Skip to main content
SpringerLink
Log in

Direct matrix-assisted laser desorption ionisation time-of-flight mass spectrometry identification of mycobacteria from colonies

  • Original Article
  • Published:
European Journal of Clinical Microbiology & Infectious Diseases Aims and scope Submit manuscript

Abstract

Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) identification of mycobacteria requires a standard acetonitrile/formic acid pre-MALDI-TOF-MS. We prospectively compared this standard protocol with direct deposit with matrix for the identification of mycobacteria cultured on solid media. We first verified that Mycobacterium tuberculosis was killed after it was mixed with matrix. Then, 111 Mycobacterium isolates previously identified by partial rpoB gene sequencing were tested in parallel by the two protocols. An identification score >1.7 was obtained in 86/111 (77.5 %) isolates after protein extraction versus 97/111 (87.4 %) isolates after direct deposit (p = 0.039, Chi-squared test). In a third step, we determined that direct deposit achieved identification for as few as 2.104 M. tuberculosis organisms. In a fourth step, we evaluated direct deposit of one colony for 116 solid medium-cultured clinical isolates finally identified as representative of 12 species (63.8 % M. tuberculosis). For 114/116 (98.3 %) isolates with an identification score >1.2, the MALDI-TOF-MS identification was in complete agreement with the reference rpoB gene sequencing identification. One isolate with a MALDI-TOF-MS identification score of 1.22 for M. fortuitum was identified as M. avium by partial rpoB gene sequencing. One other isolate with a MALDI-TOF-MS identification score of 1.22 for M. tuberculosis was identified as M. tuberculosis by genotyping. All the original MALDI-TOF-MS spectra reported here have been deposited in a public database. Direct deposit of one colony on a MALDI-TOF-MS plate allows for an accurate identification of mycobacteria for an identification score >1.3.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  1. El Khéchine A, Couderc C, Flaudrops C, Raoult D, Drancourt M (2011) Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of mycobacteria in routine clinical practice. PLoS One 6:e24720

    Article  PubMed  PubMed Central  Google Scholar 

  2. Johnson MM, Odell JA (2014) Nontuberculous mycobacterial pulmonary infections. J Thorac Dis 6:210–220

    PubMed  PubMed Central  Google Scholar 

  3. Brown-Elliott BA, Nash KA, Wallace RJ Jr (2012) Antimicrobial susceptibility testing, drug resistance mechanisms, and therapy of infections with nontuberculous mycobacteria. Clin Microbiol Rev 25:545–582

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Escobar-Escamilla N, Ramírez-González JE, González-Villa M, Torres-Mazadiego P, Mandujano-Martínez A, Barrón-Rivera C, Bäcker CE, Fragoso-Fonseca DE, Olivera-Díaz H, Alcántara-Pérez P, Hernández-Solís A, Cícero-Sabido R, Cortés-Ortíz IA (2014) Hsp65 phylogenetic assay for molecular diagnosis of nontuberculous mycobacteria isolated in Mexico. Arch Med Res 45:90–97

    Article  CAS  PubMed  Google Scholar 

  5. Butcher PD, Hutchinson NA, Doran TJ, Dale JW (1996) The application of molecular techniques to the diagnosis and epidemiology of mycobacterial diseases. Soc Appl Bacteriol Symp Ser 25:53S–71S

    Article  CAS  PubMed  Google Scholar 

  6. Dunne WM Jr, Doing K, Miller E, Miller E, Moreno E, Baghli M, Mailler S, Girard V, van Belkum A, Deol P (2014) Rapid inactivation of Mycobacterium and nocardia species before identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 52:3654–3659

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Asmar S, Chatellier S, Mirande C, van Belkum A, Canard I, Raoult D, Drancourt M (2015) A novel solid medium for culturing Mycobacterium tuberculosis isolates from clinical specimens. J Clin Microbiol 53:2566–2569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Seng P, Rolain J-M, Fournier PE, La Scola B, Drancourt M, Raoult D (2010) MALDI-TOF-mass spectrometry applications in clinical microbiology. Future Microbiol 5:1733–1754

    Article  CAS  PubMed  Google Scholar 

  9. Tran A, Alby K, Kerr A, Jones M, Gilligan PH (2015) Cost savings realized by implementation of routine microbiological identification by matrix-assisted laser desorption ionization–time of flight mass spectrometry. J Clin Microbiol 53:2473–2479

    Article  PubMed  PubMed Central  Google Scholar 

  10. Saleeb PG, Drake SK, Murray PR, Zelazny AM (2011) Identification of mycobacteria in solid-culture media by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 49(5):1790–1794

    Article  PubMed  PubMed Central  Google Scholar 

  11. Mather CA, Rivera SF, Butler-Wu SM (2014) Comparison of the Bruker Biotyper and Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry systems for identification of mycobacteria using simplified protein extraction protocols. J Clin Microbiol 52(1):130–138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Machen A, Kobayashi M, Connelly MR, Wang YF (2013) Comparison of heat inactivation and cell disruption protocols for identification of mycobacteria from solid culture media by use of vitek matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 51:4226–4229

    Article  PubMed  PubMed Central  Google Scholar 

  13. Djelouagji Z, Drancourt M (2006) Inactivation of cultured Mycobacterium tuberculosis organisms prior to DNA extraction. J Clin Microbiol 44:1594–1595

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Somerville W, Thibert L, Schwartzman K, Behr MA (2005) Extraction of Mycobacterium tuberculosis DNA: a question of containment. J Clin Microbiol 43:2996–2997

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, Rolain JM, Raoult D (2009) Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 49(4):543–551

    Article  CAS  PubMed  Google Scholar 

  16. Lotz A, Ferroni A, Beretti J-L, Dauphin B, Carbonnelle E, Guet-Revillet H, Veziris N, Heym B, Jarlier V, Gaillard J-L, Pierre-Audigier C, Frapy E, Berche P, Nassif X, Bille E (2010) Rapid identification of mycobacterial whole cells in solid and liquid culture media by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 48:4481–4486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Mareković I, Bošnjak Z, Jakopović M, Boras Z, Janković M, Popović-Grle S (2016) Evaluation of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in identification of nontuberculous mycobacteria. Chemotherapy 61:167–170

    Article  PubMed  Google Scholar 

  18. Kehrmann J, Wessel S, Murali R, Hampel A, Bange F-C, Buer J, Mosel F (2016) Principal component analysis of MALDI TOF MS mass spectra separates M. abscessus (sensu stricto) from M. massiliense isolates. BMC Microbiol 16:24

    Article  PubMed  PubMed Central  Google Scholar 

  19. Asmar S, Sassi M, Phelippeau M, Drancourt M (2016) Inverse correlation between salt tolerance and host-adaptation in mycobacteria. BMC Res Notes 9:249

    Article  PubMed  PubMed Central  Google Scholar 

  20. Asmar S, Chatellier S, Mirande C, van Belkum A, Canard I, Raoult D, Drancourt M (2016) A chlorhexidine-agar plate culture medium protocol to complement standard broth culture of Mycobacterium tuberculosis. Front Microbiol 7:30

    Article  PubMed  PubMed Central  Google Scholar 

  21. Bouricha M, Castan B, Duchene-Parisi E, Drancourt M (2014) Mycobacterium marinum infection following contact with reptiles: vivarium granuloma. Int J Infect Dis 21:17–18

    Article  PubMed  Google Scholar 

  22. Adékambi T, Colson P, Drancourt M (2003) rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J Clin Microbiol 41:5699–5708

    Article  PubMed  PubMed Central  Google Scholar 

  23. Balážová T, Makovcová J, Šedo O, Slaný M, Faldyna M, Zdráhal Z (2014) The influence of culture conditions on the identification of Mycobacterium species by MALDI-TOF MS profiling. FEMS Microbiol Lett 353:77–84

    Article  PubMed  Google Scholar 

  24. Pai M, Minion J, Sohn H, Zwerling A, Perkins MD (2009) Novel and improved technologies for tuberculosis diagnosis: progress and challenges. Clin Chest Med 30:701–716

    Article  PubMed  Google Scholar 

  25. Visconti V, La Martire G, Brunetti G, Ghezzi MC, Venditti M, Raponi G (2016) Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assay solves misidentification of rapidly growing mycobacteria. Am J Infect Control 44:614–616

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

The authors acknowledge the technical support of Gilles Liotaud, Juline Collin and Céline Perreal in their laboratory.

Author information

Authors and Affiliations

  1. Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France

    D. Zingue, C. Flaudrops & M. Drancourt

Authors
  1. D. Zingue
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. C. Flaudrops
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. Drancourt
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to M. Drancourt.

Ethics declarations

Funding

This study was supported by IHU Méditerranée Infection, Marseille, France.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures in this study involving human participants were in accordance with the ethical standards of the institutional research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethic standards.

Informed consent

Not applicable.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zingue, D., Flaudrops, C. & Drancourt, M. Direct matrix-assisted laser desorption ionisation time-of-flight mass spectrometry identification of mycobacteria from colonies. Eur J Clin Microbiol Infect Dis 35, 1983–1987 (2016). https://doi.org/10.1007/s10096-016-2750-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10096-016-2750-5

Keywords

Search

Navigation