Advertisement

Application of MALDI Biotyper System for Rapid Identification of Bacteria Isolated from a Fresh Produce Market

  • Israa Mohamad El-Nemr
  • Mohanad Mushtaha
  • Sathyavathi Sundararaju
  • Charmaine Fontejon
  • Mohammed Suleiman
  • Patrick Tang
  • Ipek Goktepe
  • Mohammad Rubayet HasanEmail author
Article
  • 63 Downloads

Abstract

MALDI-TOF MS has revolutionized the identification of microorganisms and has become an indispensable part of routine diagnostics in the clinical microbiological laboratory. However, application of this technique in microbial surveillance outside of clinical settings is limited. In this study, we have evaluated the performance of a Bruker MALDI Biotyper System for the identification of bacteria isolated from the hand palms of fresh produce handlers and their surrounding environments in a wholesale fresh produce market in Doha, Qatar. The accuracy was verified against the results obtained by bacterial 16S rRNA gene sequencing. A total of 105 isolates were tested, of which 67 (64%) isolates were identified by MALDI-TOF MS and 101 isolates (96%) were identified by 16S rRNA gene sequencing, either at the genus level or species level. However, MALDI-TOF MS identified more isolates (41%) at the species level than 16S rRNA gene sequencing (28%). MALDI-TOF MS was particularly useful in the species level identification of Enterobacteriaceae. MALDI-TOF MS successfully identified most known human pathogens in a rapid and cost-effective manner but failed to identify a significant number of isolates that were of environmental origin, suggesting room for further expansion of the reference database.

Notes

Acknowledgements

This study was partly supported by a GSRA Grant # (GSRA2-1-0615-14038) from the Qatar National Research Fund (a member of Qatar foundation) and Qatar University Student Grant (QUST-CAS-SPR-2017-12). We gratefully acknowledge the technical support from the Microbiology and Pathology Sciences Laboratories of Sidra Medicine and Center for Sustainable Development Laboratory of Qatar University.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical Approval

Produce handler’s hand swab samples were collected as per the protocols approved by Qatar University’s Institutional Review Board (QU-IRB) (No. QU-IRB 509-E/15).

Informed Consent

Written informed consent was obtained from all study participants in a form approved by QU-IRB.

Supplementary material

284_2018_1624_MOESM1_ESM.docx (26 kb)
Supplementary material 1 (DOCX 25 KB)

References

  1. 1.
    Croxatto A, Prod’hom G, Greub G (2012) Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev 36(2):380–407CrossRefGoogle Scholar
  2. 2.
    Anhalt JP, Fenselau C (1975) Identification of bacteria using mass spectrometry. Anal Chem 47:219–225CrossRefGoogle Scholar
  3. 3.
    Jang KS, Kim YH (2018) Rapid and robust MALDI-TOF MS techniques for microbial identification: a brief overview of their diverse applications. J Microbiol 56(4):209–216CrossRefGoogle Scholar
  4. 4.
    Giebel R, Worden C, Rust SM, Kleinheinz GT, Robbins M, Sandrin TR (2010) Microbial fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) applications and challenges. Adv Appl Microbiol 71:149–184CrossRefGoogle Scholar
  5. 5.
    French K, Evans J, Tanner H, Gossain S, Hussain A (2016) The clinical impact of rapid, direct MALDI-ToF identification of bacteria from positive blood cultures. PLoS ONE 11(12):e0169332CrossRefGoogle Scholar
  6. 6.
    Vlek AL, Bonten MJ, Boel CH (2012) Direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry improves appropriateness of antibiotic treatment of bacteremia. PLoS ONE 7(3):e32589CrossRefGoogle Scholar
  7. 7.
    Scott JS, Sterling SA, To H, Seals SR, Jones AE (2016) Diagnostic performance of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry in blood bacterial infections: a systematic review and meta-analysis. Infect Dis 48(7):530–536CrossRefGoogle Scholar
  8. 8.
    Wilson DA, Young S, Timm K, Novak-Weekley S, Marlowe EM, Madisen N, Lillie JL, Ledeboer NA, Smith R, Hyke J et al (2017) Multicenter evaluation of the bruker MALDI biotyper CA system for the identification of clinically important bacteria and yeasts. Am J Clin Pathol 147(6):623–631CrossRefGoogle Scholar
  9. 9.
    Cao Y, Wang L, Ma P, Fan W, Gu B, Ju S (2018) Accuracy of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of mycobacteria: a systematic review and meta-analysis. Sci Rep 8(1):4131CrossRefGoogle Scholar
  10. 10.
    Gosselin VB, Lovstad J, Dufour S, Adkins PRF, Middleton JR (2018) Use of MALDI-TOF to characterize staphylococcal intramammary infections in dairy goats. J Dairy Sci 101(7):6262–6270CrossRefGoogle Scholar
  11. 11.
    Lawton SJ, Weis AM, Byrne BA, Fritz H, Taff CC, Townsend AK, Weimer BC, Mete A, Wheeler S, Boyce WM (2018) Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing. J Vet Diagn Invest 30(3):354–361CrossRefGoogle Scholar
  12. 12.
    Avanzi IR, Gracioso LH, Baltazar MD, Karolski B, Perpetuo EA, do Nascimento CA (2017) Rapid bacteria identification from environmental mining samples using MALDI-TOF MS analysis. Environ Sci Pollut Res Int 24(4):3717–3726CrossRefGoogle Scholar
  13. 13.
    Popović NT, Kazazić SP, Strunjak-Perović I, Čož-Rakovac R (2017) Differentiation of environmental aquatic bacterial isolates by MALDI-TOF MS. Environ Res 152:7–16CrossRefGoogle Scholar
  14. 14.
    Sala-Comorera L, Vilaró C, Galofré B, Blanch AR, García-Aljaro C (2016) Use of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry for bacterial monitoring in routine analysis at a drinking water treatment plant. Int J Hyg Environ Health 219(7 Pt A):577–584CrossRefGoogle Scholar
  15. 15.
    Böhme K, Fernández-No IC, Barros-Velázquez J, Gallardo JM, Cañas B, Calo-Mata P (2011) Rapid species identification of seafood spoilage and pathogenic Gram-positive bacteria by MALDI-TOF mass fingerprinting. Electrophoresis 32(21):2951–2965CrossRefGoogle Scholar
  16. 16.
    Timperio AM, Gorrasi S, Zolla L, Fenice M (2017) 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. PLoS ONE 12(7):e0181860CrossRefGoogle Scholar
  17. 17.
    Shin HB, Yoon J, Lee Y, Kim MS, Lee K (2015) Comparison of MALDI-TOF MS, housekeeping gene sequencing, and 16S rRNA gene sequencing for identification of Aeromonas clinical isolates. Yonsei Med J 56(2):550–555CrossRefGoogle Scholar
  18. 18.
    Böhme K, Fernández-No IC, Pazos M, Gallardo JM, Barros-Velázquez J, Cañas B, Calo-Mata P (2013) Identification and classification of seafood-borne pathogenic and spoilage bacteria: 16S rRNA sequencing versus MALDI-TOF MS fingerprinting. Electrophoresis 34(6):877–887CrossRefGoogle Scholar
  19. 19.
    Vithanage NR, Yeager TR, Jadhav SR, Palombo EA, Datta N (2014) Comparison of identification systems for psychrotrophic bacteria isolated from raw bovine milk. Int J Food Microbiol 189:26–38CrossRefGoogle Scholar
  20. 20.
    Cheng YH, Perng CL, Jian MJ, Lee SY, Sun JR, Shang HS (2018) Multicentre study evaluating matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically isolated Elizabethkingia species and analysis of antimicrobial susceptibility. Clin Microbiol Infect.  https://doi.org/10.1016/j.cmi.2018.04.015 Google Scholar
  21. 21.
    Suzuki Y, Niina K, Matsuwaki T, Nukazawa K, Iguchi A (2018) Bacterial flora analysis of coliforms in sewage, river water, and ground water using MALDI-TOF mass spectrometry. J Environ Sci Health A 53(2):160–173CrossRefGoogle Scholar
  22. 22.
    U.S. Food and Drug Administration (2017) Bacteriological analytical manual. https://www.fda.gov/Food/FoodScienceResearch/LaboratoryMethods/ucm2006949.htm Accessed 26 Nov 2017
  23. 23.
    Bruker (2016) MBT compass user manual Revision C. Bruker Daltonics, Inc., BremenGoogle Scholar
  24. 24.
    Bruker (2011) Instructions for use MALDI Biotarget 48 Revision 1. Bruker Daltonics, Inc., BremenGoogle Scholar
  25. 25.
    Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9(9):868–877CrossRefGoogle Scholar
  26. 26.
    Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefGoogle Scholar
  27. 27.
    CLSI (2008) Interpretive criteria for identification of bacteria and fungi by DNA target sequencing; Approved Guideline MM18-A. Clinical and Laboratory Standards Institute, WayneGoogle Scholar
  28. 28.
    Kostrzewa M (2018) Application of the MALDI Biotyper to clinical microbiology: progress and potential. Expert Rev Proteomics 15(3):193–202CrossRefGoogle Scholar
  29. 29.
  30. 30.
    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):543–551CrossRefGoogle Scholar
  31. 31.
    Sogawa K, Watanabe M, Sato K, Segawa S, Ishii C, Miyabe A, Murata S, Saito T, Nomura F (2011) Use of the MALDI BioTyper system with MALDI-TOF mass spectrometry for rapid identification of microorganisms. Anal Bioanal Chem 400(7):1905–1911CrossRefGoogle Scholar
  32. 32.
    Fan WT, Qin TT, Bi RR, Kang HQ, Ma P, Gu B (2017) Performance of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry system for rapid identification of streptococci: a review. Eur J Clin Microbiol Infect Dis 36(6):1005–1012CrossRefGoogle Scholar
  33. 33.
    Martiny D, Busson L, Wybo I, El Haj RA, Dediste A, Vandenberg O (2012) Comparison of the Microflex LT and Vitek MS systems for routine identification of bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 50(4):1313–1325CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Israa Mohamad El-Nemr
    • 1
  • Mohanad Mushtaha
    • 1
  • Sathyavathi Sundararaju
    • 2
  • Charmaine Fontejon
    • 2
  • Mohammed Suleiman
    • 2
  • Patrick Tang
    • 2
    • 3
  • Ipek Goktepe
    • 1
  • Mohammad Rubayet Hasan
    • 2
    • 3
    Email author
  1. 1.Department of Biological and Environmental Sciences, College of Arts and SciencesQatar UniversityDohaQatar
  2. 2.Department of PathologySidra MedicineDohaQatar
  3. 3.Weill Cornell Medical College in QatarDohaQatar

Personalised recommendations