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.     

Evaluation of commercial systems for the identification of clinical yeast isolates.

The Analytab Products Inc. (API), Micro-Drop (MD), and Uni-Yeast-Tek (UYT) systems for the presumptive identification of common clinical yeast isolates were compared with the oxidation-fermentation (OF) and a conventional procedure. With 229 coded isolates, the identification accuracies were API 94, MD 83, OF 82, and UYT 99%. The API system required the greatest technical ability. The MD materials were prone to malfunction. OF media, if incubated beyond 14 days, gave an accuracy of 87%, but this offered no advantage over the conventional procedure. The UYT system was the easiest to use.     

Comparative evaluation of three identification systems for anaerobes.

The accuracy of two new 4-h identification systems for anaerobes, the AN-IDENT (Analytab Products, Plainview, N.Y.) and the RapID ANA (Innovative Diagnostic Systems, Inc., Atlanta, Ga.) was compared with that of the API 20A system (Analytab Products). A total of 132 clinical isolates were tested in each of the three systems. The overall accuracies at the genus and species level for the three systems were: API 20A, 68.9 and 56.8%, respectively; AN-IDENT, 90.2 and 73.5%; and RapID ANA, 93.9 and 81.8%. Improved identification of anaerobes with the AN-IDENT and the RapID ANA systems was observed for isolates of the genus Fusobacterium, Clostridium species other than Clostridium perfringens, non-spore-forming bacilli, and isolates of the genus Peptostreptococcus. Reproducibility studies demonstrated that the results of the individual test reactions in all three identification systems were reproducible when the interpretive guidelines of the manufacturer were followed precisely.     

Rapid identification of Candida dubliniensis with commercial yeast identification systems.

Candida dubliniensis is a newly described species that is closely related phylogenetically to Candida albicans and that is commonly associated with oral candidiasis in human immunodeficiency virus-positive patients. Several recent studies have attempted to elucidate phenotypic and genotypic characteristics of use in separating the two species. However, results obtained with simple phenotypic tests were too variable and tests that provided more definitive data were too complex for routine use in the clinical laboratory setting. The objective of this study was to determine if reproducible identification of C. dubliniensis could be obtained with commercial identification kits. The substrate reactivity profiles of 80 C. dubliniensis isolates were obtained by using the API 20C AUX, ID 32 C, RapID Yeast Plus, VITEK YBC, and VITEK 2 ID-YST systems. The percentages of C. dubliniensis isolates capable of assimilating or hydrolyzing each substrate were compared with the percentages from the C. albicans profiles in each kit's database, and the results were expressed as percent C. dubliniensis and percent C. albicans. Any substrate that showed >50% difference in reactivity was considered useful in differentiating the species. In addition, assimilation of methyl-alpha-D-glucoside (MDG), D-trehalose (TRE), and D-xylose (XYL) by the same isolates was investigated by the traditional procedure of Wickerham and Burton (L. J. Wickerham and K. A. Burton, J. Bacteriol. 56:363-371, 1948). At 48 h (the time recommended by the manufacturer for its new database), we found that the assimilation of four carbohydrates in the API 20C AUX system could be used to distinguish the species, i.e., glycerol (GLY; 88 and 14%), XYL (0 and 88%), MDG (0 and 85%), and TRE (15 and 97%). Similarly, results with the ID 32 C system at 48 h showed that XYL (0 and 98%), MDG (0 and 98%), lactate (LAT; 0 and 96%), and TRE (30 and 96%) could be used to separate the two species. Phosphatase (PHS; 9 and 76%) and alpha-D-glucosidase (23 and 94%) proved to be the most useful for separation of the species in the RapID Yeast Plus system. While at 24 h the profiles obtained with the VITEK YBC system showed that MDG (10 and 95%), XYL (0 and 95%), and GLY (26 and 80%) could be used to separate the two species, at 48 h only XYL (6 and 95%) could be used to separate the two species. The most useful substrates in the VITEK 2 ID-YST system were TRE (1 and 89%), MDG (1 and 99%), LAT (4 and 98%), and PHS (83 and 1%). While the latter kit was not yet commercially available at the time of the study, it would appear to be the most valuable for the identification of C. dubliniensis. Although assimilation of MDG, TRE, and XYL proved to be the most useful for species differentiation by the majority of commercial systems, the results with these carbohydrates by the Wickerham and Burton procedure were essentially the same for both species, albeit following protracted incubation. Thus, it is the rapidity of the assimilation achieved with the commercial systems that allows the differentiation of C. dubliniensis from C. albicans.     

Comparative evaluation of three commercial systems for nucleic acid extraction from urine specimens

A nucleic acid extraction system that can handle small numbers of specimens with a short test turnaround time and short hands-on time is desirable for emergent testing. We performed a comparative validation on three systems: the MagNA Pure compact system (Compact), the NucliSens miniMAG extraction instrument (miniMAG), and the BioRobot EZ1 system (EZ1). A total of 75 urine specimens submitted for polyomavirus BK virus detection were used. The human beta-actin gene was detected on 75 (100%), 75 (100%), and 72 (96%) nucleic acid extracts prepared by the miniMAG, EZ1, and Compact, respectively. The miniMAG produced the highest quantity of nucleic acids and the best precision among the three systems. The agreement rate was 100% for BKV detection on nucleic acid extracts prepared by the three extraction systems. When a full panel of specimens was run, the hands-on time and test turnaround time were 105.7 and 121.1 min for miniMAG, 6.1 and 22.6 min for EZ1, and 7.4 and 33.7 min for Compact, respectively. The EZ1 and Compact systems processed automatic nucleic acid extraction properly, providing a good solution to the need for sporadic but emergent specimen detection. The miniMAG yielded the highest quantity of nucleic acids, suggesting that this system would be the best for specimens containing a low number of microorganisms of interest.     

Comparative evaluation of five commercial systems for the rapid identification of pathogenic Neisseria species.

Prompt diagnosis and effective treatment of urogenital gonococcal infections require rapid isolation and identification of Neisseria gonorrhoeae from urogenital specimens. We evaluated a new, rapid (30-min) test called Gonochek II (E-Y Laboratories, San Mateo, Calif.) which utilizes chromogenic substrates for the identification of pathogenic Neisseria species. It was compared with the API NeIdent (Analytab Products, Inc., Plainview, N.Y.), Minitek (BBL Microbiology Systems, Cockeysville, Md.), and RapID NH (Innovative Diagnostics, Atlanta, Ga.), systems and the Phadebact GC (Pharmacia Diagnostics, Piscataway, N.J.) test for its performance in identifying known strains of N. gonorrhoeae (39 strains), Neisseria meningitidis (22 strains), Neisseria lactamica (12 strains), and Branhamella catarrhalis (17 strains). The Gonochek II system correctly identified 100% of N. gonorrhoeae, N. lactamica, and B. catarrhalis strains and 95.4% of N. meningitidis strains. The percent agreement for correct identification of all strains tested was 98.8%. In contrast, the Minitek, RapID NH, and API NeIdent systems correctly identified 86.6, 80.0, and 73.3% of the strains, respectively. The Phadebact GC test identified 94.9% of the N. gonorrhoeae isolates but also cross-reacted with 41.6% of the N. lactamica strains. The Gonochek II system is rapid, simple to perform, and easy to interpret, requires 1 to 2 min to set up, and more accurately identifies pathogenic Neisseria species when compared with other systems used in this study.     

Evaluation of three commercial agar preparations for the presumptive identification of significant urinary isolates

Three commercially available pre-poured chromogenic preparations--chromogenic urinary tract infection (UTI) medium (chromogenic UTI, Oxoid), CHROMagar Orientation (Becton Dickinson) and CPS ID2 (bioMérieux)--are evaluated in comparison to routine urine microbiology using cysteine lactose electrolyte-deficient (CLED) medium and conventional methods of identification and susceptibility testing by Vitek 1 for the majority of isolates. Most isolates were Escherichia coli, and a chromogenic medium has been shown to be a reliable, rapid and more economic medium on which to presumptively identify these organisms due to the substrates the strain utilises in the plate and the chromogen subsequently produced. However, the opacity of chromogenic UTI made the medium difficult to inoculate and read, although the colours were clear and strong. Although there was no statistical difference between CHROMagar Orientation and CPS ID2, the colours observed on the former were stronger. This meant that colony counting was possible at significant concentrations of 10(4) and 10(5) colony-forming units (cfu)/mL and it may be easier to detect mixtures that would indicate contamination. Chromogenic media are richer than CLED and a number of Lactobacillus spp. (normally regarded as normal flora) grew on this medium. These were not considered to be significant.     

Comparative costs of microbial identification employing conventional and prepackaged commercial systems.

The accuracy of commercially prepackaged kits for microbial identification has become well established. Laboratory workers may encounter increasing demands for production of objective data to justify replacement of systems using individual biochemical tests in tubes. The authors present a system of cost analysis in which materials and labor costs are separately computed, and to which are added the effects of (1) fringe benefits, (2) decreased productivity resulting from administration, quality control, education and development, and (3) the additional expense of indirect costs that are allocated to laboratory procedures by accepted and standardized hospital accounting methods. Labor costs should be based on time-engineered studies conducted in individual laboratories. Alternatively, various published "unit values" may be used. The result may present several alternative differences in cost, depending on which unit values are accepted as applicable to the individual laboratory. Despite these uncertainties, the method of analysis provides a more objective means of justifying the cost of introduction of prepackaged kits where accuracy and speed of identification have already been proven to have advantages over biochemical tests in tubes.     

Nonfermentative bacilli: evaluation of three systems for identification.

Three systems for the identification of nonfermentative bacilli were evaluated for their rapidity and accuracy of identification of 217 strains. Two of the systems, API 20E (API) and Oxi/Ferm tube (OxiF), are available as kits; the oxidative attack (OA) system is not commerically available. The overall accuracies of the OA, API, and OxiF systems were 91, 69, and 50%, respectively. Identification within 48 h was achieved for 98% of the strains by OA, for 50% by API, and for 18% by OxiF. Most of the organisms that were either misidentified or not identified by API and OxiF were those nonfermentative bacilli which are relatively more fastidious or rarely encountered or both. All three systems accurately identified nonfermentative bacilli commonly isolated at Olive View Medical Center, namely, Pseudomonas aeruginosa, Acinetobacter anitratus, Pseudomonas maltophilia, Acinetobacter lwoffi, saccharolytic flavobacteria (CDC IIb), moraxellae, Pseudomonas fluorescens, and Pseudomonas putida. The OA system identified 100% of the above organisms correctly, API identified 99.4%, and OxiF identified 99.3%. Since these organisms comprise 92% of the total number of nonfermentative bacilli isolated at Olive View Medical Center, we conclude that both API and OxiF may be useful alternatives to conventional methods, based on accuracy of identification alone. These two systems were considered substantially inferior to the OA system when both accuracy and rapidity of identification were taken into account.     

Evaluation of a method for identification of Candida dubliniensis bloodstream isolates

To evaluate methods for differentiating Candida albicans and Candida dubliniensis, 772 putative C. albicans bloodstream isolates were tested for growth at 37 and 42 degrees C. Isolates showing no growth at 42 degrees C, abundant chlamydospore production, and the sugar assimilation pattern of the type strain were confirmed by DNA-based procedures to be C. dubliniensis.     

Comparative evaluation of three commercial software packages for analysis of DNA polymorphism patterns

Objective   In the present study we have compared three commercial software packages, GelCompar, Molecular Analyst Fingerprinting, and BioImage, to determine if the results generated by the programs were comparable and correlated adequately with visual interpretation of electrophoretic gels, in the analysis of several well characterized incidents of infections.
Methods   Infections caused by Pseudomonas aeruginosa , Candida dubliniensis , C. albicans , and serotypes of Salmonella were characterized by restriction endonuclease analysis, macrorestriction analysis of genomic DNA with pulsed-field gel electrophoresis, and random amplified polymorphic DNA. The genotypes were visually detected based on band presence or absence in the different gels. The similarity values of DNA profiles were computed using Dice coefficient and were presented in dendrograms by upgma . The concordance or agreement between the number of genotypes obtained and their clustering, using the computerized programs, was determined.
Results   In general, agreement in number of genotypes obtained visually and by using the commercial DNA analysis software was achieved, but discrepancies were also denoted between the systems. The concordance between the visual and the computerized analysis ranged from 72% to 100%.
Conclusion   In our experience, although the programs evaluated in the present study performed acceptably well, such programs may be used as an aid in the analysis of complex banding patterns, and they do not provide an indisputably correct analysis in genotype definition.     

Comparative evaluation of a commercial test for rapid identification of methicillin-resistant Staphylococcus aureus

The performance and ease of use of the recently introduced MRSA screen test (Denka Seiken Co. Ltd., Japan) for the identification of methicillin-resistant Staphylococcus aureus was evaluated in comparison with the BBL Crystal MRSA ID System (Becton Dickinson Europe, France). A total of 109 strains of S. aureus, consisting of 57 strains of MecA-negative S. aureus and 52 strains of MecA-positive S. aureus, were tested. With MecA PCR as the gold standard, the MRSA screen test had 98% sensitivity and 98% specificity, whereas the BBL Crystal MRSA ID System had 98% sensitivity and 95% specificity. The simplicity of use and rapid result make the MRSA screen test a valuable tool in the clinical microbiology laboratory pending demonstration of the MecA gene that should still always be done.     

Species identification and antifungal susceptibility of uncommon blood yeast isolates

Background/PurposeAccurate identification of Candida species is increasingly important in the era of emergence of Candida auris. We aimed to compare the identification performance of two matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems (Vitek MS and Bruker biotyper MS) and an oligonucleotide array for uncommon blood yeast isolates and demonstrate the susceptibilities among those isolates.MethodCandida species isolates from blood culture other than Candida albicans, Candida parapsilosis, Candida tropicalis, Candida glabrata, and Candida krusei identified by biochemical methods were collected from multiple hospitals and further identified by an oligonucleotide array based on the internal transcribed spacer-1 (ITS-1) and ITS-2 sequences of the rRNA genes, Vitek MS and Bruker biotyper MS. The minimal inhibitory concentrations (MICs) of these clinical isolates were determined by the Sensititre YeastOne (SYO) system.ResultsAmong 136 isolates, Candida guilliermondii was most common (52, 38.2%), followed by C. lusitaniae (13, 9.6%) and C. haemulonii (12, 8.8%). The oligonucleotide array, Vitek MS and Bruker biotyper MS correctly identified 89.7% (122), 90.4% (123), and 92.6% (126) of these isolates, respectively. Elevated minimal inhibitory concentrations (MICs) of fluconazole were observed for C. haemulonii (MIC₉₀: 256 mg/L), and C. guilliermondii (MIC₉₀: 16 mg/L) with 28.4% of uncommon Candida isolates with MIC ≧ 8 mg/L.ConclusionsFor uncommon Candida species, the unmet need for current databases of two commercial MALDI-TOF MS systems is highlighted, and the oligonucleotide array may serve as a supplement.     

An evaluation of three commercial fecal transport systems for the recovery of enteric pathogens

Twenty-five isolates, including six strains of Shigella species, six strains of Salmonella species, five strains of Yersinia enterocolitica, six strains of Campylobacter jejuni, and two strains of Vibrio parahaemolyticus, were inoculated at a concentration of 1.5 x 10(4) colony-forming units/mL into the following transport systems: Fekal Enteric Plus (Trend Scientific, Inc., St. Paul, MN), Cary Blair Transport Medium (Remel, Inc., Lenexa, KS), and Para-Pak C & S (Meridian Diagnostics, Inc., Cincinnati, OH). The Fekal Enteric Plus system showed a greater than or equal to 50% recovery of the original bacterial inoculum after 96 hours for all Salmonella, Shigella, and Yersinia strains tested and after as long as 72 hours for Vibrio strains. The Cary Blair Transport System showed greater than or equal to 50% recovery of the initial inoculum at 96 hours for five of six Salmonella strains, four of six Shigella strains, all Yersinia strains, and one of two Vibrio strains. With the use of the Para-Pak C & S, greater than or equal to 50% recovery of the original inoculum after 96 h was demonstrated for five of six Salmonella strains, four of six Shigella strains, all Yersinia strains, and one of two Vibrio strains. All three systems did not demonstrate even 10% recovery of the initial C. jejuni inoculum at 24 hours when held at room temperature.     

Comparative evaluation of three different commercial blood culture media for recovery of anaerobic organisms.

A comparison of three different commercial media was made to assess their recovery of anaerobic organisms from the blood stream. The three media used were the 50-ml brain heart infusion broth with added CO2 (Pfizer), the 50-ml Thiol broth with added CO2 (Difco), and the 50-ml prereduced, supplemented peptone broth in a Vacutainer tube with added CO2 (Becton-Dickinson). During a period of 17 consecutive months, 12,216 specimens of blood were processed with each broth. Aerobic or anaerobic bacteria were recovered from 913 specimens (7%). Seventy-four specimens (8%) of the total positive cultures contained anaerobic organisms. When potential contaminants were removed from the totals, 7% of the positive cultures contained anaerobic organisms and 7% of the patients with positive cultures had bacteremia with anaerobic bacteria. Of the three commercial blood culture media studied, the prereduced, supplemented peptone broth recovered more anaerobic organisms than did either the brain heart infusion or Thiol broths.     

Comparative genotyping of Candida albicans bloodstream and nonbloodstream isolates at a polymorphic microsatellite locus

Molecular typing studies have shown that the predominant form of reproduction of Candida albicans is clonal and that, in a majority of situations, persistent or recurrent infections are due to a unique strain. Characterization of distinct subpopulations and correlation with clinical features may thus be important to understanding the pathogenesis of candidiasis. In a clonal model, a unique polymorphic marker may identify populations with different biological properties. We therefore compared 48 bloodstream isolates and 48 nonbloodstream matched strains of C. albicans at the elongation factor 3-encoding gene (CEF3) polymorphic microsatellite locus of C. albicans. Sizing of the alleles was performed by automated capillary electrophoresis. A new, 137-bp allele was characterized, and seven nondescribed combinations were observed, resulting in 15 and 11 distinct CEF3 profiles in bloodstream and control strains, respectively. Genotypes 126-135, 130-136, and 131-131 accounted for 60.4% of both bloodstream and control strains. Four bloodstream isolates but no control strains displayed the 135-135 combination. None of the other genotypes was present at an increased frequency in bloodstream isolates. Bloodstream and nonbloodstream strains of C. albicans thus have a heterogeneous structure at the CEF3 locus, with three major and multiple minor allelic combinations.     

Comparative evaluation of macrodilution and alamar colorimetric microdilution broth methods for antifungal susceptibility testing of yeast isolates.

A comparative evaluation of the macrodilution method and the Alamar colorimetric method for the susceptibility testing of amphotericin B, fluconazole, and flucytosine was conducted with 134 pathogenic yeasts. The clinical isolates included 28 Candida albicans, 17 Candida tropicalis, 15 Candida parapsilosis, 12 Candida krusei, 10 Candida lusitaniae, 9 Candida guilliermondii, 18 Torulopsis glabrata, and 25 Cryptococcus neoformans isolates. The macrodilution method was performed and interpreted according to the recommendations of the National Committee for Clinical Laboratory Standards (document M27-P), and the Alamar colorimetric method was performed according to the manufacturer's instructions. For the Alamar colorimetric method, MICs were determined at 24 and 48 h of incubation for Candida species and T. glabrata and at 48 and 72 h of incubation for C. neoformans. The overall agreement within +/- 1 dilution for Candida species and T. glabrata against the three antifungal agents was generally good, with the values for amphotericin B, fluconazole, and flucytosine being 85.3, 77.9, and 86.2%, respectively, at the 24-h readings and 69.3, 65.2, and 97.2%, respectively, at the 48-h readings. Most disagreement was noted with fluconazole against C. tropicalis and T. glabrata. Our studies indicate that determination of MICs at 24 h by the Alamar colorimetric method is a valid alternate method for testing amphotericin B, fluconazole, and flucytosine against Candida species but not for testing fluconazole against C. tropicalis and T. glabrata. For flucytosine, much better agreement can be demonstrated against Candida species and T. glabrata at the 48-h readings by the Alamar method.(ABSTRACT TRUNCATED AT 250 WORDS)     

Identification of viridans streptococci by three commercial systems

The API 20S (Analytab Products, Plainview, NY), the GPI card (Vitek Systems, St. Louis, MO) and the RapSTR system (Innovative Diagnostics, Atlanta, GA) were compared with conventional biochemicals for the identification of viridans streptococci. One hundred nine clinical isolates were tested that included the following species: intermedius (38) sanguis II (20), bovis (variant) (14), mitis (14), salivarius (11), sanguis I (6), constellatus (3), mutans (2), and uberis (1). With initial testing, a correct species call was made with 72% of the isolates with the GPI card, 62% with the RapSTR, and 50% with the API 20S. Identifications of viridans streptococci group or those that needed additional biochemicals for species identification occurred with 28% of isolates with the API 20S, 8% with the RapSTR, and 9% with the GPI card. Incorrect identifications occurred with 6% of the isolates tested by the GPI card, 20% with the API 20S, and 30% with the RapSTR. Most discrepancies with the RapSTR were with 66% of the intermedius isolates, whereas most, 55%, of misidentifications with the API 20S were with sanguis II isolates. No identifications were made with 2% and 13% of isolates with the API 20S and GPI, respectively.     

Comparative evaluation of three commercial products and counterimmunoelectrophoresis for the detection of antigens in cerebrospinal fluid.

Three commercial products and counterimmunoelectrophoresis were evaluated for their ability to detect microbial antigens of Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae in cerebrospinal fluid from 157 patients suspected of having meningitis. Thirty-four patients were diagnosed as having bacterial meningitis by culture, microscopy, or antigen detection. The overall results showed the following detection percentages; counterimmunoelectrophoresis, 76%; Phadebact CSF, 76%; Directigen, 82%, and Bactigen, 93%. The results with purified antigen revealed that latex agglutination was more sensitive than coagglutination, which in turn was more sensitive than counterimmunoelectrophoresis.     

Evaluation of YeastIdent and Uni-Yeast-Tek yeast identification systems.

The accuracy of the new API YeastIdent system and the Flow Laboratories Uni-Yeast-Tek identification kit with an expanded data base was evaluated in comparison to the API 20C yeast identification system by three laboratories. A total of 489 test isolates were used, biased toward yeasts commonly encountered in clinical specimens. Isolates not in a system's data base were not counted in the evaluation of that system. For isolates in their data base, YeastIdent was 55% accurate and Uni-Yeast-Tek was 40% accurate. By the manufacturer's criteria of reliable identification without additional tests, both systems failed to identify many common and uncommon species. The limited number of substrates and difficulties in assessing results obtained with 11 of the API YeastIdent substrates and apparent errors in the expanded Uni-Yeast-Tek data base appeared to be major factors limiting the accuracy of these systems.