Classification and Identification of Bacteria by Mass Spectrometry and Computational Analysis

Abstract

BackgroundIn 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.MethodologyWe 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.ConclusionsWith 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.

Characterization of Escherichia coli and other Enterobacteriaceae in producer-distributor bulk milk

“…Distance values in a dendrogram were relative and normalized to a maximal value of 10. Species with distance levels under 1.5 have been described as reliably classified into distinct strains (Sauer et al, 2008).…”

Einsatz der Matrix-Assisted Laser Desorption/ionisation-Time of Flight Massenspektrometrie (MALDI-TOF MS) in der mikrobiologischen Routinediagnostik/Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) in clinical microbiological routine diagnostics

“…Dieses massenspektrometrische Verfahren hat prinzipiell das Potenzial, die klassischen biochemischen Differenzierungsverfahren in der mikrobiologischen Diagnostik abzul ö sen, da es wesentliche Vorteile wie sehr kurze Analysenzeiten, einfache Bedienung und Automatisierbarkeit bei geringen Verbrauchskosten, sowie hohe Sensitivit ä t und Spezifi t ä t in sich vereint [1] . [7,8] . Dies ergibt eine sehr kurze Umsatzzeit bis zum positiven Ergebnis.…”

Evaluation of Intact Cell Matrix-Assisted Laser Desorption/Ionization Timeof- Flight Mass Spectrometry for Capillary Electrophoresis Detection of Controlled Bacterial Clumping

“…Therefore, a homemade database (repository) can be developed and applied to targeted identification of microorganisms and as a complementary method to classical molecular or biochemical techniques. Moreover, a local repository of reference bacterial strains can also be used for statistic evaluation of one-dimensional IC MALDI spectra [18] or in a detection approach for separation analysis of microorganisms.…”