Ribosomal proteins as biomarkers for bacterial identification by mass spectrometry in the clinical microbiology laboratory.

Whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a rapid method for identification of microorganisms that is increasingly used in microbiology laboratories. This identification is based on the comparison of the tested isolate mass spectrum with reference databases. Using Neisseria meningitidis as a model organism, we showed that in one of the available databases, the Andromas database, 10 of the 13 species-specific biomarkers correspond to ribosomal proteins. Remarkably, one biomarker, ribosomal protein L32, was subject to inter-strain variability. The analysis of the ribosomal protein patterns of 100 isolates for which whole genome sequences were available, confirmed the presence of inter-strain variability in the molecular weight of 29 ribosomal proteins, thus establishing a correlation between the sequence type (ST) and/or clonal complex (CC) of each strain and its ribosomal protein pattern. Since the molecular weight of three of the variable ribosomal proteins (L30, L31 and L32) was included in the spectral window observed by MALDI-TOF MS in clinical microbiology, i.e., 3640-12000 m/z, we were able by analyzing the molecular weight of these three ribosomal proteins to classify each strain in one of six subgroups, each of these subgroups corresponding to specific STs and/or CCs. Their detection by MALDI-TOF allows therefore a quick typing of N. meningitidis isolates.

[1]  Zaida Luthey-Schulten,et al.  Molecular signatures of ribosomal evolution , 2008, Proceedings of the National Academy of Sciences.

[2]  David Wishart,et al.  Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring. , 2004, Analytical chemistry.

[3]  Natalya Yutin,et al.  Phylogenomics of Prokaryotic Ribosomal Proteins , 2012, Genome Biology.

[4]  Joany Jackman,et al.  Microorganism identification by matrix-assisted laser/desorption ionization mass spectrometry and model-derived ribosomal protein biomarkers. , 2003, Analytical chemistry.

[5]  K. Voorhees,et al.  Rapid identification of intact whole bacteria based on spectral patterns using matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry. , 1996, Rapid communications in mass spectrometry : RCM.

[6]  J. Lay,et al.  MALDI-TOF mass spectrometry of bacteria. , 2001, Mass spectrometry reviews.

[7]  C. Fenselau,et al.  Characterization of the protein subset desorbed by MALDI from whole bacterial cells. , 2001, Analytical Chemistry.

[8]  K. Voorhees,et al.  Identification of bacterial proteins observed in MALDI TOF mass spectra from whole cells. , 1999, Analytical chemistry.

[9]  Liwei Sun,et al.  A simple intact protein analysis by MALDI-MS for characterization of ribosomal proteins of two genome-sequenced lactic acid bacteria and verification of their amino acid sequences. , 2007, Journal of proteome research.

[10]  Keith A. Jolley,et al.  Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain , 2012, Microbiology.

[11]  K. Ochi.  Heterogeneity of ribosomal proteins among Streptomyces species and its application to identification. , 1989, Journal of general microbiology.

[12]  A. Hosoda,et al.  Phylogenetic classification of Pseudomonas putida strains by MALDI-MS using ribosomal subunit proteins as biomarkers. , 2007, Analytical chemistry.

[13]  P. Limbach,et al.  Extending ribosomal protein identifications to unsequenced bacterial strains using matrix‐assisted laser desorption/ionization mass spectrometry , 2005, Proteomics.

[14]  Matthew R. Pocock,et al.  The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.

[15]  D. Falush,et al.  Genealogical typing of Neisseria meningitidis , 2009, Microbiology.

[16]  P. Siguier,et al.  Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium Deinococcus deserti , 2009, PLoS genetics.

[17]  W. Kitagawa,et al.  Phylogenetic analysis of Rhodococcus erythropolis based on the variation of ribosomal proteins as observed by matrix-assisted laser desorption ionization-mass spectrometry without using genome information. , 2009, Journal of bioscience and bioengineering.

[18]  P. Berche,et al.  Rapid Identification of Staphylococci Isolated in Clinical Microbiology Laboratories by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry , 2007, Journal of Clinical Microbiology.

[19]  J. Armengaud,et al.  Restricting Fermentative Potential by Proteome Remodeling , 2012, Molecular & Cellular Proteomics.

[20]  Martin C. J. Maiden,et al.  BIGSdb: Scalable analysis of bacterial genome variation at the population level , 2010, BMC Bioinformatics.

[21]  J. Lay,et al.  Experimental factors affecting the quality and reproducibility of MALDI TOF mass spectra obtained from whole bacteria cells , 2003, Journal of the American Society for Mass Spectrometry.

[22]  J. Parkhill,et al.  A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria , 2012, Microbiology.

[23]  J P Reilly,et al.  Fingerprint matching of E. coli strains with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of whole cells using a modified correlation approach. , 1998, Rapid communications in mass spectrometry : RCM.

[24]  T. Maier,et al.  Direct bacterial profiling by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for identification of pathogenic Neisseria. , 2009, The Journal of molecular diagnostics : JMD.

[25]  J. Robert‐Baudouy,et al.  Bacterial aminopeptidases: properties and functions. , 1996, FEMS microbiology reviews.

[26]  P. Berche,et al.  Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Nonfermenting Gram-Negative Bacilli Isolated from Cystic Fibrosis Patients , 2008, Journal of Clinical Microbiology.

[27]  Hervé Philippe,et al.  Archaeal phylogeny based on ribosomal proteins. , 2002, Molecular biology and evolution.

[28]  Andrew B. Feldman,et al.  Top-down proteomics for rapid identification of intact microorganisms. , 2005, Analytical chemistry.

[29]  J. Armengaud,et al.  Shotgun nanoLC-MS/MS proteogenomics to document MALDI-TOF biomarkers for screening new members of the Ruegeria genus. , 2013, Environmental microbiology.

[30]  M. Achtman,et al.  Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. , 1998, Proceedings of the National Academy of Sciences of the United States of America.