title: The Technical and Biological Reproducibility of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Based Typing: Employment of Bioinformatics in a Multicenter Study.
abstract: BACKGROUND
  The technical, biological, and inter-center reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS) typing data has not yet been explored. The aim of this study is to compare typing data from multiple centers employing bioinformatics using bacterial strains from two past outbreaks and non-related strains.
  
  
  METHODS
  Participants received twelve extended spectrum betalactamase-producing E. coli isolates and followed the same standard operating procedure (SOP) including a full-protein extraction protocol. All laboratories provided visually read spectra via flexAnalysis (Bruker, Germany). Raw data from each laboratory allowed calculating the technical and biological reproducibility between centers using BioNumerics (Applied Maths NV, Belgium).
  
  
  RESULTS
  Technical and biological reproducibility ranged between 96.8-99.4% and 47.6-94.4%, respectively. The inter-center reproducibility showed a comparable clustering among identical isolates. Principal component analysis indicated a higher tendency to cluster within the same center. Therefore, we used a discriminant analysis, which completely separated the clusters. Next, we defined a reference center and performed a statistical analysis to identify specific peaks to identify the outbreak clusters. Finally, we used a classifier algorithm and a linear support vector machine on the determined peaks as classifier. A validation showed that within the set of the reference center, the identification of the cluster was 100% correct with a large contrast between the score with the correct cluster and the next best scoring cluster.
  
  
  CONCLUSIONS
  Based on the sufficient technical and biological reproducibility of MALDI-TOF MS based spectra, detection of specific clusters is possible from spectra obtained from different centers. However, we believe that a shared SOP and a bioinformatics approach are required to make the analysis robust and reliable.
authors: Clinical Microbiology, Cantonal Hospital of Aarau, Aarau, Switzerland.
authors: Michael
authors: M
authors: Oberle
authors: Clinical Microbiology, labormedizinisches Zentrum Dr. Risch AG, Berne, Switzerland.
authors: Nadia
authors: N
authors: Wohlwend
authors: Institute for Environmental Health Medicine and Hospital Infection Control, University of Freiburg, Freiburg, Germany.
authors: Daniel
authors: D
authors: Jonas
authors: Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
authors: Florian P
authors: FP
authors: Maurer
authors: Clinical Microbiology, Dianalabs, Geneva, Switzerland.
authors: Geraldine
authors: G
authors: Jost
authors: Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.
authors: Sarah
authors: S
authors: Tschudin-Sutter
authors: Applied Maths NV, Sint-Martens-Latem, Belgium.
authors: Katleen
authors: K
authors: Vranckx
authors: Clinical Microbiology, University Hospital Basel, Basel, Switzerland.|Applied Microbiology Research, University of Basel, Basel Switzerland.
authors: Adrian
authors: A
authors: Egli
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D015373:Bacterial Typing Techniques; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004926:Escherichia coli / Q000145:classification / Q000235:genetics; D006801:Humans; D025341:Principal Component Analysis; D015203:Reproducibility of Results; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods / Q000592:standards; D001618:beta-Lactamases / Q000235:genetics
chemical_list: D001618:beta-Lactamases