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Antimicrobial Agents and Chemotherapy, January 2009, p. 112-122, Vol. 53, No. 1
0066-4804/09/$08.00+0 doi:10.1128/AAC.01162-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Public Health Research Institute, New Jersey Medical School-UMDNJ, Newark, New Jersey 07103
Received 29 August 2008/ Returned for modification 17 September 2008/ Accepted 16 October 2008
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2 µg/ml for caspofungin captured nearly 100% of fks1 C. albicans strains when a kinetic inhibition rise threshold of
50-fold for the Ki was used as a measure of susceptibility. A similar MIC breakpoint for micafungin and anidulafungin was less inclusive, and a projected MIC of
0.5 µg/ml was required for >95% coverage of clinical isolates. However, when MIC determinations were performed in the presence of 50% serum, all fks1 mutants showed MIC values of
2 µg/ml for the three echinocandin drugs. The 1,3-β-D-glucan synthase kinetic inhibition data support the proposed susceptibility breakpoint for caspofungin in C. albicans, but a lower susceptibility breakpoint (
0.5 µg/ml) may be more appropriate for anidulafungin and micafungin. Overall, the data indicate that MIC testing with caspofungin may serve as a surrogate marker for resistance among the class of echinocandin drugs. |
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Echinocandin resistance in susceptible species like Candida albicans is uncommon, but it has been associated with amino acid substitutions in two conserved regions of Fks1p (35). These mutations, which result in elevated MICs, reduce the sensitivity of 1,3-β-D-glucan synthase to drug by several hundredfold to a thousandfold (33). The biochemical mechanism of this reduced sensitivity is not understood. There is a complex relationship between elevated MIC and clinical success (20, 39), largely because cells can induce a variety of adaptive pathways that lead to reduced susceptibility without directly impacting the behavior of the drug on 1,3-β-D-glucan synthase (20, 25, 26). Furthermore, in vitro MIC assays of echinocandin susceptibility according to CLSI protocol M27-A3 do not take into account the strong effects of serum protein binding, which influences the relative efficacies of echinocandin drugs (30, 32, 53). Nevertheless, the CLSI Antifungal Subcommittee proposed an echinocandin MIC breakpoint for susceptibility of
2 µg/ml for Candida spp. (40). To assess the relationship between the new breakpoint and the inherent sensitivity of 1,3-β-D-glucan synthase from fks1 mutants to echinocandin drugs, a detailed kinetic analysis of mutant and wild-type enzymes was undertaken to compare kinetic inhibition parameters with the MICs for clinical and laboratory isolates of C. albicans.
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2 µg/ml), and three strains (strains 1002, 3107, and 3795) were echinocandin susceptible. Two of the echinocandin-susceptible clinical strains were fluconazole resistant (strain 3107 harbors the Y132F amino acid change in Erg11p, and strain 3795 showed CDR2 and MDR2 overexpression) (34). C. albicans strains SC5314, ATCC 90028, and ATCC 36082 were used as control strains. ANF, caspofungin (CSF) (Merck & Co., Inc., Rahway, NJ), and micafungin (MCF) (Astellas Pharma USA, Inc., Deerfield, IL) were obtained as standard powders from their manufacturers. CSF and MCF were dissolved in sterile distilled water, while ANF was dissolved in 100% dimethyl sulfoxide (Sigma-Aldrich). Stock solutions of each drug were kept at –86°C. |
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TABLE 1. In vitro whole-cell susceptibility (MIC) and GS inhibition profiles (IC50) for ECD of the C. albicans strains included in the studyh
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Antifungal susceptibility testing. Susceptibility testing was performed in triplicate in accordance with CLSI document M27-A3 (7) in the presence or absence of 50% human serum (Sigma) (32). Candida krusei ATCC 6258 and Candida parapsilosis ATCC 22019 were used as quality control strains.
FKS gene sequence analysis. The C. albicans FKS1 and FKS2 genes were amplified and sequenced from genomic DNA extracted from C. albicans cells grown overnight in YPD broth medium with the Q-Biogene (Irvine, CA) FastDNA kit. PCR and sequencing primers were designed based on the C. albicans FKS1 and FKS2 sequences (GenBank accession no. XM_716336 and XM_712867, respectively). DNA sequencing was performed with a CEQ dye terminator sequencing kit (Beckman Coulter, Fullerton, CA) according to the manufacturer's recommendations. Sequence analyses were performed with CEQ 8000 genetic analysis system software (Beckman Coulter, Fullerton, CA) and BioEdit Sequence Alignment Editor (Ibis Therapeutics, Carlsbad, CA).
C. albicans 1,3-β-D-glucan synthase isolation and inhibition assay. All the isolates used in this work were grown with vigorous shaking at 37°C to early stationary phase in YPD broth, and cells were collected by centrifugation. Cell disruption, membrane protein extraction, and 1,3-β-D-glucan synthase enrichment by-product entrapment were done as described previously (33). Sensitivity to echinocandin drugs was measured in a polymerization assay using a 96-well multiscreen HTS filtration system (Millipore Corporation, Bedford, MA) in a final reaction mixture volume of 100 µl, as previously described (33). Serial dilutions of ANF, CSF, and MCF were added (1 µl/well). Control reactions were performed in the presence of 1% dimethyl sulfoxide when ANF was used. All reactions were initiated by the addition of the product-entrapped 1,3-β-D-glucan synthase enzyme to the reaction mixture. Inhibition curves and 50% inhibitory concentrations (IC50s) were determined using a sigmoidal response (variable-slope) curve and a two-site competition-fitting algorithm with GraphPad Prism, version 4.0, software (Prism Software, Irvine, CA).
Characterization of the 1,3-β-D-glucan product.
The product of the reaction mixtures was characterized as 1,3-β-D-glucan using a Glucatell kit (Associates of Cape Cod Inc., Falmouth, MA) according to the manufacturer's instructions. The addition of the 1,3-β-D-glucan synthase-trapped enzyme was used to initiate the reaction in a 100-µl final volume. Reaction mixtures were incubated at 25°C for 60 min and were then stopped by rapid cooling on ice. Using the end-point assay Glucatell kit and comparing the results obtained with those using the [3H]UDPG incorporation assay, it was established that 2.4 x 10–2 nmol of glucose was incorporated (
10 pg of 1,3-β-D-glucan/ml).
Kinetic analyses.
All reactions were run with a 96-well multiscreen HTS filtration system (Millipore) in a final volume of 100 µl. Each well contained 50 mM HEPES (pH 7.5), 10% (wt/vol) glycerol, 1.5 mg/ml bovine serum albumin, 25 mM KF, 1 mM EDTA, 25 µM GTP-
-S, 1 µg 1,3-β-D-glucan synthase enzyme, [3H]UDPG (7,000 dpm/nmol glucose), and echinocandin drugs, as indicated below. The plates were incubated for 60 min at 25°C. All reactions were initiated by the addition of product-entrapped 1,3-β-D-glucan synthase to the mixture. [3H]UDPG was used as the substrate in concentrations varying from 0.015 to 2 mM to determine the different kinetic parameters, which were analyzed by linear regression to obtain slopes in dpm/min. This value was then converted to nM glucose incorporated per minute. The maximum velocity (Vmax) and the Michaelis-Menten constant (Km) were determined for product-entrapped 1,3-β-D-glucan synthase enzyme by varying the amount of UDPG (between 0.015 and 2 mM) using Lineweaver-Burke plots. Furthermore, Dixon plots were used to determine the inhibition constant (Ki) and the nature of kinetic inhibition by echinocandin drugs. Ki values were calculated by varying the echinocandin drug concentration (between 0.01 and 50 ng/ml for wild-type GS and between 10 and 10,000 ng/ml for mutant GS) at different fixed substrate concentrations ranging from 0.125 to 0.5 mM UDPG. All data were analyzed with GraphPad Prism 4.0 software (Prism Software).
RNA isolation and expression profiling. C. albicans strains were grown in YPD broth and incubated at 37°C with shaking (150 rpm) for 16 h. Total RNA was extracted using the RNeasy minikit (Qiagen), and gene expression profiles were performed using the one-step Sybr green QRT-PCR kit (Stratagene, La Jolla, CA) using the Stratagene Mx3005P multiplex quantitative PCR system. Differential expression was analyzed for the three C. albicans FKS genes. FKS1, FKS2, and FKS3 expression profiling primers were designed using GenBank accession numbers XM_716336, XM_712867, and XM_713421, respectively (Table 2). Relative expression was evaluated using a method described previously by Pfaffl (36). The C. albicans URA3 gene (GenBank accession no. XP_721787.1) was used for the normalization of expression (13).
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TABLE 2. Primers used in this study
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90% of the strains had Ki values for 1,3-β-D-glucan synthase at least 100-fold higher than that for the wild-type enzyme. Statistical analysis was done with the Statistical Package for the Social Sciences (version 13.0; SPSS Inc., Chicago, IL). |
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Effect of Fks1p substitutions on 1,3-β-D-glucan synthase inhibition. Evaluation of kinetic inhibition (IC50) for wild-type crude microsomes and product-entrapped enzyme demonstrated that the entrapped enzyme was approximately 10-fold more sensitive to all echinocandin drugs (Fig. 1A and Table 1). Moreover, the IC50 values obtained using different crude microsome preparations were highly variable (variation coefficient of 34.5% on average) (data not shown), making this preparation less reliable for kinetic studies. 1,3-β-D-Glucan synthase enzymes isolated from fks1 mutant strains showed higher IC50 values for ANF (243-fold) than for the other drugs (29- and 14-fold for CSF and MCF, respectively). Among the 14 mutant Fks1p enzymes studied, mutations at Ser645 (S645P, S645Y, and S645F) showed the highest IC50 increases relative to the wild type (P < 0.01). On the other hand, F641S mutants showed higher IC50 values than did F641L mutants (Fig. 1B). As demonstrated previously (33), the heterozygous R1361H mutants (strains 90 and A15) showed two IC50 values (two inflection points in the inhibition curve), demonstrating that the two isoenzymes (mutant and wild type) are present in the extracts (Fig. 1C). The spontaneous ANF mutants showed IC50 values comparable to those of clinical isolates carrying the same mutations (Table 1).
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FIG. 1. (A) ANF titration curves for strain SC5314 (wild type) 1,3-β-glucan synthase in crude microsomal membranes or in a trapped-enzyme preparation. (B) CSF titration curves for strains ATCC 90028 (wild type [WT]), 90 (R1361R/H), 85(S645F), and 194 (S645F and R1361R/H). (C) MCF titration curves for strains ATCC 36082 (wild type), 119 (F641L), and 177 (F641S). (D) Lineweaver-Burke double-reciprocal plotting for wild-type strain SC5314, Fks1p mutant S645P strain 205, and Fks1p mutant P649H strain 122. (E and F) Dixon plotting using 0.5 mM, 0.25 mM, and 0.125 mM UDPG for the 1,3-β-glucan synthase-trapped enzyme isolated from strains SC5314 (E) and strain 205 (F).
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TABLE 3. In vitro properties of the trapped 1,3-β-glucan synthase enzyme from the C. albicans strain SC5314 and its spontaneous echinocandin-resistant mutant A15-10
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TABLE 4. Kinetic properties and Ki values of strains included in the studye
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100-fold increase compared with wild-type enzymes. The mutations conferring the highest Ki values for all three echinocandin drugs were F641S, S645P, and S645Y. For CSF, the highest Ki values were observed in mutants with amino acid changes at Ser645 (S645P, S645F, and S645Y). Mutations at the C-terminal end of Fks1 hot spot 1 (D648Y and P649H) confer higher MCF Ki values than those for the other drugs tested. For Fks1 hot spot 2 amino acid substitutions, the R1361H 1,3-β-D-glucan synthase mutant showed statistically significantly higher Ki values than wild-type 1,3-β-D-glucan synthases (P < 0.001). However, the CSF Ki was three times higher than those of ANF and MCF. As expected, the R1361H homozygous mutant (strain 121) showed higher Ki values than did the heterozygous mutant (strain 90) for all three echinocandin drugs tested. Finally, in compound mutant strain 194 (S645F-R1361R/H), ANF and MCF Ki values were lower than that of the S645F mutant alone (strain 85), indicating that the two resistance sites do not synergize. Expression profiling. Real-time PCR was used to evaluate transcription levels for the three different C. albicans FKS genes. Table 5 indicates that FKS1 is expressed 2.92- and 26.9-fold more on average than FKS2 and FKS3, respectively. The level of expression for FKS2 and FKS3 increased when FKS1 harbored a resistance mutation. The spontaneous mutants selected from strain SC5314 using ANF (this study) (Table 1) and CSF (3, 33) showed similar decreases in expressed FKS1/FKS2 and FKS1/FKS3 ratios, indicating that mutations in FKS1 affect the regulation of all three genes. Heterozygous mutants (S645S/P) showed FKS1/FKS2 and FKS1/FKS3 ratios intermediate to those obtained using their parental (S645) and homozygous (S645P) counterpart strains. This phenomenon likely reflects the notion that the expression of the FKS family of genes is coordinately regulated with the level of the 1,3-β-D-glucan-synthesizing capacity in the cell.
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TABLE 5. Relative expression ratios between FKS genes
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Echinocandin susceptibility breakpoint relative to Ki.
The correlations established in Fig. 2 indicate that Ki values can be used to distinguish between susceptible and resistant strains. In order to determine if the echinocandin breakpoint includes all the strains with 1,3-β-D-glucan synthase Ki values at least 50-fold higher than the average wild-type values (ANF and CSF Ki values of >200 ng/ml and MCF Ki values of >1,500 ng/ml), a quantitative evaluation of Ki and MIC values was performed for the wild type and fks1 mutants. An evaluation of log2 MICs, in the presence and absence of 50% human serum, and the log10 Ki demonstrated for CSF that all high-Ki isolates were captured at an MIC of
2 µg/ml (Fig. 3A). The separation between susceptible and resistant strains was maximized in the presence of 50% serum (Fig. 3B). An MIC of 0.5 µg/ml was sufficient to distinguish between most strains with high-Ki 1,3-β-D-glucan synthases for ANF (Fig. 3C) and MCF (Fig. 3E). Typically, these strains at the margin showed changes in Ki values of <100-fold relative to that of wild type (Table 4). A cutoff value of 2 µg/ml for these drugs, as proposed by the new CLSI recommendation, missed several strains with fks1 mutations except those containing substitutions at Ser645 (S645P, S645Y, S645F, and S645F-R1361R/H). However, a cutoff value of 2 µg/ml was sufficient to distinguish between all resistant fks1 mutant strains and susceptible strains when MICs were obtained in the presence of 50% serum (Fig. 3D and F).
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FIG. 2. Correlation between ANF (diamonds), CSF (squares), and MCF (triangles) Ki values and MICs with and without 50% serum. Filled shapes represent wild-type glucan synthases, and open shapes represent mutants. Ki threshold lines represent >50-fold-higher-than-average wild-type glucan synthase Ki values.
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FIG. 3. Ki-MIC correlations arranged by Fks1p amino acid changes. Ki values are expressed in ng/ml (log10), and MICs are expressed in µg/ml (log2). Black lines represent the CLSI susceptibility breakpoint (2 µg/ml). Gray dotted lines represent the breakpoint suggested in this work. (A, C, and E) MICs were obtained using RPMI 1640 medium (CLSI document M27-A3) (7). (B, D, and F) MICs were obtained using RPMI 1640 medium with 50% serum. WT, wild type.
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Relationship of Ki to MIC and CLSI breakpoint.
The susceptibility of common yeasts to the three echinocandin drugs has remained largely constant since the introduction of CSF in 2001 (37). It was determined for a wide range of species that greater than 99% of isolates were inhibited by
2 µg/ml of either CSF, MCF, or ANF. Therefore, the CLSI Antifungal Subcommittee recently established an MIC of
2 µg/ml as an interpretive MIC breakpoint for susceptibility of Candida spp. to the three echinocandin drugs (7). An MIC predictive of resistance could not be assigned because of the paucity of isolates available above the proposed breakpoint (40). In this work, we have provided a detailed molecular and kinetic characterization of clinical isolates of C. albicans with FKS1 mutations resulting in high MICs. It is now well recognized that high-MIC isolates of Candida spp. from patients failing therapy often contain amino acid substitutions in Fks subunits (Fks1p and/or Fks2p) of the 1,3-β-D-glucan synthase complex (6, 8, 14, 15, 19, 22, 24, 28, 33). The elevated MIC phenotype linked to mutations in FKS is a direct consequence of a decrease in the biochemical sensitivity of 1,3-β-D-glucan synthase to drug, which is reflected as an increase of 50-fold to several thousandfold for the related enzyme inhibition constants IC50 and Ki (Tables 1 and 4). The decrease in enzyme sensitivity (IC50 or Ki) does not correlate strictly with an equivalent rise in MIC (Tables 1 and 4). However, there is an unambiguous linkage between increasing Ki and MIC values (Fig. 2). This tightly coupled interrelationship between amino acid substitutions in Fks1p, 1,3-β-D-glucan synthase sensitivity, and MIC (Tables 1 to 4 and Fig. 2) provides a window to examine resistance and, in particular, the relationship between MIC and the potential for successful clinical outcome, as proposed by the new CLSI guidelines. In principle, a plot of the inherent biochemical parameter Ki as a function of MIC should establish a drug level that correlates with enzyme insensitivity to drug, which can be operationally defined as a Ki level at least 50 times that of the average sensitive wild-type enzyme (Table 4). Using this threshold criterion for enzyme-mediated resistance, it is apparent for CSF that all clinical isolates containing FKS1 mutations, except F641L, are captured at MICs of
2 µg/ml (Fig. 3C), which fully supports the CLSI breakpoint. When MICs are obtained in the presence of serum, there is a 100% capture of all fks1 mutants above the MIC breakpoint (Fig. 2 and 3B, D, and F). However, a threshold MIC of
2 µg/ml is less inclusive when similar relationships for ANF (Fig. 3C) and MCF (Fig. 3E) in the absence of serum were evaluated. For those drugs, an MIC of >0.5 µg/ml would permit >95% capture of mutant isolates with fks1 mutations. Again, if serum is included in the growth medium, the MICs shift sufficiently for both MCF and ANF, which enables the complete capture of fks1 mutants above an MIC of
2 µg/ml. The inclusion of serum in routine testing medium would simplify matters, but in practice, it would be difficult to standardize. Nevertheless, even under CLSI testing methodology standard M27-A3, echinocandin susceptibility surveillance studies showed that more than 99% of the C. albicans strains have ANF and MCF MICs of
0.5 µg/ml, which were considered to be susceptible (38, 40). Lower breakpoints would therefore not result in false resistance detection. However, while attractive, such a view does not take into account the full range of considerations for the breakpoint determination, including the tenant that the threshold value should not bisect MIC distributions of wild-type populations such as Candida parapsilosis or Candida guillermondii. In this context, this work has immediate relevance to strains with fks1 mutant backgrounds; further studies would be required to support lower breakpoints for ANF and MCF.
FKS1 mutations influence 1,3-β-D-glucan synthase kinetics. Little is known about the inhibition kinetics of 1,3-β-D-glucan synthase and how echinocandin drugs interact with the enzyme complex. Genetic analysis of resistance can help define structural binding/interaction domains, especially when mutations are clustered in limited regions, which tend to favor direct or short-range interactions over long-range conformational rearrangements. Kinetic analysis of mutant enzymes indicates that amino acid substitutions conferring reduced drug susceptibility have little or no effect on the affinity of enzyme for substrate (Km) (Tables 3 and 4), while certain mutations alter the catalytic capacity of the enzyme (Vmax) (Tables 3 and 4). These kinetic findings suggest that the binding site for echinocandin drugs is apart from the binding site for substrate, which is also consistent with the noncompetitive inhibition kinetics observed (Fig. 1E and F) (9, 49). The reduced catalytic capacity of some mutations suggests a possible effect on a transition state intermediate in the reaction. The structural location of the binding site is not known, although the hot spot regions are predicted from topology models (29) to lie near the extracytoplasmic surface of the enzyme. The clustering of mutations in two structurally defined hot spot regions (F641-P649 and D1357-L1364) may help define a binding site for echinocandin drugs. Such a notion would imply that amino acids Phe641, Ser645, Asp648, Pro649, and Arg1361 promote echinocandin-enzyme interactions. Moreover, Ser645 would be most important in this interaction since all substitutions have the most pronounced effect on MIC for both CSF (3) and ANF, as observed in this study.
Certain FKS1 mutations are associated with decreases in Vmax, which were observed in mutant Fks1p isolated from isogenic strains (SC5314 and A15-10) (Table 3). The decreased catalytic capacity may have a fitness cost to the cell. However, the relative expression data (Table 5) presented here show a possible way for the cell to compensate for this effect, since C. albicans is able to increase the expression of the other nonmutated FKS genes. This idea was confirmed when isogenic strains showing a moderate and more important increase in FKS2 and FKS3 expression levels for heterozygous and homozygous isogenic mutants, respectively, were studied. However, this phenomenon was not seen in D648Y (strain 149) and P649H (strain 122) mutants and in other Candida spp. with equivalent mutations (13). Coincidently, these strains showed the lowest MICs in this collection. Surprisingly, our kinetic assays did not reflect elevated levels of FKS2 and FKS3 expression, since smooth curves were obtained, representing a single kinetic species. Thus, the majority of the kinetic response for C. albicans GS appears to be dominated by one enzyme type (presumably Fks1p). This phenomenon could have several possible explanations. One explanation is that the expression of FKS2 and FKS3 does not translate into assembled enzyme due to posttranscriptional control (e.g., RNA or enzyme turnover), or the enzyme extraction was more selective for Fks1p, as stated previously (13). Conversely, when heterozygous FKS1 mutants (Fks1p/fks1p) were studied, double-inflection inhibition curves (two IC50 values) and nonlinear double reciprocal plots were seen, representing two isoenzymes (18, 33).
Overall, it is apparent that the three echinocandin drugs share target, mechanism of resistance, spectrum, and in vitro potency, allowing the possibility of using CSF as a surrogate marker to predict the echinocandin susceptibility of C. albicans strains. This concept was suggested previously by Pfaller et al. (41-43) using fluconazole MIC breakpoints to assess relative voriconazole (or other azole) susceptibility, and our data with CSF support an analogous application for echinocandin drugs.
Published ahead of print on 27 October 2008. ![]()
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