Evaluation of VITEK 2 and RapID Yeast Plus Systems for Yeast Species Identification: Experience at a Large Clinical Microbiology Laboratory

Abstract

A total of 750 clinical yeast isolates were evaluated by two identification systems, VITEK 2 and RapID Yeast Plus, using sequence analysis of the rRNA gene internal transcribed spacer regions as the reference method. The VITEK 2 and RapID systems correctly identified 737 (98.2%) and 716 (95.5%) isolates, respectively.Although Candida species, including the pathogenic Candida albicans, remain the yeast species most commonly encountered in a clinical microbiology laboratory, a variety of other yeasts are recovered from patients with well-documented infections. Accurate identification of these species is clinically important, as certain yeast species are associated with specific diseases (11,22). In addition, yeast species can differ greatly in their relative virulence levels (22) as well as their susceptibilities to antifungal agents (19). While there is an increasing move toward molecular biology-based diagnostic approaches (1), identification of clinical yeast isolates is still typically performed by biochemical, morphological, and physiological tests (8). These phenotypic systems often produce results that may not be accurate, so their performance must be reassessed to enable users to have a reliable system for yeast identification. In this study, we compared the VITEK 2 (bioMérieux VITEK, Marcy l'Etoile, France) and RapID Yeast Plus (Remel Inc., Lenexa, KS) systems, with sequence analysis of the rRNA gene internal transcribed spacer (ITS) regions used as the reference method, for the identification of medically important yeasts typically found in a large clinical microbiology laboratory.A total of 750 yeast isolates, representing 24 species of six genera, were studied. Isolates were obtained from clinical samples (oral, vaginal, anorectal, urine, stool, blood, central Candida krusei ATCC 6258 were used as quality control strains. Isolates were grown on Sabouraud dextrose agar (Kima, Padua, Italy) for 48 h at 30°C prior to being tested. Each isolate was simultaneously tested with the VITEK 2 system (version 4.02), using the new colorimetric YST card (BioMérieux), and with the RapID Yeast Plus system (version 1.95), according to the instructions of their respective manufacturers, and the results were compared. In cases of discrepant results, both methods were repeated and the results for the second runs were accepted as the final results. In cases of identification with low discrimination (see below), additional tests (e.g., microscopic morphology on cornmeal-Tween 80 agar or growth at 42 to 45°C) were carried out (3). ITS sequence analysis was performed on all 750 isolates and used as the reference system. Thus, purified genomic DNA was obtained from each yeast isolate, using an EZ1 DNA tissue kit (QIAGEN, Milan, Italy) and a BioRobot EZ1 workstation (QIAGEN) in accordance with the manufacturer's instructions. This included a preliminary step in which yeast colonies were resuspended in 190 l of buffer G2, 10 l of lyticase (25 units/l) was added to each cell sample, and the resulting mixture was incubated at 3...

Are the Conventional Commercial Yeast Identification Methods Still Helpful in the Era of New Clinical Microbiology Diagnostics? A Meta-Analysis of Their Accuracy

“…The main characteristics of the 26 studies (32-57), which were published between 1993 and 2014, are shown in Table 1 (see also Table S2 in the supplemental material). Among the 26 studies, 12 (32-34, 36-38, 40-43, 45, 54) reported on the identification performance of the AuxaColor system, 5 (35,38,39,43,54) reported on the identification performance of the API ID32C system, and 13 (44,(46)(47)(48)(49)(50)(51)(52)(53)(54)(55)(56)(57) reported on the identification performance of the Vitek 2 system operating with the ID-YST (fluorimetric) card (44,(46)(47)(48)(49) and/or the YST (colorimetric) card (47,48,(50)(51)(52)(53)(54)(55)(56)(57); among them, three were direct-comparison studies, of which two were between the AuxaColor and API ID32C systems (38,43) and one was among the AuxaColor, API ID32C, and Vitek 2 systems (54). Two studies evaluating the Vitek 2 system compared the colorimetric YST card with the older fluorimetric ID-YST card (47,48); however, we decided to include the results of these studies only with respect to the YST card.…”

“…In 3 of these studies (46,48,52), phenotypic methods were used in conjunction with molecular methods (i.e., sequencing of the internal transcribed spacer [ITS] region or the 18S-28S intersequence of ribosomal DNA [rDNA]) but only to resolve discrepant results between two phenotypic methods (i.e., the method under evaluation and that used as the reference method). Among the studies that employed molecular methods as reference methods (35,51,(53)(54)(55)(56), one study employed multilocus microsatellite-based PCR fingerprinting, and rDNA sequencing of all isolates was performed in the other 5 studies.…”

Development and Validation of an In-House Database for Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry-Based Yeast Identification Using a Fast Protein Extraction Procedure

“…Molecular identification. All 156 isolates included in the UCSC yeast database, the 100 isolates from the retrospective study, and any other study isolates for which a definitive species identification needed to be achieved or randomly confirmed were characterized molecularly by sequencing the ITS1-5.8S-ITS2 ribosomal DNA (rDNA) region and, when necessary, the 28S ribosomal subunit gene region, as previously described (22).…”

Uncommon Neosartorya udagawae Fungus as a Causative Agent of Severe Corneal Infection

“…PCR amplification was performed using fungus-specific primers for the internal transcribed spacer 1 and 2 regions flanking 5.8S ribosomal DNA (rDNA) (ITS1-5.8S-ITS2) (8) and partial portions of the ␤-tubulin and calmodulin genes (2, 3). PCR products were sequenced as previously described (20), and species identification was performed by searching databases using the BLAST sequence analysis tool (http://www.ncbi.nlm.nih.gov /BLAST/). The isolate was assigned to Neosartorya udagawae based on the complete identity with the corresponding sequences of the N. udagawae type strain CBS 114217.…”