title: Species identification of invasive yeasts including Candida in Pakistan: limitations of phenotypic methods.
abstract: OBJECTIVE
  To compare phenotypic and genotypic methods of yeast identification.
  
  
  METHODS
  The in-vitro cross-sectional study was conducted from January 2006 to May 2009. Invasive yeasts isolated at the clinical microbiology laboratory at the Aga Khan University (AKU), Karachi, Pakistan, were identified. Speciation by phenotypic and molecular methods was compared. All yeasts isolated during the study period from blood and other invasive sites were identified using standard methods. Isolates were shipped to Mycotic Diseases Branch, Centres for Disease Control and Prevention, Atlanta, Georgia, USA, for identification by Luminex flow cytometric multianalyte profiling (xMAP) system. Ribosomal ITS2 DNA sequencing was performed on isolates not identified by Luminex.
  
  
  RESULTS
  Of the 214 invasive yeasts evaluated, Candida species were 209 (97.7%) while the frequency of non-Candida species was 5 (2.3%). Overall agreement between phenotypic and molecular identification was 81.3%, 90.3% amongst the more common Candida species, and only 38.8% amongst the uncommon yeasts.
  
  
  CONCLUSIONS
  Phenotypic methods of identification proved adequate for common Candida species, but were deficient in recognising rare Candida and non-Candida yeasts, highlighting the importance of molecular methods for identification.
authors.affiliation: Department of Pathology & Microbiology, Aga Khan Hospital, Karachi. joveria.farooqi@aku.edu
authors.forename: Joveria
authors.initials: J
authors.lastname: Farooqi
authors.forename: Kauser
authors.initials: K
authors.lastname: Jabeen
authors.forename: Noureen
authors.initials: N
authors.lastname: Saeed
authors.forename: Afia
authors.initials: A
authors.lastname: Zafar
authors.forename: Mary Eleanor
authors.initials: ME
authors.lastname: Brandt
authors.forename: Rumina
authors.initials: R
authors.lastname: Hasan
mesh_terms: D002175:Candida / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D003430:Cross-Sectional Studies; D005434:Flow Cytometry; D005838:Genotype; D006801:Humans; D066298:In Vitro Techniques; D016533:Mycological Typing Techniques / Q000379:methods*; D009181:Mycoses / Q000453:epidemiology / Q000382:microbiology*; D010154:Pakistan / Q000453:epidemiology; D010641:Phenotype; D016133:Polymerase Chain Reaction; D015003:Yeasts / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification