Automatic identification of mixed bacterial species fingerprints in a MALDI-TOF mass-spectrum.

Motivation: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has been broadly adopted by routine clinical microbiology laboratories for bacterial species identification. An isolated colony of the targeted microorganism is the single prerequisite. Currently, MS-based microbial identification directly from clinical specimens can not be routinely performed, as it raises two main challenges: (i) the nature of the sample itself may increase the level of technical variability and bring heterogeneity with respect to the reference database and (ii) the possibility of encountering polymicrobial samples that will yield a ‘mixed’ MS fingerprint. In this article, we introduce a new method to infer the composition of polymicrobial samples on the basis of a single mass spectrum. Our approach relies on a penalized non-negative linear regression framework making use of species-specific prototypes, which can be derived directly from the routine reference database of pure spectra. Results: A large spectral dataset obtained from in vitro mono- and bi-microbial samples allowed us to evaluate the performance of the method in a comprehensive way. Provided that the reference matrixassisted laser desorption/ionization time-of-flight mass spectrometry fingerprints were sufficiently distinct for the individual species, the method automatically predicted which bacterial species were present in the sample. Only few samples (5.3%) were misidentified, and bimicrobial samples were correctly identified in up to 61.2% of the cases. This method could be used in routine clinical microbiology practice. Availability and implementation: The complete dataset including both the reference database and the mock-up mixture spectra is available at http://archive.ics.uci.edu/ml/datasets/MicroMass. Contact: pierre.mahe@biomerieux.com Supplementary information: Supplementary data are available at Bioinformatics online.