title: Conventional Morphology Versus PCR Sequencing, rep-PCR, and MALDI-TOF-MS for Identification of Clinical Aspergillus Isolates Collected Over a 2-Year Period in a University Hospital at Kayseri, Turkey.
abstract: BACKGROUND
  Aspergillus species cause a wide range of diseases in humans, including allergies, localized infections, or fatal disseminated diseases. Rapid detection and identification of Aspergillus spp. facilitate effective patient management. In the current study we compared conventional morphological methods with PCR sequencing, rep-PCR, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for the identification of Aspergillus strains.
  
  
  METHODS
  A total of 24 consecutive clinical isolates of Aspergillus were collected during 2012-2014. Conventional morphology and rep-PCR were performed in our Mycology Laboratory. The identification, evaluation, and reporting of strains using MALDI-TOF-MS were performed by BioMérieux Diagnostic, Inc. in Istanbul. DNA sequence analysis of the clinical isolates was performed by the BMLabosis laboratory in Ankara.
  
  
  RESULTS
  Samples consisted of 18 (75%) lower respiratory tract specimens, 3 otomycosis (12.5%) ear tissues, 1 sample from keratitis, and 1 sample from a cutaneous wound. According to DNA sequence analysis, 12 (50%) specimens were identified as A. fumigatus, 8 (33.3%) as A. flavus, 3 (12.5%) as A. niger, and 1 (4.2%) as A. terreus. Statistically, there was good agreement between the conventional morphology and rep-PCR and MALDI-TOF methods; kappa values were κ = 0.869, 0.871, and 0.916, respectively (P < 0.001).
  
  
  CONCLUSIONS
  The good level of agreement between the methods included in the present study and sequence method could be due to the identification of Aspergillus strains that were commonly encountered. Therefore, it was concluded that studies conducted with a higher number of isolates, which include other Aspergillus strains, are required.
authors.affiliation: Faculty of Medicine, Department of Medical Microbiology, University of Erciyes, Kayseri, Turkey. altayatalay@gmail.com.
authors.forename: Altay
authors.initials: A
authors.lastname: Atalay
authors.affiliation: Faculty of Medicine, Department of Medical Microbiology, University of Erciyes, Kayseri, Turkey.
authors.forename: Ayse Nedret
authors.initials: AN
authors.lastname: Koc
authors.affiliation: BioMérieux Diagnostic, Inc, Istanbul, Turkey.
authors.forename: Ahmet
authors.initials: A
authors.lastname: Suel
authors.affiliation: Faculty of Medicine, Department of Medical Microbiology, University of Erciyes, Kayseri, Turkey.
authors.forename: Hafize
authors.initials: H
authors.lastname: Sav
authors.affiliation: Faculty of Medicine, Department of Medical Microbiology, University of Erciyes, Kayseri, Turkey.
authors.forename: Gonca
authors.initials: G
authors.lastname: Demir
authors.affiliation: Faculty of Medicine, Department of Biostatistics, University of Erciyes, Kayseri, Turkey.
authors.forename: Ferhan
authors.initials: F
authors.lastname: Elmali
authors.affiliation: Faculty of Medicine, Department of Medical Microbiology, University of Erciyes, Kayseri, Turkey.
authors.forename: Nuri
authors.initials: N
authors.lastname: Cakir
authors.affiliation: Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands.|Department of Medical Microbiology and Infectious Diseases, ErasmusMC, The Netherlands.|Invasive Fungi Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
authors.forename: Seyedmojtaba
authors.initials: S
authors.lastname: Seyedmousavi
mesh_terms: D001230:Aspergillus / Q000166:cytology* / Q000302:isolation & purification*; D006785:Hospitals, University; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D014421:Turkey
keywords: Aspergillus; MALDI-TOF-MS; rep-PCR; sequencing