Validation of MALDI-TOF MS for rapid classification and identification of lactic acid bacteria, with a focus on isolates from traditional fermented foods in Northern Vietnam

Letters in Applied Microbiology

Volumn 55, Issue 4, 2012, Pages 265-273

  Doan, N T L ^a,b   Van Hoorde, K ^a,c   Cnockaert, M ^a   De Brandt, E ^a   Aerts, M ^a   Le Thanh, B ^d   Vandamme, P ^a  

^a GHENT UNIVERSITY   (Belgium)

^b VIETNAM NATIONAL UNIVERSITY OF AGRICULTURE   (Viet Nam)

^c UNIVERSITY COLLEGE GHENT   (Belgium)

^d INSTITUTE OF BIOTECHNOLOGY   (Viet Nam)

Author keywords

Lactic acid bacteria; MALDI TOF MS; Nem chua; pheS analysis; Protein profiling

Indexed keywords

CLUSTER ANALYSIS; COST EFFECTIVENESS; INDUCTIVELY COUPLED PLASMA; LABORATORIES; LACTIC ACID;

CLASSIFICATION AND IDENTIFICATIONS; DENDROGRAMS; LACTIC ACID BACTERIA; MALDI TOF MS; MALDI-TOF; NEM CHUUM; PHE ANALYSE; PROTEIN PROFILING; TRADITIONAL FERMENTED FOODS; VIET NAM;

BACTERIA;

PHENYLALANINE TRANSFER RNA LIGASE;

BACTERIOLOGY; BACTERIUM; BIOTECHNOLOGY; CLASSIFICATION; CLUSTER ANALYSIS; COST-BENEFIT ANALYSIS; FERMENTATION; FOOD PROCESSING; HETEROGENEITY; IDENTIFICATION METHOD; MEAT; POLYMERASE CHAIN REACTION; PROTEIN;

ARTICLE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CLUSTER ANALYSIS; CONTROLLED STUDY; DNA FINGERPRINTING; FERMENTED PRODUCT; GENE SEQUENCE; LACTIC ACID BACTERIUM; LACTOBACILLUS; LACTOBACILLUS ACIDIPISCIS; LACTOBACILLUS PARACASEI; LACTOBACILLUS ROSSIAE; LACTOCOCCUS LACTIS; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MICROBIAL DIVERSITY; MUSTARD; NONHUMAN; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; PROTEIN POLYMORPHISM; RELIABILITY; SPECIES COMPARISON; VALIDATION PROCESS; VIET NAM; WEISSELLA; WEISSELLA PARAMESENTEROIDES;

VIET NAM;

EID: 84866154904     PISSN: 02668254     EISSN: 1472765X     Source Type: Journal    
DOI: 10.1111/j.1472-765X.2012.03287.x     Document Type: Article

References (30)

1. Barbuddhe, S.B., Maier, T., Schwarz, G., Kostrzewa, M., Hof, H., Domann, E., Chakraborty, T. and Hain, T. (2008) Rapid identification and typing of Listeria species by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 74, 5402-5407.
2. Ben Amor, K., Vaughan, E.E. and de Vos, W.M. (2007) Advanced molecular tools for the identification of lactic acid bacteria. J Nutr 137, 741S-747S.
3. Bizzini, A. and Greub, G. (2010) Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolution in clinical microbial identification. Clin Microbiol Infect 16, 1614-1619.
4. Cain, T.C., Lubman, D.M., Weber, W.J. and Vertes, A. (1994) Differentiation of bacteria using protein profiles from matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 8, 1026-1030.
5. Carson, C.A., Shear, B.L., Ellersieck, M.R. and Schnell, J.D. (2003) Comparison of ribotyping and repetitive extragenic palindromic-PCR for identification of fecal Escherichia coli from humans and animals. Appl Environ Microbiol 69, 1836-1839.
6. Cherkaoui, A., Hibbs, J., Emonet, S., Tangomo, M., Girard, M., Francois, P. and Schrenzel, J. (2010) 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. J Clin Microbiol 48, 1169-1175.
7. Christner, M., Rohde, H., Wolters, M., Sobottka, I., Wegscheider, K. and Aepfelbacher, M. (2010) 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 48, 1584-1591.
8. Cocolin, L., Rantsiou, K., Iacumin, L., Urso, R., Cantoni, C. and Comi, G. (2004) Study of the ecology of fresh sausages and characterization of populations of lactic acid bacteria by molecular methods. Appl Environ Microbiol 70, 1883-1894.
9. Cocolin, L., Dolci, P. and Rantsiou, K. (2008) Molecular methods for identification of microorganisms in traditional meat products. In Meat Biotechnology ed. Toldrá, F. pp. 91-127. New York: Springer.
10. Comi, G., Urso, R., Iacumin, L., Rantsiou, K., Cattaneo, P., Cantoni, C. and Cocolin, L. (2005) Characterisation of naturally fermented sausages produced in the North East of Italy. Meat Sci 69, 381-392.
11. De Bruyne, K., Schillinger, U., Caroline, L., Boehringer, B., Cleenwerck, I., Vancanneyt, M., De Vuyst, L., Franz, C.M.A.P. et al. (2007) Leuconostoc holzapfelii sp. nov., isolated from Ethiopian coffee fermentation and assessment of sequence analysis of housekeeping genes for delineation of Leuconostoc species. Int J Syst Evol Micr 57, 2952-2959.
12. De Bruyne, K., Slabbinck, B., Waegeman, W., Vauterin, P., De Baets, B. and Vandamme, P. (2011) Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning. Syst Appl Microbiol 34, 20-29.
13. Freiwald, A. and Sauer, S. (2009) Phylogenetic classification and identification of bacteria by mass spectrometry. Nat Protoc 4, 732-742.
14. Gevers, D., Huys, G. and Swings, J. (2001) Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol Lett 205, 31-36.
15. Ghyselinck, J., Van Hoorde, K., Hoste, B., Heylen, K. and De Vos, P. (2011) Evaluation of MALDI-TOF MS as a tool for high-throughput dereplication. J Microbiol Methods 86, 327-336.
16. Gilson, E., Clement, J.-M., Brutlag, D. and Hofnung, M. (1984) A family of dispersed repetitive extragenic palindromic DNA sequences in E.coli. EMBO J 3, 1417-1421.
17. Healy, M., Huong, J., Bittner, T., Lising, M., Frye, S., Raza, S., Schrock, R., Manry, J. et al. (2005) Microbial DNA typing by automated repetitive-sequence-based PCR. J Clin Microbiol 43, 199-207.
18. Ishii, S. and Sadowsky, M.J. (2009) Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution. Environ Microbiol 11, 733-740.
19. Johnson, J.R. and Clabots, C. (2000) Improved repetitive-element PCR fingerprinting of Salmonella enterica with the use of extremely elevated annealing temperatures. Clin Diagn Lab Immunol 7, 258-264.
20. Lay, J.O. and Holland, R.D. (2000) Rapid identification of bacteria based on spectral patterns using MALDI-TOF MS. In Mass Spectrometry of Proteins and Peptid ed. Chapman, J.R. pp. 461-487. New York, USA: Humana Press Inc.
21. Naser, S.M., Thompson, F.L., Hoste, B., Gevers, D., Dawyndt, P., Vancanneyt, M. and Swings, J. (2005) Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology 151, 2141-2150.
22. 5-PCR fingerprinting. Appl Environ Microbiol 73, 7128-7137.
23. Sato, H., Yanagida, F., Shinohara, T. and Yokotsuka, K. (2000) Restriction fragment length polymorphism analysis of 16S rRNA genes in lactic acid bacteria isolated from red wine. J Biosci Bioeng 90, 335-337.
24. Scheirlinck, I., Van der Meulen, R., Van Schoor, A., Vancanneyt, M., De Vuyst, L., Vandamme, P. and Huys, G. (2007) Influence of geographical origin and flour type on diversity of lactic acid bacteria in traditional Belgian sourdoughs. Appl Environ Microbiol 73, 6262-6269.
25. Schlegel, L., Grimont, F., Collins, M.D., Regnault, B., Grimont, P.A. and Bouvet, A. (2000) Streptococcus infantarius sp. nov., Streptococcus infantarius subsp. infantarius subsp. nov. and Streptococcus infantarius subsp. coli subsp. nov., isolated from humans and food. Int J Syst Evol Micr 50, 1425-1434.
26. 5-PCR for identification of Enterococcus spp. FEMS Microbiol Lett 247, 59-63.
27. Tanigawa, K., Kawabata, H. and Watanabe, K. (2010) Identification and typing of Lactococcus lactis by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 76, 4055-4062.
28. Tran, K.T.M., May, B.K., Smooker, P.M., Van, T.T.H. and Coloe, P.J. (2011) Distribution and genetic diversity of lactic acid bacteria from traditional fermented sausage. Food Res Int 44, 338-344.
29. Van Hoorde, K., Verstraete, T., Vandamme, P. and Huys, G. (2008) Diversity of lactic acid bacteria in two Flemish artisan raw milk Gouda-type cheeses. Food Microbiol 25, 929-935.
30. Wieser, M. and Busse, H. (2000) Rapid identification of Staphylococcus epidermidis. Int J Syst Evol Micr 50, 1087-1093.