Characterization and identification of clinically relevant microorganisms using rapid evaporative ionization mass spectrometry.

Rapid evaporative ionization mass spectrometry (REIMS) was investigated for its suitability as a general identification system for bacteria and fungi. Strains of 28 clinically relevant bacterial species were analyzed in negative ion mode, and corresponding data was subjected to unsupervised and supervised multivariate statistical analyses. The created supervised model yielded correct cross-validation results of 95.9%, 97.8%, and 100% on species, genus, and Gram-stain level, respectively. These results were not affected by the resolution of the mass spectral data. Blind identification tests were performed for strains cultured on different culture media and analyzed using different instrumental platforms which led to 97.8-100% correct identification. Seven different Escherichia coli strains were subjected to different culture conditions and were distinguishable with 88% accuracy. In addition, the technique proved suitable to distinguish five pathogenic Candida species with 98.8% accuracy without any further modification to the experimental workflow. These results prove that REIMS is sufficiently specific to serve as a culture condition-independent tool for the identification and characterization of microorganisms.

[1]  D. Williamson,et al.  The isolation and estimation of the poly-beta-hydroxybutyrate inclusions of Bacillus species. , 1958, Journal of general microbiology.

[2]  C. Fenselau,et al.  Identification of bacteria using mass spectrometry , 1975 .

[3]  C. Fenselau,et al.  Profiling of bacteria by fast atom bombardment mass spectrometry. , 1987, Analytical chemistry.

[4]  H. Wenschuh,et al.  The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins. , 1999, Analytical chemistry.

[5]  B. Spengler,et al.  Electrospray Post-Ionization Mass Spectrometry of Electrosurgical Aerosols , 2011, Journal of the American Society for Mass Spectrometry.

[6]  S. Abbott,et al.  16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls , 2007, Journal of Clinical Microbiology.

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

[8]  Josephine Bunch,et al.  Inclusive sharing of mass spectrometry imaging data requires a converter for all. , 2012, Journal of proteomics.

[9]  B. Wanner,et al.  In vivo recognition of Bacillus subtilis by desorption electrospray ionization mass spectrometry (DESI-MS). , 2009, The Analyst.

[10]  Anthony B. Costa,et al.  Rapid direct lipid profiling of bacteria using desorption electrospray ionization mass spectrometry , 2011 .

[11]  T. Tanaka,et al.  Mass spectral analysis of complex lipids desorbed directly from lyophilized membranes and cells. , 1987, Biochemical and biophysical research communications.

[12]  D. Raoult,et al.  Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. , 2009, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[13]  I. Yano,et al.  Occurrence of free ceramides in Bacteroides fragilis NCTC 9343. , 1979, Journal of biochemistry.

[14]  M. Lanéelle,et al.  Structure des acides corynomycoliques de Corynebacterium hofmanii et leur implication biogénétique , 1970 .

[15]  Takayuki Ezaki,et al.  Proposal of Burkholderia gen. nov. and Transfer of Seven Species of the Genus Pseudomonas Homology Group II to the New Genus, with the Type Species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. , 1992, Microbiology and immunology.

[16]  L. Rahme,et al.  Electrospray/mass spectrometric identification and analysis of 4-hydroxy-2-alkylquinolines (HAQs) produced by Pseudomonas aeruginosa , 2004, Journal of the American Society for Mass Spectrometry.

[17]  A. Madonna,et al.  Rapid analysis of intact phospholipids from whole bacterial cells by matrix-assisted laser desorption/ionization mass spectrometry combined with on-probe sample pretreatment. , 2002, Rapid communications in mass spectrometry : RCM.

[18]  V. Havlíček,et al.  Current trends in microbial diagnostics based on mass spectrometry. , 2013, Analytical chemistry.

[19]  K. Carroll,et al.  Prospective Evaluation of a Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System in a Hospital Clinical Microbiology Laboratory for Identification of Bacteria and Yeasts: a Bench-by-Bench Study for Assessing the Impact on Time to Identification and Cost-Effectiveness , 2012, Journal of Clinical Microbiology.

[20]  T. Ebbels,et al.  Recursive segment-wise peak alignment of biological (1)h NMR spectra for improved metabolic biomarker recovery. , 2009, Analytical chemistry.

[21]  Nari Talaty,et al.  Rapid ambient mass spectrometric profiling of intact, untreated bacteria using desorption electrospray ionization. , 2007, Chemical communications.

[22]  Ara Darzi,et al.  Chemo-informatic strategy for imaging mass spectrometry-based hyperspectral profiling of lipid signatures in colorectal cancer , 2014, Proceedings of the National Academy of Sciences.

[23]  S. Ranque,et al.  Evaluation of four pretreatment procedures for MALDI-TOF MS yeast identification in the routine clinical laboratory. , 2013, Medical mycology.

[24]  A. Snyder,et al.  Characterization of bacterial phospholipids by electrospray ionization tandem mass spectrometry. , 1995, Analytical chemistry.

[25]  M. Klouche,et al.  Rapid methods for diagnosis of bloodstream infections , 2008, Clinical chemistry and laboratory medicine.

[26]  Changgeng Liu,et al.  Rapid lipid profiling of bacteria by online MALDI-TOF mass spectrometry , 2012 .

[27]  A. Stipanovic,et al.  Production and characterization of poly‐3‐hydroxybutyrate from biodiesel‐glycerol by Burkholderia cepacia ATCC 17759 , 2009, Biotechnology progress.

[28]  G Greub,et al.  Performance of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Bacterial Strains Routinely Isolated in a Clinical Microbiology Laboratory , 2010, Journal of Clinical Microbiology.

[29]  Z. Takáts,et al.  In vivo, in situ tissue analysis using rapid evaporative ionization mass spectrometry. , 2009, Angewandte Chemie.

[30]  K. Veselkov,et al.  Analysis of intact bacteria using rapid evaporative ionisation mass spectrometry. , 2013, Chemical communications.

[31]  P. Woo,et al.  Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. , 2008, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[32]  Lechevalier Mp.  Lipids in Bacterial Taxonomy - A Taxonomist's View , 1977 .

[33]  F. Lépine,et al.  Rhamnolipids: diversity of structures, microbial origins and roles , 2010, Applied Microbiology and Biotechnology.

[34]  P. François,et al.  Comparison of Two Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Methods with Conventional Phenotypic Identification for Routine Identification of Bacteria to the Species Level , 2010, Journal of Clinical Microbiology.

[35]  D. Kell,et al.  Flow-injection electrospray ionization mass spectrometry of crude cell extracts for high-throughput bacterial identification , 2002, Journal of the American Society for Mass Spectrometry.

[36]  Pieter C Dorrestein,et al.  Real-time metabolomics on living microorganisms using ambient electrospray ionization flow-probe. , 2013, Analytical chemistry.

[37]  E. Claas,et al.  High-Throughput Identification of Bacteria and Yeast by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Conventional Medical Microbiology Laboratories , 2010, Journal of Clinical Microbiology.

[38]  S. N. Davey,et al.  The rapid identification of intact microorganisms using mass spectrometry , 1996, Nature Biotechnology.

[39]  Nuno Bandeira,et al.  Mass spectral molecular networking of living microbial colonies , 2012, Proceedings of the National Academy of Sciences.

[40]  B. Thiede,et al.  Shotgun mass mapping of Lactobacillus species and subspecies from caries related isolates by MALDI‐MS , 2009, Proteomics.

[41]  T. Ebbels,et al.  Optimized preprocessing of ultra-performance liquid chromatography/mass spectrometry urinary metabolic profiles for improved information recovery. , 2011, Analytical chemistry.

[42]  H. Meuzelaar,et al.  A technique for fast and reproducible fingerprinting of bacteria by pyrolysis mass spectrometry. , 1973, Analytical chemistry.

[43]  H. Meuzelaar,et al.  High resolution field ionization mass spectrometry of bacterial pyrolysis products. , 1973, Analytical chemistry.

[44]  Douglas B. Kell,et al.  Characterisation of intact microorganisms using electrospray ionisation mass spectrometry , 1999 .