One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes.

The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1-D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial ß -tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5-6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1α. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1α, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.

In vitro antifungal and antileishmanial activities of steroidal saponins from Allium leucanthum C. Koch -- a Caucasian endemic species.

Five steroidal saponins were isolated for the first time in the flower of Allium leucanthum C.Koch. In vitro antifungal and antileishmanial activities of pure compounds as well as crude extract, spirostanoid and furostanoid fractions were evaluated. Spirostanol saponins (25R),5alpha- spirostan -3beta,6beta- diol 3-0-{beta-D-glucopyranosyl-(1-->2)- 0-[beta-D-xylopyranosyl-(1-->3)]- 0-beta-D- glucopyranosyl -(1-->4)-beta-D- galactopyranoside } compound 3 were more antifungal active especially with a MCF ranging from 6,25 to 12,5 microg/ml on the most yeast stains tested. Spirostanol fraction was more active on amastigote forms of leishmania with IC(50) 0,9 microg/ml.

Results obtained with various antifungal susceptibility testing methods do not predict early clinical outcome in patients with cryptococcosis.

The in vitro susceptibilities of Cryptococcus neoformans isolates from consecutive human immunodeficiency virus-positive and -negative patients to the antifungal agents fluconazole, amphotericin B, and flucytosine were determined by different techniques, including the CLSI method, Etest, and broth microdilution in yeast nitrogen base (YNB) medium, during a multicenter prospective study in France. The relationship between the in vitro data and the clinical outcome 2 weeks after the initiation of antifungal therapy was assessed. In addition, the correlation between the strain serotype and the in vitro activities of the antifungals was determined, and the susceptibility results obtained with the different techniques were also compared. Thirty-seven patients received a combination of amphotericin B with flucytosine as first-line therapy, 22 were treated with amphotericin B alone, and 15 received fluconazole alone. Whatever the antifungal tested, there was no trend toward higher MICs for strains isolated from patients who failed to respond to a given therapy compared to those from patients who did not with either the CLSI method, Etest, or broth microdilution in YNB medium. The MICs obtained by the CLSI or Etest method were significantly lower for serotype D strains than for serotype A strains for both fluconazole and amphotericin B, while flucytosine MICs were not different according to serotype. These findings suggest that the in vitro antifungal susceptibility of C. neoformans, as determined with the techniques used, is not able to predict the early clinical outcome in patients with cryptococcosis.

In vitro cytotoxic, antileishmanial and antifungal activities of ethnopharmacologically selected Gabonese plants.

Seventy-seven crude extracts from leaves and stem barks of 15 Gabonese plants used in traditional medicine were evaluated for their cytotoxic, antileishmanial and antifungal activities. Most of the extracts exhibited cytotoxic activities toward human monocytes, and most particularly the hydromethanolic 50% (v/v) fraction of Ganophyllum giganteum leaves (IC(50)=1.3 microg/ml) as well as the methanolic extracts of Polyalthia suaveolens, Dioscorea preussii, Augouardia letestui leaves and Cola lizae stem barks (IC(50)<5 microg/ml). The methanolic extract of Polyalthia suaveolens displayed a strong antiproliferative activity against the promastigote form of Leishmania infantum parasites and presented a good antifungal activity on all the tested strains (IC(50)<1mg/ml). This extract was divided into six fractions: fraction F6 demonstrated a cytotoxic activity stronger than those of the crude extract (IC(50)=0.6 microg/ml), fractions F4 and F5 were devoid of cytotoxicity (IC(50)>100 microg/ml) and displayed interesting antileishmanial activity against the intracellular amastigote form of the parasite (IC(50)=5.6 and 12.4 microg/ml), respectively. However, the antifungal activity observed for the crude extract could not be recovered in the corresponding fractions.

Antifungal activity of steroidal glycosides from Yucca gloriosa L.

The antifungal activity of a crude steroidal glycoside extract from Yucca gloriosa flowers, named alexin, was investigated in vitro against a panel of human pathogenic fungi, yeasts as well as dermatophytes and filamentous species. The minimal inhibitory concentration (MIC) was determined by an agar dilution method. Alexin had a broad spectrum of antifungal activity, found to reside entirely in the spirostanoid fraction. The major tigogenyl glycosides, yuccaloeside B and yuccaloeside C, exhibited MICs between 0.39 and 6.25 microg[sol ]mL for all the tested yeast strains except for two (C. lusitaniae and C. kefyr). They were also active against several clinical Candida isolates known to be resistant to the usual antifungal agents. The MICs for the dermatophytes were between 0.78 and 12.5 microg[sol ]mL. The most sensitive filamentous species was A. fumigatus (MIC = 1.56 microg[sol ]mL). For most of the strains, the MICs of both glycosides were similar to those of the reference antifungal agent.

Sterol and fatty acid composition of Candida lusitaniae clinical isolates.

The sterol and fatty acid compositions of four amphotericin B-resistant and of two amphotericin B-susceptible Candida lusitaniae clinical isolates were determined. A flow cytofluorometric susceptibility test (FCST) with a membrane potential-sensitive cationic dye was used as a complement to the conventional method for selecting the isolates. Compared to susceptible isolates, resistant ones showed a greatly reduced ergosterol content and changes in sterol composition, consistent with a defect in Delta8-->7 isomerase. Within each group, no correlation between the sterol or fatty acid pattern or composition and both the degree of in vitro susceptibility and FCST MIC was found.

Alternative identification test relying upon sexual reproductive abilities of Candida lusitaniae strains isolated from hospitalized patients.

The in vitro mating ability of Candida lusitaniae (teleomorph Clavispora lusitaniae) clinical isolates has been investigated. Studying the effects of culture conditions, we showed that ammonium ion depletion in the medium is a major trigger of the sexual cycle. Moreover, a solid support is required for mating, suggesting a role for adhesion factors in addition to the mating type gene recognition function. Monitoring of mating and meiosis efficiency with auxotrophic strains showed great variations in ascospore yields, which appeared to be strain and temperature dependent, with an optimal range of 18 to 28 degrees C. The morphogenetic events taking place from mating to ascospore release were studied by scanning and electron microscopy, and the ultrastructure of the conjugation canal, through which intercellular nuclear exchanges occur, was revealed. Labeling experiments with a lectin-fluorochrome system revealed that the nuclear transfer was predominantly polarized, thus allowing a distinction between the nucleus donor and the nucleus acceptor strains. The direction of the transfer depended on the strain combination used, rather than on the genotypes of the strains, and did not appear to be controlled by the mating type genes. Finally, we demonstrated that all of the 76 clinical isolates used in this study were able to reproduce sexually when mated with an opposite mating type strain, and we identified a 1:1 MATa/MATalpha ratio in the collection. These results support the idea that there is no anamorph state in C. lusitaniae. Accordingly, the mating type test, which is easy to use and can usually be completed within 48 h, is a reliable alternative identification system for C. lusitaniae.

Improved detection of amphotericin B-resistant isolates of Candida lusitaniae by Etest.

Both intrinsic and acquired resistance to amphotericin B have been documented for Candida lusitaniae. Amphotericin B remains the drug of choice for many critical fungal infections, and the detection of resistance is essential to monitor treatment effectively. The limitations of the National Committee for Clinical Laboratory Standards (NCCLS) reference methodology for detection of amphotericin B resistance are well documented, and several alternative methods have been proposed. Etest assays with RPMI and antibiotic medium 3 (AM3) agar were compared to the NCCLS M27-A broth macrodilution method using AM3 for amphotericin B resistance testing with 49 clinical isolates of C. lusitaniae. The panel included nine isolates with known or presumed resistance to amphotericin B on the basis of in vivo and/or in vitro data. The distribution of amphotericin B MICs by Etest with RPMI ranged from 0. 032 to 16 microg/ml and was bimodal. All of the putatively resistant isolates were inhibited by amphotericin B at >/=0.38 microg/ml and could be categorized as resistant using this breakpoint. Etest with AM3 yielded a broader amphotericin B MIC range (0.047 to 32 microg/ml), and there were six putatively resistant isolates for which MICs were >1 microg/ml. The separation of putatively susceptible and resistant isolates was less obvious. Broth macrodilution with AM3 generated a unimodal distribution of MICs (ranging from 0.032 to 2 microg/ml) and failed to discriminate most of the putatively resistant isolates at both 24 and 48 h. Etest using RPMI and, to a lesser extent, using AM3 provided better discrimination between amphotericin B-resistant and -susceptible isolates of C. lusitaniae.

Comparative evaluation of a commercial system for identification of Candida lusitaniae.

The ability of the API Candida system (bioMérieux, France) to identify Candida lusitaniae isolates was evaluated in comparison to the Auxacolor and ID 32C systems using 52 clinical isolates previously identified on the basis of their morphology and their biochemical reactions in the Auxacolor and ID 32C systems. The API Candida system failed to definitively identify most of the strains tested within 24 h. No beta-maltosidase activity was detected in 28 strains, and supplementary tests were required to discriminate Candida lusitaniae, Candida famata and Candida guilliermondii. The API Candida system is not suitable for identification of Candida lusitaniae. In comparison, the Auxacolor system is easy to use and interpret, allowing rapid identification of this species; however, the ID 32C system is required for identification of atypical strains.

Evaluation of the E test for antifungal susceptibility testing of Candida glabrata.

The E test was compared to the reference NCCLS broth macrodilution method for susceptibility testing of Candida (Torulopsis) glabrata. The MICs of amphotericin B, flucytosine, fluconazole and itraconazole were determined using the appropriate culture media (RPMI 1640 agar with 2% glucose, Casitone agar or Antibiotic Medium 3 agar) according to the drug tested. Agreement between the two methods was within plus/minus two dilutions for 77-100% of test results, according to the drug/medium combination. The study revealed problems in determining the MICs of azoles using the E test, and confirmed the suitability of Casitone agar for susceptibility testing of fluconazole even if results were read within 24 h.

Amphotericin B susceptibility testing of Candida lusitaniae isolates by flow cytofluorometry: comparison with the Etest and the NCCLS broth macrodilution method.

A flow cytofluorometric susceptibility test (FCST) was used for rapid determination of the susceptibility of Candida lusitaniae isolates to amphotericin B. The test is based on the decrease in fluorescence intensity of cells stained with 3,3'-dipentyloxacarbocyanine iodide (DiOC5(3)), a membrane potential-sensitive cationic dye, after drug treatment. A total of 58 C. lusitaniae clinical isolates including strains known to be amphotericin B-resistant on the basis of in-vivo and/or in-vitro data were tested. MICs were determined concurrently by the NCCLS broth macrodilution method and the Etest, both with antibiotic medium 3. Regression analysis demonstrated that the data from the FCST and the Etest were better correlated (r = 0.93, n = 59, P < 0.001) than those from the FCST and the NCCLS method (r = 0.63, n = 59, P < 0.001). The FCST readily identified a series of putatively susceptible and resistant isolates. Our study points out the advantages of the flow cytometry approach in antifungal susceptibility testing of yeasts, since speed remains a major problem in conventional tests.

Study of the action of alpha-hederin on the ultrastructure of Candida albicans.

alpha-Hederin, a saponin isolated from Hedera helix (L.) (Araliaceae), was tested on Candida albicans ultrastructure. The concentrations used were 6.25, 12.5, and 25 micrograms ml-1 for an exposure time of 24 h. Transmission electron microscopy observations indicated that compared with untreated control yeasts, alpha-hederin induced modifications of cellular contents and alterations of cell envelope with degradation and death of the yeasts. The impact of alpha-hederin on the biomembranes and in particular on the plasmalemma is discussed. The antifungal activity of alpha-hederin was confirmed, as was the minimal inhibitory concentration (25 micrograms ml-1).

Evaluation of a flow cytofluorometric method for rapid determination of amphotericin B susceptibility of yeast isolates.

A rapid-flow cytofluorometric susceptibility test for in vitro amphotericin B testing of yeasts was evaluated and compared to the National Committee for Clinical Laboratory Standards (NCCLS) M27-T reference broth macrodilution method. The flow cytofluorometric method is based on the detection of decreased green fluorescence intensity of cells stained with DiOC5(3), a membrane potential-sensitive cationic dye, after drug treatment. Testing was performed on 134 clinical isolates (Candida spp. and Torulopsis glabrata). From the dose-response curve obtained for each isolate, three endpoints were calculated by computer analysis (the concentrations at which the fluorescence intensity was reduced by 50, 80, and 90%, i.e., 50% inhibitory concentration [IC50], IC80, and IC90, respectively). A regression analysis correlating these endpoints with the M27-T MICs showed that the best agreement was obtained with IC80. The flow cytofluorometric method showed good reproducibility with control strains. These initial results suggest that the flow cytofluorometric method is a valid alternative to the NCCLS reference method.

In-vitro susceptibility pattern of Candida lusitaniae and evaluation of the Etest method.

The antifungal susceptibility of 35 Candida lusitaniae isolates was determined in vitro by the National Committee for Clinical Laboratory Standards (NCCLS) M27-P macrodilution methodology. All the isolates were susceptible to ketoconazole, itraconazole and fluconazole. Of the 35 isolates, eight (23%) were resistant to flucytosine. For amphotericin B, M27-P yielded a narrow range of MICs (0.06-0.5 mg/L). We therefore investigated the activity of this drug by reading MICs at 72 h and by using alternative media, namely casitone complex medium (CCM) and antibiotic medium 3 (M-3). Reading at 72 h did not generate reproducible results. CCM and M-3 provided better discrimination between the isolates but did not change the rank order of the MICs. We thus concluded that all the isolates were susceptible to amphotericin B. We also conducted an evaluation with the Etest method according to the manufacturer's instructions with RPMI 1640 agar, CCM and the alternative semi-synthetic medium (SSM). For RPMI 1640, agreements +/-2 dilutions were 58% for amphotericin B, 92% for flucytosine, 57% for ketoconazole, 92% for fluconazole and 74% for itraconazole. CCM did not improve the agreement rates between the two methods but it led to better growth of all the isolates. The suitability of SSM was pointed out with itraconazole. The poor agreement rates for amphotericin B and ketoconazole call for further evaluation of the Etest method to assess several drug-organism combinations.

Screening for in vitro antifungal activities of some indole alkaloids.

Several indole alkaloids were tested by the agar dilution technique on a panel of human pathogenic fungi, yeasts, and dermatophytes. Our results indicate that the most active compounds possess a beta-carboline skeleton and that the presence of a 3-4 double bond enhances the activity. Our results also show that antifungal activities are not linked to the cytotoxic, antimicrobial or antiparasitic properties.

In vitro antifungal activity of triterpenoid saponins.

The antifungal activity of triterpenoid saponins, with hederagenin or oleanolic acid as aglycone, was investigated in vitro by the agar dilution method. Monodesmosidic hederagenin derivatives were shown to exhibit a broad spectrum of activity against yeast as well as dermatophyte species. alpha-Hederin was the most active compound, and Candida glabrata was the most susceptible strain. The structure-activity relationships are discussed.

Molecular recognition between serine proteases and new bioactive microproteins with a knotted structure.

Microproteins with proteinase inhibitory activity, 28 to 30 amino acids long, with 3 disulfide bridges have been isolated from Ecballium elaterium seeds. A peptide (EETI II) was isolated and behaved as a powerful trypsin inhibitor (Kd = 10(-11) to 10(-12) M). It was sequenced, chemically synthesized and the 3-D structure determined by 2-D 1H NMR. The information gained in the process enabled us to synthesize modified derivatives with inhibitory activity towards pancreatic elastase, chymotrypsin and human leucocyte elastase (Kd = 10(-7) to 10(-9) respectively). The most striking characteristic that appeared during the synthetic approach was the unfailing ability of the 28 amino acid peptides to refold and correctly close the 3 disulfide bridges, giving in each case an active compound. These disulfide bridges are assembled in a particular knotted structure, shared by few other bioactive peptides and called the 'knottin' structure. Molecular modeling of the peptide and a comparison with the other active molecules with similar topology allowed the synthesis of a chimaeric peptide, bearing 1 active site against a seryl-protease (trypsin), and 1 against a metallo-protease (carboxypeptidase A). The bis-headed peptide was able to inhibit both enzymes separately and concomitantly.