Comparison of the new API Candida system to the ID 32C system for identification of clinically important yeast species

Evaluation of a Method for Long-Term Cryopreservation of Fungal Strains

The conservation of microorganisms is essential for their in-depth study. However, today's most widely used conservation methods, based on the use of distilled water, soil, oils, or silica, do not guarantee the stability of fungal cells, especially dermatophytes. This problem led us to evaluate the conservation capacity of a cryogenic vials system containing glass beads covered in a cryopreservant hypertonic solution as an alternative method of storage of fungal cells at -80°C. Up to 570 strains of fungi belonging to 27 different species, isolated from clinical samples, were inoculated into cryotubes containing 25 glass beads covered in a cryopreserving hypertonic solution. Suspensions were mixed vigorously and the cryopreserving solution was discarded. The tubes were frozen at -80°C for a period of 42 months and periodically, a glass bead was removed from each cryotube and inoculated onto Sabouraud dextrose agar, and incubated at 30°C for 7-14 days to evaluate the number of colonies recovered, their purity, and phenotypic characteristics. All yeast isolates were recovered, unlike 2 isolates (4.4%) of the mold group and 21 (10.7%) of the dermatophytes. Survival rates were close to 100% for yeasts and molds, with expiration times being estimated for almost indefinite stocks, and 62% for dermatophytes, with an average expiration date of 25.5 years. The phenotypic characteristics remained comparable to those of the strains before storage. Conservation at -80°C using cryogenic vials is a reliable and efficient system for the conservation of fungal collections, and although the behavior differs by groups, stratified survival data are obtained to avoid extinction.

Applicability of Fourier transform infrared (FTIR) spectroscopy in rapid identification of some Candida and dermatophyte species infections in humans

Traditional systems of identifying yeasts and dermatophytes have many disadvantages. Preliminary data on a radically different approach based on optical spectroscopic techniques suggest that these techniques may offer some advantages. We conducted a trial to verify the practical applicability of Fourier transform infrared (FTIR) spectroscopy in the identification of some yeast and dermatophyte species, in which samples from 50 patients with superficial fungal infections were cultured on Sabouraud dextrose agar with chloramphenicol and cycloheximide (actidione) and studied using FTIR microspectroscopy. Spectra of the same species were identical, whereas spectra of different species did not show similarity. This study showed that FTIR microspectroscopy is promising and can be used to obtain, with a single measurement, a "molecular fingerprint" of Candida and dermatophyte species. It can be improved further in terms of reliability.

COMPARISON BETWEEN FOUR USUAL METHODS OF IDENTIFICATION OF Candida SPECIES

Infection by Candidaspp. is associated with high mortality rates, especially when treatment is not appropriate and/or not immediate. Therefore, it is necessary to correctly identify the genus and species of Candida. The aim of this study was to compare the identification of 89 samples of Candida spp. by the manual methods germ tube test, auxanogram and chromogenic medium in relation to the ID 32C automated method. The concordances between the methods in ascending order, measured by the Kappa index were: ID 32C with CHROMagar Candida(κ = 0.38), ID 32C with auxanogram (κ = 0.59) and ID 32C with germ tube (κ = 0.9). One of the species identified in this study was C. tropicalis,which demonstrated a sensitivity of 46.2%, a specificity of 95.2%, PPV of 80%, NPV of 81.1%, and an accuracy of 80.9% in tests performed with CHROMagar Candida;and a sensitivity of 76.9%, a specificity of 96.8%, PPV of 90.9%, NPV of 91%, and an accuracy of 91% in the auxanogram tests. Therefore, it is necessary to know the advantages and limitations of methods to choose the best combination between them for a fast and correct identification of Candidaspecies.

Fungal diagnostics: review of commercially available methods

Fungi and yeasts are critical causes of acute infection. As such, the detection and identification of these organisms are crucial in the diagnosis of affected patient populations. There is a vast array of commercial tests currently available for diagnostic purposes. These vary from traditional culture and biochemical methods to advanced multiparameter molecular tests. Recent technological advances have driven the development of rapid tests which are complementing and in some cases replacing the more traditional methods of detection. Irrespective of the method used the ultimate goal is timely detection of the infectious agent allowing appropriate treatment and improved outcome for the patient.

In vitro susceptibility of a large collection of Candida Strains against fluconazole and voriconazole by using the CLSI disk diffusion assay

We evaluated all Candida spp. isolates obtained from patients admitted to two tertiary care hospitals between 1999 and 2003 in the city of São Paulo, Brazil. The in vitro activities of fluconazole (FCZ) and voriconazole were determined by the agar disk diffusion test using the Clinical and Laboratory Standards Institute M44-A guidelines. The inhibition zone diameters were read and interpreted automatically by the BIOMIC(®) image-analysis plate reader system. We tested a total of 4,625 strains, including 2,393 strains of C. albicans (51.7%), 658 of C. tropicalis (14.2%), 503 of C. glabrata (10.9%), 495 of C. parapsilosis (10.7%), 292 of C. rugosa (6.3%), 195 of C. guilliermondii (4.2%) and 89 of other Candida species (2.0%). Only 2.0% of the strains tested were classified as dose-dependent susceptible (DDS), and 5.8% of them were resistant to FCZ. The resistance or DDS to fluconazole was verified mainly among C. glabrata (7.8%), C. krusei (67.9%) and C. rugosa (65.1%). Voriconazole exhibited better activity in vitro than fluconazole, even in isolates fluconazole resistant. The resistance of fluconazole and voriconazole did not increase in the isolates of Candida spp. during the evaluated period.

The combination of minocycline and fluconazole causes synergistic growth inhibition against Candida albicans: an in vitro interaction of antifungal and antibacterial agents

Combination therapy can be used for the treatment of fungal infections, especially for those caused by antifungal-resistant fungi. In the present study, in vitro interactions and mechanisms between fluconazole and minocycline against Candida albicans were evaluated. The nature of the interactions determined by spectrophotometric method in a checkerboard assay was interpreted using nonparametric models of fractional inhibitory concentration index (FICI) and percentages of growth difference (ΔE). In the mechanism study, we evaluated the potential activity of minocycline on fluconazole penetrating the C. albicans biofilm. Furthermore, the effect of fluconazole and minocycline alone and in combination on the cellular calcium balance, as well as on the uptake and efflux of fluconazole were evaluated. It was found that fluconazole can work synergistically with minocycline against fluconazole-resistant C. albicans; the minimum inhibitory concentration of fluconazole decreased from 512 to 2 microgmL(-1) when fluconazole and minocycline were given in combination, with an FICI of 0.035 and 0.064 and high-percentage synergistic interactions of 1250% and 988% for the two resistant strains. The mechanism of action was suggested to be the enhancement of minocycline on fluconazole penetrating biofilm, and inducing the intracellular calcium release, instead of impacting on the uptake and efflux of fluconazole. Our results suggest that the combination of fluconazole and minocycline can reduce the fluconazole resistance of C. albicans in vitro.

Antifungal activity of low molecular weight chitosan against clinical isolates of Candida spp

Chitosan is a natural polymer derived from chitin, a structural component of fungi, insects and shrimp, which exerts antimicrobial effects against bacteria and fungi. The aim of this study was to investigate the in vitro antifungal activity of low molecular weight chitosan (LMWC), and the potential synergy between chitosan and a currently used antifungal drug, fluconazole. The in vitro minimal inhibitory concentrations (MICs) of chitosan and fluconazole against 105 clinical Candida isolates were measured by the broth microdilution method. LMWC exhibited a significant antifungal activity, inhibiting over 89.9% of the clinical isolates examined (68.6% of which was completely inhibited). The species included several fluconazole-resistant strains and less susceptible species such as C. glabrata, which was inhibited at a concentration of 4.8 mg/l LMWC. Although some strains were susceptible at pH 7.0, a greater antifungal activity of LMWC was observed at pH 4.0. There was no evidence of a synergistic effect of the combination of LMWC and fluconazole at pH 7.0. This is the first report in which the antifungal activity of LMWC was investigated with clinical Candida strains. The use of LMWC as an antifungal compound opens new therapeutic perspectives, as the low toxicity of LMWC in humans supports its use in new applications in an environment of pH 4.0-4.5, such as a topical agent for vulvovaginal candidiasis.

Spectrum and prevalence of fungi infecting deep tissues of lower-limb wounds in patients with type 2 diabetes

The prevalence rate and spectrum of fungi infecting deep tissues of diabetic lower-limb wounds (DLWs) have not been previously studied. Five hundred eighteen (382 male and 136 female) consecutive patients with type 2 diabetes hospitalized due to infected lower-limb wounds were enlisted in this study. Deep tissue (approximately 0.5- x 0.5-cm size) taken perioperatively from the wound bed was cultured for fungi. Fungi was found in 27.2% (141/518) of the study population. Candida parapsilosis (25.5%), Candida tropicalis (22.7%), Trichosporon asahii (12.8%), Candida albicans (10.6%), and Aspergillus species (5.0%) were the most predominant fungal isolates. Of the fungal isolates, 17.7% were resistant to itraconazole, 6.9% were resistant to amphotericin B, 6.9% were resistant to voriconazole, 3.9% were resistant to fluconazole, and 1.5% were resistant to flucytosine. Of the population, 79.7% (413/518) had bacterial infection in deep tissue. The predominant isolates were Enterococcus faecalis (14.1%), Staphylococcus aureus (12.2%), and Pseudomonas aeruginosa (10.8%). Mixed fungal and bacterial infections were seen in 21.4% of patients, while 5.8% had only fungal infection and 58.3% had only bacterial infections. Another 14.5% had neither bacteria nor fungi in the deep tissue. Patients with higher glycosylated hemoglobin levels had significantly more fungal infections. Our study reveals that deep-seated fungal infections are high in DLWs. In the context of delayed wound healing and amputation rates due to DLWs, it is important to study the pathogenicity of fungi in deep tissues of DLWs and their possible contribution to delayed wound healing. The role of antifungal agents in wound management needs to be evaluated further.

Enzymatic substrates in microbiology

Enzymatic substrates are powerful tools in biochemistry. They are widely used in microbiology to study metabolic pathways, to monitor metabolism and to detect, enumerate and identify microorganisms. Synthetic enzymatic substrates have been customized for various microbial assays, to detect an expanding range of both new enzymatic activities and target microorganisms. Recent developments in synthetic enzymatic substrates with new spectral, chemical and biochemical properties allow improved detection, enumeration and identification of food-borne microorganisms, clinical pathogens and multi-resistant bacteria in various sample types. In the past 20 years, the range of synthetic enzymatic substrates used in microbiology has been markedly extended supporting the development of new multi-test systems (e.g., Microscan, Vitek 2, Phoenix) and chromogenic culture media. The use of such substrates enables an improvement in time to detection and specificity over conventional tests that employ natural substrates. In the era of intense developments in molecular biology, phenotypic tests involving enzymatic substrates remain useful to analyse both simple and complex samples. Such tests are applicable to diagnostic and research laboratories all over the world.

Synergistic activity of azoles with amiodarone against clinically resistant Candida albicans tested by chequerboard and time–kill methods

Candida albicans is the most common candidal pathogen, causing serious systemic disease in immunocompromised patients. Azoles are widely applied and largely effective; however, they are generally fungistatic and clinically resistant isolates are emerging increasingly. The present study provided in vitro evidence using a chequerboard technique that amiodarone is strongly synergistic with azoles against resistant C. albicans, with mean fractional inhibitory concentration indices of 0.01 and high-percentage synergistic interactions of 1250 %. A time–kill study performed by both colony counting and a colorimetric reduction assay confirmed the synergistic interaction, with a ≥2 log10 decrease in c.f.u. ml−1 compared with the corresponding azoles alone. These results suggest the possibility of supplementing azoles with amiodarone to treat resistant C. albicans infections.

Evaluation of the new Micronaut-Candida system compared to the API ID32C method for yeast identification

A new system, Micronaut-Candida, was compared to API ID32C to identify 264 yeast (Candida albicans, C. parapsilosis, C. tropicalis, C. krusei, C. inconspicua, C. norvegensis, C. lusitaniae, C. guilliermondii, C. dubliniensis, C. pulcherrima, C. famata, C. rugosa, C. glabrata, C. kefyr, C. lipolytica, C. catenulata, C. neoformans, Geotrichum and Trichosporon species, Rhodotorula glutinis, and Saccharomyces cerevisiae) clinical isolates. Results were in concordance in 244 cases. Eighteen out of the 20 of discordant results were correctly identified by Micronaut-Candida but not by API ID32C, as confirmed by PCR ribotyping.

In vitro interactions between tacrolimus and azoles against Candida albicans determined by different methods

Combination therapy could be of use for the treatment of fungal infections, especially those caused by drug-resistant fungi. However, the methods and approaches used for data generation and result interpretation need further optimizing. The fractional inhibitory concentration index (FICI) is the most commonly used method, but it has several drawbacks in characterizing antifungal drug interaction. Alternatively, some new methods can be used such as the DeltaE model (difference between the predicted and measured fungal growth percentages) and the response surface approach, which uses the concentration-effect relationship over the whole concentration range instead of just the MIC. In the present study, in vitro interactions between tacrolimus (FK506) and three azoles-fluconazole (FLC), itraconazole (ITR), and voriconazole (VRC)-against Candida albicans were evaluated by the checkerboard microdilution method and time-killing test. The intensity of the interactions was determined by visual reading and the spectrophotometric method in a checkerboard assay, and the nature of the interactions was assessed by nonparametric models of FICI and DeltaE. Colony counting and colorimetric viable detection methods (2,3-bis {2-methoxy-4-nitro-5-[(sulfenylamino) carbonyl]-2H-tetrazolium hydroxide} [XTT] reduction test) were used for evaluating the combination antifungal effects over time. Synergistic and indifferent effects were found for the combination of FK506 and azoles against azole-sensitive strains, while strong synergy was found against azole-resistant strains analyzed by FICI. The DeltaE model gave more consistent results with FICI. The positive interactions were also confirmed by the time-killing test. Our findings suggest a potential role for combination therapy with calcineurin pathway inhibitors and azoles to augment activity against resistant C. albicans.

Yeast identification--past, present, and future methods

The focus of this review is the evolution of biochemical phenotypic yeast identification methods with emphasis on conventional approaches, rapid screening tests, chromogenic agars, comprehensive commercial methods, and the eventual migration to genotypic methods. As systemic yeast infections can be devastating and resistance is common in certain species, accurate identification to the species level is paramount for successful therapy and appropriate patient care.

Rapid identification of Candida species by FT-IR microspectroscopy

Due to the continuous increase of human candidiasis and the great diversity of yeasts of the Candida genera, it is indispensable to identify this yeast as early as possible. Early identification enables an early diagnostic and patient-adapted anti-fungal therapy, thus reducing morbidity and mortality related to these infections. In view of this, we have in this study investigated microcolonies using a method based on Fourier transform-infrared microspectroscopy (FTIRM) for a rapid and early identification of the most frequent Candida species encountered in human pathology. FTIR spectroscopy is a whole-cell "fingerprinting" method by which microorganisms can be identified. By exploiting the huge discriminating capacity of this technique, we identified 6 species (Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, Candida krusei, and Candida kefyr) from a collection of 57 clinical strains of Candida, isolated from hospitalised patients. Data obtained on 10- to 18-h-old microcolonies were compared to cultures of 24 h. Our results clearly show the efficiency and the robustness of FTIR (micro)spectroscopy in identifying species with a classification rate of 100% for both microcolonies and 24-h cultures. FTIR microspectroscopy is thus a promising clinical approach, because compared to conventional and molecular techniques, it is time and money saving, has great identification and discriminating potentials, and is amenable to an automated high-throughput routine system.

The combination effects of phenolic compounds and fluconazole on the formation of ergosterol in Candida albicans determined by high-performance liquid chromatography/tandem mass spectrometry

A liquid chromatography/tandem mass spectrometry (LC/MS) with atmospheric pressure chemical ionization (APCI) for the quantification of ergosterol, lanosterol, and squalene was developed to evaluate the combination effects of phenolic compounds with fluconazole on ergosterol biosynthesis in Candida albicans. The three analytes were separated by a column of C18 and were quantified without interference with each other using positive mode tandem mass spectrometry (MS/MS). Molecular ions of ergosterol and lanosterol were detected as the [M+H-H2O]+ ion species at m/z 380 and 410, whereas squalene appeared as the [M+H]+ ion species at m/z 412. On fragmentation of ergosterol, lanosterol, and squalene, the product ions at m/z 69, 149, and 109, respectively, were present as major fragments. These product ions were used for the quantification of them in multiple reaction monitoring acquisition mode. The relationship between signal intensity and the analytes' concentration was linear over the concentration range of 0.05-10 microg/ml. Following the treatment of C. albicans with fluconazole in combination with albicanyl caffeate, resveratrol, and 3,4'-difluorostilbene, respectively, the content of ergosterol in both the sensitive and resistant C. albicans showed depletion, whereas the squalene showed accumulation especially in the sensitive isolates determined with the method developed.

Comparison of VITEK 2 with ITS2-fragment length polymorphism analysis for identification of yeast species

A total of 61 clinical yeast isolates of Candida, Cryptococcus, Blastoschizomyces, and Saccharomyces spp. were used to compare two identification techniques, VITEK 2 and ITS2-fragment length polymorphism analysis (ITS2-FLP), with ID32C as the reference method. ID32C identified 58 isolates correctly. ITS2-FLP with Instagene DNA extraction identified 59 isolates. ITS2-FLP combined with boiling-freezing DNA extraction identified 55 isolates. VITEK 2 identified 41 isolates correctly.

Liquid chromatography–tandem mass spectrometric method for the analysis of fluconazole and evaluation of the impact of phenolic compounds on the concentration of fluconazole in Candida albicans

A bioanalytical method using liquid chromatography-tandem mass spectrometry was developed for the analysis of fluconazole in Candida albicans after incubation with phenolic compounds, which have been proved possessing antifungal properties and have synergetic activity against C. albicans when in combination with fluconazole. Samples of C. albicans thallus obtained by centrifuging the mixed culture after 24 h incubation were saponified and centrifuged. The supernatant was evaporated to dryness, reconstituted, and injected on a C18 column using an organic-aqueous mobile phase. The chromatographic run time was 3.5 min per injection, with retention times of 2.4 min for fluconazole. The detection was by monitoring fluconazole at m/z 305-->191. The standard curve range was 1.0-100.0 ng ml(-1) with a mean correlation coefficient 0.9992. The precision and accuracy of the quality control (QC) samples were R.S.D < 5.5%, R.E. <3% for intra-day and R.S.D. <6.2%, R.E. <4% for inter-day. The concentration of fluconazole in C. albicans was found to be increased with the increment of the tested compounds concentration when they were in combination.

Epidemiology of clinical isolates of Candida albicans and their susceptibility to triazoles

The study comprised strains of Candida albicans isolated from patients hospitalised in a tertiary care hospital during a 2-year period. In total 851 strains were cultured, including 379 (44.5%) strains from internal medicine patients, 243 (28.6%) from surgical patients and 229 (26.9%) from patients in the surgical intensive care unit. The strains were tested for susceptibility to the triazoles: fluconazole and itraconazole. There were 523 (61.5%) strains susceptible, 11 strains (1.3%) showed intermediate susceptibility and 317 (37.2%) were resistant to fluconazole, while 403 (47.3%) strains were susceptible, 43 (5.1%) intermediately susceptible and 405 (47.6%) resistant to itraconazole. Regular surveillance of fungal resistance patterns should be carried out and there should be prudent use of hospital triazole usage.

Yeast identification in the clinical microbiology laboratory: phenotypical methods

Emerging yeast pathogens are favoured by increasing numbers of immunocompromised patients and by certain current medical practices. These yeasts differ in their antifungal drug susceptibilities, and rapid species identification is imperative. A large variety of methods have been developed with the aim of facilitating rapid, accurate yeast identification. Significant recent commercial introductions have included species-specific direct enzymatic colour tests, differential chromogenic isolation plates, direct immunological tests, and enhanced manual and automated biochemical and enzymatic panels. Chromogenic isolation media demonstrate better detection rates of yeasts in mixed cultures than traditional media, and allow the direct identification of Candida albicans by means of colony colour. Comparative evaluation of rapid methods for C. albicans identification, including the germ tube test, shows that chromogenic media may be economically advantageous. Accurate tests for single species include the Bichrolatex Albicans and Krusei Color tests, both immunologically based, as well as the Remel Rapid Trehalose Assimilation Broth for C. glabrata. Among broad-spectrum tests, the RapID Yeast Plus system gives same-day identification of clinical yeasts, but performance depends on inoculum density and geographic isolate source. The API 20 C AUX system is considered a reference method, but newer systems such as Auxacolor and Fungichrom are as accurate and are more convenient. Among automated systems, the ID 32 C strip, the Vitek Yeast Biochemical Card and the Vitek 2 ID-YST system correctly identify >93% of common yeasts, but the ID-YST is the most accurate with uncommon yeasts, including C. dubliniensis. Spectroscopic methods such as Fourier transformed-infrared spectroscopy offer potential advantages for the future. Overall, the advantages of rapid yeast identification methods include relative simplicity and low cost. For all rapid methods, meticulous, standardized multicenter comparisons are needed before tests are fully accepted.

Identification of yeast species by fatty acid profiling as measured by gas-liquid chromatography

An improved rapid method for the identification of yeasts and yeast-like fungi from clinical sources which is based on fatty acid profiles obtained by gas-liquid chromatography (GLC) is described. The fatty acid profile database is based upon internal standardisation and using the relative retention times and the retention index of the analysed fatty acids. Differentiation between yeast species was achieved by the quantitative and qualitative comparison of measured fatty acid profiles with those in the database. A total of 1024 clinical isolates were analysed by GLC to test the validity of the database. 96.2% of all tested samples were identified correctly to the species level by the improved GLC method.

The ins and outs of DNA fingerprinting the infectious fungi

DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as the method of choice, and some methods perform better than others at different levels of resolution. In this review, requirements for an effective DNA fingerprinting method are proposed and procedures are described for testing the efficacy of a method. In light of the proposed requirements, the most common methods now being used to DNA fingerprint the infectious fungi are described and assessed. These methods include restriction fragment length polymorphisms (RFLP), RFLP with hybridization probes, randomly amplified polymorphic DNA and other PCR-based methods, electrophoretic karyotyping, and sequencing-based methods. Procedures for computing similarity coefficients, generating phylogenetic trees, and testing the stability of clusters are then described. To facilitate the analysis of DNA fingerprinting data, computer-assisted methods are described. Finally, the problems inherent in the collection of test and control isolates are considered, and DNA fingerprinting studies of strain maintenance during persistent or recurrent infections, microevolution in infecting strains, and the origin of nosocomial infections are assessed in light of the preceding discussion of the ins and outs of DNA fingerprinting. The intent of this review is to generate an awareness of the need to verify the efficacy of each DNA fingerprinting method for the level of genetic relatedness necessary to answer the epidemiological question posed, to use quantitative methods to analyze DNA fingerprint data, to use computer-assisted DNA fingerprint analysis systems to analyze data, and to file data in a form that can be used in the future for retrospective and comparative studies.

Evaluation of the VITEK 2 system for rapid identification of yeasts and yeast-like organisms

The new VITEK 2 system is a fully automated system dedicated to the identification and susceptibility testing of microorganisms. In conjunction with the VITEK ID-YST card the VITEK 2 system allows the identification of clinically important yeasts and yeast-like organisms in 15 h due to a sensitive fluorescence-based technology. The ID-YST card consists of 47 biochemical reactions. The database comprises 51 taxa, including newly described species. In this study we evaluated the reliability of the VITEK ID-YST card for the identification of yeasts and yeast-like organisms encountered in a clinical microbiology laboratory. A total of 241 strains representing 21 species were studied. The strains were isolated from clinical samples within a period of 60 days prior to the identification. The tests were performed using 24-h to 55-h subcultures on Sabouraud-gentamicin-chloramphenicol agar. Each strain was tested in parallel using the ID 32C strip as a comparison method combined with microscopic morphology and an agglutination test for C. krusei. Overall, 222 strains (92.1%) were unequivocally identified including 11 isolates (4.6%) identified with low discrimination resolved by simple additional tests. Ten strains (4. 1%) for which results were given with low discrimination could not be unequivocally identified with supplemental tests, 4 strains (1. 7%) were misidentified and 5 strains (2.1%) could not be identified. In conclusion, we found that the VITEK 2 system is a rapid and accurate method for the identification of medically important yeasts and yeast-like organisms.

The ins and outs of DNA fingerprinting the infectious fungi

DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as the method of choice, and some methods perform better than others at different levels of resolution. In this review, requirements for an effective DNA fingerprinting method are proposed and procedures are described for testing the efficacy of a method. In light of the proposed requirements, the most common methods now being used to DNA fingerprint the infectious fungi are described and assessed. These methods include restriction fragment length polymorphisms (RFLP), RFLP with hybridization probes, randomly amplified polymorphic DNA and other PCR-based methods, electrophoretic karyotyping, and sequencing-based methods. Procedures for computing similarity coefficients, generating phylogenetic trees, and testing the stability of clusters are then described. To facilitate the analysis of DNA fingerprinting data, computer-assisted methods are described. Finally, the problems inherent in the collection of test and control isolates are considered, and DNA fingerprinting studies of strain maintenance during persistent or recurrent infections, microevolution in infecting strains, and the origin of nosocomial infections are assessed in light of the preceding discussion of the ins and outs of DNA fingerprinting. The intent of this review is to generate an awareness of the need to verify the efficacy of each DNA fingerprinting method for the level of genetic relatedness necessary to answer the epidemiological question posed, to use quantitative methods to analyze DNA fingerprint data, to use computer-assisted DNA fingerprint analysis systems to analyze data, and to file data in a form that can be used in the future for retrospective and comparative studies.

Comparative study of seven commercial yeast identification systems

AIMS

To compare the performance of seven commercial yeast identification methods with that of a reference method, and to compare the costs of the commercial kits.

METHODS

Clinical yeast isolates (n = 52), comprising 19 species, were identified using Vitek, Api ID 32C, Api 20C AUX, Yeast Star, Auxacolor, RapID Yeast Plus system, and Api Candida and compared with a reference method which employed conventional tests.

RESULTS

The percentage of correctly identified isolates varied between 59.6% and 80.8%. Overall, the highest performance was obtained with Api Candida (78.8%) and Auxacolor (80.8%). Among germ tube negative yeast isolates, Auxacolor and Api Candida both identified 93.1% of isolates correctly. All systems failed to identify C norvegensis, C catenulata, C haemulonii, and C dubliniensis. In comparison with Auxacolor, the Api Candida is less expensive and requires less bench time.

CONCLUSIONS

Auxacolor and Api Candida appeared to be the most useful systems for identification of germ tube negative yeast isolates in clinical microbiology laboratories, although one should be aware that several germ tube negative Candida species cannot be identified by these systems.

Comparison of the API Candida system with the AUXACOLOR system for identification of common yeast pathogens

Two commercial systems for the identification of yeasts were evaluated by using 159 clinical isolates that had also been identified by conventional biochemical and morphological methods. The API Candida system correctly identified 146 isolates (91.8%), and the AUXACOLOR system correctly identified 145 isolates (91.2%). However, of the 146 isolates identified by the API Candida system, 23 required supplemental biochemical tests or morphological assessment to obtain the correct identification. The AUXACOLOR system gave no identification in 13 cases (8.2%), while the API Candida system gave an unreadable profile in only one case. Incorrect identifications were more common with the API Candida system (12 isolates; 7.5%) than with the AUXACOLOR system (1 isolate; 0.6%).

Efficacy of API 20C and ID 32C systems for identification of common and rare clinical yeast isolates

The abilities of the API 20C and ID 32C yeast identification systems to identify 123 common and 120 rare clinical yeast isolates were compared. API 20C facilitated correct identification of 97% common and 88% rare isolates while ID 32C facilitated correct identification of 92% common and 85% rare isolates.

Evaluation of the new API Candida system for identification of the most clinically important yeast species

The API Candida system (bioMérieux) a new yeast identification system, was evaluated for its reliability in identifying 198 clinical yeast isolates in comparison with the API 20C system (bioMérieux) that was used as reference standard. The API Candida system correctly identified 91.4% and 71.7% of the isolates, with and without additional tests, respectively. The API Candida system identified 96.3% of common isolates studied, and 66.6% of uncommon isolates. We think that API Candida system is an easy and good yeast identification system and it could be used in a routine clinical microbiology laboratory.

Evaluation of six commercial systems for identification of medically important yeasts

Six commercially available systems for the identification of yeasts were evaluated using 133 clinical isolates and four reference strains that had been previously identified by conventional methods and 19 recent clinical isolates that had been identified by the ID32C system (bioMérieux, France). The total identification rates (TIR) established for the total number of strains tested and the database identification rates (DBIR) established for the strains included in the respective manufacturer databases were both determined. After incubation for 4 h, the TIR and DBIR were 78% and 84%, respectively, for the RapID Yeast Plus system (Innovative Diagnostic Systems, USA). After incubation for 24 h, the TIR and DBIR were 32% and 32%, respectively, for the ID32C, 65% and 67% for the Auxacolor system (Sanofi Diagnostics Pasteur, France), 62% and 65% for the Fungichrom I system (International Microbio, France), 52% and 65% for the Fungifast I twin system (International Microbio), and 62% and 68% for the API Candida system (bioMérieux). The maximum TIR and DBIR (+/- 1%) obtained after incubation for 48 h were 86% and 88% for the Auxacolor, 85% and 89% for the Fungichrom I, 78% and 98% for the Fungifast I twin, and 82% and 91% for the API Candida. For the ID32C, the maximum TIR and DBIR were 98% and 98%, respectively, but these values were obtained only after 72 h of incubation. In addition, the six systems varied in their ease of use and readings. In conclusion, based on results obtained with 156 strains, the Auxacolor and Fungichrom systems seem the most appropriate for use in a clinical microbiology laboratory, due to their ease of use and reading, their rapidity, their cost per test, and their relatively high TIR results, which indicated acceptable performance with strains frequently isolated in our hospital. For a reference identification, the ID32C remains the sole system usable.

Identification of Candida species by randomly amplified polymorphic DNA fingerprinting of colony lysates

We have characterized a method that produces simple yet diagnostic fingerprints that are unique to isolates of Candida species. DNA from individual colonies can be amplified from crude single-colony lysates. Randomly amplified polymorphic DNA (RAPD) fingerprints generated from a single primer correctly identified the species of most (>98%) of the isolates identified with CHROMagar Candida plates as non-Candida albicans Candida species. RAPD fingerprints were much more informative than the plates, since they distinguished between all tested species and required less time. Most (91%) of these identifications agreed with those assigned by API 20C tests. In almost every incident of species identity mismatch, electrophoretic karyotyping showed that the RAPD fingerprint was correct. This underscores the improved objectivity and reliability of this method over those of conventional diagnostic tools. The identities of approximately 30% of C. albicans isolates identified in clinical laboratories by positive germ tube tests are not verified by either testing on CHROMagar Candida plates or RAPD fingerprinting. Data suggest that clinical isolates conventionally identified as C. albicans in clinical settings are heterogeneous, consisting of both misidentified and atypical yeasts. RAPD fingerprints obtained from primary culture plate colonies allows for rapid, highly accurate determinations of Candida species, hence permitting earlier selection of appropriate antifungal agents in the clinical setting.