Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species

Genomic epidemiology and antifungal resistance of emerging Trichophyton indotineae in China

The emergence and spread of antifungal-resistant Trichophyton indotineae pose an increasing public health concern worldwide. Multidrug-resistant T. indotineae infections have been reported in China in the past few years. To understand the genetic relationship and the origin of these Chinese isolates, as well as their relationship to the global collections, we sequenced the whole genomes of 31 isolates using the Illumina platforms. Genomic epidemiology was performed on a dataset of 181 T. indotineae isolates from China and 8 other countries, representing the largest genome-wide analysis. Single nucleotide polymorphism analysis revealed that T. indotineae can be divided into four distinct phylogenetic groups (I, II, III, IV), with regional clonal transmission clusters identified in eastern China; T. indotineae was introduced into China more than once given the genetic variability. The isolates from South Asia may be the source of Chinese isolates based on epidemiological information. There were differences in the prevalence and resistance profiles among four phylogenetic groups, with Group III being predominant and exhibiting a higher terbinafine resistance rate of 88.24% and azole resistance. Also, we characterized the role of gene mutation, copy number variation, and gene expression in antifungal drug resistance. Terbinafine resistance could be mainly associated with Phe397Leu substitution in SQLE, and azole resistance might be related to increased copy number of CYP51B, as well as elevated MDR2 and MDR3 expression. Given the clinical challenges posed by T. indotineae, this emerging dermatophyte should be recognized as a global threat, necessitating urgent collaborative surveillance and management strategies.

Candida auris cells form giant lipid droplets to survive in harsh environments

The emerging fungal pathogen Candida auris is notorious for environmental persistence, which is a major contributor to outbreaks in healthcare settings. Here we report that giant lipid droplets (gLDs) inside C. auris cells play critical roles in the ability to survive harsh environments. C. auris cells that contain gLDs exhibit an increased tolerance to environmental stresses, antifungals, and host-associated antimicrobial peptides. These cells often undergo significant cell wall remodeling and sloughing of the outer layer of the cell wall. Lipidomics analysis indicates that cells with gLDs contain a significantly higher level of triacylglycerols, sterol esters, and other lipids, such as glycerolipids, sphingolipids, and sterol lipids. At the transcriptional level, a large set of differentially expressed genes was observed between C. auris cells with and without gLDs. Our study reveals that gLDs are a new strategy used by C. auris to adapt to stressful conditions and to persist in hospital environments.

A clinical and molecular analysis of Candidozyma auris strains from Romania, 2022-2023

Candidozyma auris (formerly Candida auris; C. auris) raises significant concerns for healthcare facilities due to its ability to cause severe systemic infections, increased resistance to antifungals, and high intra-hospital transmissibility. We conducted a retrospective study on 102 patients diagnosed in 2022 and 2023. Demographic, clinical, and epidemiologic data were collected from the hospital databases. C. auris was identified using MALDI-TOF systems, and antifungal susceptibility was determined with Micronaut. The isolates were sequenced using Illumina next-generation sequencing platforms. Molecular epidemiology analysis was performed with multiple bioinformatics approaches (phylogenetic tools, resistance genes-related predictions, and variant analyses). Most patients (80/102) were admitted to or had been recently transferred from intensive care units at the moment of C. auris detection. Most cases (57/102) were classified as infections; 29 of them were bloodstream infections. All patients had been treated with broad-spectrum antibiotics before C. auris isolation, and 75/102 had received antifungals. All 31 tested isolates showed resistance to fluconazole, 5 were resistant to amphotericin B, and they were all susceptible to echinocandins. Crude mortality for infected patients was 68.18%. The 31 analyzed sequences belonged to clade I and bore multiple resistance markers.IMPORTANCEHighly antifungal-resistant Candidozyma auris keeps spreading in regions previously free of this pathogen, stressing once again the need for active surveillance, flexible control measures, and antimicrobial stewardship. This study is seminal for our understanding of the C. auris outbreak in Romania, providing insights into the evolutionary dynamics and genomic diversity of the pathogen and highlighting clade-specific mutations possibly linked to antifungal resistance. By joining these molecular characteristics with clinical, epidemiological, and microbiology data, such as risk factors for acquiring C. auris and phenotypic antifungal susceptibility, the study can be instrumental for surveillance and infection control strategies that are essential due to the pathogen's high transmissibility and the global health threat that it poses.

Signaling pathways governing the pathobiological features and antifungal drug resistance of Candida auris

Candida auris is an emerging multidrug-resistant fungal pathogen that poses a significant global health threat. Since its discovery in 2009, C. auris has rapidly spread worldwide, causing severe infections with high mortality rates, particularly in healthcare settings. Its ability to persist in the environment, form biofilms, and resist multiple antifungal drugs underscores the urgent need to understand its pathogenicity mechanisms and associated signaling pathways. Such insights are crucial for elucidating its unique virulence traits and developing targeted therapeutic strategies. Current studies have identified several key pathways involved in its pathogenicity and antifungal drug resistance. The Ras/cAMP/PKA pathway regulates critical virulence factors, including thermotolerance, morphological plasticity, and biofilm formation. The mitogen-activated protein kinase (MAPK) and calcineurin pathways contribute to stress responses and antifungal drug resistance. The regulation of Ace2 and morphogenesis (RAM) pathway influences cell aggregation, while the target of rapamycin (TOR) pathway affects filamentous growth and biofilm development. However, the distinct characteristics of C. auris, such as its rapid environmental spread and clade-specific traits, warrant further investigation into additional signaling pathways. This review provides a comprehensive analysis of known signaling pathways associated with C. auris pathogenicity and antifungal drug resistance, integrating insights from other fungal pathogens. By synthesizing current knowledge and identifying research gaps, this review offers new perspectives on future research directions and potential therapeutic targets against this formidable pathogen.

Molecular mechanism of host-yeast interactions and prevention by nanoformulation approaches

Fungal infections are a major source of morbidity and mortality in people with compromised immune systems, such as those with human immunodeficiency virus, cancer, organ transplant recipients, and patients undergoing chemotherapy in healthcare settings. According to a recent World Health Organization (WHO) fungal priority pathogens list, Cryptococcus spp., Candida spp., Aspergillus spp., and Candida auris cause severe invasive infections in human. These opportunistic pathogens cause a significant number of mycoses, which affect over a billion people annually. Around two million infections can be fatal, especially for those with compromised immune systems. To diagnose and treat mycoses, we need to understand the complex interactions between the fungus and the host during pathogenesis, the virulence-causing traits of the fungus, and how the host fights infection through the immune system. Although several antifungal drugs are available against fungal infections, their effectiveness is highly variable, with adverse effects. In addition, the increasing resistance to traditional antifungal treatments poses serious risks to the healthcare industry. Therefore, new therapeutic strategies are required to combat these potentially fatal fungal infections. Nanostructure-based formulations can improve the therapeutic efficacy of conventional medications by broadening their activities, decreasing toxicity, enhancing bioactivity, and improving biodistribution. The review highlights host and fungus interaction and how nanoformulations can be targeted against fungal infections.

Rapid in vitro evolution of flucytosine resistance in Candida auris

The pan-antifungal-resistant pathogen Candida auris has been causing high-mortality infection outbreaks in hospitals and healthcare settings. The prodrug 5-fluorocytosine (5FC) is one of four chemical entities, but its clinical use as an antifungal drug has been limited owing to pronounced resistance. However, antifungal combination therapy with 5FC appears as a promising strategy for treating C. auris infections. Here, we show that a C. auris clinical isolate can rapidly acquire genetic mutations to mount 5FC resistance after only one to two passages under drug selection. We exploit a new bioinformatics workflow to identify genetic polymorphisms from RNA-seq data. Strikingly, we identify several mutations in the FUR1 gene encoding the 5-fluorouracil convertase that normally generates the active drug. A single nonsense mutation truncates the enzyme at residue Q30*, leading to 5FC resistance due to inactive Fur1. Whole-genome sequencing analysis revealed that an indel mutation in FCY2 also contributes to 5FC resistance. Furthermore, at least one out of seven adapted strains acquired enhanced 5FC tolerance without mutations in the 5FC conversion pathway. Thus, we demonstrate that FUR1 mutations are critical drivers of 5FC resistance in C. auris.IMPORTANCECandida auris is a high-priority human fungal pathogen, causing infection outbreaks of high mortality in healthcare settings. Antifungal combination therapy with 5-fluorocytosine (5FC) is one of the emerging approaches in treatment. However, acquired 5FC resistance traits have been a matter of concern. 5FC is taken up by fungal cells via a cytosine permease and further metabolized by a cytosine deaminase to 5-fluorouracil (5FU). 5FU is then converted by the Fur1 uracil phosphoribosyltransferase into a toxic antimetabolite that disrupts fungal RNA and DNA syntheses. Mutations in these proteins are commonly associated with 5FC resistance in fungal species. Here, we show that C. auris can rapidly develop resistance under 5FC selective stress owing to mutational inactivation of Fur1 function. Moreover, other mechanisms that bypass mutations in the 5FC conversion pathway may also contribute to 5FC resistance traits. Finally, we have developed a tailored bioinformatics workflow that facilitates the identification of polymorphisms associated with 5FC resistance in clinical isolates.

The Emerging Fungal Pathogen Candida auris Induces IFNγ to Colonize the Skin

Candida auris is an emerging multidrug-resistant skin-tropic fungal pathogen that causes serious human infections. However, the factors that regulate C. auris skin infection in vivo are still unclear. In this study, we identified that, unlike Candida albicans, which induces IL-17-secreting protective effector Th17 cells, C. auris predominately induces IFNγ-secreting pathogenic Th1 cells during reinfection. Surprisingly, we found that IFNγ enhances skin infection of C. auris but not C. albicans. Mechanistically, IFNγ enhances skin infection of C. auris by dampening the protective IL-17 responses and increasing dermal damage. Furthermore, we identified that the development of Th1 cells occurs through IL-12, produced by C. auris-induced inflammatory macrophages and monocyte-derived dendritic cells. In addition, our findings reveal that C. auris unique cell wall outer mannan layer regulates the development of Th1 and Th17 cells. Collectively, our findings, for the first time, identified that C. auris induces IFNγ to persist in the skin. These findings help explain why C. auris but not C. albicans preferentially persist in the skin long-term, with the potential to identify novel therapeutic approaches to prevent and treat this emerging fungal pathogen in humans.

Deciphering Fluconazole Resistance in Candida auris clade V: The Role of Efflux Pump Gene Expression and Ergosterol Pathway Mutations

Candida auris is an emerging multidrug-resistant yeast pathogen that poses a serious global health threat. In particular, fluconazole resistance is common in C. auris, posing challenges for treating invasive infections. Understanding the genetic and molecular mechanisms underlying fluconazole resistance in C. auris is crucial for developing effective control strategies. The current study investigated the genetic and molecular basis of fluconazole resistance in C. auris clade V isolates. Furthermore, we examined mutations in ergosterol biosynthesis genes and expression of efflux pump genes in fluconazole-resistant versus susceptible in strains Clade V. Two C. auris isolates, one fluconazole-resistant, and one fluconazole-susceptible, were subjected to qPCR analysis of efflux pump gene (CDR1, CDR2, MDR1, MDR2) expression. Protein structure modeling was also performed to assess the impact of mutation in the ergosterol biosynthesis gene (ERG11) on antifungal drug accessibility. qPCR analysis revealed no significant difference in the expression levels of the efflux pump genes CDR1, CDR2, and MDR1 between the resistant and susceptible strains. Protein structure modeling indicated that the Y132F mutation in ERG11 likely altered fluconazole binding and accessibility. This study provides insights into the genetic and molecular mechanisms underpinning fluconazole resistance in C. auris Clade V. The findings highlight the critical roles of ERG11 mutation in mediating azole resistance in this emerging fungal pathogen.

How does antifungal resistance vary in Candida (Candidozyma) auris and its clades? Quantitative and qualitative analyses and their clinical implications

BACKGROUND

Candida (Candidozyma) auris is a multidrug-resistant yeast that emerged as a significant health care-associated pathogen. It is classified as an urgent threat to public health due to the high resistance to available antifungal agents. Globally six distinct clades of C. auris have been identified with varying antifungal susceptibility patterns and geographical distributions.

OBJECTIVES

The aim of this review is to investigate the (published) antifungal susceptibility profiles of different C. auris clades to identify those with a higher prevalence of resistance.

SOURCES

A comprehensive literature review was conducted using PubMed, SciELO, Google Scholar, and MEDLINE databases to collect data on MIC distributions and clade designations of C. auris strains.

CONTENT

A total of 1031 C. auris strains were included. Clades I and III, which are closely related phylogenetically, displayed the highest resistance rates, particularly to fluconazole, with 94% and 96% of isolates, respectively. Clade IV also exhibited resistance to both azoles and echinocandins. In contrast, clades II, V, and VI had lower resistance rates, with clade VI being entirely susceptible to fluconazole. Anidulafungin demonstrated the greatest efficacy across all clades, with resistance rates ranging from 0% to 3.67%. Furthermore, clades V and VI showed complete susceptibility to all antifungal agents evaluated.

IMPLICATIONS

This study highlights significant variations in antifungal resistance profiles across the six C. auris clades. Clades I, III, and IV stand out because of their multidrug resistance, particularly to fluconazole and amphotericin B, posing serious challenges for treatment. Continuous global surveillance and tailored management strategies are essential for controlling C. auris infections, especially in highly resistant clades. Enhanced diagnostic capabilities and further genomic studies are critical to understanding the evolving nature of resistance in this emerging pathogen and improving therapeutic outcomes. Clade-specific antifungal resistance in C. auris requires monitoring to optimize therapy selection during outbreaks.

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.

Dry Surface Biofilm Formation by Candida auris Facilitates Persistence and Tolerance to Sodium Hypochlorite

Candida auris is an enigmatic fungal pathogen, recently elevated as a critical priority group pathogen by the World Health Organisation, linked with its ability to cause outbreaks within nosocomial care units, facilitated through environmental persistence. We investigated the susceptibility of phenotypically distinct C. auris isolates to sodium hypochlorite (NaOCl), and evaluated the role of biofilms in surviving disinfection using a dry-surface biofilm (DSB) model and transcriptomic profiling. Planktonic cells were tested for susceptibility to NaOCl, with biofilm formation using the 12-day DSB model, assessed using viable counts, biomass assays and microscopy. Disinfection efficacy was assessed using clinical protocols of 500-1,000 ppm for 1-5 min. RNA sequencing was performed on untreated DSBs in comparison to planktonic cells. Isolates were found to be susceptible planktonically, but grew NaOCl-tolerant biofilms, with only 2-4 log10 reductions in viable cells observed at highest concentrations. Transcriptomics identified DSB upregulation of ABC transporters and iron acquisition pathways relative to planktonic cells. Our findings optimized a DSB protocol in which C. auris can mediate tolerance to NaOCl disinfection, suggesting a lifestyle through which this problematic yeast can environmentally persist. Mechanistically, it has been shown for the first time that upregulation of small-molecule and iron transport pathways are potential facilitators of environmental survival.

Biofilm production by the multidrug-resistant fungus Candida haemulonii is affected by aspartic peptidase inhibitor

Candida haemulonii is an emerging, opportunistic, and multidrug-resistant fungal pathogen. Recently, our group reported the ability of C. haemulonii to form biofilm and secrete aspartic-type peptidases (Saps). Herein, we investigated the correlation between Saps production and biofilm formation along C. haemulonii growth in yeast carbon base medium supplemented with albumin (a Sap-inducing condition) and in the presence of the classical Sap inhibitor pepstatin A. Under these conditions, the biofilm biomass increased on a polystyrene surface, reaching its maximum at 96 h, while maximum biofilm viability was detected at 48 h. The release of Saps during biofilm formation showed an inverse trend, with the highest enzymatic activity measured after 24 h. In the presence of pepstatin A, a significant reduction in biofilm parameters (biomass and viability), as well as in albumin consumption by biofilm-forming cells was detected. These findings underscore the importance of Saps during the biofilm development in C. haemulonii.

The high-osmolarity glycerol (HOG) pathway in Candida auris

The emerging fungal pathogen Candida auris is known for its strong skin tropism and resilience against antifungal and disinfection treatment, posing a significant challenge for healthcare units. Although efforts to identify the effectors of its unique pathogenic behavior have been insightful, the role of the high-osmolarity glycerol (HOG) pathway in this context remains unexplored. The study by Shivarathri and co-workers (R. Shivarathri, M. Chauhan, A. Datta, D. Das et al., mBio 15:e02748-24, 2024, https://doi.org/10.1128/mbio.02748-24) sought to address this gap. This report indeed advances our understanding of the critical role of the HOG pathway in C. auris pathogenicity by emphasizing its involvement in skin colonization, biofilm formation, and evasion of phagocyte attack.

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.

Molecular characterization of some multidrug resistant Candida Auris in egypt

Candida auris is an emerging multidrug-resistant yeast that causes healthcare-associated and deep-seated infections. Notably, the emergence of this yeast is alarming as it exhibits resistance to azoles, echinocandins, and amphotericin B, which may lead to clinical treatment failure in patients. This study aims to identify and characterize the genetic determinants of antifungal resistance in C. auris among some local clinical isolates to contribute for understanding the molecular epidemiology of C. auris in Egypt. Four test strains were identified based on the ribosomal internal transcribed spacer (ITS) region sequence and phylogenetic analysis. Antifungal susceptibility was determined using the VITEK 2 system. Molecular analysis of ERG11, ERG3, FKS1, and FKS2 was used to identify mutations associated with antifungal resistance. The four test strains were identified as C. auris. Evolutionary analysis was conducted, and sequences of ITS regions were submitted to GenBank. The mutations Y132F in ERG11 and F635Y in FKS2 were identified, which are known to confer resistance to azoles and echinocandins, respectively. The emergence of C. auris in Egypt represents a public health concern. Hospitals should implement strict infection control measures to prevent its spread. Effective treatment guidelines and ongoing monitoring of antifungal resistance are essential to combat this emerging pathogen.

Short-term evolution and dispersal patterns of fluconazole-resistance in Candida auris clade III

The rapid increase in infections caused by the emerging fungal pathogen Candida auris is of global concern, and understanding its expansion is a priority. The phylogenetic diversity of the yeast is clustered in five major clades, among which clade III is particularly relevant, as most of its strains exhibit resistance to fluconazole, reducing the therapeutic alternatives and provoking outbreaks that are difficult to control. In this study, we have investigated the phylogenetic structure of clade III by analyzing a global collection of 566 genomes. We have identified three subgroups within clade III, among which two are genetically most closely related. Moreover, we have estimated the evolutionary rate of clade III to be 2.25e-7 s/s/y (2.87 changes per year). We found that one of these subgroups shows intrinsic resistance to fluconazole and is responsible for the majority of cases within this clade globally. We inferred that this subgroup may have originated around December 2010 (95% High Probability Density (HPD): April 2010-June 2011), and since then it has spread across continents, generating multiple large outbreaks, each with a unique pattern of transmission and dissemination. These results highlight the remarkable ability of the pathogen to adapt to its environment and its rapid global spread, underscoring the urgent need to address this epidemiological challenge effectively.IMPORTANCEThe number of cases affected by Candida auris has increased worryingly worldwide. Among the currently recognized clades, clade III has the highest proportion of fluconazole-resistant cases and is spreading very rapidly, causing large nosocomial outbreaks across the globe. By analyzing complete fungal genomes from around the world, we have confirmed the origin of this clade and unraveled its dispersal patterns in the early 2010s. This finding provides knowledge that may be helpful to the public health authorities for the control of the disease.

Suppressed Protein Translation Caused by MSP-8 Deficiency Determines Fungal Multidrug Resistance with Fitness Cost

Antifungal resistance, particularly the rise of multidrug-resistance strains, poses a significant public health threat. In this study, the study identifies a novel multidrug-resistance gene, msp-8, encoding a helicase, through experimental evolution with Neurospora crassa as a model. Deletion of msp-8 conferred multidrug resistance in N. crassa, Aspergillus fumigatus, and Fusarium verticillioides. However, the transcript levels of genes encoding known drug targets or efflux pumps remain unaltered with msp-8 deletion. Interestingly, MSP-8 interacted with ribosomal proteins, and this mutant displays compromised ribosomal function, causing translational disturbance. Notably, inhibition of protein translation enhances resistance to azoles, amphotericin B, and polyoxin B. Furthermore, MSP-8 deficiency or inhibition of translation reduces intracellular ketoconazole accumulation and membrane-bound amphotericin B content, directly causing antifungal resistance. Additionaly, MSP-8 deficiency induces cell wall remodeling, and decreases intracellular ROS levels, further contributing to resistance. The findings reveal a novel multidrug resistance mechanism independent of changes in drug target or efflux pump, while MSP-8 deficiency suppresses protein translation, thereby facilitating the development of resistance with fitness cost. This study provides the first evidence that MSP-8 participates in protein translation and that translation suppression can cause multidrug resistance in fungi, offering new insights into resistance mechanisms in clinical and environmental fungal strains.

Two outbreaks and sporadic occurrences of Candida auris from one hospital in China: an epidemiological, genomic retrospective study

OBJECTIVES

To investigate the clinical relevance, origin, transmission, and resistance of Candida auris (C. auris) isolates from two outbreaks and sporadic occurrences from one hospital in China.

METHODS

A total of 135 C. auris isolates were collected. Clinical characteristics were obtained and antifungal susceptibility testing (AFST) was performed using the method of broth microdilution. Phylogenetic tree, WGS analysis, and single nucleotide polymorphisms (SNPs) were used to determine the origin, transmission, and resistance mechanisms.

RESULTS

A total of 31 patients (91.2%, 31/34) received invasive medical procedures and 13 patients (38.2%, 13/34) had antifungal agents before C. auris infection/colonization, except one patient whose clinical information was missing. Only 4 cases of C. auris candidemia were observed. 18 patients died, 13 patients recovered, and the outcomes of 3 patients were not available. A total of 35 C. auris isolates, which were successfully cultivated and the first isolated or harbored specific drug-resistant phenotype from each patient, were selected to be sequenced and further analyzed. C. auris isolates presented low genetic variability and belonged to clade I, possibly originating from BJ004-H7 in Beijing. All 35 isolates were resistant to Fluconazole (FCZ) and amphotericin B (AMB), and 3 isolates were resistant to caspofungin (CAS). Mutations in ERG11 and FKS1 were linked to reduced azole and echinocandin susceptibility, respectively.

CONCLUSIONS

Two outbreaks of highly clonal, multidrug-resistant C. auris isolates within the medical facility were reported. The intensive performance of disinfection measures helped block in-hospital transmission. Understanding the epidemiology, drug resistance and management of C. auris will be helpful for implementing effective infection control and treatment strategies.

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.

A comparative evaluation of CRISPR-Cas9 allele editing systems in Candida auris: challenging research in a challenging bug

Candida auris is an emergent fungal pathogen of significant interest for molecular research because of its unique nosocomial persistence, high stress tolerance and common multidrug resistance. To investigate the molecular mechanisms of these or other phenotypes, a handful of CRISPR-Cas9 based allele editing tools have been optimized for C. auris. Nonetheless, allele editing in this species remains a significant challenge, and different systems have different advantages and disadvantages. In this work, we compare four systems to introduce the genetic elements necessary for the production of Cas9 and the guide RNA molecule in the genome of C. auris, replacing the ENO1, LEU2 and HIS1 loci respectively, while the fourth system makes use of an episomal plasmid. We observed that the editing efficiency of all four systems was significantly different and strain dependent. Alarmingly, we did not detect correct integration of linear CRISPR cassette constructs in integration-based systems, in over 4,900 screened transformants. Still, all transformants, whether correctly edited or not, grew on selective nourseothricin media, suggesting common random ectopic integration of the CRISPR cassette. Although the plasmid-based system showed a low transformation success compared to the other systems, it has the highest editing efficiency with 41.9% correct transformants on average. In an attempt to improve editing efficiencies of integration-based systems by silencing the non-homologous end joining (NHEJ) DNA repair pathway, we deleted two main NHEJ factors, KU70 and LIG4. However, no improved editing or targeting efficiencies were detected in ku70Δ, lig4Δ, or ku70Δ/lig4Δ backgrounds. Our research highlights important challenges in precise genome editing of C. auris and sheds light on the advantages and limitations of several methods with the aim to guide scientists in selecting the most appropriate tool for molecular work in this enigmatic fungal pathogen.

Population Structure Based on Microsatellite Length Polymorphism, Antifungal Susceptibility Profile, and Enzymatic Activity of Candida auris Clinical Isolates in Russia

Candida auris is an emerging multidrug-resistant fungal pathogen causing nosocomial transmission and invasive infections with high mortality. This study aimed to investigate the genetic relationships, enzymatic activities, and drug-resistance profiles of C. auris isolates to evaluate the population and epidemiological diversity of candidiasis in Russia. A total of 112 clinical isolates of C. auris were analyzed from May 2017 to March 2023 in 18 hospitals across Saint Petersburg, the Leningrad Region, and Moscow. Species identification was confirmed by ITS sequencing, and genotyping was performed using 12 short tandem repeat (STR) markers. Antifungal susceptibility was tested using Sensititre™ YeastOne™ plates, and hydrolytic enzyme production was measured by the plate method. ITS sequencing confirmed that all isolates belonged to a single ITS cluster (clades I and III). Fifteen distinct STR genotypes were identified, with genotype I being dominant (n = 53). The most variable of the analyzed markers turned out to be M3-Ia, which was represented in the Russian population by eight different variants. Fluconazole resistance was found in 111 isolates, 17% were resistant to amphotericin B, and 3.6% to 5-flucytosine. Phospholipase activity was strong in most strains, especially in urine isolates (p = 0.014). Conclusion: The predominance of STR genotype I and its variability at the M3-Ia locus suggest its association with nosocomial outbreaks and transmissibility in Russia.

Genetic and Phenotypic Intra-Clade Variation in Candida auris Isolated from Critically Ill Patients in a New York City Tertiary Care Center

BACKGROUND

Candida auris is an emerging multidrug-resistant pathogen. Interpretation of susceptibility testing can be difficult since minimum inhibitory concentration (MIC) breakpoints have not been fully established.

METHODS

All C. auris isolates from unique patients identified at a large urban hospital between 2020 and 2024 (n = 66) underwent whole-genome sequencing (WGS). Genomic DNA was extracted from pure culture isolates and underwent PCR-free library preparation. WGS was performed on an Illumina platform (NextSeq2000) with an average coverage of 50×. Genomic analysis was conducted via an adapted GATK-based pipeline using the B11205 strain as the reference genome based on the CDC (MycoSNP) protocol. All isolates underwent FKS1 gene Sanger sequencing for confirmation of WGS results. Genotypic results were correlated with antifungal susceptibility testing.

RESULTS

All clinical isolates were part of Clade I and carried azole resistance mutations in ERG11, TAC1b, and CDR1, consistent with 100% phenotypic fluconazole resistance. Across all isolates, 5 distinct missense variants in FKS1 were identified: one case with p.Ser639Tyr, one case with both a p.Arg1354Ser and a p.Asp642His, 7 cases with p.Met690Ile, and 9 cases with p.Val1818Ile. Isolates with known echinocandin resistance conferring mutations p.Ser639Tyr and p.Arg1354Ser were resistant to micafungin and anidulafungin. Two isolates with Met690Ile were resistant to caspofungin alone.

CONCLUSIONS

With potential resistance to all 3 major antifungal classes of drugs, C. auris is an emerging public health threat. Early detection of echinocandin resistance by molecular methods could impact treatment course to include novel antifungal agents. Further study of the FKS1 Met690Ile variant is warranted.

First Identification of Domestic Clade I Candida auris in Japanese Otitis Externa Patients Without Travel History

BACKGROUND

Candida auris is an emerging fungus causing nosocomial infections and outbreaks, with many strains exhibiting multidrug resistance. This study analyzed the C. auris clinical isolates at The Jikei University School of Medicine Kashiwa Hospital from December 2019 to March 2021.

METHODS

Clinical data were reviewed retrospectively for patients from whom C. auris was isolated from clinical specimens. Clade analysis and drug susceptibility testing were conducted.

RESULTS

Three strains of C. auris were isolated, all from otorrhea in patients with otitis externa. Case A was a 69-year-old female with aural pain, Case B was an 82-year-old female with left ear deafness, and Case C was a 76-year-old male with left otorrhea and hearing loss; all cases were immunocompetent. Strains from Clade I (South Asian clade) were found in Cases A and C, and a strain from Clade II (East Asian clade) was isolated from Case B. None had a travel history overseas or contact with foreigners. Drug susceptibility testing showed that one C. auris strain of Clade Ⅰ had a high minimal inhibitory concentration for fluconazole. No severe infection was observed, and all cases improved with local treatment, including ketoconazole ointment for Case A.

CONCLUSION

The presence of Clade I C. auris strains in Japan without travel history raises concerns about domestic or in-hospital transmission. Accurate identification and rigorous infection control are essential to manage the spread of C. auris. Ongoing surveillance, research, and international cooperation are needed.

Molecular Epidemiology and Antifungal Susceptibility Profile of Candidozyma Isolates From Argentina

BACKGROUND

Epidemiological surveillance of Candidozyma sp. has become important because many species of this new genus have been reported to be responsible for nosocomial outbreaks and to exhibit elevated minimal inhibitory concentrations (MIC) to one or more classes of antifungal drugs.

OBJECTIVES

To describe the genetic relationships among Argentinian clinical isolates belonging to the Candidozyma genus and to study the molecular mechanisms associated with antifungal resistance.

METHODS

We performed whole-genome sequencing of 41 isolates. Identification was based on ribosomal DNA sequencing and susceptibility testing was determined according to the EUCAST document. Phylogenetic analysis, non-synonymous mutations in genes associated with antifungal resistance and the presence of copy number variations (CNVs) were investigated.

RESULTS

We identified 12 Candidozyma haemuli, 11 Candidozyma haemuli var. vulneris, 5 Cz. haemuli/ Cz. haemuli var. vulneris ITS hybrids, 8 Candidozyma duobushaemuli and 5 Candidozyma cf. pseudohaemuli. Phylogenetic analysis, together with clinical data, demonstrated nosocomial transmission events. In addition, Cz. haemuli and Cz. haemuli var. vulneris were not separated in the phylogenetic tree; the Cz. cf. pseudohaemuli isolates clustered distantly from the Cz. pseudohaemuli type strain. Most isolates were resistant to amphotericin B, and two Cz. haemuli isolates showed fluconazole resistance and Y132F mutation in ERG11. We did not find CNV in genes associated with antifungal resistance.

CONCLUSIONS

These findings highlight the need for epidemiological surveillance of these species and the study of molecular mechanisms associated with antifungal resistance. Furthermore, we propose a taxonomic revision for Cz. haemuli var. vulneris and Cz. pseudohaemuli based on genomic data.

Anticandidal Efficacy of Green Synthesized Silver Nanoparticles Using Trans-Himalayan Plant Extracts Against Drug Resistant Clinical Isolates of Candida auris

Candida auris is the most common, globally detected nosocomial fungal pathogen with multi-drug resistance. The high prevalence of C. auris infections has raised concern about drug resistance and adverse effects, compounded by a lack of effective alternative drugs. Bioengineered nanomaterials play a significant role in combating nosocomial infections. Silver nanoparticles (AgNPs) have emerged as an extensively used nanomaterial due to their prominent antimicrobial properties. One of the most promising approaches is to incorporate herbal extracts that contain a range of phytoconstituents, being used for curing various chronic illnesses. This study aimed to produce eco-friendly, cost-effective green synthesized AgNPs with trans-Himalayan medicinal plant extracts (Trillium govanianum & Bergenia ligulata) and assess their anticandidal and antibiofilm potential. The green-synthesized AgNPs formation and crystalline nature were confirmed by UV-visible spectroscopy, dynamic light scattering and X-ray diffraction analysis. The UV-Vis spectra of the AgNPs revealed bands in the range of 415-430 nm. Phytoconstituents as reducing agents were involved in the stabilization of AgNPs as identified by FTIR spectra. HR-TEM of AgNPs' displayed a spherical shape with size in the range of 10-100 nm. Results of activity tests performed using various C. auris clinical strains showed half maximum growth inhibition (IC50) at 8.02 µg/mL, which inhibited 65% of biofilm for T. govanianum extract. The free radical scavenging activity evaluated for green synthesized AgNPs using DPPH showed more than 90% antioxidant activity. Green synthesized AgNPs displayed potent growth inhibition (IC50) at 4.01 µg/mL with 87.0% biofilm inhibition. Green synthesized AgNPs coated bandages and catheters inhibited the growth of C. auris. This study concluded that green synthesized AgNPs formulation in conjunction with antifungal agents exhibits potential biomedical application and also could be used as alternative therapeutics.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-024-01277-8.

Genetic microevolution of clinical Candida auris with reduced Amphotericin B sensitivity in China

The global rate of Amphotericin B (AmB) resistance in Candida auris has surpassed 12%. However, there is limited data on available clinical treatments and microevolutionary analyses concerning reduced AmB sensitivity. In this study, we collected 18 C. auris isolates from five patients between 2019 and 2022. We employed clinical data mining, genomic, and transcriptomic analyses to identify genetic evolutionary features linked to reduced AmB sensitivity in these isolates during clinical treatment. We identified six isolates with a minimum inhibitory concentration (MIC) of AmB below 0.5 µg/mL (AmB0.5) and 12 isolates with an AmB-MIC of 1 µg/mL (AmB1) or ≥ 2 µg/mL (AmB2). All five patients received 24-hour AmB (5 mg/L) bladder irrigation treatment. Evolutionary analyses revealed an ERG3 (c923t) mutation in AmB1 C. auris. Additionally, AmB2 C. auris was found to contain a t2831c mutation in the RAD2 gene. In the AmB1 group, membrane lipid-related gene expression (ERG1, ERG2, ERG13, and ERG24) was upregulated, while in the AmB2 group, expression of DNA-related genes (e.g. DNA2 and PRI1) was up-regulated. In a series of C.auris strains with reduced susceptibility to AmB, five key genes were identified: two upregulated (IFF9 and PGA6) and three downregulated (HGT7, HGT13,and PRI32). In this study, we demonstrate the microevolution of reduced AmB sensitivity in vivo and further elucidate the relationship between reduced AmB sensitivity and low-concentration AmB bladder irrigation. These findings offer new insights into potential antifungal drug targets and clinical markers for the "super fungus", C. auris.

Blood cultures contain populations of genetically diverse Candida albicans strains that may differ in echinocandin tolerance and virulence

It is unknown whether within-patient Candida albicans diversity is common during bloodstream infections (BSIs). We determined whole genome sequences of 10 C. albicans strains from blood cultures (BCs) in each of 4 patients. BCs in 3 patients contained mixed populations of strains that differed by large-scale genetic variants, including chromosome (Chr) 5 or 7 aneuploidy (n=2) and Chr1 loss of heterozygosity (n=1). Chr7 trisomy (Tri7) strains from patient MN were attenuated for hyphal and biofilm formation in vitro compared to euploid strains, due at least in part to NRG1 over-expression. Nevertheless, representative Tri7 strain M1 underwent filamentation during disseminated candidiasis (DC) in mice. M1 was more fit than euploid strain M2 during DC and mouse gastrointestinal colonization, and in blood ex vivo. M1 and M2 exhibited identical echinocandin minimum inhibitory concentrations, but M2 was more tolerant to micafungin in vitro. Furthermore, M2 was more competitive with M1 in mouse kidneys following micafungin treatment than it was in absence of micafungin. Tri7 strains represented 74% of patient MN's baseline BC population, but after 1d and 3d of echinocandin treatment, euploid strains were 93% and 98% of the BC population, respectively. Findings suggest that echinocandin tolerant, euploid strains were a subpopulation to more virulent Tri7 strains at baseline and then were selected upon echinocandin exposure. In conclusion, BCs in at least some patients are comprised of diverse C. albicans populations not recognized by the clinical lab, rather than single strains. Clinical relevance of C. albicans diversity and antifungal tolerance merits further investigation.

Collateral sensitivity counteracts the evolution of antifungal drug resistance in Candida auris

Antifungal drug resistance represents a serious global health threat, necessitating new treatment strategies. Here we investigated collateral sensitivity (CS), in which resistance to one drug increases sensitivity to another, and cross-resistance (XR), in which one drug resistance mechanism reduces susceptibility to multiple drugs, since CS and XR dynamics can guide treatment design to impede resistance development, but have not been systematically explored in pathogenic fungi. We used experimental evolution and mathematical modelling of Candida auris population dynamics during cyclic and combined drug exposures and found that especially CS-based drug cycling can effectively prevent the emergence of drug resistance. In addition, we found that a CS-based treatment switch can actively select against or eradicate resistant sub-populations, highlighting the potential to consider CS in therapeutic decision-making upon resistance detection. Furthermore, we show that some CS trends are robust among different strains and resistance mechanisms. Overall, these findings provide a promising direction for improved antifungal treatment approaches.

Complete genome assembly of Candida auris representative strains of three geographical clades

The complete genome assembly of Candida auris strains B11103, B11221, and B11244 is reported in this manuscript. These strains represent the three geographical clades, namely, South Asian (Clade I), South African (Clade III), and South American (Clade IV).

Improved genome assembly of Candida auris strain B8441 and annotation of B11205

Candida auris is a fungal pathogen of significant worldwide concern, typically resistant to one or more antifungal drugs. We report a completed genome for clade Ia isolate B8441 and gene annotations of clade Ic isolate B11205. These resources will support public health investigations and population genomic studies of this pathogen.

What makes Candida auris pan-drug resistant? Integrative insights from genomic, transcriptomic, and phenomic analysis of clinical strains resistant to all four major classes of antifungal drugs

The global epidemic of drug-resistant Candida auris continues unabated. The initial report on pan-drug resistant (PDR) C. auris strains in a hospitalized patient in New York was unprecedented. PDR C. auris showed both known and unique mutations in the prominent gene targets of azoles, amphotericin B, echinocandins, and flucytosine. However, the factors that allow C. auris to acquire pan-drug resistance are not known. Therefore, we conducted a genomic, transcriptomic, and phenomic analysis to better understand PDR C. auris. Among 1,570 genetic variants in drug-resistant C. auris, 299 were unique to PDR strains. The whole-genome sequencing results suggested perturbations in genes associated with nucleotide biosynthesis, mRNA processing, and nuclear export of mRNA. Whole transcriptome sequencing of PDR C. auris revealed two genes to be significantly differentially expressed-a DNA repair protein and DNA replication-dependent chromatin assembly factor 1. Of 59 novel transcripts, 12 transcripts had no known homology. We observed no fitness defects among multi-drug resistant (MDR) and PDR C. auris strains grown in nutrient-deficient or -enriched media at different temperatures. Phenotypic profiling revealed wider adaptability to nitrogenous nutrients and increased utilization of substrates critical in upper glycolysis and tricarboxylic acid cycle. Structural modeling of a 33-amino acid deletion in the gene for uracil phosphoribosyl transferase suggested an alternate route in C. auris to generate uracil monophosphate that does not accommodate 5-fluorouracil as a substrate. Overall, we find evidence of metabolic adaptations in MDR and PDR C. auris in response to antifungal drug lethality without deleterious fitness costs.

Unveiling the antifungal mechanisms of CTP, a new copper(II)-theophylline/1,10-phenanthroline complex, on drug-resistant non-albicans Candida species

Candida species undeniably rank as the most prevalent opportunistic human fungal pathogens worldwide, with Candida albicans as the predominant representative. However, the emergence of non-albicans Candida species (NACs) has marked a significant shift, accompanied by rising incidence rates and concerning trends of antifungal resistance. The search for new strategies to combat antifungal-resistant Candida strains is of paramount importance. Recently, our research group reported the anti-Candida activity of a coordination compound containing copper(II) complexed with theophylline (theo) and 1,10-phenanthroline (phen), known as "CTP" - Cu(theo)2phen(H2O).5H2O. In the present work, we investigated the mechanisms of action of CTP against six medically relevant, antifungal-resistant NACs, including C. auris, C. glabrata, C. haemulonii, C. krusei, C. parapsilosis and C. tropicalis. CTP demonstrated significant efficacy in inhibiting mitochondrial dehydrogenases, leading to heightened intracellular reactive oxygen species production. CTP treatment resulted in substantial damage to the plasma membrane, as evidenced by the passive incorporation of propidium iodide, and induced DNA fragmentation as revealed by the TUNEL assay. Scanning electron microscopy images of post-CTP treatment NACs further illustrated profound alterations in the fungal surface morphology, including invaginations, cavitations and lysis. These surface modifications significantly impacted the ability of Candida cells to adhere to a polystyrene surface and to form robust biofilm structures. Moreover, CTP was effective in disassembling mature biofilms formed by these NACs. In conclusion, CTP represents a promising avenue for the development of novel antifungals with innovative mechanisms of action against clinically relevant NACs that are resistant to antifungals commonly used in clinical settings.

Do morphogenetic switching and intraspecies variation enhance virulence of Candida auris?

Intraspecies variations that affect pathogenicity and antifungal resistance traits pose a serious obstacle to efficient therapy of Candida auris infections. Recent reports indicate that mutations determine drug susceptibility and virulence. However, mutations alone cannot fully explain a bewildering variety of phenotypes in clinical isolates from known C. auris clades, suggesting an unprecedented complexity underlying virulence traits and antifungal resistance. Hence, we wish to discuss how phenotypic plasticity promotes morphogenetic switching and how that contributes to intraspecies variations in the human fungal pathogen C. auris. Further, we will also discuss how intraspecies variations and morphogenetic events can impact the progress in molecular mycology research that aims to find better treatments for C. auris infections. Finally, we will present our opinion as to the most relevant questions to be addressed when trying to better understand the pathophysiology of C. auris.

Genomic epidemiology describes introduction and outbreaks of antifungal drug-resistant Candida auris

Candida auris is a globally emerged fungal pathogen causing nosocomial invasive infections. Here, we use cutting-edge genomic approaches to elucidate the temporal and geographic epidemiology of drug-resistant C. auris within the UK. We analysed a representative sample of over 200 isolates from multiple UK hospitals to assess the number and timings of C. auris introductions and infer subsequent patterns of inter- and intra-hospital transmission of azole drug-resistant isolates. We identify at least one introduction from Clade I and two from Clade III into the UK, and observe temporal and geographical evidence for multiple transmission events of antifungal drug resistant isolates between hospitals and identified local within-hospital patient-to-patient transmission events. Our study confirms outbreaks of drug-resistant C. auris are linked and that transmission amongst patients occurs, explaining local hospital outbreaks, and demonstrating a need for improved epidemiological surveillance of C. auris to protect patients and healthcare services.

Evolutionary origin and population diversity of a cryptic hybrid pathogen

Cryptic fungal pathogens pose disease management challenges due to their morphological resemblance to known pathogens. Here, we investigated the genomes and phenotypes of 53 globally distributed isolates of Aspergillus section Nidulantes fungi and found 30 clinical isolates-including four isolated from COVID-19 patients-were A. latus, a cryptic pathogen that originated via allodiploid hybridization. Notably, all A. latus isolates were misidentified. A. latus hybrids likely originated via a single hybridization event during the Miocene and harbor substantial genetic diversity. Transcriptome profiling of a clinical isolate revealed that both parental subgenomes are actively expressed and respond to environmental stimuli. Characterizing infection-relevant traits-such as drug resistance and growth under oxidative stress-revealed distinct phenotypic profiles among A. latus hybrids compared to parental and closely related species. Moreover, we identified four features that could aid A. latus taxonomic identification. Together, these findings deepen our understanding of the origin of cryptic pathogens.

Detection and characterisation of a sixth Candida auris clade in Singapore: a genomic and phenotypic study

BACKGROUND

The emerging fungal pathogen Candida auris poses a serious threat to global public health due to its worldwide distribution, multidrug resistance, high transmissibility, propensity to cause outbreaks, and high mortality. We aimed to characterise three unusual C auris isolates detected in Singapore, and to determine whether they constitute a novel clade distinct from all previously known C auris clades (I-V).

METHODS

In this genotypic and phenotypic study, we characterised three C auris clinical isolates, which were cultured from epidemiologically unlinked inpatients at a large tertiary hospital in Singapore. The index isolate was detected in April, 2023. We performed whole-genome sequencing (WGS) and obtained hybrid assemblies of these C auris isolates. The complete genomes were compared with representative genomes of all known C auris clades. To provide a global context, 3651 international WGS data from the National Center for Biotechnology Information (NCBI) database were included in a high-resolution single nucleotide polymorphism (SNP) analysis. Antifungal susceptibility testing was done and antifungal resistance genes, mating-type locus, and chromosomal rearrangements were characterised from the WGS data of the three investigated isolates. We further implemented Bayesian logistic regression models to classify isolates into known clades and simulate the automatic detection of isolates belonging to novel clades as their WGS data became available.

FINDINGS

The three investigated isolates were separated by at least 37 000 SNPs (range 37 000-236 900) from all existing C auris clades. These isolates had opposite mating-type allele and different chromosomal rearrangements when compared with their closest clade IV relatives. The isolates were susceptible to all tested antifungals. Therefore, we propose that these isolates represent a new clade of C auris, clade VI. Furthermore, an independent WGS dataset from Bangladesh, accessed via the NCBI Sequence Read Archive, was found to belong to this new clade. As a proof-of-concept, our Bayesian logistic regression model was able to flag these outlier genomes as a potential new clade.

INTERPRETATION

The discovery of a new C auris clade in Singapore and Bangladesh in the Indomalayan zone, showing a close relationship to clade IV members most commonly found in South America, highlights the unknown genetic diversity and origin of C auris, particularly in under-resourced regions. Active surveillance in clinical settings, along with effective sequencing strategies and downstream analysis, will be essential in the identification of novel strains, tracking of transmission, and containment of adverse clinical effects of C auris infections.

FUNDING

Duke-NUS Academic Medical Center Nurturing Clinician Researcher Scheme, and the Genedant-GIS Innovation Program.

Vertebrate and invertebrate animal infection models of Candida auris pathogenicity

Candida auris is an emerging fungal pathogen with several concerning qualities. First recognized in 2009, it has arisen in multiple geographically distinct genomic clades nearly simultaneously. C. auris strains are typically multidrug resistant and colonize the skin much better than most other pathogenic fungi; it also persists on abiotic surfaces, enabling outbreaks due to transmission in health care facilities. All these suggest a biology substantially different from the 'model' fungal pathogen, Candida albicans and support intensive investigation of C. auris biology directly. To uncover novel virulence mechanisms in this species requires the development of appropriate animal infection models. Various studies using mice, the definitive model, are inconsistent due to differences in mouse and fungal strains, immunosuppressive regimes, doses, and outcome metrics. At the same time, developing models of skin colonization present a route to new insights into an aspect of fungal pathogenesis that has not been well studied in other species. We also discuss the growing use of nonmammalian model systems, including both vertebrates and invertebrates, such as zebrafish, C. elegans, Drosophila, and Galleria mellonella, that have been productively employed in virulence studies with other fungal species. This review will discuss progress in developing appropriate animal models, outline current challenges, and highlight opportunities in demystifying this curious species.

The intricate link between iron, mitochondria and azoles in Candida species

Invasive fungal infections are rapidly increasing, and the opportunistic pathogenic Candida species are the fourth most common cause of nosocomial systemic infections. The current antifungal classes, of which azoles are the most widely used, all have shortcomings. Azoles are generally considered fungistatic rather than fungicidal, they do not actively kill fungal cells and therefore resistance against azoles can be rapidly acquired. Combination therapies with azoles provide an interesting therapeutic outlook and agents limiting iron are excellent candidates. We summarize how iron is acquired by the host and transported towards both storage and iron-utilizing organelles. We indicate whether these pathways alter azole susceptibility and/or tolerance, to finally link these transport mechanisms to mitochondrial iron availability. In this review, we highlight putative novel intracellular iron shuffling mechanisms and indicate that mitochondrial iron dynamics in relation to azole treatment and iron limitation is a significant knowledge gap.

Clavispora lusitaniae: From a saprophytic yeast to an emergent pathogen

Clavispora lusitaniae has been isolated from different substrates, such as soil, water, fruit, vegetables, plants, and the gastrointestinal tract of animals and humans. However, its importance lies in being isolated from in invasive infections, particularly in pediatric patients with hematologic malignancies. It is an emerging nosocomial pathogen commonly associated with fatal prognosis in immunocompromised hosts. C. lusitaniae has attracted attention in the last decade because of resistance to amphotericin B, 5- flucytosine, and fluconazole. The adaptations of this yeast to the human host may contribute to its pathogenicity. Further study will be needed to understand C. lusitaniae's ability as a potential pathogen. This mini-review highlights the importance of the growing number of invasive disease cases caused by this yeast.

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.

Emergence of the novel sixth Candida auris Clade VI in Bangladesh

Candida auris, initially identified in 2009, has rapidly become a critical concern due to its antifungal resistance and significant mortality rates in healthcare-associated outbreaks. To date, whole-genome sequencing (WGS) has identified five unique clades of C. auris, with some strains displaying resistance to all primary antifungal drug classes. In this study, we presented the first WGS analysis of C. auris from Bangladesh, describing its origins, transmission dynamics, and antifungal susceptibility testing (AFST) profile. Ten C. auris isolates collected from hospital settings in Bangladesh were initially identified by CHROMagar Candida Plus, followed by VITEK2 system, and later sequenced using Illumina NextSeq 550 system. Reference-based phylogenetic analysis and variant calling pipelines were used to classify the isolates in different clades. All isolates aligned ~90% with the Clade I C. auris B11205 reference genome. Of the 10 isolates, 8 were clustered with Clade I isolates, highlighting a South Asian lineage prevalent in Bangladesh. Remarkably, the remaining two isolates formed a distinct cluster, exhibiting >42,447 single-nucleotide polymorphism differences compared to their closest Clade IV counterparts. This significant variation corroborates the emergence of a sixth clade (Clade VI) of C. auris in Bangladesh, with potential for international transmission. AFST results showed that 80% of the C. auris isolates were resistant to fluconazole and voriconazole, whereas Clade VI isolates were susceptible to azoles, echinocandins, and pyrimidine analogue. Genomic sequencing revealed ERG11_Y132F mutation conferring azole resistance while FCY1_S70R mutation found inconsequential in describing 5-flucytosine resistance. Our study underscores the pressing need for comprehensive genomic surveillance in Bangladesh to better understand the emergence, transmission dynamics, and resistance profiles of C. auris infections. Unveiling the discovery of a sixth clade (Clade VI) accentuates the indispensable role of advanced sequencing methodologies.IMPORTANCECandida auris is a nosocomial fungal pathogen that is commonly misidentified as other Candida species. Since its emergence in 2009, this multidrug-resistant fungus has become one of the five urgent antimicrobial threats by 2019. Whole-genome sequencing (WGS) has proven to be the most accurate identification technique of C. auris which also played a crucial role in the initial discovery of this pathogen. WGS analysis of C. auris has revealed five distinct clades where isolates of each clade differ among themselves based on pathogenicity, colonization, infection mechanism, as well as other phenotypic characteristics. In Bangladesh, C. auris was first reported in 2019 from clinical samples of a large hospital in Dhaka city. To understand the origin, transmission dynamics, and antifungal-resistance profile of C. auris isolates circulating in Bangladesh, we conducted a WGS-based surveillance study on two of the largest hospital settings in Dhaka, Bangladesh.

Essential Oils against Candida auris-A Promising Approach for Antifungal Activity

The emergence of Candida auris as a multidrug-resistant fungal pathogen represents a significant global health challenge, especially given the growing issue of antifungal drug resistance. This review aims to illuminate the potential of essential oils (EOs), which are volatile plant secretions containing complex mixtures of chemicals, as alternative antifungal agents to combat C. auris, thus combining traditional insights with contemporary scientific findings to address this critical health issue. A systematic literature review was conducted using the PubMed, Scopus, and Web of Science databases from 2019 to 2024, and using the Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) protocol to identify relevant studies on the antifungal efficacy of EOs or their components against C. auris. Of the 90 articles identified, 16 were selected for detailed review. The findings highlight the diverse mechanisms of action of EOs and their components, such as disrupting fungal cell membranes, inducing the production of reactive oxygen species (ROS), and impeding biofilm formation, suggesting that some of them may be as effective as, or better than, traditional antifungal drugs while potentially limiting the development of resistance. However, issues such as variability in the composition of EOs and a paucity of clinical trials have been identified as significant obstacles. In conclusion, EOs and their active ingredients are emerging as viable candidates for creating effective treatments for C. auris, underscoring their importance as alternative or complementary antifungal agents in the face of increasing drug resistance. The call for future research underscores the need for clinical trials and standardization to unlock the full antifungal potential of EOs against C. auris.

What makes Candida auris pan-drug resistant? Integrative insights from genomic, transcriptomic, and phenomic analysis of clinical strains resistant to all four major classes of antifungal drugs

The global epidemic of drug-resistant Candida auris continues unabated. We do not know what caused the unprecedented appearance of pan-drug resistant (PDR) Candida auris strains in a hospitalized patient in New York; the initial report highlighted both known and unique mutations in the prominent gene targets of azoles, amphotericin B, echinocandins, and flucytosine antifungal drugs. However, the factors that allow C. auris to acquire multi-drug resistance and pan-drug resistance are not known. Therefore, we conducted a comprehensive genomic, transcriptomic, and phenomic analysis to better understand PDR C. auris . Among 1,570 genetic variants in drug-resistant C. auris , 299 were unique to PDR strains. The whole genome sequencing results suggested perturbations in genes associated with nucleotide biosynthesis, mRNA processing, and nuclear export of mRNA. Whole transcriptome sequencing of PDR C. auris revealed two genes to be significantly differentially expressed - a DNA repair protein and DNA replication-dependent chromatin assembly factor 1. Of 59 novel transcripts, 12 candidate transcripts had no known homology among expressed transcripts found in other organisms. We observed no fitness defects among multi-drug resistant (MDR) and PDR C. auris strains grown in nutrient-deficient or - enriched media at different temperatures. Phenotypic profiling revealed wider adaptability to nitrogenous nutrients with an uptick in the utilization of substrates critical in upper glycolysis and tricarboxylic acid cycle. Structural modelling of 33-amino acid deletion in the gene for uracil phosphoribosyl transferase suggested an alternate route in C. auris to generate uracil monophosphate that does not accommodate 5-fluorouracil as a substrate. Overall, we find evidence of metabolic adaptations in MDR and PDR C. auris in response to antifungal drug lethality without deleterious fitness costs.

A correlative study of the genomic underpinning of virulence traits and drug tolerance of Candida auris

Candida auris is an opportunistic fungal pathogen with high mortality rates which presents a clear threat to public health. The risk of C. auris infection is high because it can colonize the body, resist antifungal treatment, and evade the immune system. The genetic mechanisms for these traits are not well known. Identifying them could lead to new targets for new treatments. To this end, we present an analysis of the genetics and gene expression patterns of C. auris carbon metabolism, drug resistance, and macrophage interaction. We chose to study two C. auris isolates simultaneously, one drug sensitive (B11220 from Clade II) and one drug resistant (B11221 from Clade III). Comparing the genomes, we confirm the previously reported finding that B11220 was missing a 12.8 kb region on chromosome VI. This region contains a gene cluster encoding proteins related to alternative sugar utilization. We show that B11221, which has the gene cluster, readily assimilates and utilizes D-galactose and L-rhamnose as compared to B11220, which harbors the deletion. B11221 exhibits increased adherence and drug resistance compared to B11220 when grown in these sugars. Transcriptomic analysis of both isolates grown on glucose or galactose showed that the gene cluster was upregulated when grown on D-galactose. These findings reinforce growing evidence of a link between metabolism and drug tolerance. B11221 resists phagocytosis by macrophages and exhibits decreased β-1,3-glucan exposure, a key determinant that allows Candida to evade the host immune system, as compared to B11220. In a transcriptomic analysis of both isolates co-cultured with macrophages, we find upregulation of genes associated with transport and transcription factors in B11221. Our studies show a positive correlation between membrane composition and immune evasion, alternate sugar utilization, and drug tolerance in C. auris.

Comparative Genomics of the First Resistant Candida auris Strain Isolated in Mexico: Phylogenomic and Pan-Genomic Analysis and Mutations Associated with Antifungal Resistance

Candida auris is an emerging multidrug-resistant and opportunistic pathogenic yeast. Whole-genome sequencing analysis has defined five major clades, each from a distinct geographic region. The current study aimed to examine the genome of the C. auris 20-1498 strain, which is the first isolate of this fungus identified in Mexico. Based on whole-genome sequencing, the draft genome was found to contain 70 contigs. It had a total genome size of 12.86 Mbp, an N50 value of 1.6 Mbp, and an average guanine-cytosine (GC) content of 45.5%. Genome annotation revealed a total of 5432 genes encoding 5515 proteins. According to the genomic analysis, the C. auris 20-1498 strain belongs to clade IV (containing strains endemic to South America). Of the two genes (ERG11 and FKS1) associated with drug resistance in C. auris, a mutation was detected in K143R, a gene located in a mutation hotspot of ERG11 (lanosterol 14-α-demethylase), an antifungal drug target. The focus on whole-genome sequencing and the identification of mutations linked to the drug resistance of fungi could lead to the discovery of new therapeutic targets and new antifungal compounds.

Antifungal Plant Defensins as an Alternative Tool to Combat Candidiasis

Currently, the spread of fungal infections is becoming an urgent problem. Fungi of the Candida genus are opportunistic microorganisms that cause superficial and life-threatening systemic candidiasis in immunocompromised patients. The list of antifungal drugs for the treatment of candidiasis is very limited, while the prevalence of resistant strains is growing rapidly. Therefore, the search for new antimycotics, including those exhibiting immunomodulatory properties, is of great importance. Plenty of natural compounds with antifungal activities may be extremely useful in solving this problem. This review evaluates the features of natural antimicrobial peptides, namely plant defensins as possible prototypes of new anticandidal agents. Plant defensins are important components of the innate immune system, which provides the first line of defense against pathogens. The introduction presents a brief summary regarding pathogenic Candida species, the pathogenesis of candidiasis, and the mechanisms of antimycotic resistance. Then, the structural features of plant defensins, their anticandidal activities, their mechanisms of action on yeast-like fungi, their ability to prevent adhesion and biofilm formation, and their combined action with conventional antimycotics are described. The possible mechanisms of fungal resistance to plant defensins, their cytotoxic activity, and their effectiveness in in vivo experiments are also discussed. In addition, for the first time for plant defensins, knowledge about their immunomodulatory effects is also presented.

Antifungal drug resistance in Candida: a special emphasis on amphotericin B

Invasive fungal infections in humans caused by several Candida species, increased considerably in immunocompromised or critically ill patients, resulting in substantial morbidity and mortality. Candida albicans is the most prevalent species, although the frequency of these organisms varies greatly according to geographic region. Infections with C. albicans and non-albicans Candida species have become more common, especially in the past 20 years, as a result of aging, immunosuppressive medication use, endocrine disorders, malnourishment, extended use of medical equipment, and an increase in immunogenic diseases. Despite C. albicans being the species most frequently associated with human infections, C. glabrata, C. parapsilosis, C. tropicalis, and C. krusei also have been identified. Several antifungal drugs with different modes of action are approved for use in clinical settings to treat fungal infections. However, due to the common eukaryotic structure of humans and fungi, only a limited number of antifungal drugs are available for therapeutic use. Furthermore, drug resistance in Candida species has emerged as a result of the growing use of currently available antifungal drugs against fungal infections. Amphotericin B (AmB), a polyene class of antifungal drugs, is mainly used for the treatment of serious systemic fungal infections. AmB interacts with fungal plasma membrane ergosterol, triggering cellular ion leakage via pore formation, or extracting the ergosterol from the plasma membrane inducing cellular death. AmB resistance is primarily caused by changes in the content or structure of ergosterol. This review summarizes the antifungal drug resistance exhibited by Candida species, with a special focus on AmB.