Advertisement
Review Article| Volume 33, ISSUE 3, P611-628, September 2013

Beyond Identification

Emerging and Future Uses for MALDI-TOF Mass Spectrometry in the Clinical Microbiology Laboratory

      Keywords

      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'

      Subscribers receive full online access to your subscription and archive of back issues up to and including 2002.

      Content published before 2002 is available via pay-per-view purchase only.

      Subscribe:

      Subscribe to Clinics in Laboratory Medicine
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect

      References

        • van Belkum A.
        • Welker M.
        • Erhard M.
        • et al.
        Biomedical mass spectrometry in today’s and tomorrow’s clinical microbiology laboratories.
        J Clin Microbiol. 2012; 1: 1513-1517
        • Sandrin T.R.
        • Goldstein J.E.
        • Schumaker S.
        MALDI TOF MS profiling of bacteria at the strain level: a review.
        Mass Spectrom Rev. 2013; 32: 188-217
        • Carbonnelle E.
        • Grohs P.
        • Jacquier H.
        • et al.
        Robustness of two MALDI-TOF mass spectrometry systems for bacterial identification.
        J Microbiol Methods. 2012; 89: 133-136
        • Benagli C.
        • Rossi V.
        • Dolina M.
        • et al.
        Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the identification of clinically relevant bacteria.
        PLoS One. 2011; 6: e16424
        • Justesen U.S.
        • Holm A.
        • Knudsen E.
        • et al.
        Species identification of clinical isolates of anaerobic bacteria: a comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry systems.
        J Clin Microbiol. 2011; 1: 4314-4318
        • Marko D.C.
        • Saffert R.T.
        • Cunningham S.A.
        • et al.
        Evaluation of the Bruker Biotyper and Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry systems for identification of nonfermenting gram-negative bacilli isolated from cultures from cystic fibrosis patients.
        J Clin Microbiol. 2012; 1: 2034-2039
        • Rosenvinge F.S.
        • Dzajic E.
        • Knudsen E.
        • et al.
        Performance of matrix-assisted laser desorption-time of flight mass spectrometry for identification of clinical yeast isolates.
        Mycoses. 2013; 56: 229-235
        • Bille E.
        • Dauphin B.
        • Leto J.
        • et al.
        MALDI-TOF MS Andromas strategy for the routine identification of bacteria, mycobacteria, yeasts, Aspergillus spp. and positive blood cultures.
        Clin Microbiol Infect. 2012; 18: 1117-1125
        • Meetani M.A.
        • Voorhees K.J.
        MALDI mass spectrometry analysis of high molecular weight proteins from whole bacterial cells: pretreatment of samples with surfactants.
        J Am Soc Mass Spectrom. 2005; 16: 1422-1426
        • Williams T.L.
        • Andrzejewski D.
        • Lay Jr., J.O.
        • et al.
        Experimental factors affecting the quality and reproducibility of MALDI TOF mass spectra obtained from whole bacteria cells.
        J Am Soc Mass Spectrom. 2003; 14: 342-351
        • Buchan B.W.
        • Riebe K.M.
        • Ledeboer N.A.
        Comparison of the MALDI Biotyper system using Sepsityper specimen processing to routine microbiological methods for identification of bacteria from positive blood culture bottles.
        J Clin Microbiol. 2012; 1: 346-352
        • Leibovici L.
        • Shraga I.
        • Drucker M.
        • et al.
        The benefit of appropriate empirical antibiotic treatment in patients with bloodstream infection.
        J Intern Med. 1998; 244: 379-386
        • Kollef M.H.
        Inadequate antimicrobial treatment: an important determinant of outcome for hospitalized patients.
        Clin Infect Dis. 2000; 31: S131-S138
        • Dellinger R.P.
        • Levy M.M.
        • Rhodes A.
        • et al.
        Surviving Sepsis Campaign.
        Crit Care Med. 2013; 41: 580-637
        • Weinstein M.P.
        • Reller L.B.
        • Murphy J.R.
        • et al.
        The clinical significance of positive blood cultures: a comprehensive analysis of 500 episodes of bacteremia and fungemia in adults. I. Laboratory and epidemiologic observations.
        Clin Infect Dis. 1983; 1: 35-53
        • Stevenson L.G.
        • Drake S.K.
        • Murray P.R.
        Rapid identification of bacteria in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry.
        J Clin Microbiol. 2010; 1: 444-447
        • Prod’hom G.
        • Bizzini A.
        • Durussel C.
        • et al.
        Matrix-assisted laser desorption ionization-time of flight mass spectrometry for direct bacterial identification from positive blood culture pellets.
        J Clin Microbiol. 2010; 48: 1481-1483
        • La Scola B.
        • Raoult D.
        Direct identification of bacteria in positive blood culture bottles by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry.
        PLoS One. 2009; 4: e8041
        • Ferroni A.
        • Suarez S.
        • Beretti J.L.
        • et al.
        Real-time identification of bacteria and Candida species in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry.
        J Clin Microbiol. 2010; 48: 1542-1548
        • Marinach-Patrice C.
        • Fekkar A.
        • Atanasova R.
        • et al.
        Rapid species diagnosis for invasive candidiasis using mass spectrometry.
        PLoS One. 2010; 5: e8862
        • Meex C.
        • Neuville F.
        • Descy J.
        • et al.
        Direct identification of bacteria from BacT/ALERT anaerobic positive blood cultures by MALDI-TOF MS: MALDI Sepsityper kit versus an in-house saponin method for bacterial extraction.
        J Med Microbiol. 2012; 61: 1511-1516
        • Fothergill A.
        • Kasinathan V.
        • Hyman J.
        • et al.
        Rapid identification of bacteria and yeasts from positive BacT/ALERT blood culture bottles by using a lysis-filtration method and MALDI-TOF mass spectrum analysis with SARAMIS database.
        J Clin Microbiol. 2013; 51: 805-809
        • Croxatto A.
        • Prod’hom G.
        • Greub G.
        Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology.
        FEMS Microbiol Rev. 2012; 36: 380-407
        • Loonen A.J.
        • Jansz A.R.
        • Stalpers J.
        • et al.
        An evaluation of three processing methods and the effect of reduced culture times for faster direct identification of pathogens from BacT/ALERT blood cultures by MALDI-TOF MS.
        Eur J Clin Microbiol Infect Dis. 2012; 31: 1575-1583
        • Romero-Gómez M.P.
        • Gómez-Gil R.
        • Paño-Pardo J.R.
        • et al.
        Identification and susceptibility testing of microorganism by direct inoculation from positive blood culture bottles by combining MALDI-TOF and Vitek-2 Compact is rapid and effective.
        J Infect. 2012; 65: 513-520
        • Szabados F.
        • Michels M.
        • Kaase M.
        • et al.
        The sensitivity of direct identification from positive BacT/ALERTTM (bioMérieux) blood culture bottles by matrix-assisted laser desorption ionization time-of-flight mass spectrometry is low.
        Clin Microbiol Infect. 2011; 1: 192-195
        • Christner M.
        • Rohde H.
        • Wolters M.
        • et al.
        Rapid identification of bacteria from positive blood culture bottles by use of matrix-assisted laser desorption-ionization time of flight mass spectrometry fingerprinting.
        J Clin Microbiol. 2010; 48: 1584-1591
        • Qian J.
        • Cutler J.E.
        • Cole R.B.
        • et al.
        MALDI-TOF mass signatures for differentiation of yeast species, strain grouping and monitoring of morphogenesis markers.
        Anal Bioanal Chem. 2008; 392: 439-449
        • Reisner B.S.
        • Woods G.L.
        Times to detection of bacteria and yeasts in BACTEC 9240 blood culture bottles.
        J Clin Microbiol. 1999; 37: 2024-2026
        • Lagacé-Wiens P.R.
        • Adam H.J.
        • Karlowsky J.A.
        • et al.
        Identification of blood culture isolates directly from positive blood cultures by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry and a commercial extraction system: analysis of performance, cost, and turnaround time.
        J Clin Microbiol. 2012; 50: 3324-3328
        • Spanu T.
        • Posteraro B.
        • Fiori B.
        • et al.
        Direct MALDI-TOF mass spectrometry assay of blood culture broths for rapid identification of Candida species causing bloodstream infections: an observational study in two large microbiology laboratories.
        J Clin Microbiol. 2012; 50: 176-179
        • Santos C.
        • Paterson R.R.
        • Venâncio A.
        • et al.
        Filamentous fungal characterizations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
        J Appl Microbiol. 2010; 108: 375-385
        • Kwon J.H.
        • Fausone M.K.
        • Du H.
        • et al.
        Impact of laboratory-reported urine culture colony counts on the diagnosis and treatment of urinary tract infection for hospitalized patients.
        Am J Clin Pathol. 2012; 137: 778-784
        • Ferreira L.
        • Sánchez-Juanes F.
        • González-Avila M.
        • et al.
        Direct identification of urinary tract pathogens from urine samples by matrix-assisted laser desorption ionization-time of flight mass spectrometry.
        J Clin Microbiol. 2010; 48: 2110-2115
        • Köhling H.L.
        • Bittner A.
        • Müller K.D.
        • et al.
        Direct identification of bacteria in urine samples by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and relevance of defensins as interfering factors.
        J Med Microbiol. 2012; 61: 339-344
        • DeMarco M.L.
        • Burnham C.D.
        Direct identification of microbes in urine specimens using mass spectrometry.
        Clin Chem. 2012; 58: A137
        • Gibb S.
        • Strimmer K.
        MALDIquant: a versatile R package for the analysis of mass spectrometry data.
        Bioinformatics. 2012; 1: 2270-2271
        • Ihaka R.
        • Gentleman R.R.
        A language for data analysis and graphics.
        J Comput Graph Stat. 1996; 5: 299-314
        • Ketterlinus R.
        • Hsieh S.Y.
        • Teng S.H.
        • et al.
        Fishing for biomarkers: analyzing mass spectrometry data with the new ClinProTools software.
        Biotechniques. 2005; : 37-40
        • Du P.
        • Kibbe W.A.
        • Lin S.M.
        Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.
        Bioinformatics. 2006; 1: 2059-2065
        • Vu T.
        • Valkenborg D.
        • Smets K.
        • et al.
        An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.
        BMC Bioinformatics. 2011; 20: 405
        • Chang C.C.
        • Lin C.J.
        LIBSVM: a library for support vector machines.
        ACM Trans Intell Syst Technol. 2011; 2: 1-27
        • Chen P.
        • Lu Y.
        • Harrington P.B.
        Biomarker profiling and reproducibility study of MALDI-MS measurements of Escherichia coli by analysis of variance-principal component analysis.
        Anal Chem. 2008; 1: 1474-1481
        • Seibold E.
        • Maier T.
        • Kostrzewa M.
        • et al.
        Identification of Francisella tularensis by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry: fast, reliable, robust, and cost-effective differentiation on species and subspecies levels.
        J Clin Microbiol. 2010; 1: 1061-1069
        • Ikryannikova L.N.
        • Filimonova A.V.
        • Malakhova M.V.
        • et al.
        Discrimination between S. pneumoniae and S. mitis based on sorting of their MALDI mass spectra.
        Clin Microbiol Infect. 2012; ([Epub ahead of print])https://doi.org/10.1111/1469-0691.12113
        • Barla A.
        • Jurman G.
        • Riccadonna S.
        • et al.
        Machine learning methods for predictive proteomics.
        Brief Bioinform. 2008; 1: 119-128
        • Centor R.M.
        Signal detectability the use of ROC curves and their analyses.
        Med Decis Making. 1991; 1: 102-106
      1. Provost F. The case against accuracy estimation for comparing induction algorithms. Proceeding ICML ‘98 Proceedings of the Fifteenth International Conference on Machine Learning. San Francisco (CA): Morgan Kaufmann Publishers Inc; 1998. p. 445-53.

        • Nantasenamat C.
        • Preeyanon L.
        • Isarankura-Na-Ayudhya C.
        • et al.
        PyBact: an algorithm for bacterial identification.
        EXCLI J. 2011; 10: 240-245
        • Hall M.
        • Frank E.
        • Holmes G.
        • et al.
        The WEKA data mining software: an update.
        SIGKDD Explor Newsl. 2009; 11 (Available at:): 10-18
        • Petricoin III, E.F.
        • Ardekani A.M.
        • Hitt B.A.
        • et al.
        Use of proteomic patterns in serum to identify ovarian cancer.
        Lancet. 2002; 16: 572-577
        • Check E.
        Proteomics and cancer: running before we can walk?.
        Nature. 2004; 3: 496-497
        • Falkow S.
        Molecular Koch’s postulates applied to microbial pathogenicity.
        Rev Infect Dis. 1988; 1: S274-S276
        • Gagnaire J.
        • Dauwalder O.
        • Boisset S.
        • et al.
        Detection of staphylococcus aureus delta-toxin production by whole-cell MALDI-TOF mass spectrometry.
        PLoS One. 2012; 6: 7
        • De Bruyne K.
        • Slabbinck B.
        • Waegeman W.
        • et al.
        Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning.
        Syst Appl Microbiol. 2011; 34: 20-29
        • Reil M.
        • Erhard M.
        • Kuijper E.J.
        • et al.
        Recognition of Clostridium difficile PCR-ribotypes 001, 027 and 126/078 using an extended MALDI-TOF MS system.
        Eur J Clin Microbiol Infect Dis. 2011; 1: 1431-1436
        • Davies A.P.
        • Reid M.
        • Hadfield S.J.
        • et al.
        Identification of clinical isolates of α-haemolytic streptococci by 16S rRNA gene sequencing, MALDI TOF MS by MALDI Biotyper and conventional phenotypic methods—a comparison.
        J Clin Microbiol. 2012; 50: 4087-4090
        • Werno A.M.
        • Christner M.
        • Anderson T.P.
        • et al.
        Differentiation of Streptococcus pneumoniae from nonpneumococcal streptococci of the Streptococcus mitis group by matrix-assisted laser desorption ionization–time of flight mass spectrometry.
        J Clin Microbiol. 2012; 1: 2863-2867
        • Griffin P.M.
        • Price G.R.
        • Schooneveldt J.M.
        • et al.
        The use of MALDI-TOF MS to identify vancomycin resistant enterococci and investigate the epidemiology of an outbreak.
        J Clin Microbiol. 2012; 50: 2918-2931
        • Edwards-Jones V.
        • Claydon M.A.
        • Evason D.J.
        • et al.
        Rapid discrimination between methicillin-sensitive and methicillin-resistant Staphylococcus aureus by intact cell mass spectrometry.
        J Med Microbiol. 2000; 1: 295-300
        • Jackson K.A.
        • Edwards-Jones V.
        • Sutton C.W.
        • et al.
        Optimisation of intact cell MALDI method for fingerprinting of methicillin-resistant Staphylococcus aureus.
        J Microbiol Methods. 2005; 62: 273-284
        • Du Z.
        • Yang R.
        • Guo Z.
        • et al.
        Identification of staphylococcus aureus and determination of its methicillin resistance by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
        Anal Chem. 2002; 1: 5487-5491
        • Wolters M.
        • Rohde H.
        • Maier T.
        • et al.
        MALDI-TOF MS fingerprinting allows for discrimination of major methicillin-resistant Staphylococcus aureus lineages.
        Int J Med Microbiol. 2011; 301: 64-68
        • Freiwald A.
        • Sauer S.
        Phylogenetic classification and identification of bacteria by mass spectrometry.
        Nat Protoc. 2009; 4: 732-742
        • Smole S.C.
        • King L.A.
        • Leopold P.E.
        • et al.
        Sample preparation of Gram-positive bacteria for identification by matrix assisted laser desorption/ionization time-of-flight.
        J Microbiol Methods. 2002; 48: 107-115
        • Hrabák J.
        • Chudáčková E.
        • Walková R.
        Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry for detection of antibiotic resistance mechanisms: from research to routine diagnosis.
        Clin Microbiol Rev. 2013; 1: 103-114
        • Wybo I.
        • Bel A.D.
        • Soetens O.
        • et al.
        Differentiation of cfiA-negative and cfiA-positive Bacteroides fragilis isolates by matrix-assisted laser desorption ionization-time of flight mass spectrometry.
        J Clin Microbiol. 2011; 1: 1961-1964
        • Livermore D.M.
        • Woodford N.
        Carbapenemases: a problem in waiting?.
        Curr Opin Microbiol. 2000; 3: 489-495
        • Podglajen I.
        • Breuil J.
        • Casin I.
        • et al.
        Genotypic identification of two groups within the species Bacteroides fragilis by ribotyping and by analysis of PCR-generated fragment patterns and insertion sequence content.
        J Bacteriol. 1995; 1: 5270-5275
        • O’Callaghan C.H.
        • Morris A.
        • Kirby S.M.
        • et al.
        Novel method for detection of β-lactamases by using a chromogenic cephalosporin substrate.
        Antimicrob Agents Chemother. 1972; 1: 283-288
        • Sparbier K.
        • Schubert S.
        • Weller U.
        • et al.
        Matrix-assisted laser desorption ionization-time of flight mass spectrometry-based functional assay for rapid detection of resistance against B-lactam antibiotics.
        J Clin Microbiol. 2012; 1: 927-937
        • Burckhardt I.
        • Zimmermann S.
        Using matrix-assisted laser desorption ionization-time of flight mass spectrometry to detect carbapenem resistance within 1 to 2.5 hours.
        J Clin Microbiol. 2011; 1: 3321-3324
        • Hrabák J.
        • Walková R.
        • Študentová V.
        • et al.
        Carbapenemase activity detection by matrix-assisted laser desorption ionization-time of flight mass spectrometry.
        J Clin Microbiol. 2011; 1: 3222-3227
        • Delcour A.H.
        Outer membrane permeability and antibiotic resistance.
        Biochim Biophys Acta. 2009; 1794: 808-816
        • Dunne W.M.
        • Hardin D.J.
        Use of several inducer and substrate antibiotic combinations in a disk approximation assay format to screen for AmpC induction in patient isolates of Pseudomonas aeruginosa, Enterobacter spp., Citrobacter spp., and Serratia spp.
        J Clin Microbiol. 2005; 1: 5945-5949