Evaluation of MALDI-TOF mass spectrometry and MALDI BioTyper in comparison to 16S rDNA sequencing for the identification of bacteria isolated from Arctic sea water

MALDI-TOF Mass Spectrometry in association with the MALDI BioTyper 3.1 software has been evaluated for the identification and classification of 45 Arctic bacteria isolated from Kandalaksha Bay (White Sea, Russia). The high reliability of this method has been already demonstrated, in clinical microbiology, by a number of studies showing high attribution concordance with other credited analyses. Recently, it has been employed also in other branches of microbiology with controversial performance. The phyloproteomic results reported in this study were validated with those obtained by the “gold standard” 16S rDNA analysis. Concordance between the two methods was 100% at the genus level, while at the species level it was 48%. These percentages appeared to be quite high compared with other studies regarding environmental bacteria. However, the performance of MALDI BioTyper changed in relation to the taxonomical group analyzed, reflecting known identification problems related to certain genera. In our case, attribution concordance for Pseudomonas species was rather low (29%), confirming the problematic taxonomy of this genus, whereas that of strains from other genera was quite high (> 60%). Among the isolates tested in this study, two strains (Exiguobacterium oxidotolerans and Pseudomonas costantinii) were misidentified by MALDI BioTyper due to absence of reference spectra in the database. Accordingly, missing spectra were acquired for the database implementation.

[1]  O. Prakash,et al.  Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists , 2016, Front. Microbiol..

[2]  Z. Hildenbrand,et al.  Applications of MALDI-TOF MS in environmental microbiology. , 2016, The Analyst.

[3]  J. Antón,et al.  Diversity of extremely halophilic cultivable prokaryotes in Mediterranean, Atlantic and Pacific solar salterns: Evidence that unexplored sites constitute sources of cultivable novelty. , 2015, Systematic and applied microbiology.

[4]  M. Fenice,et al.  Relationship between phylogenetic and nutritional diversity in Arctic (Kandalaksha Bay) seawater planktonic bacteria , 2015, Annals of Microbiology.

[5]  J. Mulec,et al.  Microbiology of Healing Mud (Fango) from Roman Thermae Aquae Iasae Archaeological Site (Varaždinske Toplice, Croatia) , 2015, Microbial Ecology.

[6]  A. Al-Ahmad,et al.  Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing , 2014, BMC Microbiology.

[7]  A. Godány,et al.  Need for database extension for reliable identification of bacteria from extreme environments using MALDI TOF mass spectrometry , 2014, Chemical Papers.

[8]  F. Gunzer,et al.  Comparison of VITEK2, MALDI-TOF MS, and 16S rDNA sequencing for identification of Myroides odoratus and Myroides odoratimimus. , 2014, Diagnostic microbiology and infectious disease.

[9]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[10]  R. Zbinden,et al.  Identification of Gram-Positive Cocci by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Comparison of Different Preparation Methods and Implementation of a Practical Algorithm for Routine Diagnostics , 2013, Journal of Clinical Microbiology.

[11]  M. Dybwad,et al.  Large scale MALDI-TOF MS based taxa identification to identify novel pigment producers in a marine bacterial culture collection , 2013, Antonie van Leeuwenhoek.

[12]  Bin Xu,et al.  Identification and Cluster Analysis of Streptococcus pyogenes by MALDI-TOF Mass Spectrometry , 2012, PloS one.

[13]  Prasanna D. Khot,et al.  Optimization of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Analysis for Bacterial Identification , 2012, Journal of Clinical Microbiology.

[14]  D. Mack,et al.  Identification of Clinical Isolates of α-Hemolytic Streptococci by 16S rRNA Gene Sequencing, Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Using MALDI Biotyper, and Conventional Phenotypic Methods: a Comparison , 2012, Journal of Clinical Microbiology.

[15]  T. Tan,et al.  Comparison of phenotypic methods and matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for the identification of aero-tolerant Actinomyces spp. isolated from soft-tissue infections , 2012, European Journal of Clinical Microbiology & Infectious Diseases.

[16]  J. Klimentova,et al.  Evaluation of sample preparation methods for MALDI‐TOF MS identification of highly dangerous bacteria , 2012, Letters in applied microbiology.

[17]  C. Neut,et al.  Chemical extraction versus direct smear for MALDI-TOF mass spectrometry identification of anaerobic bacteria. , 2012, Anaerobe.

[18]  T. Macek,et al.  Whole-cell MALDI-TOF: Rapid screening method in environmental microbiology , 2012 .

[19]  M. Kostrzewa,et al.  Identification of Trueperella (Arcanobacterium) bernardiae by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis and by species-specific PCR. , 2012, Journal of medical microbiology.

[20]  L. Selbmann,et al.  Temperature preferences of bacteria isolated from seawater collected in Kandalaksha Bay, White Sea, Russia , 2012, Polar Biology.

[21]  Marius Dybwad,et al.  Characterization of Airborne Bacteria at an Underground Subway Station , 2012, Applied and Environmental Microbiology.

[22]  P. de Vos,et al.  Evaluation of MALDI-TOF MS as a tool for high-throughput dereplication. , 2011, Journal of microbiological methods.

[23]  M. Millar,et al.  Improved Performance of Bacterium and Yeast Identification by a Commercial Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System in the Clinical Microbiology Laboratory , 2011, Journal of Clinical Microbiology.

[24]  Robin Patel,et al.  Comparison of Direct Colony Method versus Extraction Method for Identification of Gram-Positive Cocci by Use of Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry , 2011, Journal of Clinical Microbiology.

[25]  Fumio Nomura,et al.  Use of the MALDI BioTyper system with MALDI–TOF mass spectrometry for rapid identification of microorganisms , 2011, Analytical and bioanalytical chemistry.

[26]  E. Moore,et al.  Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. , 2011, Systematic and applied microbiology.

[27]  J. M. Gallardo,et al.  Comparative analysis of protein extraction methods for the identification of seafood-borne pathogenic and spoilage bacteria by MALDI-TOF mass spectrometry , 2010 .

[28]  J. Schrenzel,et al.  Application and use of various mass spectrometry methods in clinical microbiology. , 2010, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[29]  J. Lalucat,et al.  DNA sequence-based analysis of the Pseudomonas species. , 2010, Environmental microbiology.

[30]  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.

[31]  M. Alispahic,et al.  Species-specific identification and differentiation of Arcobacter, Helicobacter and Campylobacter by full-spectral matrix-associated laser desorption/ionization time of flight mass spectrometry analysis. , 2010, Journal of medical microbiology.

[32]  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.

[33]  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.

[34]  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.

[35]  E. Stackebrandt,et al.  Culturable aerobic bacteria from the upstream region of a karst water rivulet. , 2008, International microbiology : the official journal of the Spanish Society for Microbiology.

[36]  S. Brisse,et al.  Comparative phylogenies of Burkholderia, Ralstonia, Comamonas, Brevundimonas and related organisms derived from rpoB, gyrB and rrs gene sequences. , 2008, Research in microbiology.

[37]  Johanna E. Camara,et al.  Discrimination between wild-type and ampicillin-resistant Escherichia coli by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry , 2007, Analytical and bioanalytical chemistry.

[38]  K. Konstantinidis,et al.  Toward a More Robust Assessment of Intraspecies Diversity, Using Fewer Genetic Markers , 2006, Applied and Environmental Microbiology.

[39]  U. Szewzyk,et al.  Rapid screening and dereplication of bacterial isolates from marine sponges of the Sula Ridge by Intact-Cell-MALDI-TOF mass spectrometry (ICM-MS) , 2005, Applied Microbiology and Biotechnology.

[40]  H. Kasai,et al.  Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. , 2000, Microbiology.

[41]  Catherine Fenselau,et al.  Rapid Characterization of Spores of Bacillus cereusGroup Bacteria by Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry , 2000, Applied and Environmental Microbiology.

[42]  Ju-Young Park,et al.  Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. , 2000, International journal of systematic and evolutionary microbiology.

[43]  A. Fox,et al.  Rapid discrimination between methicillin-sensitive and methicillin-resistant Staphylococcus aureus by intact cell mass spectrometry. , 2000, Journal of medical microbiology.

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

[45]  A. Wichels,et al.  A polyphasic approach for the differentiation of environmental Vibrio isolates from temperate waters. , 2011, FEMS microbiology ecology.

[46]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[47]  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.