Molecular mechanisms of azole resistance in Candida bloodstream isolates

A MALDI-TOF MS-based multiple detection panel of drug resistance-associated multiple single-nucleotide polymorphisms in Candida tropicalis

Candida tropicalis is one of the main causes of invasive candidiasis. Rapid identification of antifungal resistance is crucial for selection of an appropriate antifungal to improve patient outcomes. Mutations at specific loci are strongly correlated with resistance to antifungal agents. In this study, we developed a multi-single-nucleotide polymorphism (SNP) panel to accurately identify 36 mutation sites across seven genes of C. tropicalis that are associated with resistance to azoles and/or echinocandins. Ten isolates were selected to test repeatability, and another 20 isolates of C. tropicalis were selected to validate consistency. Intra-assay and inter-assay repeatability of the panel was 100%, with the loci accuracy being 99.44% (716 of 720). Furthermore, 109 isolates were examined for clinical research, and the most commonly detected mutations were G751A and A866T of UPC2, A491T of TAC1, and A395T and C461T of ERG11. The G751A and A866T mutations of UPC2 as well as the A395T and C461T mutations of ERG11 co-existed. The SNP panel enables identification of specific mutations at critical sites of drug-resistant strains to facilitate the rapid selection of appropriate antifungal agents and efficient monitoring of the regional epidemiological trends of resistance of C. tropicalis.IMPORTANCEC. tropicalis infections pose a growing global public health challenge, with mortality rates approaching 40%. C. tropicalis is one of the top four Candida spp. responsible for candidiasis, particularly in the Asia-Pacific region and Latin America, notably affecting patients with neutropenia and malignancies. The azole resistance rate of C. tropicalis ranges from 0% to 30%. Between 2009 and 2018, the China Hospital Invasive Fungal Surveillance Network reported an increase in fluconazole and voriconazole resistance from 5.7% to ~30%. Although resistance to echinocandins and amphotericin B remains low, multi-resistance to echinocandins and azoles has been observed. Current methods for detecting drug resistance are limited by the long turnaround time of antifungal susceptibility testing, low throughput of Sanger sequence to target resistance mutations, complex data analysis, and high costs of second-generation sequencing. We developed and validated a rapid, high-throughput, and cost-effective panel to detect and monitor drug-resistance mutations of C. tropicalis.

Candida tropicalis morphotypes show altered cellular structure and gene expression pre- and post-exposure to fluconazole

A feature of Candida tropicalis is its ability to undergo phenotypic switching that can affect antifungal sensitivity and virulence traits. Here, we investigated the effect of switching on alterations at the cellular structure level of C. tropicalis morphotypes and whether exposure to fluconazole (FLC) in vitro could be associated with these alterations in a morphotype-dependent manner. Candida tropicalis morphotypes included clinical isolate (Parental) and two switch strains (Crepe variant and revertant of Crepe-RC). The minimum inhibitory concentration (MIC50) of fluconazole was determined according to EUCAST. Cell wall porosity, quantification of cell wall components, cell size/complexity, and expression of ERG11 and CDR1 genes in morphotypes pre- and post-exposure to fluconazole were determined. Crepe and RC showed an eightfold higher MIC50 (1 µg/ml) than the Parental (0.125 µg/ml). Exposure to FLC resulted in twofold higher MIC50 for Parental and RC. The Crepe variant exhibited a fourfold higher expression of ERG11, and the RC showed 10-fold higher expression of CDR1 than the clinical isolate. Switch strains showed reduced cell wall porosity compared to Parental, and exposure to FLC resulted in a significant reduction in the porosity of Parental and RC cells. Furthermore, phenotypic switching affected cell wall β-1,3-glucan and chitin contents in a morphotype-dependent manner. Our findings indicate that switching affects cellular structure in C. tropicalis and the occurrence of differential alterations between the clinical isolate and its switched states in response to fluconazole exposure.

Genome-wide profiling of piggyBac transposon insertion mutants reveals loss of the F1F0 ATPase complex causes fluconazole resistance in Candida glabrata

Invasive candidiasis caused by non-albicans species has been on the rise, with Candida glabrata emerging as the second most common etiological agent. Candida glabrata possesses an intrinsically lower susceptibility to azoles and an alarming propensity to rapidly develop high-level azole resistance during treatment. In this study, we have developed an efficient piggyBac (PB) transposon-mediated mutagenesis system in C. glabrata to conduct genome-wide genetic screens and applied it to profile genes that contribute to azole resistance. When challenged with the antifungal drug fluconazole, PB insertion into 270 genes led to significant resistance. A large subset of these genes has a role in the mitochondria, including almost all genes encoding the subunits of the F1F0 ATPase complex. We show that deleting ATP3 or ATP22 results in increased azole resistance but does not affect susceptibility to polyenes and echinocandins. The increased azole resistance is due to increased expression of PDR1 that encodes a transcription factor known to promote drug efflux pump expression. Deleting PDR1 in the atp3Δ or atp22Δ mutant resulted in hypersensitivity to fluconazole. Our results shed light on the mechanisms contributing to azole resistance in C. glabrata. This PB transposon-mediated mutagenesis system can significantly facilitate future genome-wide genetic screens.

Analysis of CDR1 and MDR1 Gene Expression and ERG11 Substitutions in Clinical Candida tropicalis Isolates from Alexandria, Egypt

INTRODUCTION

Candida tropicalis is a common non-albicans Candida (NAC) species that causes numerous fungal infections. Increasing antifungal resistance to azoles in NAC is becoming a major health problem worldwide; however, in Egypt, almost no data is available regarding fluconazole resistance mechanisms in C. tropicalis. The current study aims to investigate two possible important molecular mechanisms involved in fluconazole resistance in C. tropicalis isolates.

MATERIALS

Fifty-four clinical C. tropicalis isolates were included. Identification and antifungal susceptibility profiles of the isolates were carried out using the VITEK 2 compact system. The molecular investigation of fluconazole resistance included the expression of the CDR1 and MDR1 genes by quantitative real-time RT-PCR as well as the sequence analysis of the ERG11 gene.

RESULTS

Antifungal susceptibility testing identified 30 fluconazole-non-susceptible isolates. Statistically, CDR1 gene expression in fluconazole-non-susceptible isolates was significantly higher than that in fluconazole-susceptible isolates, with MDR1 gene expression levels that were similar in both non-susceptible and susceptible isolates. Sequence analysis of the ERG11 gene of 26 fluconazole-resistant isolates identified two missense mutations: A395T (Y132F) and G1390A (G464S).

CONCLUSIONS

This study has highlighted the role of overexpression of the CDR1 gene and ERG11 gene mutations in fluconazole non-susceptibility. Further studies in Egypt are required to investigate other possible molecular mechanisms involved in azole resistance.

Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures

The longstanding model is that most bloodstream infections (BSIs) are caused by a single organism. We perform whole genome sequencing of five-to-ten strains from blood culture (BC) bottles in each of ten patients with Candida glabrata BSI. We demonstrate that BCs contain mixed populations of clonal but genetically diverse strains. Genetically distinct strains from two patients exhibit phenotypes that are potentially important during BSIs, including differences in susceptibility to antifungal agents and phagocytosis. In both patients, the clinical microbiology lab recovered a fluconazole-susceptible index strain, but we identify mixed fluconazole-susceptible and -resistant populations. Diversity in drug susceptibility is likely clinically relevant, as fluconazole-resistant strains were subsequently recovered by the clinical laboratory during persistent or relapsing infections. In one patient, unrecognized respiration-deficient small colony variants are fluconazole-resistant and significantly attenuated for virulence during murine candidiasis. Our data suggest a population-based model of C. glabrata genotypic and phenotypic diversity during BSIs.

Antifungal drug susceptibility profiles and molecular mechanisms of azole resistance in Candida blood stream isolates

PURPOSE

The purpose of this study was to determine the activity of fluconazole, voriconazole, posaconazole, amphotericin B, micafungin and caspofungin against Candida blood stream isolates and to investigate the molecular mechanisms of azole resistance in fluconazole resistant isolates.

METHODS

The in vitro susceptibilities of Candida isolates to fluconazole, voriconazole, posaconazole, amphotericin B, micafungin and caspofungin were tested by E-test ERG11, CDR1, CDR2 and MDR1 genes expression of fluconazole resistant, fluconazole (S-DD) and fluconazole intermediate resistant isolates were investigated by quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR).

RESULTS

C. albicans (41%) was the most frequently isolated fungal species from blood stream infections followed by C. parapsilosis (22%). All C. albicans isolates except one and all C. tropicalis isolates were found to be susceptible to fluconazole. Overall, 21% of C. glabrata isolates were resistant to fluconazole. None of the Candida isolates were found to be resistant to caspofungin except 2 ​C. glabrata isolates. Overexpression of ERG11 and CDR1 genes were detected in all fluconazole S-DD and fluconazole resistant C. glabrata isolates, while CDR2 overexpression was observed in 91% fluconazole S-DD and 67 of % fluconazole resistant C.glabrata isolates. The overexpression of MDR1, ERG11 and CDR1 genes were found 100%, 80% and 80%, respectively, in fluconazole resistant C. parapsilosis isolates.

CONCLUSION

Most of the Candida isolates were susceptible to posaconazole and caspofungin. Our data also highlighted that overexpression of efflux pump genes major cause of azole resistance.

Encapsulation of Zataria multiflora essential oil in polyvinyl alcohol/chitosan/gelatin thermo-responsive hydrogel: Synthesis, physico-chemical properties, and biological investigations

Zataria multiflora essential oil is a natural volatile plant product whose therapeutic applications require a delivery platform. Biomaterial-based hydrogels have been extensively used in biomedical applications, and they are promising platforms to encapsulate essential oils. Among different hydrogels, intelligent hydrogels have recently attracted many interests because of their response to environmental stimuli such as temperature. Herein, Zataria multiflora essential oil is encapsulated in a polyvinyl alcohol/chitosan/gelatin hydrogel as a positive thermo-responsive and antifungal platform. According to the optical microscopic image, the encapsulated spherical essential oil droplets reveal a mean size of 1.10 ± 0.64 μm, which are in consistent with the SEM imaging results. Encapsulation efficacy and loading capacity are 98.66 % and 12.98 %, respectively. These results confirm the successful efficient encapsulation of the Zataria multiflora essential oil within the hydrogel. The chemical compositions of the Zataria multiflora essential oil and the fabricated hydrogel are analyzed by gas chromatography-mass spectroscopy (GC-MS) and Fourier transform infrared (FTIR) techniques. It is found that thymol (44.30 %) and γ-terpinene (22.62 %) are the main constituents of the Zataria multiflora essential oil. The produced hydrogel inhibits the metabolic activity of Candida albicans biofilms (~60-80 %), which can be related to the antifungal activity of the essential oil constituents and chitosan. Based on the rheological results, the produced thermo-responsive hydrogel shows a gel-sol viscoelastic transition at a temperature of 24.5 °C. This transition leads to a facile release of the loaded essential oil. The release test depicts that about 30 % of Zataria multiflora essential oil is released during the first 16 min. In addition, 2, 5-diphenyl-2H-tetrazolium bromide (MTT) assay demonstrates that the designed thermo-sensitive formulation is biocompatible with high cell viability (over 96 %). The fabricated hydrogel can be deemed as a potential intelligent drug delivery platform for controlling cutaneous candidiasis due to antifungal effectiveness and less toxicity, which can be a promising alternative to traditional drug delivery systems.

Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures

The longstanding paradigm is that most bloodstream infections (BSIs) are caused by a single organism. We performed whole genome sequencing of five-to-ten strains from blood culture (BC) bottles in each of ten patients with Candida glabrata BSI. We demonstrated that BCs contained mixed populations of clonal but genetically diverse strains. Genetically distinct strains from two patients exhibited phenotypes that were potentially important during BSIs, including differences in susceptibility to antifungal agents and phagocytosis. In both patients, the clinical microbiology lab recovered a fluconazole-susceptible index strain, but we identified mixed fluconazole-susceptible and â€"resistant populations. Diversity in drug susceptibility was likely clinically relevant, as fluconazole-resistant strains were subsequently recovered by the clinical laboratory during persistent or relapsing infections. In one patient, unrecognized respiration-deficient small colony variants were fluconazole-resistant and significantly attenuated for virulence during murine candidiasis. Our data suggest a new population-based paradigm of C. glabrata genotypic and phenotypic diversity during BSIs.

Myriocin enhances the antifungal activity of fluconazole by blocking the membrane localization of the efflux pump Cdr1

Introduction: Extrusion of azoles from the cell, mediated by an efflux pump Cdr1, is one of the most frequently used strategies for developing azole resistance in pathogenic fungi. The efflux pump Cdr1 is predominantly localized in lipid rafts within the plasma membrane, and its localization is sensitive to changes in the composition of lipid rafts. Our previous study found that the calcineurin signal pathway is important in transferring sphingolipids from the inner to the outer membrane. Methods: We investigated multiple factors that enhance the antifungal activity of fluconazole (FLC) using minimum inhibitory concentration (MIC) assays and disk diffusion assays. We studied the mechanism of action of myriocin through qRT-PCR analysis and confocal microscopy analysis. We tested whether myriocin enhanced the antifungal activity of FLC and held therapeutic potential using a mouse infection model. Results: We found that this signal pathway has no function in the activity of Cdr1. We found that inhibiting sphingolipid biosynthesis by myriocin remarkably increased the antifungal activity of FLC with a broad antifungal spectrum and held therapeutic potential. We further found that myriocin potently enhances the antifungal activity of FLC against C. albicans by blocking membrane localization of the Cdr1 rather than repressing the expression of Cdr1. In addition, we found that myriocin enhanced the antifungal activity of FLC and held therapeutic potential. Discussion: Our study demonstrated that blocking the membrane location and inactivating Cdr1 by inhibiting sphingolipids biogenesis is beneficial for enhancing the antifungal activity of azoles against azole-resistant C. albicans due to Cdr1 activation.

<i>CDR1, CDR2, MDR1</i> and <i>ERG11</i> expression in azole resistant <i>Сandida albicans</i> isolated from HIV-infected patients in city of Moscow

Candida fungi are common opportunistic microorganisms capable of causing infections of various localization, as well as life-threatening conditions in immunocompromised patients, such as HIV-infected individuals, oncology patients, subjects undergoing HSCT, which number has been steadily increasing in recent years. In addition, resistance to anti-fungal drugs has been spreading as well. Naturally sensitive to azoles, C. albicans possess a variety of mechanisms of acquired resistance, including efflux transporters and target protein-encoding gene amplification. This study was conducted to assess a prevalence of such mechanisms in the isolates sample obtained from HIV-infected patients in the Moscow region of the Russian Federation, characterize a relationship between these mechanisms and patterns of developing drug resistance. 18 strains of C. albicans resistant to fluconazole and voriconazole were isolated from HIV-infected patients with recurrent oropharyngeal candidiasis in the Moscow region. The expression levels of the ERG11, MDR1, CDR1, CDR2 genes involved in the formation of acquired azole resistance were measured using quantitative PCR, the 2CT method with ACT and PMA genes as control genes and reference values of sensitive isolates. Expression levels exceeding the average values of sensitive isolates by more than 3 standard deviations were considered significantly elevated. In most of the isolates, elevated levels of CDR1 and CDR2 gene expression were found: 89% and 78%, respectively. The expression level of the MDR1 gene was increased only in 28% of cases. ERG11 expression levels were significantly elevated in 78% of the isolates. Expression levels of all resistance genes studied were significantly increased in 4 strains. In this sample of C. albicans isolates, acquired resistance is mainly associated with efflux vectors encoded by the CDR1 and CDR2 genes. Also, in most isolates, an increased expression level for the azole target protein gene ERG11 was detected. The expression level of the efflux transporter gene MDR1 was increased in the smallest number of samples. It is also impossible to exclude a potential role of other mechanisms in developing acquired resistance, such as mutations in the ERG11 gene. It can be assumed that the identified mechanisms of resistance result from long-term, widespread, and sometimes uncontrolled use of azoles, including those in treatment and prevention of candidiasis in HIV-infected patients.

Azole Resistance in Candida albicans Isolates from Oropharyngeal Candidiasis is Associated with ERG11 Mutation and Efflux Overexpression

Background: Azole resistance rates are rising in Candida species. Fluconazole is one of the most important antifungal drugs used in candidiasis treatment. Objectives: We identified the molecular mechanisms of fluconazole resistance of Candida albicans oropharyngeal candidiasis (OPC) isolates obtained from head and neck cancer patients, a study carried out between 2018 and 2020. Methods: One hundred and twenty-five Candida albicans clinical isolates were collected. Antifungal susceptibilities were determined by the CLSI- M27-A3 method. The ERG11 gene was amplified and sequenced to discover SNP mutation. Moreover, real-time PCR was carried out to measure the mRNA levels of ERG11, CDR1, CDR2, and MDR1. Results: Resistance to fluconazole was found in 15 C. albicans isolates. Amino acid substitutions E266D and D116E were observed in resistant, sensitive dose-dependent (SDD), and susceptible C. albicans isolates. K128T, G465S, A114S, Y257H and V488I were in relation to fluconazole resistance. D504A, P375A, W520C, G59S, and V51L were novel substitutions detected in the isolates; except for D504A, other mutations were observed only in resistance isolates. The expression levels of CDR2, CDR1, MDR1, and ERG11 were increased compared to susceptible isolates, respectively. Conclusions: ERG11 mutation was the principal mechanism for fluconazole resistance in C. albicans isolated from oropharyngeal candidiasis patients, and caspofungin can be used as the effective antifungal substance in fluconazole resistance situation for C. albicans infection.

The Risk Factors and Mechanisms of Azole Resistance of Candida tropicalis Blood Isolates in Thailand: A Retrospective Cohort Study

In recent decades, an epidemiological shift has been observed from Candida infections to non-albicans species and resistance to azoles. We investigated the associated factors and molecular mechanisms of azole-resistant blood isolates of C. tropicalis. Full-length sequencing of the ERG11 gene and quantitative real-time RT-PCR for the ERG11, MDR1, and CDR1 genes were performed. Male sex (odds ratio, 0.38), leukemia (odds ratio 3.15), and recent administration of azole (odds ratio 10.56) were associated with isolates resistant to azole. ERG11 mutations were found in 83% of resistant isolates, with A395T as the most common mutation (53%). There were no statistically significant differences in the expression of the ERG11, MDR1, and CDR1 genes between the groups resistant and susceptible to azole. The prevalence of azole-resistant isolates was higher than the usage of antifungal drugs, suggesting the possibility of environmental transmission in the healthcare setting. The unknown mechanism of the other 17% of the resistant isolates remains to be further investigated.

The emerging threat antifungal-resistant Candida tropicalis in humans, animals, and environment

Antifungal resistance in humans, animals, and the environment is an emerging problem. Among the different fungal species that can develop resistance, Candida tropicalis is ubiquitous and causes infections in animals and humans. In Asia and some Latin American countries, C. tropicalis is among the most common species related to candidemia, and mortality rates are usually above 40%. Fluconazole resistance is especially reported in Asian countries and clonal spread in humans and the environment has been investigated in some studies. In Brazil, high rates of azole resistance have been found in animals and the environment. Multidrug resistance is still rare, but recent reports of clinical multidrug-resistant isolates are worrisome. The molecular apparatus of antifungal resistance has been majorly investigated in clinical C. tropicalis isolates, revealing that this species can develop resistance through the conjunction of different adaptative mechanisms. In this review article, we summarize the main findings regarding antifungal resistance and Candida tropicalis through an "One Health" approach.

Comparative Analysis of Epidemiological and Clinical Characteristics Between Invasive Candida Infection versus Colonization in Critically Ill Patients in a Tertiary Hospital in Anhui, China

Objective

Invasive infections due to Candida spp. have unique epidemiology, strain distribution, antimicrobial susceptibility, and clinical features. This study aimed to compare and evaluate these characteristic variables between invasive Candida infection and colonization of critically ill patients in local China to potentially improve differential diagnosis and therapy.

Methods

A total of 193 critically ill patients were recruited and followed up for the study, and 133 Candida isolates were obtained from invasive Candida-infected or -colonized subjects. The strains were identified to species level through matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry, assisted by DNA sequencing. Candida susceptibility to common antifungals, including azoles, was determined by microbroth ATB Fungus 3 methodology. Azole resistance–related gene sequencing and homologous 3D-structure modeling were employed. Patient demographics and clinical risk factors were documented and comparatively analyzed from the hospital information-management system.

Results

Non–C. albicans Candida (56%) principally caused invasive Candida infections, while C. albicans (55.17%) contributed more to Candida colonization in critically ill patients. Additional risk factors exerted significant impact on both Candida cohorts, primarily including invasive interventions, cancers, and concurrent infections in common. Most colonized Candida spp. harbored relatively higher sensitivity to azoles. ERG11 gene mutations of T348A and A1309G, A395T and C461T, and a novel G1193T to our knowledge were identified in azole-resistant C. albicans, C. tropicalis, and C. parapsilosis respectively, and their corresponding homologous 3D-structure modeling was putatively achieved.

Conclusion

Distinct epidemiological and clinical characteristics existed between invasive Candida infection and colonization in critically ill patients. Multiple risk factors significantly involved both the Candida cohorts. Colonized Candida exhibited generally higher azole sensitivity than invasively infectious counterparts. ERG11 point mutations had mechanistically potential ties with local Candida resistance to azoles.

In vitro synergistic antifungal activities with caspofungin plus fluconazole or voricanazole against Candida species determined by Etest method

OBJECTIVES

Increased resistance of Candida species, especially C.glabrata is problematic. Combination antifungal therapies were studied to solve the problem.

METHODS

In this study, combinations of caspofungin with fluconazole and voricanazole were evaluated in 28 Candida species (included 15 C.glabrata and 12 with FKS mutation) at 24 and 48 h by two Etest methods (direct cover method and MIC/MIC method).

RESULTS

For Candida isolates, direct cover method showed synergy of caspofungin-fluconazole and caspofungin-voriconazole against 12/28 (43%) isolates at 24 h, and against 16/28 (57%) isolates at 48 h. MIC/MIC method showed synergy of caspofungin-fluconazole and caspofungin-voriconazole against 11/28 (39%) and 12/28 (43%) isolates at 24 h, and against 16/28 (57%) and 17/28 (61%) isolates at 48 h, respectively. For C.glabrata, direct cover method showed synergy of caspofungin-fluconazole and caspofungin-voriconazole against 11/15 (73%) and 10/15 (67%) isolates at 24 h, and 11/15 (73%) and 13/15 (87%) isolates at 48 h, respectively. MIC/MIC method showed synergy of caspofungin-fluconazole and caspofungin-voriconazole against both 11/15 (73%) isolates at 24 h, and 10/15 (67%) and 14/15 (93%) isolates at 48 h, respectively.

CONCLUSION

A combination of caspofungin and fluconazole or voriconazole might be effective in infections due to Candida species, especially for C.glabrata with FKS mutation.

A New Variant of Mutational and Polymorphic Signatures in the ERG11 Gene of Fluconazole-Resistant Candida albicans

Background

Resistance to antifungal drugs for treating Candida infections remains a major concern globally despite the range of medications available. Most of these drugs target key proteins essential to the life cycle of the organism. An enzyme essential for fungal cell membrane integrity, lanosterol 14–α demethylase (CYP51), is encoded by the ERG11 gene in Candida species. This enzyme is the target of azole–based drugs. The organism has, however, devised molecular adaptations to evade the activity of these drugs.

Materials and Methods

Classical methods were employed to characterize clinical isolates sampled from women and dogs of reproductive age. For fluconazole efficacy studies, CLSI guidelines on drug susceptibility testing were used. To understand the susceptibility pattern, various molecular and structural analytic approaches, including sequencing, in silico site-directed mutagenesis, and protein-ligand profiling, were applied to the ERG11 gene and CYP51 protein sequences. Several platforms, comprising Clustal Omega, Pymol plugin manager, Pymol molecular visualizer, Chimera–curated Dynameomics rotamer library, protein–ligand interaction profiler, Charmm36 force field, GROMACS, Geneious, and Mega7, were employed for this analysis.

Results

The following Candida species distribution was obtained: 37.84% C. albicans, 8.12% C. glabrata, 10.81% C. krusei, 5.41% C. tropicalis, and 37.84% of other unidentified Candida species. Two codons in the nucleotide sequence of the wild-type (CTC and CCA) coding for LEU–370 and PRO–375, respectively, were mutated to L370S and P375H in the resistant strain. The mutation stabilized the protein at the expense of the heme moiety. We found that the susceptible isolate from dogs (Can–iso–029/dog) is closely related to the most resistant isolate from humans.

Conclusion

Taken together, our results showed new mutations in the heme-binding pocket of caCYP51 that explain the resistance to fluconazole exhibited by the Candida isolates. So far, the L370S and P375H resistance-linked mutations have not been previously reported.

Collateral consequences of agricultural fungicides on pathogenic yeasts: A One Health perspective to tackle azole resistance

Candida and Cryptococcus affect millions of people yearly, being responsible for a wide array of clinical presentations, including life-threatening diseases. Interestingly, most human pathogenic yeasts are not restricted to the clinical setting, as they are also ubiquitous in the environment. Recent studies raise concern regarding the potential impact of agricultural use of azoles on resistance to medical antifungals in yeasts, as previously outlined with Aspergillus fumigatus. Thus, we undertook a narrative review of the literature and provide lines of evidence suggesting that an alternative, environmental route of azole resistance, may develop in pathogenic yeasts, in addition to patient route. However, it warrants sound evidence to support that pathogenic yeasts cross border between plants, animals and humans and that environmental reservoirs may contribute to azole resistance in Candida or other yeasts for humans. As these possibilities could concern public health, we propose a road map for future studies under the One Health perspective.

Unmasking of CgYor1-Dependent Azole Resistance Mediated by Target of Rapamycin (TOR) and Calcineurin Signaling in Candida glabrata

In this study, 18 predicted membrane-localized ABC transporters of Candida glabrata were deleted individually to create a minilibrary of knockouts (KO). The transporter KOs were analyzed for their susceptibility toward antimycotic drugs. Although CgYOR1 has previously been reported to be upregulated in various azole-resistant clinical isolates of C. glabrata, deletion of this gene did not change the susceptibility to any of the tested azoles. Additionally, Cgyor1Δ showed no change in susceptibility toward oligomycin, which is otherwise a well-known substrate of Yor1 in other yeasts. The role of CgYor1 in azole susceptibility only became evident when the major transporter CgCDR1 gene was deleted. However, under nitrogen-depleted conditions, Cgyor1Δ demonstrated an azole-susceptible phenotype, independent of CgCdr1. Notably, Cgyor1Δ cells also showed increased susceptibility to target of rapamycin (TOR) and calcineurin inhibitors. Moreover, increased phytoceramide levels in Cgyor1Δ and the deletions of regulators downstream of TOR and the calcineurin signaling cascade (Cgypk1Δ, Cgypk2Δ, Cgckb1Δ, and Cgckb2Δ) in the Cgyor1Δ background and their associated fluconazole (FLC) susceptibility phenotypes confirmed their involvement. Collectively, our findings show that TOR and calcineurin signaling govern CgYor1-mediated azole susceptibility in C. glabrata. IMPORTANCE The increasing incidence of Candida glabrata infections in the last 40 years is a serious concern worldwide. These infections are usually associated with intrinsic azole resistance and increasing echinocandin resistance. Efflux pumps, especially ABC transporter upregulation, are one of the prominent mechanisms of azole resistance; however, only a few of them are characterized. In this study, we analyzed the mechanisms of azole resistance due to a multidrug resistance-associated protein (MRP) subfamily ABC transporter, CgYor1. We demonstrate for the first time that CgYor1 does not transport oligomycin but is involved in azole resistance. Under normal growing conditions its function is masked by major transporter CgCdr1; however, under nitrogen-depleted conditions, it displays its azole resistance function independently. Moreover, we propose that the azole susceptibility due to removal of CgYor1 is not due to its transport function but involves modulation of TOR and calcineurin cascades.

Candida Isolates From Blood and Other Normally Sterile Foci From ICU Patients: Determination of Epidemiology, Antifungal Susceptibility Profile and Evaluation of Associated Risk Factors

Background: The clinical diagnosis and therapy for ICU patients with invasive candidiasis are challenged by the changes of Candida community composition and antimicrobial resistance. The epidemiology and drug sensitivity of candidiasis in ICU as well as its risk factors and drug resistance mechanism were investigated. Methods: In the present study, 115 patients in ICU were recruited from June 2019 through July 2020. Among them, 83 Candida isolates were identified with MALDI-TOF mass spectrometry. The susceptibility to antifungals was measured by microdilution method. The molecular mechanisms of azole-resistant Candida tropicalis were explored by sequencing, and their outcomes were explicitly documented. Results: Candida glabrata and C. tropicalis were the predominant non-C. albicans Candida. The specimen sources were mainly urine, bronchoalveolar lavage fluid and blood. The age, length of hospitalization, tracheotomy, diabetes and concomitant bacterial infection were the main risk factors for candidiasis. The majority of Candida species exhibited susceptibility to antifungals. However, certain C. tropicalis were frequently resistant to azoles. The polymorphism of the ERG11 in C. tropicalis was likely associated with azole resistance. Conclusion: The multiple risk factors for candidiasis in ICU patients need to be considered. Certain C. tropicalis exhibit resistance to azoles likely due to the ERG11 gene polymorphism.

Azole and echinocandin resistance mechanisms and genotyping of Candida tropicalis in Japan: cross-boundary dissemination and animal-human transmission of C. tropicalis infection

OBJECTIVES

To assess the prevalence and genetic basis of antifungal resistance mechanisms as well as the genotyping of Candida tropicalis from clinical and non-clinical sources in Japan.

METHODS

Eighty C. tropicalis isolates, including 32 clinical isolates recovered from 29 patients and 48 non-clinical isolates recovered from 24 different sources (animals and the environment) were evaluated. All isolates were tested phenotypically for resistance to a wide range of antifungals and genotypically for resistance mechanisms to azole and echinocandin. Furthermore, all the isolates were genotyped by multilocus sequence typing (MLST).

RESULTS

Phenotypically, 30.2% (16/53) of the isolates were azole-resistant, with high levels of azole resistance among clinical isolates (51.7%; 15/29) and low levels (4.2%; 1/24) among non-clinical isolates. None of the isolates were reported as echinocandin resistant, with 60.4% (32/53) of the isolates intermediate to caspofungin. Azole resistance was basically attributed to high expression levels of drug efflux transporter genes (CDR2 and CDR3), transcription factors (TAC1 and UPC2) and ergosterol biosynthesis pathway HMG gene. No FKS1 hot spot 1 (HS1) or HS2 missense mutations were detected in any of the isolates. MLST analysis revealed 36 different sequence types (STs), with the first identification of 23 new STs. Phylogenetic analysis confirmed the close relationship between the clinical and non-clinical isolates, with identifications of ST232 and ST933 among patients and marine mammals.

CONCLUSION

Our results confirmed the emergence of azole resistance in C. tropicalis in Japan. Furthermore, phylogenetic analysis confirmed the transboundary dissemination and cross-transmission of C. tropicalis between humans and animals.

Mechanisms of Azole Resistance and Trailing in Candida tropicalis Bloodstream Isolates

Objectives: Azole-resistant Candida tropicalis has emerged in Asia in the context of its trailing nature, defined by residual growth above minimum inhibitory concentrations (MICs). However, limited investigations in C. tropicalis have focused on the difference of genotypes and molecular mechanisms between these two traits. Methods: Sixty-four non-duplicated C. tropicalis bloodstream isolates collected in 2017 were evaluated for azole MICs by the EUCAST E.def 7.3.1 method, diploid sequence type (DST) by multilocus sequencing typing, and sequences and expression levels of genes encoding ERG11, its transcription factor, UPC2, and efflux pumps (CDR1, CDR2 and MDR1). Results: Isavuconazole showed the highest in vitro activity and trailing against C. tropicalis, followed by voriconazole and fluconazole (geometric mean [GM] MIC, 0.008, 0.090, 1.163 mg/L, respectively; trailing GM, 27.4%, 20.8% and 19.5%, respectively; both overall p < 0.001). Fourteen (21.9%) isolates were non-WT to fluconazole/voriconazole, 12 of which were non-WT to isavuconazole and clustered in clonal complex (CC) 3. Twenty-five (39.1%) isolates were high trailing WT, including all CC2 isolates (44.0%) (containing DST140 and DST98). All azole non-WT isolates carried the ERG11 mutations A395T/W and/or C461T/Y, and most carried the UPC2 mutation T503C/Y. These mutations were not identified in low and high trailing WT isolates. Azole non-WT and high trailing WT isolates exhibited the highest expression levels of ERG11 and MDR1, 3.91- and 2.30-fold, respectively (both overall p < 0.01). Conclusions: Azole resistance and trailing are phenotypically and genotypically different in C. tropicalis. Interference with azole binding and MDR1 up-regulation confer azole resistance and trailing, respectively.

A novel use for an old drug: resistance reversal in Candida albicans by combining dihydroartemisinin with fluconazole

Aim: To investigate the effects of dihydroartemisinin combined with fluconazole against C. albicans in vitro and to explore the underlying mechanisms. Materials & methods: Checkerboard microdilution assay and time-kill curve method were employed to evaluate the static and dynamic antifungal effects against C. albicans. Reactive oxygen species (ROS) was measured by a fluorescent probe. Results: Combination of dihydroartemisinin and fluconazole exerted potent synergy against planktonic cells and biofilms of fluconazole-resistant C. albicans, with the fractional inhibitory concentration index values less than 0.07. A potent fungistatic activity of this drug combination could still be observed after 18 h. The accumulation of ROS induced by the drug combination might contribute to the synergy. Conclusion: Dihydroartemisinin reversed the resistance of C. albicans to fluconazole.

A Review on Molecular Mechanisms of Antifungal Resistance in Candida glabrata: Update and Recent Advances

Candida glabrata is the second frequent etiologic agent of mucosal and invasive candidiasis. Based on the recent developments in molecular methods, C. glabrata has been introduced as a complex composed of C. glabrata, Candida nivariensis, and Candida bracarensis. The four main classes of antifungal drugs effective against C. glabrata are pyrimidine analogs (flucytosine), azoles, echinocandins, and polyenes. Although the use of antifungal drugs is related to the predictable development of drug resistance, it is not clear why C. glabrata is able to rapidly resist against multiple antifungals in clinics. The enhanced incidence and antifungal resistance of C. glabrata and the high mortality and morbidity need more investigation regarding the resistance mechanisms and virulence associated with C. glabrata; additional progress concerning the drug resistance of C. glabrata has to be further prevented. The present review highlights the mechanism of resistance to antifungal drugs in C. glabrata.

Molecular Diagnosis of Yeast Infections

PURPOSE OF REVIEW

The use of molecular tests to aid the diagnosis of invasive yeast infection, in particular invasive candidosis, has been described for over two decades, yet widespread application is limited, and diagnosis remains heavily dependent on classical microbiology. This article will review developments from the past decade in attempt to build on existing knowledge. It will highlight clinical performance and limitations while reviewing developments on recognized procedures; it will also provide insight into novel approaches incorporated in response to clinical demand (e.g. C. auris and antifungal resistance) or technological advances (e.g. next-generation sequencing).

RECENT FINDINGS

Limited methodological standardization and, until recently, unavailability of commercial options have hindered the integration of molecular diagnostics for yeasts. The development of certain, novel commercial methods has received considerable evaluation allowing a greater understanding of individual assay performance, but widespread multicentre evaluation of most commercial kits is lacking. The detection of emerging pathogens (e.g. C. auris) has been enhanced by the development of molecular tests. Molecular methods are providing a better understanding of the mycobiome, mechanisms of resistance and epidemiology/phylogeny.

SUMMARY

Despite over two decades of use, the incorporation of molecular methods to enhance the diagnosis of yeast infections remains limited to certain specialist centres. While the development of commercial tests will provide stimulus for broader application, further validation and reduced costs are required. Over the same period of time, Aspergillus PCR has become more widely accepted driven by international efforts to standardize methodology; it is critical that yeast PCR follows suit. Next-generation sequencing will provide significant information on the mycobiome, antifungal resistance mechanism and even broad-range detection directly from the specimen, which may be critical for the molecular detection of yeasts other than Candida species, which is currently limited.

Interaction of Styrylpyridinium Compound with Pathogenic Candida albicans Yeasts and Human Embryonic Kidney HEK-293 Cells

Candida albicans-caused local and systemic diseases are a serious health issue worldwide, leading to high mycosis-associated morbidity and mortality. Efficient combinations of novel compounds with commonly used antifungals could be an important tool for fighting infections. The aim of this study was to evaluate the interaction of synthesized 4-(4-cyanostyryl)-1-dodecylpyridin-1-ium (CSDP⁺) bromide alone or in combination with fluconazole with yeast and mammalian cells. We investigated cytotoxicity of the tested agents to mammalian HEK-293 cells and the influence of CSDP⁺ on the ability of C. albicans wt and a clinical isolate to adhere to HEK-293. Accumulation of lipophilic cation ethidium (Et⁺) was used to monitor the activity of efflux pumps in HEK-293 cells. The effect of CSDP⁺ on the expression of the main efflux transporter genes and transcription factors in C.albicans cells as well as HEK-293 efflux pump gene ABCB1 was determined. The study showed that CSDP⁺ alone and in combination with fluconazole was nontoxic to HEK-293 cells and was able to reduce C.albicans adhesion. The treatment of C.albicans cells with CSDP⁺ in combination with fluconazole resulted in a considerable overexpression of the MDR1 and MRR1 genes. The findings suggest that these genes could be associated with efflux-related resistance to fluconazole. Measurements of Et⁺ fluorescence and analysis of ABCB1 gene expression demonstrated that mammalian cells were not sensitive to concentrations of CSDP⁺ affecting C. albicans.

Sterol 14α-Demethylase Ligand-Binding Pocket-Mediated Acquired and Intrinsic Azole Resistance in Fungal Pathogens

The fungal cytochrome P450 enzyme sterol 14α-demethylase (SDM) is a key enzyme in the ergosterol biosynthesis pathway. The binding of azoles to the active site of SDM results in a depletion of ergosterol, the accumulation of toxic intermediates and growth inhibition. The prevalence of azole-resistant strains and fungi is increasing in both agriculture and medicine. This can lead to major yield loss during food production and therapeutic failure in medical settings. Diverse mechanisms are responsible for azole resistance. They include amino acid (AA) substitutions in SDM and overexpression of SDM and/or efflux pumps. This review considers AA affecting the ligand-binding pocket of SDMs with a primary focus on substitutions that affect interactions between the active site and the substrate and inhibitory ligands. Some of these interactions are particularly important for the binding of short-tailed azoles (e.g., voriconazole). We highlight the occurrence throughout the fungal kingdom of some key AA substitutions. Elucidation of the role of these AAs and their substitutions may assist drug design in overcoming some common forms of innate and acquired azole resistance.

Potent Synergistic Interactions between Lopinavir and Azole Antifungal Drugs against Emerging Multidrug-Resistant Candida auris

The limited therapeutic options and the recent emergence of multidrug-resistant Candida species present a significant challenge to human medicine and underscore the need for novel therapeutic approaches. Drug repurposing appears as a promising tool to augment the activity of current azole antifungals, especially against multidrug-resistant Candida auris In this study, we evaluated the fluconazole chemosensitization activities of 1,547 FDA-approved drugs and clinical molecules against azole-resistant C. auris This led to the discovery that lopinavir, an HIV protease inhibitor, is a potent agent capable of sensitizing C. auris to the effect of azole antifungals. At a therapeutically achievable concentration, lopinavir exhibited potent synergistic interactions with azole drugs, particularly with itraconazole against C. auris (fractional inhibitory concentration index [ΣFICI] ranged from 0.04 to 0.09). Additionally, the lopinavir/itraconazole combination enhanced the survival rate of C. auris-infected Caenorhabditis elegans by 90% and reduced the fungal burden in infected nematodes by 88.5% (P < 0.05) relative to that of the untreated control. Furthermore, lopinavir enhanced the antifungal activity of itraconazole against other medically important Candida species, including C. albicans, C. tropicalis, C. krusei, and C. parapsilosis Comparative transcriptomic profiling and mechanistic studies revealed that lopinavir was able to significantly interfere with the glucose permeation and ATP synthesis. This compromised the efflux ability of C. auris and consequently enhanced the susceptibility to azole drugs, as demonstrated by Nile red efflux assays. Altogether, these findings present lopinavir as a novel, potent, and broad-spectrum azole-chemosensitizing agent that warrants further investigation against recalcitrant Candida infections.

The Quiet and Underappreciated Rise of Drug-Resistant Invasive Fungal Pathogens

Human fungal pathogens are attributable to a significant economic burden and mortality worldwide. Antifungal treatments, although limited in number, play a pivotal role in decreasing mortality and morbidities posed by invasive fungal infections (IFIs). However, the recent emergence of multidrug-resistant Candida auris and Candida glabrata and acquiring invasive infections due to azole-resistant C. parapsilosis, C. tropicalis, and Aspergillus spp. in azole-naïve patients pose a serious health threat considering the limited number of systemic antifungals available to treat IFIs. Although advancing for major fungal pathogens, the understanding of fungal attributes contributing to antifungal resistance is just emerging for several clinically important MDR fungal pathogens. Further complicating the matter are the distinct differences in antifungal resistance mechanisms among various fungal species in which one or more mechanisms may contribute to the resistance phenotype. In this review, we attempt to summarize the burden of antifungal resistance for selected non-albicansCandida and clinically important Aspergillus species together with their phylogenetic placement on the tree of life. Moreover, we highlight the different molecular mechanisms between antifungal tolerance and resistance, and comprehensively discuss the molecular mechanisms of antifungal resistance in a species level.

Marked virulence and azole resistance in Candida albicans isolated from patients with periodontal disease

Candida albicans is an opportunistic fungus frequently associated with periodontal diseases. The objective of this study was to determine the expression patterns of virulence genes associated with those of azole resistance among the strains of C. albicans isolated from patients with periodontal disease. We isolated 80 strains of C. albicans from patients with periodontal disease enrolled from two dental clinics and their antifungal susceptibilities were evaluated using the disc diffusion method. C. albicans and its virulence genes were identified using PCR. The expressions of the virulence genes of C. albicans were analyzed using real-time PCR post in vitro infection of the cell line A549. The phenotype for resistance against azoles such as ketoconazole and fluconazole was observed in all analyzed strains (n = 80), which coincided with the high frequency of occurrence of the genes CDR1 and MDR1 associated with resistance. The frequencies of detection and expression of the genes HWP1 (47/15), ALS1 (80/66), ALS3 (70/30), LIP1 (78/44), LIP4 (77/65), LIP5 (79/58), LIP6 (79/58), PLB1 (79/65), and PLB2 (80/66) were found to be higher in the strains of C. albicans isolated from patients with moderate periodontitis and different expression patterns associated with those for azole resistance were identified. It could be elucidated that the high expression of virulence markers associated with azole resistance in C. albicans might be contributing to the chronicity of periodontal infections.

Diclofenac exhibits synergism with azoles against planktonic cells and biofilms of Candida tropicalis

This study aimed to evaluate the effect of diclofenac on minimum inhibitory concentrations of antifungals against planktonic cells and biofilms of Candida tropicalis. Susceptibility testing of planktonic cells was evaluated using the broth microdilution assay and checkerboard method. Biofilm formation by C. tropicalis in the presence of diclofenac, alone or in combination with antifungals, was also evaluated, and scanning electron microscope (SEM) and confocal microscope (CLSM) analyses were performed. Diclofenac showed an MIC of 1024 μg ml^-1 against planktonic cells. The MICs of fluconazole and voriconazole against azole-resistant isolates were reduced 8- to 32-fold and 16- to 256-fold, respectively, when in combination with diclofenac. When in combination with fluconazole or voriconazole, diclofenac reduced the antifungal concentration necessary to inhibit C. tropicalis biofilm formation. In conclusion, diclofenac presents synergism with fluconazole and voriconazole against resistant C. tropicalis strains and improves the activity of these azole drugs against biofilm formation.

The yeast, the antifungal, and the wardrobe: a journey into antifungal resistance mechanisms of Candida tropicalis

Candida tropicalis is a prominent non-Candida albicans Candida species involved in cases of candidemia, mainly causing infections in patients in intensive care units and (or) those presenting neutropenia. In recent years, several studies have reported an increase in the recovery rates of azole-resistant C. tropicalis isolates. Understanding C. tropicalis resistance is of great importance, since resistant strains are implicated in persistent or recurrent and breakthrough infections. In this review, we address the main mechanisms underlying C. tropicalis resistance to the major antifungal classes used to treat candidiasis. The main genetic basis involved in C. tropicalis antifungal resistance is discussed. A better understanding of the epidemiology of resistant strains and the mechanisms involved in C. tropicalis resistance can help improve diagnosis and assessment of the antifungal susceptibility of this Candida species to improve clinical management.

A comprehensive overview of the medicinal chemistry of antifungal drugs: perspectives and promise

The emergence of new fungal pathogens makes the development of new antifungal drugs a medical imperative that in recent years motivates the talents of numerous investigators across the world. Understanding not only the structural families of these drugs but also their biological targets provides a rational means for evaluating the merits and selectivity of new agents for fungal pathogens and normal cells. An equally important aspect of modern antifungal drug development takes a balanced look at the problems of drug potency and drug resistance. The future development of new antifungal agents will rest with those who employ synthetic and semisynthetic methodology as well as natural product isolation to tackle these problems and with those who possess a clear understanding of fungal cell architecture and drug resistance mechanisms. This review endeavors to provide an introduction to a growing and increasingly important literature, including coverage of the new developments in medicinal chemistry since 2015, and also endeavors to spark the curiosity of investigators who might enter this fascinatingly complex fungal landscape.

Overexpression of efflux pump transporter genes and mutations in ERG11 pave the way to fluconazole resistance in Candida tropicalis: A study from a North India region

INTRODUCTION

Fluconazole resistance in Candida tropicalis health care-associated infections is increasing. We investigated the role of efflux pump and mutations in ERG11p conferring fluconazole resistance in C. tropicalis.

MATERIALS AND METHODS

A total of 17 C. tropicalis clinical isolates, including fluconazole-resistant and fluconazole-susceptible/fluconazole-susceptible dose-dependent isolates, were collected from a tertiary care centre in a North India region between 2015 and 2018. Antifungal susceptibility, reversal of fluconazole resistance by tacrolimus, ERG11 amplification and its sequencing and a quantitative polymerase chain reaction (PCR) assay for expression analysis of ERG11, MDR1 and CDR1 genes were performed.

RESULTS AND DISCUSSION

Synergism between fluconazole and tacrolimus was observed in all resistant C. tropicalis isolates. Overexpression of all the three genes, MDR1, ERG11 and CDR1, was observed in resistant isolates (P = 0.05). Among resistant isolates, mutations leading to amino acid substitution were seen in two, Ct10 (glysine464serine) and Ct16 (tyrosine132phenylalanine; serine154phenylalanine).

CONCLUSION

Overexpression in efflux pump transporter genes, together with mutations in ERG11, lead to fluconazole resistance among C. tropicalis. To the best of our knowledge, this is the first study on the C. tropicalis fluconazole resistance mechanism from the North India region.

Elevated minimum inhibitory concentrations to antifungal drugs prevail in 14 rare species of candidemia-causing Saccharomycotina yeasts

Antifungal susceptibility profiles of rare Saccharomycotina yeasts remain missing, even though an increase in prevalence of such rare Candida species was reported in candidemia. Majority of these rare yeast species carry intrinsic resistances against at least one antifungal compound. Some species are known to be cross-resistant (against multiple drugs of the same drug class) or even multi-drug resistant (against multiple drugs of different drug classes). We performed antifungal susceptibility testing (AFST) according to EUCAST broth microdilution for 14 rare species (Clavispora lusitaniae, Candida intermedia, Candida auris, Diutina rugosa, Wickerhamiella pararugosa, Yarrowia lipolytica, Pichia norvegensis, Candida nivariensis, Kluyveromyces marxianus, Wickerhamomyces anomalus, Candida palmioleophila, Meyerozyma guilliermondii, Meyerozyma caribbica, and Debaryomyces hansenii) known to cause candidemia. In total, 234 isolates were tested for amphotericin B, fluconazole, itraconazole, voriconazole, posaconazole, anidulafungin, micafungin, and caspofungin. Amphothericin B had the broadest efficiency against the 14 tested rare yeast species, while high minimum inhibitory concentrations (MICs) against azole drugs and echinocandins were common. Voriconazole was the most efficient azole drug. Multidrug resistance was observed for the species C. auris and K. marxianus. Multidrug resistant individual isolates were found for Y. lipolytica and M. caribbica. In conclusion, the observed high MIC values of the rare Saccharomycotina species tested limit antifungal treatment options, complicating the management of such infections.