Hotspot mutations and genomic expansion of ERG11 are major mechanisms of azole resistance in environmental and human commensal isolates of Candida tropicalis

Emergence and characterization of mixed Candida auris strain infections in China

PURPOSE

The multidrug-resistant fungal pathogen Candida auris poses an increasing global health threat due to its high transmissibility and persistence in healthcare environments. We aimed to explore the potential cases of mixed C. auris-strain colonizations or infections in China and to investigate the genetic and biological diversity of the associated isolates.

METHODS

C. auris isolates from 5 colonization or infection cases were distinguished by colony morphology and verified by D1/D2-ITS alignment. Phylogenetic and genomic diversity analysis of all isolates were conducted using whole genome sequences. Comparative biological analysis of all isolates, including cellular and colony morphology, antifungal susceptibility, biofilm formation, SAP activity, and both in vitro and in vivo survival capabilities were performed.

RESULTS

Five cases of potential mixed C. auris-strain colonization or infections in China were identified. Comparative genomic analysis revealed these cases involved strains from two distinct genetic clades (I and III) or strains from the same clade but with genetic alterations. Comparative biological analysis demonstrated the strains from mixed colonization or infections exhibit differences in several key aspects, including colony morphology, biofilm formation, SAP activity, and both in vitro and in vivo survival capabilities.

CONCLUSION

Comparative analyses revealed notable differences in biofilm formation, environmental survival, and secretion of virulence factors between the co-colonizing or co-infecting strains of C. auris. These biological and genetic disparities may present significant challenges for the diagnosis and treatment of C. auris infections, as strains with different genetic backgrounds may exhibit varying abilities to colonize host or environmental niches.

An agricultural triazole induces genomic instability and haploid cell formation in the human fungal pathogen Candida tropicalis

The human fungal pathogen Candida tropicalis is widely distributed in clinical and natural environments. It is known to be an obligate diploid organism with an incomplete and atypical sexual cycle. Azole-resistant C. tropicalis isolates have been observed with increasing prevalence in many countries in recent years. Here, we report that tebuconazole (TBZ), a triazole fungicide widely used in agriculture, can induce ploidy plasticity and the formation of haploid cells in C. tropicalis. The evolved C. tropicalis strains with ploidy variations exhibit a cross-resistance between TBZ and standard azoles used in clinical settings (such as fluconazole and voriconazole). Similar to its diploid cells, these newly discovered C. tropicalis haploid cells are capable of undergoing filamentation, white-opaque switching, and mating. However, compared to its diploid cells, these haploid C. tropicalis cells grow more slowly under in vitro culture conditions and are less virulent in a mouse model of systemic infection. Interestingly, flow cytometry analysis of a clinical strain with extremely low genome heterozygosity indicates the existence of natural C. tropicalis haploids. Discovery of this C. tropicalis haploid state sheds new light into the biology and genetic plasticity of C. tropicalis and could provide the framework for the development of new genetic tools in the field.

Ploidy plasticity drives fungal resistance to azoles used in agriculture and clinics

The rapid growth in antimicrobial resistance is of great medical concern. A new study in PLOS Biology unveils the link between ploidy plasticity and the emergence of antifungal resistance in Candida tropicalis.

Genomics insights of candidiasis: mechanisms of pathogenicity and drug resistance

Candidiasis, a prevalent class of human infections caused by fungi belonging to the Candida genus, is garnering increasing attention due to its pathogenicity and the emergence of drug resistance. The advancement of genomics technologies has offered powerful tools for investigating the pathogenic mechanisms and drug resistance characteristics of Candida. This comprehensive review provides an overview of the applications of genomics in candidiasis research, encompassing genome sequencing, comparative genomics, and functional genomics, along with the pathogenic features and core virulence factors of Candida. Moreover, this review highlights the role of genomic variations in the emergence of drug resistance, further elucidating the evolutionary and adaptive mechanisms of Candida. In conclusion, the review underscores the current state of research and prospective avenues for exploration of candidiasis, providing a theoretical basis for clinical treatments and public health strategies.

Multi-locus sequence typing of Candida tropicalis among Candiduria shows an outbreak in azole-susceptible isolates and clonal cluster enriched in azole-resistant isolates

BACKGROUND

The increasing detection rate of C. tropicalis and its azole resistance have made clinical treatment difficult. The presence of candiduria seems to correlate with invasive candida infection, especially for patients admitted to ICUs. However, the prevalence and antifungal resistance of C. tropicalis isolates in urine samples has not been well studied.

AIM

To retrospectively investigate the clinical features, antifungal resistance, and genetic relatedness of C. tropicalis isolates from urine samples.

METHODS

A total of 107 clinical C. tropicalis isolates were retrospectively studied, including phenotypes of isolates and characteristics of patients. The genetic profiles of 107 isolates were genotyped using multi-locus sequence typing (MLST). Phylogenetic analysis was inferred using unweighted pair group method with arithmetic averages. MLST clonal clusters (CCs) were analysed by goeBURST.

FINDINGS

Of the 107 isolates, 27.1% were resistant to fluconazole, and there was a notable increasing trend of fluconazole resistance from 16.1% in 2019 to 40.0% in 2021. Forty-seven diploid sequence types (DSTs) were assigned to ten major CCs. CC1 was the predominant fluconazole-susceptible group; 24 isolates from CC1 belonged to DST333, an outbreak clone in NICU ward. The azole-resistant CC4 contained 19 isolates, accounting for 65.5% of the azole-resistant isolates in this study. CC4 belongs to a prevalent FNS CC1 globally, of which the putative founder genotype was DST225.

CONCLUSION

This study revealed an outbreak of azole-susceptible C. tropicalis isolates in urine specimens and a high azole resistance rate of C. tropicalis in candiduria, and the MLST type showed clonal aggregation in azole-resistant isolates from urine samples.

Mechanisms of Azole Potentiation: Insights from Drug Repurposing Approaches

The emergence of azole resistance and tolerance in pathogenic fungi has emerged as a significant public health concern, emphasizing the urgency for innovative strategies to bolster the efficacy of azole-based treatments. Drug repurposing stands as a promising and practical avenue for advancing antifungal therapy, with the potential for swift clinical translation. This review offers a comprehensive overview of azole synergistic agents uncovered through drug repurposing strategies, alongside an in-depth exploration of the mechanisms by which these agents augment azole potency. Drawing from these mechanisms, we delineate strategies aimed at enhancing azole effectiveness, such as inhibiting efflux pumps to elevate azole concentrations within fungal cells, intensifying ergosterol synthesis inhibition, mitigating fungal cell resistance to azoles, and disrupting biological processes extending beyond ergosterol synthesis. This review is beneficial for the development of these potentiators, as it meticulously examines instances and provides nuanced discussions on the mechanisms underlying the progression of azole potentiators through drug repurposing strategies.

Biology and genetic diversity of Candida krusei isolates from fermented vegetables and clinical samples in China

Candida krusei, also known as Pichia kudriavzevii, is an emerging non-albicans Candida (NAC) species causing both superficial and deep-seated infections in humans. This fungal pathogen is inherently resistant to the first-line antifungal drug, fluconazole, and is widely distributed in natural environments such as soil, foods, vegetables, and fruits. In this study, we collected 86 C. krusei strains from clinical settings and traditional fermented vegetables from different areas of China. Compared to C. krusei strains from fermented vegetables, clinical isolates exhibited a higher ability to undergo filamentation and biofilm development, which could facilitate its host colonization and infections. Isolates from fermented vegetables showed higher resistance to several antifungal drugs including fluconazole, voriconazole, itraconazole, amphotericin B, and caspofungin, than clinical strains, while they were more susceptible to posaconazole than clinical strains. Although C. krusei has been thought to be a diploid organism, we found that one-fourth of clinical strains and the majority of isolates from fermented vegetables (87.5%) are triploid. Whole-genome sequencing and population genetic analyses demonstrated that isolates from clinical settings and fermented food are genetically associated, and distributed across a wide range of genetic clusters. Additionally, we found that six nucleotide substitutions at the promoter region of the ABC11 gene, encoding a multidrug efflux pump, could play a critical role in antifungal resistance in this species. Given the ubiquitous distribution of C. krusei strains in fermented vegetables and their genetic association with clinical strains, a One Health approach will be necessary to control the prevalence of this pathogen.

Yeast supplementation potentiates fluoxetine's anti-depressant effect in mice via modulation of oxido-inflammatory, CREB, and MAPK signaling pathways

Introduction

The therapeutic potential of yeast in the management of depression is unknown. Thus, we evaluated the modulatory effect of nutritional yeast supplementation on antidepressant activity of fluoxetine in mice models of depressive-like behaviors (DLB).

Methods

A total of 112 mice were divided into 16 groups (n = 7 each) for a 3-stage study. Stage I (non-DLB study) had groups Ia (10 mL/kg vehicle), Ib (20 mg/kg fluoxetine), Ic - If (2% yeast diet for all, but Id - If additionally received 5 mg/kg, 10 mg/kg, and 20 mg/kg fluoxetine respectively). Stage II (lipopolysaccharide [LPS] model of DLB) had groups IIa - IIb (10 mL/kg vehicle), IIc (20 mg/kg fluoxetine), IId (yeast) and IIe (yeast + 20 mg/kg fluoxetine). After these treatments for 24 days, animals in IIb - IIe received 0.83 mg/kg of LPS on the 25th day. Except for group IIIa (10 mL/kg vehicle), animals in other groups of stage III (unpredictable chronic mild stress [UCMS] model) were exposed to UCMS for 24 days along with 10 mL/kg vehicle (IIIb), 20 mg/kg fluoxetine (IIIc), yeast (IIId), or yeast + fluoxetine (IIIe).

Results

Yeast and fluoxetine attenuated LPS- and UCMS-induced immobility, derangement of oxido-inflammatory (TNF-α, IL-6, NO, MDA, SOD, GSH, CAT, and AChE) and CREB/MAPK pathways. While fluoxetine had more potent effect than yeast when used separately, pre-treatment of mice with their combination had more pronounced effect than either of them.

Conclusion

Yeast supplementation improves the antidepressant activity of fluoxetine in mice by modulating oxido-inflammatory, CREB, and MAPK pathways.

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.