title: Direct identification of clinically relevant bacterial and yeast microcolonies and macrocolonies on solid culture media by Raman spectroscopy.
abstract: Decreasing turnaround time is a paramount objective in clinical diagnosis. We evaluated the discrimination power of Raman spectroscopy when analyzing colonies from 80 strains belonging to nine bacterial and one yeast species directly on solid culture medium after 24-h (macrocolonies) and 6-h (microcolonies) incubation. This approach, that minimizes sample preparation and culture time, would allow resuming culture after identification to perform downstream antibiotic susceptibility testing. Correct identification rates measured for macrocolonies and microcolonies reached 94.1% and 91.5%, respectively, in a leave-one-strain-out cross-validation mode without any correction for possible medium interference. Large spectral differences were observed between macrocolonies and microcolonies, that were attributed to true biological differences. Our results, conducted on a very diversified panel of species and strains, were obtained by using simple and robust sample preparation and preprocessing procedures, while still confirming published results obtained by using more complex elaborated protocols. Instrumentation is simplified by the use of 532-nm laser excitation yielding a Raman signal in the visible range. It is, to our knowledge, the first side-by-side full classification study of microorganisms in the exponential and stationary phases confirming the excellent performance of Raman spectroscopy for early species-level identification of microorganisms directly from an agar culture.
authors: CEA, LIST, Département Métrologie, Instrumentation et Information, 91191 Gif-sur-Yvette, France.
authors: Isabelle
authors: I
authors: Espagnon
authors: bioMérieux, Technology Research Department, 5 rue des Berges, 38000 Grenoble, France.
authors: Denis
authors: D
authors: Ostrovskii
authors: bioMérieux, Technology Research Department, 5 rue des Berges, 38000 Grenoble, France.
authors: Raphaël
authors: R
authors: Mathey
authors: CEA, LETI, MINATEC Campus, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France.
authors: Mathieu
authors: M
authors: Dupoy
authors: CEA, LETI, MINATEC Campus, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France.
authors: Pierre L
authors: PL
authors: Joly
authors: bioMérieux, Technology Research Department, 5 rue des Berges, 38000 Grenoble, France.
authors: Armelle
authors: A
authors: Novelli-Rousseau
authors: bioMérieux, Technology Research Department, 5 rue des Berges, 38000 Grenoble, France.
authors: Frédéric
authors: F
authors: Pinston
authors: CEA, LIST, Département Métrologie, Instrumentation et Information, 91191 Gif-sur-Yvette, France.
authors: Olivier
authors: O
authors: Gal
authors: bioMérieux, Technology Research Department, 5 rue des Berges, 38000 Grenoble, France.
authors: Frédéric
authors: F
authors: Mallard
authors: bioMérieux, Technology Research Department, Chemin de l'Orme, 69280 Marcy l'Etoile, France.
authors: Denis F
authors: DF
authors: Leroux
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000737:chemistry / Q000145:classification* / Q000302:isolation & purification; D003470:Culture Media; D008828:Microbiological Techniques / Q000379:methods*; D012815:Signal Processing, Computer-Assisted; D013059:Spectrum Analysis, Raman / Q000379:methods*; D015003:Yeasts / Q000737:chemistry / Q000145:classification* / Q000302:isolation & purification
chemical_list: D003470:Culture Media