Classification and identification of bacteria by mass spectrometry and computational analysis

• Published in: PloS one 2008-07, Vol.3 (7), p.e2843-e2843
• Main Authors: Sauer, Sascha, Freiwald, Anja, Maier, Thomas, Kube, Michael, Reinhardt, Richard, Kostrzewa, Markus, Geider, Klaus
• Format: Article
• Language: English
• Subjects: Algorithms; Analysis; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - metabolism; Bacterial analysis; Biotechnology/Applied Microbiology; Biotechnology/Plant Biotechnology; Blight; Computational Biology - methods; Computer applications; Databases, Protein; Desorption; Ecology/Environmental Microbiology; Erwinia; Erwinia - metabolism; Erwinia amylovora; Erwinia billingiae; Erwinia pyrifoliae; Erwinia rhapontici; Feasibility studies; Gene Expression Regulation, Bacterial; Genera; Genomes; Genomics; Genotype; Genotyping; Ions; Lasers; Mass spectra; Mass spectrometry; Mass Spectrometry - methods; Mass spectroscopy; Microbiology; Microbiology/Applied Microbiology; Microbiology/Plant-Biotic Interactions; Models, Biological; Phylogeny; Plant diseases; Proteomes; Proteomics - methods; Reliability analysis; Salmonella; Sequence Analysis, DNA; Shigella; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Software; Software development tools; Species; Species classification; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Spectroscopy; Strains (organisms); Technology application
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0002843

In general, the definite determination of bacterial species is a tedious process and requires extensive manual labour. Novel technologies for bacterial detection and analysis can therefore help microbiologists in minimising their efforts in developing a number of microbiological applications. We present a robust, standardized procedure for automated bacterial analysis that is based on the detection of patterns of protein masses by MALDI mass spectrometry. We particularly applied the approach for classifying and identifying strains in species of the genus Erwinia. Many species of this genus are associated with disastrous plant diseases such as fire blight. Using our experimental procedure, we created a general bacterial mass spectra database that currently contains 2800 entries of bacteria of different genera. This database will be steadily expanded. To support users with a feasible analytical method, we developed and tested comprehensive software tools that are demonstrated herein. Furthermore, to gain additional analytical accuracy and reliability in the analysis we used genotyping of single nucleotide polymorphisms by mass spectrometry to unambiguously determine closely related strains that are difficult to distinguish by only relying on protein mass pattern detection. With the method for bacterial analysis, we could identify fire blight pathogens from a variety of biological sources. The method can be used for a number of additional bacterial genera. Moreover, the mass spectrometry approach presented allows the integration of data from different biological levels such as the genome and the proteome.