456
Views
0
CrossRef citations to date
0
Altmetric
Review

How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota

, , &
Pages 217-229 | Received 30 Mar 2017, Accepted 15 Jan 2018, Published online: 19 Jan 2018

References

  • Ley RE, Backhed F, Turnbaugh P, et al. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA. 2005;102:11070–11075. Epub 2005/07/22.
  • Turnbaugh PJ, Ley RE, Mahowald MA, et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027–1031. Epub 2006/12/22.
  • Brooks JP, Edwards DJ, Harwich MD Jr., et al.The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. BMC Microbiol. 2015;15:66. Epub 2015/04/17.
  • Claesson MJ, Wang Q, O’Sullivan O, et al. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res. 2010;38:e200. Epub 2010/10/01.
  • Fouhy F, Clooney AG, Stanton C, et al. 16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform. BMC Microbiol. 2016;16:123. Epub 2016/06/28.
  • Angelakis E, Bachar D, Henrissat B, et al. Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies. Sci Rep. 2016;6:26276. Epub 2016/05/18.
  • Lagier JC, Armougom F, Million M, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect. 2012;18:1185–1193. Epub 2012/10/05.
  • Kaeberlein T, Lewis K, Epstein SS Isolating ‘uncultivable’ microorganisms in pure culture in a simulated natural environment. Science 2002;296(5570):1127–1129.
  • Seng P, Drancourt M, Gouriet F, et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis. 2009;49:543–551. Epub 2009/07/09.
  • Lagier JC, Khelaifia S, Alou MT, et al. Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol. 2016;1:16203. Epub 2016/11/08.
  • Abdallah RA, Beye M, Diop A, et al. The impact of culturomics on taxonomy in clinical microbiology. Antonie Van Leeuwenhoek. 2017; 110(10):1327–1337.
  • Browne HP, Forster SC, Anonye BO, et al. Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature. 2016;533:543–546. Epub 2016/05/05.
  • Nichols D, Cahoon N, Trakhtenberg EM, et al. Use of ichip for high-throughput in situ cultivation of ‘uncultivable’ microbial species. Appl Environ Microbiol. 2010;76:2445–2450. Epub 2010/02/23.
  • Sizova MV, Hohmann T, Hazen A, et al. New approaches for isolation of previously uncultivated oral bacteria. Appl Environ Microbiol. 2012;78:194–203. Epub 2011/11/08
  • Lagkouvardos I, Overmann J, Clavel T Cultured microbes represent a substantial fraction of the human and mouse gut microbiota. Gut Microbes. 2017; 8(5):493–503.
  • Levi Mortera S, Del Chierico F, Vernocchi P, et al. Monitoring perinatal gut microbiota in mouse models by mass spectrometry approaches: parental genetic background and breastfeeding effects. Front Microbiol. 2016;7:1523
  • Miescher Schwenninger S, Freimuller Leischtfeld S, Gantenbein-Demarchi C High-throughput identification of the microbial biodiversity of cocoa bean fermentation by MALDI-TOF MS. Lett Appl Microbiol. 2016;63:347–355. Epub 2016/07/28.
  • Tandina F, Almeras L, Kone AK, et al. Use of MALDI-TOF MS and culturomics to identify mosquitoes and their midgut microbiota. Parasit Vectors. 2016;9:495. Epub 2016/09/11.
  • Wolochow H Detection of airborne microorganisms through their unique compounds. Naval Biosciences Laboratory Technical Reports Arlington, Virginia: Armed Services Technical Information Agency 1959; Report No 211170.
  • Abel K, Deschmertzing H, Peterson JI Classification of microorganisms by analysis of chemical composition. I. Feasibility of utilizing gas chromatography. J Bacteriol. 1963;85:1039–1044.
  • Anhalt JP, Fenselau C Identification of bacteria using mass spectrometry. Anal Chem. 1975;47(2):219–225.
  • Cain TC, Lubman DM, Weber WJ, et al. Differentiation of bacteria using protein profiles from matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry. Rapid Commun Mass Spectrom. 1994;8(12):1026–1030.
  • Claydon MA, Davey SN, Edwards-Jones V, et al. The rapid identification of intact microorganisms using mass spectrometry. Nat Biotechnol. 1996;14(11):1584–1586.
  • Holland RD, Wilkes JG, Rafii F, et al. Rapid identification of intact whole bacteria based on spectral patterns using matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry. Rapid Commun Mass Spectrom. 1996;10:1227–1232. Epub 1996/01/01.
  • Demirev PA, Fenselau C Mass spectrometry in biodefense. J Mass Spectrom. 2008 Nov;43(11):1441–1457.
  • Fenselau C, Demirev PA Characterization of intact microorganisms by MALDI mass spectrometry. Mass Spectrom Rev. 2001;20(4):157–171.
  • Lay JO Jr. MALDI-TOF mass spectrometry of bacteria. Mass Spectrom Rev.2001;20(4):172–194.
  • Sandrin TR, Goldstein JE, Schumaker S MALDI TOF MS profiling of bacteria at the strain level: a review. Mass Spectrom Rev. 2013;32(3):188–217.
  • Albrethsen J Reproducibility in protein profiling by MALDI-TOF mass spectrometry. Clin Chem. 2007;53(5):852–858.
  • Wunschel SC, Jarman KH, Petersen CE, et al. Bacterial analysis by MALDI-TOF mass spectrometry: an inter-laboratory comparison. J Am Soc Mass Spectrom. 2005;16:456–462. Epub 2005/03/29.
  • Valentine N, Wunschel S, Wunschel D, et al. Effect of culture conditions on microorganism identification by matrix-assisted laser desorption ionization mass spectrometry. Appl Environ Microbiol. 2005;71:58–64. Epub 2005/01/11.
  • Williams TL, Andrzejewski D, Lay JO, 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. Epub 2003/04/11.
  • Freiwald A, Sauer S Phylogenetic classification and identification of bacteria by mass spectrometry. Nat Protoc. 2009;4(5):732–742.
  • Goyer M, Lucchi G, Ducoroy P, et al. Optimization of the preanalytical steps of matrix-assisted laser desorption ionization-time of flight mass spectrometry identification provides a flexible and efficient tool for identification of clinical yeast isolates in medical laboratories. J Clin Microbiol. 2012;50:3066–3068. Epub 2012/06/22.
  • Mellmann A, Bimet F, Bizet C, et al. High interlaboratory reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry-based species identification of nonfermenting bacteria. J Clin Microbiol 2009;47:3732–3734. Epub 2009/09/25.
  • Ghyselinck J, Van Hoorde K, Hoste B, et al. Evaluation of MALDI-TOF MS as a tool for high-throughput dereplication. J Microbiol Methods 2011;86:327–336. Epub 2011/06/28.
  • Ilina EN, Borovskaya AD, Malakhova MM, et al. Direct bacterial profiling by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for identification of pathogenic Neisseria. J Mol Diagn 2009;11:75–86. Epub 2008/12/20.
  • Sauer S, Kliem M Mass spectrometry tools for the classification and identification of bacteria. Nat Rev Microbiol. 2010;8:74–82. Epub 2009/12/17.
  • Holland RD, Duffy CR, Rafii F, et al. Identification of bacterial proteins observed in MALDI TOF mass spectra from whole cells. Anal Chem. 1999;71:3226–3230. Epub 1999/08/18.
  • Carbonnelle E, Mesquita C, Bille E, et al. MALDI-TOF mass spectrometry tools for bacterial identification in clinical microbiology laboratory. Clin Biochem. 2011;44:104–109. Epub 2010/07/14.
  • Keys CJ, Dare DJ, Sutton H, et al. Compilation of a MALDI-TOF mass spectral database for the rapid screening and characterisation of bacteria implicated in human infectious diseases. Infect Genet Evol. 2004;4:221–242. Epub 2004/09/29.
  • Sauer S, Freiwald A, Maier T, et al. Classification and identification of bacteria by mass spectrometry and computational analysis. PloS One. 2008;3:e2843. Epub 2008/07/31.
  • Seng P, Abat C, Rolain JM, et al. Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol. 2013;51:2182–2194. Epub 2013/05/03.
  • Almuzara M, Barberis C, Traglia G, et al. Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry for species identification of nonfermenting Gram-negative bacilli. J Microbiol Methods. 2015;112:24–27. Epub 2015/03/15.
  • Barreau M, Pagnier I, La Scola B Improving the identification of anaerobes in the clinical microbiology laboratory through MALDI-TOF mass spectrometry. Anaerobe. 2013;22:123–125. Epub 2013/05/04.
  • 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. Epub 2011/02/02.
  • Bizzini A, Durussel C, Bille J, 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. J Clin Microbiol. 2010;48:1549–1554. Epub 2010/03/12.
  • Bruin JP, Kostrzewa M, van der Ende A, et al. Identification of Haemophilus influenzae and Haemophilus haemolyticus by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Eur J Clin Microbiol Infect Dis. 2014;33:279–284. Epub 2013/09/11.
  • Carpaij N, Willems RJ, Bonten MJ, et al. Comparison of the identification of coagulase-negative staphylococci by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and tuf sequencing. Eur J Clin Microbiol Infect Dis. 2011;30:1169–1172. Epub 2011/03/02.
  • Cheng WC, Jan IS, Chen JM, et al. Evaluation of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of blood isolates of Vibrio species. J Clin Microbiol. 2015;53:1741–1744. Epub 2015/03/06.
  • Cherkaoui A, Emonet S, Fernandez J, et al. Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for rapid identification of Beta-hemolytic streptococci. J Clin Microbiol. 2011;49:3004–3005. Epub 2011/06/24.
  • Clark AE, Kaleta EJ, Arora A, et al. Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev. 2013;26:547–603. Epub 2013/07/05.
  • Couturier MR, Mehinovic E, Croft AC, et al. Identification of HACEK clinical isolates by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol. 2011;49:1104–1106. Epub 2011/01/14.
  • Deng J, Fu L, Wang R, et al. Comparison of MALDI-TOF MS, gene sequencing and the Vitek 2 for identification of seventy-three clinical isolates of enteropathogens. J Thorac Dis. 2014;6:539–544. Epub 2014/05/14.
  • Djelouadji Z, Roux V, Raoult D, et al. Rapid MALDI-TOF mass spectrometry identification of Leptospira organisms. Vet Microbiol. 2012;158:142–146. Epub 2012/03/06.
  • Dridi B, Raoult D, Drancourt M Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of Archaea: towards the universal identification of living organisms. APMIS. 2012;120:85–91. Epub 2012/01/11.
  • El Khechine A, Couderc C, Flaudrops C, et al. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of mycobacteria in routine clinical practice. PloS One. 2011;6:e24720. Epub 2011/09/22.
  • Fang H, Ohlsson AK, Ullberg M, et al. Evaluation of species-specific PCR, Bruker MS, VITEK MS and the VITEK 2 system for the identification of clinical Enterococcus isolates. Eur J Clin Microbiol Infect Dis. 2012;31:3073–3077. Epub 2012/06/19.
  • Fedorko DP, Drake SK, Stock F, et al. Identification of clinical isolates of anaerobic bacteria using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Eur J Clin Microbiol Infect Dis. 2012;31:2257–2262. Epub 2012/03/01.
  • Fournier PE, Couderc C, Buffet S, et al. Rapid and cost-effective identification of Bartonella species using mass spectrometry. J Med Microbiol. 2009;58:1154–1159. Epub 2009/06/17.
  • Hsueh PR, Kuo LC, Chang TC, et al. Evaluation of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of blood isolates of Acinetobacter species. J Clin Microbiol. 2014;52:3095–3100. Epub 2014/06/06.
  • Hsueh PR, Lee TF, Du SH, et al. Bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of Nocardia, Rhodococcus, Kocuria, Gordonia, Tsukamurella, and Listeria species. J Clin Microbiol. 2014;52:2371–2379. Epub 2014/04/25.
  • Krishnamurthy T, Ross PL Rapid identification of bacteria by direct matrix-assisted laser desorption/ionization mass spectrometric analysis of whole cells. Rapid Commun Mass Spectrom. 1996;10:1992–1996. Epub 1996/01/01.
  • Lasch P, Wahab T, Weil S, et al. Identification of highly pathogenic microorganisms by matrix-assisted laser desorption ionization-time of flight mass spectrometry: results of an interlaboratory ring trial. J Clin Microbiol. 2015;53:2632–2640. Epub 2015/06/13.
  • Lista F, Reubsaet FA, De Santis R, et al. Reliable identification at the species level of Brucella isolates with MALDI-TOF-MS. BMC Microbiol. 2011;11:267. Epub 2011/12/24.
  • Lynch T, Gregson D, Church DL Species-level identification of actinomyces isolates causing invasive infections: multiyear comparison of Vitek MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) to partial sequencing of the 16S rRNA gene. J Clin Microbiol. 2016;54:712–717. Epub 2016/01/08.
  • Martiny D, Cremagnani P, Gaillard A, et al. Feasibility of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) networking in university hospitals in Brussels. Eur J Clin Microbiol Infect Dis. 2014;33:745–754. Epub 2013/11/08.
  • Nagy E Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a new possibility for the identification and typing of anaerobic bacteria. Future Microbiol. 2014;9:217–233. Epub 2014/02/28.
  • Pavlovic M, Konrad R, Iwobi AN, et al. A dual approach employing MALDI-TOF MS and real-time PCR for fast species identification within the Enterobacter cloacae complex. FEMS Microbiol Lett. 2012;328:46–53. Epub 2011/12/14.
  • Rettinger A, Krupka I, Grunwald K, et al. Leptospira spp. strain identification by MALDI TOF MS is an equivalent tool to 16S rRNA gene sequencing and multi locus sequence typing (MLST). BMC Microbiol. 2012;12:185. Epub 2012/08/29.
  • Rychert J, Burnham CA, Bythrow M, et al. Multicenter evaluation of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of gram-positive aerobic bacteria. J Clin Microbiol. 2013;51:2225–2231. Epub 2013/05/10.
  • Tseng SP, Teng SH, Lee PS, et al. Rapid identification of M. abscessus and M. massiliense by MALDI-TOF mass spectrometry with a comparison to sequencing methods and antimicrobial susceptibility patterns. Future Microbiol. 2013;8:1381–1389. Epub 2013/11/10.
  • Tuuminen T, Suomala P, Harju I Actinobaculum schaalii: identification with MALDI-TOF. New Microbes New Infect. 2014;2:38–41. Epub 2014/10/31.
  • van Veen SQ, Claas EC, Kuijper EJ High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories. J Clin Microbiol. 2010;48:900–907. Epub 2010/01/08.
  • Verroken A, Janssens M, Berhin C, et al. Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of nocardia species. J Clin Microbiol. 2010;48:4015–4021. Epub 2010/09/24.
  • Werno AM, Christner M, Anderson TP, 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;50:2863–2867. Epub 2012/06/22.
  • Xiao D, Zhao F, Zhang H, et al. Novel strategy for typing Mycoplasma pneumoniae isolates by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry coupled with ClinProTools. J Clin Microbiol. 2014;52:3038–3043. Epub 2014/06/13.
  • Zangenah S, Guleryuz G, Borang S, et al. Identification of clinical Pasteurella isolates by MALDI-TOF – a comparison with VITEK 2 and conventional microbiological methods. Diagn Microbiol Infect Dis. 2013;77:96–98. Epub 2013/07/28.
  • Krásný L, Hynek R, Hochel I Identification of bacteria using mass spectrometry techniques. Int J Mass Spectrom. 2013;353:67–79.
  • Gaia V, Casati S, Tonolla M Rapid identification of Legionella spp. by MALDI-TOF MS based protein mass fingerprinting. Syst Appl Microbiol 2011;34:40–44.
  • Khot PD, Fisher MA Novel approach for differentiating Shigella species and Escherichia coli by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol. 2013;51:3711–3716. Epub 2013/08/30.
  • Paauw A, Jonker D, Roeselers G, et al. Rapid and reliable discrimination between Shigella species and Escherichia coli using MALDI-TOF mass spectrometry. Int J Med Microbiol. 2015;305:446–452. Epub 2015/04/29.
  • Ikryannikova LN, Filimonova AV, Malakhova MV, et al. Discrimination between Streptococcus pneumoniae and Streptococcus mitis based on sorting of their MALDI mass spectra. Clin Microbiol Infect. 2013;19:1066–1071. Epub 2013/01/22.
  • Ikryannikova LN, Lapin KN, Malakhova MV, et al. Misidentification of alpha-hemolytic streptococci by routine tests in clinical practice. Infect Genet Evol. 2011;11:1709–1715. Epub 2011/07/30.
  • TeKippe EM, Shuey S, Winkler DW, et al. Optimizing identification of clinically relevant gram-positive organisms using the Bruker Biotyper MALDI-TOF MS system. J Clin Microbiol. 2013; 51(5):1421–1427.
  • Barbuddhe SB, Maier T, Schwarz G, et al. Rapid identification and typing of listeria species by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol. 2008;74:5402–5407.
  • Wilen CB, McMullen AR, Burnham C-AD Comparison of sample preparation, instrumentation platforms, and contemporary commercial databases for MALDI-TOF MS identification of clinically relevant mycobacteria. J Clin Microbiol. 2015;53(7):2308–2315.
  • Xiao D, Zhang H, He L, et al. High natural variability bacteria identification and typing: Helicobacter pylori analysis based on peptide mass fingerprinting. J Proteomics. 2014;98:112–122.
  • Sedo O, Sedlacek I, Zdrahal Z Sample preparation methods for MALDI-MS profiling of bacteria. Mass Spectrom Rev. 2011;30(3):417–434.
  • Miller NS Commentary. Clin Chem. 2016;62:40. Epub 2016/01/01.
  • Boyer AE, Gallegos-Candela M, Quinn CP, et al. High-sensitivity MALDI-TOF MS quantification of anthrax lethal toxin for diagnostics and evaluation of medical countermeasures. Anal Bioanal Chem. 2015;407:2847–2858. Epub 2015/02/13.
  • Chen JH, Ho PL, Kwan GS, et al. Direct bacterial identification in positive blood cultures by use of two commercial matrix-assisted laser desorption ionization-time of flight mass spectrometry systems. J Clin Microbiol. 2013;51:1733–1739. Epub 2013/03/22.
  • 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. Epub 2009/12/01.
  • 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. Epub 2010/02/19.
  • Burillo A, Rodriguez-Sanchez B, Ramiro A, et al. Gram-stain plus MALDI-TOF MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) for a rapid diagnosis of urinary tract infection. PloS One. 2014;9:e86915. Epub 2014/01/28.
  • Demarco ML, Burnham CA. Diafiltration MALDI-TOF mass spectrometry method for culture-independent detection and identification of pathogens directly from urine specimens. Am J Clin Pathol. 2014;141:204–212. Epub 2014/01/18.
  • Nyvang Hartmeyer G, Kvistholm Jensen A, Böcher S, et al. spectrometry: pneumococcal meningitis verified and Brucella species identified in less than half an hour. Scand J Infect Dis 2010;42:716–718
  • Segawa S, Sawai S, Murata S, et al. Direct application of MALDI-TOF mass spectrometry to cerebrospinal fluid for rapid pathogen identification in a patient with bacterial meningitis. Clin Chim Acta. 2014;435:59–61.
  • Fournier PE, Dubourg G, Raoult D Clinical detection and characterization of bacterial pathogens in the genomics era. Genome Med. 2014;6(11):114.
  • Sauget M, Valot B, Bertrand X, et al. Can MALDI-TOF mass spectrometry reasonably type bacteria? Trends Microbiol. 2017;25(6):447–455.
  • Moura H, Woolfitt AR, Carvalho MG, et al. MALDI-TOF mass spectrometry as a tool for differentiation of invasive and noninvasive Streptococcus pyogenes isolates. FEMS Immunol Med Microbiol. 2008;53:333–342. Epub 2008/06/10.
  • Williamson YM, Moura H, Woolfitt AR, et al. Differentiation of Streptococcus pneumoniae conjunctivitis outbreak isolates by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol. 2008;74:5891–5897. Epub 2008/08/19.
  • Pinto TC, Costa NS, Castro LF, et al. Potential of MALDI-TOF MS as an alternative approach for capsular typing Streptococcus pneumoniae isolates. Sci Rep. 2017;7:45572
  • Clark CG, Kruczkiewicz P, Guan C, et al. Evaluation of MALDI-TOF mass spectroscopy methods for determination of Escherichia coli pathotypes. J Microbiol Methods. 2013;94:180–191. Epub 2013/07/03.
  • Kuhns M, Zautner AE, Rabsch W, et al. Rapid discrimination of Salmonella enterica serovar Typhi from other serovars by MALDI-TOF mass spectrometry. PloS One. 2012;7:e40004. Epub 2012/07/07.
  • Berrazeg M, Diene SM, Drissi M, et al. Biotyping of multidrug-resistant Klebsiella pneumoniae clinical isolates from France and Algeria using MALDI-TOF MS. PloS One. 2013;8:e61428. Epub 2013/04/27.
  • Boggs SR, Cazares LH, Drake R Characterization of a Staphylococcus aureus USA300 protein signature using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. JMed Microbiol. 2012;61:640–644. Epub 2012/02/11.
  • Cabrolier N, Sauget M, Bertrand X, et al. Matrix-assisted laser desorption ionization-time of flight mass spectrometry identifies Pseudomonas aeruginosa high-risk clones. J Clin Microbiol. 2015;53:1395–1398. Epub 2015/02/06
  • Freitas AR, Sousa C, Novais C, et al. Rapid detection of high-risk Enterococcus faecium clones by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Diagn Microbiol Infect Dis. 2017;87:299–307. Epub 2017/01/23.
  • Josten M, Reif M, Szekat C, et al. Analysis of the matrix-assisted laser desorption ionization-time of flight mass spectrum of Staphylococcus aureus identifies mutations that allow differentiation of the main clonal lineages. J Clin Microbiol. 2013;51:1809–1817. Epub 2013/04/05.
  • Mencacci A, Monari C, Leli C, et al. Typing of nosocomial outbreaks of Acinetobacter baumannii by use of matrix-assisted laser desorption ionization–time of flight mass spectrometry. J Clin Microbiol. 2013;51:603–606.
  • Rizzardi K, Akerlund T High molecular weight typing with MALDI-TOF MS – a novel method for rapid typing of Clostridium difficile. PloS One. 2015;10:e0122457. Epub 2015/04/30.
  • Reil M, Erhard M, Kuijper EJ, 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;30:1431–1436. Epub 2011/04/20.
  • Rodrigues C, Novais A, Sousa C, et al. Elucidating constraints for differentiation of major human Klebsiella pneumoniae clones using MALDI-TOF MS. Eur J Clin Microbiol Infect Dis. 2017;36:379–386. Epub 2016/11/05.
  • Sachse S, Bresan S, Erhard M, et al. Comparison of multilocus sequence typing, RAPD, and MALDI-TOF mass spectrometry for typing of beta-lactam-resistant Klebsiella pneumoniae strains. Diagn Microbiol Infect Dis. 2014;80:267–271. Epub 2014/10/01
  • Sousa C, Botelho J, Grosso F, et al. Unsuitability of MALDI-TOF MS to discriminate Acinetobacter baumannii clones under routine experimental conditions. Front Microbiol. 2015;6:481.
  • Cheng K, She YM, Chui H, et al. Mass spectrometry-based Escherichia coli H antigen/flagella typing: validation and comparison with traditional serotyping. Clin Chem. 2016;62:839–847. Epub 2016/04/08.
  • Cheng K, Sloan A, Meakin J, et al. Sequence-level and dual-phase identification of Salmonella flagellum antigens by liquid chromatography-tandem mass spectrometry (LC-MS/MS). J Clin Microbiol. 2014;52:2189–2192. Epub 2014/04/04.
  • Cheng K, Sloan A, Peterson L, et al. Comparative study of traditional flagellum serotyping and liquid chromatography-tandem mass spectrometry-based flagellum typing with clinical Escherichia coli isolates. J Clin Microbiol. 2014;52:2275–2278. Epub 2014/03/29.
  • Chui H, Chan M, Hernandez D, et al. Rapid, sensitive, and specific Escherichia coli H antigen typing by matrix-assisted laser desorption ionization-time of flight-based peptide mass fingerprinting. J Clin Microbiol. 2015;53:2480–2485. Epub 2015/05/29.
  • Griffin PM, Price GR, Schooneveldt JM, et al. Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry to identify vancomycin-resistant enterococci and investigate the epidemiology of an outbreak. J Clin Microbiol. 2012;50:2918–2931. Epub 2012/06/29.
  • Schlebusch S, Price GR, Gallagher RL, et al. MALDI-TOF MS meets WGS in a VRE outbreak investigation. Eur J Clin Microbiol Infect Dis. 2017;36:495–499. Epub 2016/11/28.
  • Mather CA, Werth BJ, Sivagnanam S, et al. Rapid detection of vancomycin-intermediate Staphylococcus aureus by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol. 2016;54:883–890. Epub 2016/01/15.
  • Rhoads DD, Wang H, Karichu J, et al. The presence of a single MALDI-TOF mass spectral peak predicts methicillin resistance in staphylococci. Diagn Microbiol Infect Dis. 2016;86:257–261. Epub 2016/08/29.
  • Szabados F, Kaase M, Anders A, et al. Identical MALDI TOF MS-derived peak profiles in a pair of isogenic SCCmec-harboring and SCCmec-lacking strains of Staphylococcus aureus. J Infect. 2012;65:400–405. Epub 2012/07/04.
  • 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. Epub 2010/08/24.
  • 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 beta-lactam antibiotics. J Clin Microbiol. 2012;50:927–937. Epub 2011/12/30.
  • Foschi C, Compri M, Smirnova V, et al. Ease-of-use protocol for the rapid detection of third-generation cephalosporin resistance in Enterobacteriaceae isolated from blood cultures using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. J Hosp Infect. 2016;93:206–210. Epub 2016/04/24.
  • 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;49:3321–3324. Epub 2011/07/29.
  • Kempf M, Bakour S, Flaudrops C, et al. Rapid detection of carbapenem resistance in Acinetobacter baumannii using matrix-assisted laser desorption ionization-time of flight mass spectrometry. PloS One. 2012;7:e31676. Epub 2012/02/24.
  • Jung JS, Popp C, Sparbier K, et al. Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for rapid detection of beta-lactam resistance in Enterobacteriaceae derived from blood cultures. J Clin Microbiol. 2014;52:924–930. Epub 2014/01/10.
  • Oviano M, Ramirez CL, Barbeyto LP, et al. Rapid direct detection of carbapenemase-producing Enterobacteriaceae in clinical urine samples by MALDI-TOF MS analysis. J Antimicrob Chemother. 2017;72(5):1350–1354. Epub 2017/01/26.
  • Oviano M, Sparbier K, Barba MJ, et al. Universal protocol for the rapid automated detection of carbapenem-resistant gram-negative bacilli directly from blood cultures by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Int J Antimicrob Agents. 2016;48:655–660. Epub 2016/11/12.
  • Lagier JC, Hugon P, Khelaifia S, et al. The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev. 2015;28(1):237–264.
  • Dubourg G, Lagier JC, Armougom F, et al. The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics. Eur J Clin Microbiol Infect Dis. 2013;32:637–645. Epub 2013/01/08.
  • Dubourg G, Lagier JC, Robert C, et al. Culturomics and pyrosequencing evidence of the reduction in gut microbiota diversity in patients with broad-spectrum antibiotics. Int J Antimicrob Agents. 2014;44:117–124. Epub 2014/07/27.
  • Pfleiderer A, Lagier JC, Armougom F, et al. Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample. Eur J Clin Microbiol Infect Dis. 2013;32:1471–1481. Epub 2013/06/04.
  • Cassir N, Benamar S, Khalil JB, et al. Clostridium butyricum strains and dysbiosis linked to necrotizing enterocolitis in preterm neonates. Clin Infect Dis. 2015;61:1107–1115.
  • Seng P, Rolain JM, Fournier PE, et al. MALDI-TOF-mass spectrometry applications in clinical microbiology. Future Microbiol. 2010;5:1733–1754. Epub 2010/12/08.
  • Fournier PE, Lagier JC, Dubourg G, et al. From culturomics to taxonomogenomics: a need to change the taxonomy of prokaryotes in clinical microbiology. Anaerobe. 2015;36:73–78. Epub 2015/10/31.
  • Ramasamy D, Mishra AK, Lagier JC, et al. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol. 2014;64:384–391. Epub 2014/02/08.
  • Dubourg G, Lagier J-C, Robert C, et al. Risungbinella massiliensis sp. nov., a new member of Thermoactinomycetaceae isolated from human gut. Antonie Van Leeuwenhoek. 2016;109:773–784.
  • Togo AH, Durand G, Khelaifia S, et al., Fournierella massiliensis, gen. nov., sp. nov., a new human-associated member of the family Ruminococcaceae. Int J Syst Evol Microbiol. 2017;67(5):1393–1399.
  • Durand GA, Pham T, Ndongo S, et al. Blautia massiliensis sp. nov., isolated from a fresh human fecal sample and emended description of the genus Blautia. Anaerobe. 2017;43:47–55. Epub 2016/12/08.
  • Fournier PE, Raoult D, Drancourt M. New species announcement: a new format to prompt the description of new human microbial species. New Microbes New Infect. 2017;15:136–137. Epub 2017/01/26.
  • Fournier P-E, Raoult D, Drancourt M Republication of ‘new species announcement’, a new format to prompt the description of new human microbial species. Hum Microbiome J. 2016;1:A1–A2.
  • Hugon P, Dufour JC, Colson P, et al. A comprehensive repertoire of prokaryotic species identified in human beings. Lancet Infect Dis. 2015;15(10):1211–1219.
  • Ferrario C, Alessandri G, Mancabelli L, et al. Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses. Environ Microbiol. 2017;19(11):4771–4783.
  • Kaspar U, Kriegeskorte A, Schubert T, et al. The culturome of the human nose habitats reveals individual bacterial fingerprint patterns. Environ Microbiol. 2016;18(7):2130–2142.
  • Mlaga KD, Dubourg G, Abat C, et al. Using MALDI-TOF MS typing method to decipher outbreak: the case of Staphylococcus saprophyticus causing urinary tract infections (UTIs) in Marseille, France. Eur J Clin Microbiol Infect Dis. 2017;36(12):2371–2377.
  • Vétizou M, Pitt JM, Daillère R, et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science. 2015;350:1079–1084.
  • Cassagne C, Normand AC, L’Ollivier C, et al. Performance of MALDI-TOF MS platforms for fungal identification. Mycoses 2016;59(11):678–690.
  • Hamad I, Ranque S, Azhar E, et al., Culturomics and amplicon-based metagenomic approaches for the study of fungal population in human gut microbiota. Sci Rep. 2017;7(1):16788.
  • Jansson J, Willing B, Lucio M, et al. Metabolomics reveals metabolic biomarkers of Crohn’s disease. PloS One. 2009;4(7):e6386.
  • Erickson AR, Cantarel BL, Lamendella R, et al. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn’s disease. PloS One. 2012;7(11):e49138.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.