotechnological innovation. CRISPR/Cas9's advantages-unmatched precision, cost-effectiveness, and therapeutic potential-are tempered by challenges like off-target effects, ethical dilemmas, and regulatory gaps. Integrating nanoparticle delivery systems and multi-omics approaches may overcome technical barriers, but responsible innovation requires addressing these limitations. CRISPR-driven fungal genome editing promises to redefine solutions for drug-resistant infections, sustainable bioproduction, and beyond as the field evolves. In conclusion, genome editing technologies have enhanced our capacity to dissect fungal biology and expanded fungi's practical applications across various scientific and industrial domains. Continued innovation in this field promises to unlock the vast potential of fungal systems further, enabling more profound understanding and transformative biotechnological progress.

Genotypic Diversity and Molecular Basis of Fluconazole Resistance in Candida parapsilosis Clinical Isolates Collected Over 7 Years in a Tertiary-Care Hospital in North India

BACKGROUND

The recent rise in the global incidence of fluconazole resistance in C. parapsilosis has become a significant public health concern. Epidemiological studies suggest that fluconazole resistance in C. parapsilosis spreads through endemic clones. We, therefore, investigated the molecular epidemiology of fluconazole-resistant C. parapsilosis in our centre.

METHODS

C. parapsilosis isolates from 2016 through 2022 were investigated for antifungal susceptibility. Fluconazole-resistant isolates were analysed for ERG11 mutation using Sanger sequencing. Gene expression profiles of ERG11, CDR1 and MDR1 were assessed by real-time qPCR. The epidemiological relationship of resistant and susceptible isolates of C. parapsilosis was investigated using short tandem repeat typing. Additionally, biofilm production and cell wall ergosterol contents were also quantified and compared.

RESULTS

Among 572 C. parapsilosis isolates, 48 (8.4%) were resistant to fluconazole. Of 28 recoverable resistant isolates, 17.9% (5/28) were wild-type and 82.1% (23/28) harboured the following ERG11 mutations: Y132F (n = 3), K143R (n = 10) and K143R + R398I (10/28). Significant fold-changes were observed in ERG11 (p = 0.037) and MDR1 (p = 0.008) gene expressions in fluconazole resistant compared to susceptible isolates. Contrary to global reports, STR typing suggested a limited clonal transmission of resistant C. parapsilosis with multiple introductions of resistant isolates in our centre. On fluconazole exposure, ergosterol content significantly increased (p < 0.01) in resistant isolates, particularly in isolates harbouring ERG11K143R + R398I mutations. In contrast, fluconazole-susceptible isolates formed comparatively higher baseline biofilm (p < 0.05) than resistant isolates with ERG11K143R mutation.

CONCLUSION

The current study underscores the need for continuous molecular surveillance and tailored therapeutic options for effective management of fluconazole resistance in C. parapsilosis.

2-Nonanol produced by Bacillus velezensis EM-1: a new biocontrol agent against tobacco brown spot

Tobacco brown spot disease, caused by Alternaria alternata, poses a significant threat to crop production. Traditional control methods, particularly chemical fungicides, have raised concerns about environmental impact and resistance. Although our previous research has shown that volatile compounds produced by Bacillus velezensis EM-1 can effectively suppress A. alternata, the specific antifungal compounds and their mechanisms remain unclear. In this study, exposure to the volatiles from strain EM-1 significantly inhibited the mycelial growth and spore germination of A. alternata, with 2-nonanol identified as the most potent antifungal compound. Fumigation experiments revealed that 2-nonanol exhibited strong dose-dependent toxicity, with an EC50 of 0.1055 μL/cm3 and a minimum inhibitory concentration of 0.2166 μL/cm3. In vivo experiments on tobacco leaves confirmed that 2-nonanol effectively reduced tobacco brown spot disease incidence and slowed lesion expansion. Transcriptome analysis indicated that 2-nonanol downregulated the expression of genes encoding D-glucose synthesis in carbon metabolism, which limited energy acquisition by A. alternata. Moreover, the expression of antioxidant enzymes, including superoxide dismutase (SOD) and catalase (CAT), was markedly suppressed by 2-nonanol, thereby exacerbating cellular damage induced by oxidative stress. These findings suggest that 2-nonanol holds potential as a biocontrol agent for managing tobacco brown spot disease, underscoring the promising role of volatile organic compounds (VOCs) in the development of environmentally friendly biocontrol products.

Resistance to Azoles in Candida parapsilosis Isolates from Spain Is Associated with an Impairment in Filamentation and Biofilm Formation

In recent years, there has been an increase in the incidence of fluconazole-non-susceptible (FNS) Candida parapsilosis. The reasons why these strains are able to colonize hospitals remain unknown. It is also unclear whether these strains exhibit resistance to the disinfectants used in hospitals, facilitating their spread. For these reasons, in this work, we aimed to investigate whether fluconazole resistance was associated with virulence traits and the resistance of these strains to common hospital disinfectants. The general conclusion of the study was that more than 95% of the FNS strains, regardless of the resistance mutation they carried, had filamentation problems, whereas around 75% of the susceptible strains formed pseudohyphae and were capable of filamentation. This 95% of the FNS strains did not form pseudohyphae, did not invade agar, and did not form biofilms, while the susceptible strains exhibited the opposite behaviour. Through microfluidics experiments, we observed that both the susceptible and FNS strains were capable of adhering to a plastic surface under dynamic conditions, but the FNS strains formed unstable aggregates that did not remain attached to the surface, confirming the filamentation defect of these strains. In the second part of the study, we observed that FNS strains are susceptible to clinical disinfectants, although they presented a slight resistance to some of them, such as chlorhexidine, compared to susceptible isolates. In this work, we address important aspects to understand the dissemination of FNS strains in clinical outbreaks.

Adaptation of Candida albicans to specific host environments by gain-of-function mutations in transcription factors

The yeast Candida albicans is usually a harmless member of the normal microbiota in healthy persons but is also a major fungal pathogen that can colonize and infect almost every human tissue. A successful adaptation to environmental changes encountered in different host niches requires an appropriate regulation of gene expression. The zinc cluster transcription factors are the largest family of transcriptional regulators in C. albicans and are involved in the control of virtually all aspects of its biology. Under certain circumstances, mutations in these transcription factors that alter their activity and the expression of their target genes confer a selective advantage, which results in the emergence of phenotypically altered variants that are better adapted to new environmental challenges. This review describes how gain-of-function mutations in different zinc cluster transcription factors enable C. albicans to overcome antifungal therapy and to successfully establish itself in specific host niches.

High-Resolution Melting Assay to Detect the Mutations That Cause the Y132F and G458S Substitutions at the ERG11 Gene Involved in Azole Resistance in Candida parapsilosis

BACKGROUND

Candida parapsilosis is a pathogenic yeast that has reduced susceptibility to echinocandins and ranks as the second or third leading cause of candidaemia, depending on the geographical region. This yeast often causes nosocomial infections, which are frequently detected as outbreaks. In recent years, resistance to azoles in C. parapsilosis has increased globally, primarily due to the accumulation of mutations in the ERG11 gene.

OBJECTIVES

In this study, we have developed an assay based on real-time PCR and high-resolution melting (HRM) curve analysis to detect two of the most prevalent mutations at ERG11 that confer resistance to fluconazole (Y132F and G458S).

METHODS

We designed allele-specific oligonucleotides that selectively bind to either the wild type or mutated sequences and optimised the conditions to ensure amplification of the specific allele, followed by detection via high-resolution melting (HRM) analysis.

RESULTS

The designed oligonucleotides to detect the Erg11Y132F and Erg11G458S mutations produced specific amplification of either WT or mutated alleles. We conducted a duplex real-time PCR combining oligonucleotides for the wild-type sequences in one mix, and oligonucleotides for the mutated alleles in another. Following this, we performed an analysis of the HRM curve to identify the amplified allele in each case. This technique was blindly evaluated on a set of 114 C. parapsilosis isolates, all of which were unequivocally identified using our approach.

CONCLUSION

This technique offers a new method for the early detection of azole resistance mechanism in C. parapsilosis.

Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches

Invasive fungal diseases (IFDs) comprise a growing healthcare burden, especially given the expanding population of immunocompromised hosts. Early diagnosis of IFDs is required to optimise therapy with antifungals, especially in the setting of rising rates of antifungal resistance. Molecular techniques including nucleic acid amplification tests and whole genome sequencing have potential to offer utility in overcoming limitations with traditional phenotypic testing. However, standardisation of methodology and interpretations of these assays is an ongoing undertaking. The utility of targeted Aspergillus detection has been well-defined, with progress in investigations into the role of targeted assays for Candida, Pneumocystis, Cryptococcus, the Mucorales and endemic mycoses. Likewise, whilst broad-range polymerase chain reaction assays have been in use for some time, pathology stewardship and optimising diagnostic yield is a continuing exercise. As costs decrease, there is also now increased access and experience with whole genome sequencing, including metagenomic sequencing, which offers unparalleled resolution especially in the investigations of potential outbreaks. However, their role in routine diagnostic use remains uncommon and standardisation of techniques and workflow are required for wider implementation.

Precise genome editing underlines the distinct contributions of mutations in ERG11, ERG3, MRR1, and TAC1 genes to antifungal resistance in Candida parapsilosis

Candida parapsilosis has recently emerged as a major threat due to the worldwide emergence of fluconazole-resistant strains causing clonal outbreaks in hospitals and poses a therapeutic challenge due to the limited antifungal armamentarium. Here, we used precise genome editing using CRISPR-Cas9 to gain further insights into the contribution of mutations in ERG11, ERG3, MRR1, and TAC1 genes and the influence of allelic dosage to antifungal resistance in C. parapsilosis. Seven of the most common amino acid substitutions previously reported in fluconazole-resistant clinical isolates (including Y132F in ERG11) were engineered in two fluconazole-susceptible C. parapsilosis lineages (ATCC 22019 and STZ5). Each mutant was then challenged in vitro against a large array of antifungals, with a focus on azoles. Any possible change in virulence was also assessed in a Galleria mellonella model. We successfully generated a total of 19 different mutants, using CRISPR-Cas9. Except for R398I (ERG11), all remaining amino acid substitutions conferred reduced susceptibility to fluconazole. However, the impact on fluconazole in vitro susceptibility varied greatly according to the engineered mutation, the stronger impact being noted for G583R acting as a gain-of-function mutation in MRR1. Cross-resistance with newer azoles, non-medical azoles, but also non-azole antifungals such as flucytosine, was occasionally noted. Posaconazole and isavuconazole remained the most active in vitro. Except for G583R, no fitness cost was associated with the acquisition of fluconazole resistance. We highlight the distinct contributions of amino acid substitutions in ERG11, ERG3, MRR1, and TAC1 genes to antifungal resistance in C. parapsilosis.

Analysis of clinical Candida parapsilosis isolates reveals copy number variation in key fluconazole resistance genes

We used whole-genome sequencing to analyze a collection of 35 fluconazole-resistant and 7 susceptible Candida parapsilosis isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. Phylogenetic analysis shows that although the collection is diverse, two persistent clinical lineages were identified. We identified copy number variation (CNV) of two genes, ERG11 and CDR1B, in resistant isolates. Two strains have a CNV at the ERG11 locus; the entire ORF is amplified in one, and only the promoter region is amplified in the other. We show that the annotated telomeric gene CDR1B is actually an artifactual in silico fusion of two highly similar neighboring CDR genes due to an assembly error in the C. parapsilosis CDC317 reference genome. We report highly variable copy numbers of the CDR1B region across the collection. Several strains have increased the expansion of the two genes into a tandem array of new chimeric genes. Other strains have experienced a deletion between the two genes creating a single gene with a reciprocal chimerism. We find translocations, duplications, and gene conversion across the CDR gene family in the C. parapsilosis species complex, showing that it is a highly dynamic family.

Analysis of clinical Candida parapsilosis isolates reveals copy number variation in key fluconazole resistance genes

We used whole-genome sequencing to analyse a collection of 35 fluconazole resistant and 7 susceptible Candida parapsilosis isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. Phylogenetic analysis shows that although the collection is diverse, two probable outbreak groups were identified. We identified copy number variation of two genes, ERG11 and CDR1B, in resistant isolates. Two strains have a CNV at the ERG11 locus; the entire ORF is amplified in one, and only the promoter region is amplified in the other. We show the annotated telomeric gene CDR1B is actually an artefactual in silico fusion of two highly similar neighbouring CDR genes due to an assembly error in the C. parapsilosis CDC317 reference genome. We report highly variable copy numbers of the CDR1B region across the collection. Several strains have increased expansion of the two genes into a tandem array of new chimeric genes. Other strains have experienced a deletion between the two genes creating a single gene with a reciprocal chimerism. We find translocations, duplications, and gene conversion across the CDR gene family in the C. parapsilosis species complex, showing that it is a highly dynamic family.