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

Abstract

Accurate identification of pathogenic species is important for early appropriate patient management, but growing diversity of infectious species/strains makes the identification of clinical yeasts increasingly difficult. Among conventional methods that are commercially available, the API ID32C, AuxaColor, and Vitek 2 systems are currently the most used systems in routine clinical microbiology. We performed a systematic review and meta-analysis to estimate and to compare the accuracy of the three systems, in order to assess whether they are still of value for the species-level identification of medically relevant yeasts. After adopting rigorous selection criteria, we included 26 published studies involving Candida and non-Candida yeasts that were tested with the API ID32C (674 isolates), AuxaColor (1,740 T he epidemiology of yeast infections, particularly those involving the bloodstream (i.e., fungemia) or other normally sterile sites, continues to evolve throughout the world (1), likely due to the diversity of susceptible hosts, including mainly patients undergoing transplantations or receiving treatment for underlying malignant diseases (2). Prophylactic use of antifungals has also contributed to alterations in the patterns of such infections, leading to increases in the incidence of non-albicans Candida species, compared to Candida albicans (3-6). Although the latter species is the most frequently isolated yeast in hospital settings (7), the emergence of less-common or "cryptic" non-albicans Candida species, as well as uncommon yeasts such as Rhodotorula, Geotrichum, Pichia, Malassezia, Saccharomyces, and cryptococci other than Cryptococcus neoformans (8), poses a threat due to their potential to develop antifungal resistance (9-12) or their intrinsically decreased susceptibility to one or more antifungal agents (13-15). As differences in antifungal drug susceptibilities can exist not only among genera but also among members of the same genus or species complex (8), accurate species identification is important for initiating early effective antifungal therapy, especially when susceptibility testing results are not promptly available.As simple, rapid, reliable alternatives to traditional methods based on the Wickerham assimilation/fermentation patterns (16), manual (e.g., AuxaColor [Bio-Rad, Marnes-la-Coquette, France]) and automated (i.e., Vitek 2 [bioMérieux, Marcy l'Etoile, France]) commercial identification systems are currently being used in clinical microbiology laboratories, but their ability to identify yeast isolates to the species level is dependent on the types and numbers of biochemical (carbohydrate/enzyme) substrates tested (17). Although with a limited database of only 26 taxa/species (updated to include 33 yeast species in a newer version of the system [AuxaColor 2], which was launched in 2002), the AuxaColor system uses colorimetric tests for assimilation substrates,

Misidentification of a Rare Species, Cryptococcus laurentii, by Commonly Used Commercial Biochemical Methods and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Systems: Challenges for Clinical Mycology Laboratories

“…It is widely recognized that commercial biochemical systems have limited accuracy in identifying rare yeast species (accuracy, 50 to 65%) (14)(15)(16). The present study further confirms these findings, as the Vitek 2 system was highly unreliable in the identification of C. laurentii.…”

Rapid Evaporative Ionisation Mass Spectrometry (REIMS) Provides Accurate Direct from Culture Species Identification within the Genus Candida

“…For example, whilst C. albicans is typically susceptible to azoles, C. krusei and C. inconspicua are innately resistant5. Furthermore, species specific antifungal interpretative breakpoints have been introduced; making it a necessity to accurately speciate Candida isolates6789.…”

“…Traditionally, the identification of members of the genus Candida within a clinical laboratory relied upon biochemical assays and the germ tube test913. Molecular methods including sequencing of the 18S rRNA gene and Internal Transcribed Spacer (ITS) regions can be used in instances where species delineations are poor.…”

Comparision of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF MS) with API ID 32C and VITEK 2 for the identification of Trichosporon species

“…Mayaların tanımlanmasında kullanılan API ID 32C, AuxaColor ve VITEK 2 ticari testlerinin değerlendirildiği bir metaanaliz çalışmasında, 26 literatür incelenmiş, sonuçlara göre VITEK 2 sistemi ile 61 T. asahii suşunun %85'inin, 21 T. mucoides suşunun tamamının; API ID 32C sistemi ile ise 11 Trichosporon beigelii suşunun %90'ının doğru tanımlandığı belirtilmiştir (10) .…”