Combined Antifungal Resistance and Biofilm Tolerance: the Global Threat of Candida auris

ABSTRACT The enigmatic yeast Candida auris has emerged over the last decade and rapidly penetrated our consciousness. The global threat from this multidrug-resistant yeast has generated a call to arms from within the medical mycology community. Over the past decade, our understanding of how this yeast has spread globally, its clinical importance, and how it tolerates and resists antifungal agents has expanded. This review highlights the clinical importance of antifungal resistance in C. auris and explores our current understanding of the mechanisms associated with azole, polyene, and echinocandin resistance. We also discuss the impact of phenotypic tolerance, with particular emphasis on biofilm-mediated resistance, and present new pipelines of antifungal drugs that promise new hope in the management of C. auris infection.

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Multi-omics Signature of Candida auris, an Emerging and Multidrug-Resistant Pathogen

mSystems ◽

10.1128/msystems.00257-19 ◽

2019 ◽

Vol 4 (4) ◽

Cited By ~ 20

Author(s):

Daniel Zamith-Miranda ◽

Heino M. Heyman ◽

Levi G. Cleare ◽

Sneha P. Couvillion ◽

Geremy C. Clair ◽

...

Keyword(s):

Drug Resistance ◽

Protein Content ◽

Pathogenic Fungus ◽

Multidrug Resistant ◽

Antifungal Resistance ◽

Clinical Isolates ◽

Medical Mycology ◽

Carbon Utilization ◽

Candida Auris ◽

Content Type

ABSTRACT Candida auris is a recently described pathogenic fungus that is causing invasive outbreaks on all continents. The fungus is of high concern given the numbers of multidrug-resistant strains that have been isolated in distinct sites across the globe. The fact that its diagnosis is still problematic suggests that the spreading of the pathogen remains underestimated. Notably, the molecular mechanisms of virulence and antifungal resistance employed by this new species are largely unknown. In the present work, we compared two clinical isolates of C. auris with distinct drug susceptibility profiles and a Candida albicans reference strain using a multi-omics approach. Our results show that, despite the distinct drug resistance profile, both C. auris isolates appear to be very similar, albeit with a few notable differences. However, compared to C. albicans both C. auris isolates have major differences regarding their carbon utilization and downstream lipid and protein content, suggesting a multifactorial mechanism of drug resistance. The molecular profile displayed by C. auris helps to explain the antifungal resistance and virulence phenotypes of this new emerging pathogen. IMPORTANCE Candida auris was first described in Japan in 2009 and has now been the cause of significant outbreaks across the globe. The high number of isolates that are resistant to one or more antifungals, as well as the high mortality rates from patients with bloodstream infections, has attracted the attention of the medical mycology, infectious disease, and public health communities to this pathogenic fungus. In the current work, we performed a broad multi-omics approach on two clinical isolates isolated in New York, the most affected area in the United States and found that the omic profile of C. auris differs significantly from C. albicans. In addition to our insights into C. auris carbon utilization and lipid and protein content, we believe that the availability of these data will enhance our ability to combat this rapidly emerging pathogenic yeast.

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In Vitro Evaluation of Antifungal Drug Combinations against Multidrug-Resistant Candida auris Isolates from New York Outbreak

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02195-19 ◽

2020 ◽

Vol 64 (4) ◽

Cited By ~ 6

Author(s):

Brittany O’Brien ◽

Sudha Chaturvedi ◽

Vishnu Chaturvedi

Keyword(s):

New York ◽

Drug Combination ◽

Multidrug Resistant ◽

Drug Combinations ◽

Health Care Facilities ◽

Antifungal Drugs ◽

Candida Auris ◽

Pathogenic Yeast ◽

Content Type

ABSTRACT Since 2016, New York hospitals and health care facilities have faced an unprecedented outbreak of the pathogenic yeast Candida auris. We tested over 1,000 C. auris isolates from affected facilities and found high resistance to fluconazole (MIC > 256 mg/liter) and variable resistance to other antifungal drugs. Therefore, we tested if two-drug combinations are effective in vitro against multidrug-resistant C. auris. Broth microdilution antifungal combination plates were custom manufactured by TREK Diagnostic System. We used 100% inhibition endpoints for the drug combination as reported earlier for the intra- and interlaboratory agreements against Candida species. The results were derived from 12,960 readings, for 15 C. auris isolates tested against 864 two-drug antifungal combinations for nine antifungal drugs. Flucytosine (5FC) at 1.0 mg/liter potentiated the most combinations. For nine C. auris isolates resistant to amphotericin B (AMB; MIC ≥ 2.0 mg/liter), AMB-5FC (0.25/1.0 mg/liter) yielded 100% inhibition. Six C. auris isolates resistant to three echinocandins (anidulafungin [AFG], MIC ≥ 4.0 mg/liter; caspofungin [CAS], MIC ≥ 2.0 mg/liter; and micafungin [MFG], MIC ≥ 4.0 mg/liter) were 100% inhibited by AFG-5FC and CAS-5FC (0.0078/1 mg/liter) and MFG-5FC (0.12/1 mg/liter). None of the combinations were effective for C. auris 18-1 and 18-13 (fluconazole [FLC] > 256 mg/liter, 5FC > 32 mg/liter) except MFG-5FC (0.1/0.06 mg/liter). Thirteen isolates with a high voriconazole (VRC) MIC (>2 mg/liter) were 100% inhibited by the VRC-5FC (0.015/1 mg/liter). The simplified two-drug combination susceptibility test format would permit laboratories to provide clinicians and public health experts with additional data to manage multidrug-resistant C. auris.

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In Vitro Activity of Manogepix against Multidrug-Resistant and Panresistant Candida auris from the New York Outbreak

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01124-20 ◽

2020 ◽

Vol 64 (11) ◽

Cited By ~ 1

Author(s):

YanChun Zhu ◽

Shannon Kilburn ◽

Mili Kapoor ◽

Sudha Chaturvedi ◽

Karen Joy Shaw ◽

...

Keyword(s):

New York ◽

Fungal Infections ◽

Geometric Mean ◽

Multidrug Resistant ◽

Antifungal Drugs ◽

New Drugs ◽

Wild Type ◽

Candida Auris ◽

Content Type

ABSTRACT An ongoing Candida auris outbreak in the New York metropolitan area is the largest recorded to date in North America. Laboratory surveillance revealed NY C. auris isolates are resistant to fluconazole, with variable resistance to other currently used broad-spectrum antifungal drugs, and that several isolates are panresistant. Thus, there is an urgent need for new drugs with a novel mechanism of action to combat the resistance challenge. Manogepix (MGX) is a first-in-class agent that targets the fungal Gwt1 enzyme. The prodrug fosmanogepix is currently in phase 2 clinical development for the treatment of fungal infections. We evaluated the susceptibility of 200 New York C. auris isolates to MGX and 10 comparator drugs using CLSI methodology. MGX demonstrated lower MICs than comparators (MIC50 and MIC90, 0.03 mg/liter; range, 0.004 to 0.06 mg/liter). The local epidemiological cutoff value (ECV) for MGX indicated all C. auris isolates were within the population of wild-type (WT) strains; 0.06 mg/liter defines the upper limit of wild type (UL-WT). MGX was 8- to 32-fold more active than the echinocandins, 16- to 64-fold more active than the azoles, and 64-fold more active than amphotericin B. No differences were found in the MGX or comparators’ MIC50, MIC90, or geometric mean (GM) values when subsets of clinical, surveillance, and environmental isolates were evaluated. The range of MGX MIC values for six C. auris panresistant isolates was 0.008 to 0.015 mg/liter, and the median and mode MIC values were 0.015 mg/liter, demonstrating that MGX retains activity against these isolates. These data support further clinical evaluation of fosmanogepix for the treatment of C. auris infections, including highly resistant isolates.

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Pseudohyphal Growth of the Emerging Pathogen Candida auris Is Triggered by Genotoxic Stress through the S Phase Checkpoint

mSphere ◽

10.1128/msphere.00151-20 ◽

2020 ◽

Vol 5 (2) ◽

Cited By ~ 6

Author(s):

Gustavo Bravo Ruiz ◽

Zoe K. Ross ◽

Neil A. R. Gow ◽

Alexander Lorenz

Keyword(s):

Fungal Pathogens ◽

Genotoxic Stress ◽

Multidrug Resistant ◽

S Phase ◽

Antifungal Drugs ◽

Yeast Cells ◽

Candida Auris ◽

Content Type ◽

Pseudohyphal Growth ◽

S Phase Checkpoint

ABSTRACT The morphogenetic switching between yeast cells and filaments (true hyphae and pseudohyphae) is a key cellular feature required for full virulence in many polymorphic fungal pathogens, such as Candida albicans. In the recently emerged yeast pathogen Candida auris, occasional elongation of cells has been reported. However, environmental conditions and genetic triggers for filament formation have remained elusive. Here, we report that induction of DNA damage and perturbation of replication forks by treatment with genotoxins, such as hydroxyurea, methyl methanesulfonate, and the clinically relevant fungistatic 5-fluorocytosine, cause filamentation in C. auris. The filaments formed were characteristic of pseudohyphae and not parallel-sided true hyphae. Pseudohyphal growth is apparently signaled through the S phase checkpoint and, interestingly, is Tup1 independent in C. auris. Intriguingly, the morphogenetic switching capability is strain specific in C. auris, highlighting the heterogenous nature of the species as a whole. IMPORTANCE Candida auris is a newly emerged fungal pathogen of humans. This species was first reported in 2009 when it was identified in an ear infection of a patient in Japan. However, despite intense interest in this organism as an often multidrug-resistant fungus, there is little knowledge about its cellular biology. During infection of human patients, fungi are able to change cell shape from ellipsoidal yeast cells to elongated filaments to adapt to various conditions within the host organism. There are different types of filaments, which are triggered by reactions to different cues. Candida auris fails to form filaments when exposed to triggers that stimulate yeast filament morphogenesis in other fungi. Here, we show that it does form filaments when its DNA is damaged. These conditions might arise when Candida auris cells interact with host immune cells or during growth in certain host tissues (kidney or bladder) or during treatment with antifungal drugs.

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Drug Repurposing in Medical Mycology: Identification of Compounds as Potential Antifungals to Overcome the Emergence of Multidrug-Resistant Fungi

Pharmaceuticals ◽

10.3390/ph14050488 ◽

2021 ◽

Vol 14 (5) ◽

pp. 488

Author(s):

Lucie Peyclit ◽

Hanane Yousfi ◽

Jean-Marc Rolain ◽

Fadi Bittar

Keyword(s):

Opportunistic Infections ◽

Fungal Infections ◽

Drug Repurposing ◽

Multidrug Resistant ◽

Resistance Mechanisms ◽

Antifungal Drugs ◽

New Drugs ◽

Medical Community ◽

Medical Mycology ◽

Candida Auris

Immunodepression, whether due to HIV infection or organ transplantation, has increased human vulnerability to fungal infections. These conditions have created an optimal environment for the emergence of opportunistic infections, which is concomitant to the increase in antifungal resistance. The use of conventional antifungal drugs as azoles and polyenes can lead to clinical failure, particularly in immunocompromised individuals. Difficulties related to treating fungal infections combined with the time required to develop new drugs, require urgent consideration of other therapeutic alternatives. Drug repurposing is one of the most promising and rapid solutions that the scientific and medical community can turn to, with low costs and safety advantages. To treat life-threatening resistant fungal infections, drug repurposing has led to the consideration of well-known and potential molecules as a last-line therapy. The aim of this review is to provide a summary of current antifungal compounds and their main resistance mechanisms, following by an overview of the antifungal activity of non-traditional antimicrobial drugs. We provide their eventual mechanisms of action and the synergistic combinations that improve the activity of current antifungal treatments. Finally, we discuss drug repurposing for the main emerging multidrug resistant (MDR) fungus, including the Candida auris, Aspergillus or Cryptococcus species.

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The Two-Component Response Regulator Ssk1 and the Mitogen-Activated Protein Kinase Hog1 Control Antifungal Drug Resistance and Cell Wall Architecture of Candida auris

mSphere ◽

10.1128/msphere.00973-20 ◽

2020 ◽

Vol 5 (5) ◽

Author(s):

Raju Shivarathri ◽

Sabrina Jenull ◽

Anton Stoiber ◽

Manju Chauhan ◽

Rounik Mazumdar ◽

...

Keyword(s):

Cell Wall ◽

Multidrug Resistance ◽

Response Regulator ◽

Multidrug Resistant ◽

Antifungal Drugs ◽

Antifungal Drug ◽

Candida Auris ◽

Content Type ◽

Antifungal Drug Resistance ◽

Two Component

ABSTRACT Candida auris is an emerging multidrug-resistant human fungal pathogen refractory to treatment by several classes of antifungal drugs. Unlike other Candida species, C. auris can adhere to human skin for prolonged periods of time, allowing for efficient skin-to-skin transmission in the hospital environments. However, molecular mechanisms underlying pronounced multidrug resistance and adhesion traits are poorly understood. Two-component signal transduction and mitogen-activated protein (MAP) kinase signaling are important regulators of adherence, antifungal drug resistance, and virulence. Here, we report that genetic removal of SSK1 encoding a response regulator and the mitogen-associated protein kinase HOG1 restores the susceptibility to both amphotericin B (AMB) and caspofungin (CAS) in C. auris clinical strains. The loss of SSK1 and HOG1 alters membrane lipid permeability, cell wall mannan content, and hyperresistance to cell wall-perturbing agents. Interestingly, our data reveal variable functions of SSK1 and HOG1 in different C. auris clinical isolates, suggesting a pronounced genetic plasticity affecting cell wall function, stress adaptation, and multidrug resistance. Taken together, our data suggest that targeting two-component signal transduction systems could be suitable for restoring C. auris susceptibility to antifungal drugs. IMPORTANCE Candida auris is an emerging multidrug-resistant (MDR) fungal pathogen that presents a serious global threat to human health. The Centers for Disease Control and Prevention (CDC) have classified C. auris as an urgent threat to public health for the next decade due to its major clinical and economic impact and the lack of effective antifungal drugs and because of future projections concerning new C. auris infections. Importantly, the Global Antimicrobial Resistance Surveillance System (GLASS) has highlighted the need for more robust and efficacious global surveillance schemes enabling the identification and monitoring of antifungal resistance in Candida infections. Despite the clinical relevance of C. auris infections, our overall understanding of its pathophysiology and virulence, its response to human immune surveillance, and the molecular basis of multiple antifungal resistance remains in its infancy. Here, we show a marked phenotypic plasticity of C. auris clinical isolates. Further, we demonstrate critical roles of stress response mechanisms in regulating multidrug resistance and show that cell wall architecture and composition are key elements that determine antifungal drug susceptibilities. Our data promise new therapeutic options to treat drug-refractory C. auris infections.

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00684-20 ◽

2020 ◽

Vol 65 (1) ◽

pp. e00684-20 ◽

Cited By ~ 1

Author(s):

Hassan E. Eldesouky ◽

Ehab A. Salama ◽

Nadia A. Lanman ◽

Tony R. Hazbun ◽

Mohamed N. Seleem

Keyword(s):

Nile Red ◽

Atp Synthesis ◽

Multidrug Resistant ◽

Antifungal Drugs ◽

Hiv Protease ◽

Candida Auris ◽

Content Type ◽

Azole Antifungals ◽

Synergistic Interactions ◽

Recent Emergence

ABSTRACTThe 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.

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Candida auris: multi-omics signature of an emerging and multidrug-resistant pathogen

10.1101/528232 ◽

2019 ◽

Cited By ~ 1

Author(s):

Daniel Zamith-Miranda ◽

Heino M. Heyman ◽

Levi G. Cleare ◽

Sneha Couvillion ◽

Geremy Clair ◽

...

Keyword(s):

Drug Resistance ◽

Protein Content ◽

Pathogenic Fungus ◽

Multidrug Resistant ◽

Antifungal Resistance ◽

Clinical Isolates ◽

Medical Mycology ◽

Carbon Utilization ◽

Candida Auris ◽

Pathogenic Yeast

AbstractCandida auris is a recently described pathogenic fungus that is causing invasive outbreaks on all continents. The fungus is of high concern given the numbers of multidrug-resistant strains that have been isolated in distinct sites across the globe. The fact that its diagnosis is still problematic suggests that the spreading of the pathogen remains underestimated. Notably, the molecular mechanisms of virulence and antifungal resistance employed by this new species are largely unknown. In the present work, we compared two clinical isolates of C. auris with distinct drug susceptibility profiles and a Candida albicans reference strain using a multi-omics approach. Our results show that, despite the distinct drug-resistance profile, both C. auris strains appear to be very similar, albeit with a few notable differences. However, when compared to C. albicans both C. auris strains have major differences regarding their carbon utilization and downstream lipid and protein content, suggesting a multi-factorial mechanism of drug resistance. The molecular profile displayed by C. auris helps to explain the antifungal resistance and virulence phenotypes of this new emerging pathogen.ImportanceCandida auris was firstly described in Japan in 2009 and has now been the cause of significant outbreaks across the globe. The high number of isolates that are resistant to one or more antifungals, as well as the high mortality rates from patients with bloodstream infections, has caught the attention of the medical mycology, infectious disease and public health communities to this pathogenic fungus. In the current work, we performed a broad multi-omics approach on two clinical isolates isolated in New York, the most affected area in the USA and found that the omic profile of C. auris differs significantly from C. albicans. Besides our insights into C. auris carbon utilization and lipid and protein content, we believe that the availability of these data will enhance our ability to combat this rapidly emerging pathogenic yeast.

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Absence of Azole or Echinocandin Resistance inCandida glabrataIsolates in India despite Background Prevalence of Strains with Defects in the DNA Mismatch Repair Pathway

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00195-18 ◽

2018 ◽

Vol 62 (6) ◽

Cited By ~ 25

Author(s):

Ashutosh Singh ◽

Kelley R. Healey ◽

Priyanka Yadav ◽

Gargi Upadhyaya ◽

Neelam Sachdeva ◽

...

Keyword(s):

Mismatch Repair ◽

Dna Mismatch Repair ◽

Geometric Mean ◽

Antifungal Susceptibility ◽

Antifungal Resistance ◽

Antifungal Drugs ◽

The Novel ◽

Content Type ◽

Dna Mismatch ◽

The Impact

ABSTRACTCandida glabratainfections are increasing worldwide and exhibit greater rates of antifungal resistance than those with other species. DNA mismatch repair (MMR) gene deletions, such asmsh2Δ, inC. glabrataresulting in a mutator phenotype have recently been reported to facilitate rapid acquisition of antifungal resistance. This study determined the antifungal susceptibility profiles of 210C. glabrataisolates in 10 hospitals in India and investigated the impact of novelMSH2polymorphisms on mutation potential. No echinocandin- or azole-resistant strains and no mutations inFKShot spot regions were detected among theC. glabrataisolates, supporting ourin vitrosusceptibility testing results. CLSI antifungal susceptibility data showed that the MICs of anidulafungin (geometric mean [GM], 0.12 μg/ml) and micafungin (GM, 0.01 μg/ml) were lower and below the susceptibility breakpoint compared to that of caspofungin (CAS) (GM, 1.31 μg/ml). Interestingly, 69% of theC. glabratastrains sequenced contained six nonsynonymous mutations inMSH2, i.e., V239L and the novel mutations E459K, R847C, Q386K, T772S, and V239/D946E. Functional analysis ofMSH2mutations revealed that 49% of the tested strains (40/81) contained a partial loss-of-functionMSH2mutation. The novelMSH2substitution Q386K produced higher frequencies of CAS-resistant colonies upon expression in themsh2Δmutant. However, expression of two other novelMSH2alleles, i.e., E459K or R847C, did not confer selection of resistant colonies, confirming that not all mutations in theMSH2MMR pathway affect its function or generate a phenotype of resistance to antifungal drugs. The lack of drug resistance prevented any correlations from being drawn with respect toMSH2genotype.

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1579. Multidrug-Resistant Candida auris Isolates From New York Hospitals and Healthcare Facilities Are Susceptible to Antifungal Combinations

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.1443 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S576-S577

Author(s):

Brittany O’Brien ◽

Sudha Chaturvedi ◽

Vishnu Chaturvedi

Keyword(s):

New York ◽

Diagnostic System ◽

Multidrug Resistant ◽

Drug Combinations ◽

Antifungal Drugs ◽

Drug Resistant ◽

Candida Auris ◽

Current Case ◽

Healthcare Facilities ◽

Broth Microdilution Method

Abstract Background Candida auris outbreak continues unabated in New York with the current case counts exceeding 300 patients. We used a modification of standard CLSI broth microdilution method (BMD) if two-drug combinations are efficacious against C. auris isolates with high-resistance to fluconazole (FZ, MIC50 >256 mg/L), and variable resistance to other broad-spectrum antifungal drugs. Methods BMD plates were custom-designed and quality controlled by TREK Diagnostic System. The combination tests of 15 drug-resistant C. auris involved microtiter wells with the initial 144 two-drug combinations and their two-fold dilutions (1/2–1/32) to get 864 two-drug combinations finally. We utilized MIC100 endpoints for the drug combination readings as reported earlier for the intra- and inter-laboratory agreements obtained against Candida species and Aspergillus fumigatus (Antimicrob Agents Chemother. 2015. 59:1759–1766). We also tested minimum fungicidal concentrations (MFC). Results We tested all possible 864 two-drug antifungal combinations for nine antifungal drugs in use to yield 12,960 MIC100 readings, and MFC readings for 15 C. auris isolates. Flucytosine (FLC) at 2.0 mg/L potentiated most successful combinations with other drugs. Micafungin (MFG), Anidulafungin (AFG), Caspofungin (CAS) at individual concentrations of 0.25 mg/L combined well with FLC (2.0 mg/L) to yield MIC100 for 14, 13, and 12 of 15 C. auris isolates tested, respectively. MFG/FLC combination was also fungicidal for 4 of 15 isolates. AMB / FLC (0.25/1.0 mg/L) yielded MIC100 for 13 isolates and MFC for three test isolates. Posaconazole (POS), and Isavuconazole (ISA) and Voriconazole (VRC) also combined well with FLC (0.25/2.0 mg/L) to yield MIC100 for 12, 13, and 13 isolates, respectively. POS/FLC combination was fungicidal for three isolates. Conclusion We identified seven two drug-combinations of antifungals efficacious against drug-resistant C. auris strains. The modified BMD combination susceptibility testing could be used by the clinical laboratories to assist providers with the selection of optimal treatment for C. auris candidemia. Disclosures All authors: No reported disclosures.

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