title: Decision criteria for MALDI-TOF MS-based identification of filamentous fungi using commercial and in-house reference databases.
abstract: BACKGROUND
  Several Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry protocols, which differ in identification criteria, have been developed for mold and dermatophyte identification. Currently, the most widely used approach is Bruker technology, although no consensus concerning the log(score) threshold has been established. Furthermore, it remains unknown how far increasing the number of spots to compare results might improve identification performance. In this study, we used in-house and Bruker reference databases as well as a panel of 422 isolates belonging to 126 species to test various thresholds. Ten distinct identification algorithms requiring one to four spots were tested.
  
  
  RESULTS
  Our findings indicate that optimal results were obtained by applying a decisional algorithm in which only the highest score of four spots was taken into account with a 1.7 log(score) threshold. Testing the entire panel enabled identification of 87.41% (in-house database) and 35.15% (Bruker database) of isolates, with a positive predictive value (PPV) of 1 at the genus level for both databases as well as 0.89 PPV (in-house database) and 0.72 PPV (Bruker database) at the species level. Applying the same rules to the isolates for which the species were represented by at least three strains in the database enabled identification of 92.1% (in-house database) and 46.6% (Bruker database) of isolates, with 1 PPV at the genus level for both databases as well as 0.95 PPV (in-house database) and 0.93 PPV (Bruker database) at the species level.
  
  
  CONCLUSIONS
  Depositing four spots per extract and lowering the threshold to 1.7, a threshold which is notably lower than that recommended for bacterial identification, decreased the number of unidentified specimens without altering the reliability of the accepted results. Nevertheless, regardless of the criteria used for mold and dermatophyte identification, commercial databases require optimization.
authors.affiliation: Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, France. anne-cecile.normand@ap-hm.fr.
authors.forename: Anne-Cécile
authors.identifier: http://orcid.org/0000-0002-7307-4380
authors.initials: AC
authors.lastname: Normand
authors.affiliation: Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, France.
authors.forename: Carole
authors.initials: C
authors.lastname: Cassagne
authors.affiliation: Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, France.
authors.forename: Magali
authors.initials: M
authors.lastname: Gautier
authors.affiliation: Service of Mycology and Aerobiology, BCCM/IHEM Fungal Collection, Scientific Institute of Public Health, Brussels, Belgium.
authors.forename: Pierre
authors.initials: P
authors.lastname: Becker
authors.affiliation: Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Ranque
authors.affiliation: Service of Mycology and Aerobiology, BCCM/IHEM Fungal Collection, Scientific Institute of Public Health, Brussels, Belgium.
authors.forename: Marijke
authors.initials: M
authors.lastname: Hendrickx
authors.affiliation: Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, France.
authors.forename: Renaud
authors.initials: R
authors.lastname: Piarroux
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004271:DNA, Fungal; D016208:Databases, Factual; D005658:Fungi / Q000145:classification / Q000302:isolation & purification*; D005800:Genes, Fungal; D016533:Mycological Typing Techniques / Q000379:methods*; D015203:Reproducibility of Results; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
chemical_list: D004271:DNA, Fungal
keywords: Filamentous Fungi; Interpretation criteria; Mass Spectrometry; Matrix-Assisted Laser Desorption/Ionization; log(score) threshold