text: Introduction
  Yeast infections cause significant mortality in critically ill and immunocompromised patients. In particular, Candida species are the 4th most common cause of nosocomial bloodstream infections in the United States, and Cryptococcus neoformans, the commonest cause of fungal meningitis worldwide [1], [2]. Whilst Candida albicans remains the leading pathogenic yeast, infections due to non-C. albicans species such as Candida glabrata, as well as previously rare opportunists such as Trichosporon and Geotrichum species, are increasingly reported [1], [3]-[6]. Novel pathogenic Candida species such as Candida nivariensis and Candida bracarensis have also been described [7]. Since many non-C. albicans Candida and non-Candida yeasts are resistant or less susceptible to antifungal agents, rapid accurate species identification is central to timely, effective antifungal therapy [3]-[6], [8], [9].
  Conventional phenotypic-based methods for yeast identification, however, are slow (24-72 h), insensitive and often unable to identify more unusual species. Various molecular techniques including real-time PCR, DNA sequence analysis, microarray analysis, and fluorescence in-situ hybridization provide accurate identification [10], [11] but are expensive, require substantial specimen processing time (hours to a day) and are not easily implemented as routine techniques in the clinical laboratory.
  Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a powerful and rapid tool for the identification of bacterial and yeast pathogens [12]-[17]. Using MALDI-TOF MS, the protein spectral "fingerprint" of an isolate is compared to a reference spectral database for identification [18]. Previous studies have reported species identification rates of 92-99% amongst collections of yeasts and yeast-like organisms [14]-[17], [19], [20]. However, taken collectively, the results may not be directly comparable since these studies have used different approaches to assign species - from comparing spectra from test organisms to reference spectra in MALDI-TOF MS databases [16], [20], to enhancing these databases, and in some instances developing study-specific databases, with "in-house" spectral signatures [14], [15]. There also is a continuing need to extend the repository of reference spectra in MALDI-TOF MS databases.
  We therefore undertook the present study to evaluate the utility of the MALDI Biotyper 2.0 Microflex LT spectrometer (Bruker Daltonik GmbH; Bremen, Germany) with its current spectral database in comparison with phenotypic-based methods for the identification of a broad range of yeasts in a diagnostic laboratory. The first part of the study comprised testing of reference and clinical strains from our culture collection. The second was a blinded prospective analysis of freshly-collected yeast isolates recovered during routine laboratory work flow; discrepant results between MALDI TOF MS and phenotypic methods were resolved using sequence analysis of the fungal internal transcribed spacer (ITS) regions [21], [22]. Results obtained by preparation of yeasts by extraction of fungal proteins and by direct application of yeast colonies onto the MALDI TOF MS plate were also compared.
  
entities: ['blood']
entities: Organism_substance
entities: PMC-3192753-sec-05_T1