Beyond the matrix-assisted laser desorption ionization (MALDI) biotyping workflow: In search of microorganism-specific tryptic peptides enabling discrimination of subspecies

Applied and Environmental Microbiology

Volumn 80, Issue 14, 2014, Pages 4234-4241

  Gekenidis, Maria Theresia ^a   Studer, Patrick ^a,c   Wüthrich, Simone ^b   Brunisholz, René ^b   Drissner, David ^a  

^a AGROSCOPE   (Switzerland)

^b FUNCTIONAL GENOMICS CENTER ZURICH   (Switzerland)

^c ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

IONIZATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MICROORGANISMS; MOLECULAR BIOLOGY; PEPTIDES;

ANALYSIS SOFTWARES; CLINICAL DIAGNOSTICS; FLIGHT MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION; MATRIX-ASSISTED LASER DESORPTION IONIZATION; NANO LIQUID CHROMATOGRAPHY; PHYLOGENETIC CLASSIFICATIONS; TARGETED PROTEOMICS;

LASER DIAGNOSTICS;

BACTERIUM; MATRIX; MICROORGANISM; PEPTIDE; PHYLOGENETICS; PROTEIN; SOLVENT; YEAST;

BACTERIAL PROTEIN; CULTURE MEDIUM; PEPTIDE;

BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; CULTURE MEDIUM; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PHENOTYPE; PHYLOGENY; PROCEDURES; PROTEOMICS; SALMONELLA; SPECIES DIFFERENCE;

BACTERIAL PROTEINS; BACTERIAL TYPING TECHNIQUES; CHROMATOGRAPHY, LIQUID; CULTURE MEDIA; PEPTIDES; PHENOTYPE; PHYLOGENY; PROTEOMICS; SALMONELLA; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84903126708     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00740-14     Document Type: Article

References (34)

1. Claydon MA, Davey SN, Edwards-Jones V, Gordon DB. 1996. The rapid identification of intact microorganisms using mass spectrometry. Nat. Biotechnol. 14:1584-1586. http://dx.doi.org/10.1038/nbt1196-1584.
2. Dieckmann R, Strauch E, Alter T. 2010. Rapid identification and characterization of Vibrio species using whole-cell MALDI-TOF mass spectrometry. J. Appl. Microbiol. 109:199-211. http://dx.doi.org/10.1111/j.1365-2672.2009.04647.x.
3. Fenselau C, Demirev PA. 2001. Characterization of intact microorganisms by MALDI mass spectrometry. Mass Spectrom. Rev. 20:157-171. http://dx.doi.org/10.1002/mas.10004.
4. Holland RD, Wilkes JG, Rafii F, Sutherland JB, Persons CC, Voorhees KJ, Lay JO, Jr. 1996. Rapid identification of intact whole bacteria based on spectral patterns using matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry. RapidCommun.Mass Spectrom. 10:1227-1232. http://dx.doi.org /10.1002/(SICI)1097-0231(19960731)10:10<1227::AID-RCM659>3.0.CO;2-6.
5. Krishnamurthy T, Ross PL, Rajamani U. 1996. Detection of pathogenic and non-pathogenic bacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 10:883-888. http://dx.doi.org/10.1002/(SICI)1097-0231(19960610)10:8883::AID-RCM5943.0.CO;2-V.
6. Valentine N, Wunschel S, Wunschel D, Petersen C, Wahl K. 2005. Effect of culture conditions on microorganism identification by matrixassisted laser desorption ionization mass spectrometry. Appl. Environ. Microbiol. 71:58-64. http://dx.doi.org/10.1128/AEM.71.1.58-64.2005.
7. Wunschel DS, Hill EA, McLean JS, Jarman K, Gorby YA, Valentine N, Wahl K. 2005. Effects of varied pH, growth rate and temperature using controlled fermentation and batch culture on matrix assisted laser desorption/ionization whole cell protein fingerprints. J. Microbiol. Methods 62: 259-271. http://dx.doi.org/10.1016/j.mimet.2005.04.033.
8. Wunschel SC, Jarman KH, Petersen CE, Valentine NB, Wahl KL, Schauki D, Jackman J, Nelson CP, White EV. 2005. Bacterial analysis by MALDI-TOF mass spectrometry: an inter-laboratory comparison. J. Am. Soc. Mass Spectrom. 16:456-462. http://dx.doi.org/10.1016/j.jasms.2004.12.004.
9. Kliem M, Sauer S. 2012. The essence on mass spectrometry based microbial diagnostics. Curr. Opin. Microbiol. 15:397-402. http://dx.doi.org/10.1016/j.mib.2012.02.006.
10. van Veen SQ, Claas ECJ, Kuijper EJ. 2010. High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionizationtime of flight mass spectrometry in conventional medical microbiology laboratories. J. Clin. Microbiol. 48:900-907. http://dx.doi.org/10.1128 /JCM.02071-09.
11. 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-offlight mass spectrometry. Clin. Infect. Dis. 49:543-551. http://dx.doi.org /10.1086/600885.
12. 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. 400:1905-1911. http://dx.doi.org/10.1007 /s00216-011-4877-7.
13. Cherkaoui A, Hibbs J, Emonet S, Tangomo M, Girard M, Francois P, 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. http://dx.doi.org/10.1128 /JCM.01881-09.
14. Bizzini A, Durussel C, Bille J, Greub G, Prod'hom G. 2010. 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. 48:1549-1554. http://dx.doi.org/10.1128/JCM.01794-09.
15. Croxatto A, Prod'hom G, Greub G. 2012. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol. Rev. 36:380-407. http://dx.doi.org/10.1111/j.1574-6976.2011.00298.x.
16. Sandrin TR, Goldstein JE, Schumaker S. 2013. MALDI TOF MS profiling of bacteria at the strain level: a review. Mass Spectrom. Rev. 32:188-217. http://dx.doi.org/10.1002/mas.21359.
17. López-Ferrer D, Capelo JL, Vázquez J. 2005. Ultra fast trypsin digestion of proteins by high intensity focused ultrasound. J. Proteome Res. 4:1569-1574. http://dx.doi.org/10.1021/pr050112v.
18. Sauer S, Freiwald A, Maier T, Kube M, Reinhardt R, Kostrzewa M, Geider K. 2008. Classification and identification of bacteria by mass spectrometry and computational analysis. PLoS One 3:e2843. http://dx.doi.org/10.1371/journal.pone.0002843.
19. Barbuddhe SB, Maier T, Schwarz G, Kostrzewa M, Hof H, Domann E, Chakraborty T, 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. http://dx.doi.org /10.1128/AEM.02689-07.
20. Dubois D, Leyssene D, Chacornac JP, Kostrzewa M, Schmit PO, Talon R, Bonnet R, Delmas J. 2010. Identification of a variety of Staphylococcus species by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 48:941-945. http://dx.doi.org/10.1128 /JCM.00413-09.
21. Mellmann A, Cloud J, Maier T, Keckevoet U, Ramminger I, Iwen P, Dunn J, Hall G, Wilson D, LaSala P, Kostrzewa M, Harmsen D. 2008. Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria. J. Clin. Microbiol. 46:1946-1954. http://dx.doi.org/10.1128/JCM.00157-08.
22. Wensing A, Zimmermann S, Geider K. 2010. Identification of the corn pathogen Pantoea stewartii by mass spectrometry of whole-cell extracts and its detection with novel PCR primers. Appl. Environ. Microbiol. 76: 6248-6256. http://dx.doi.org/10.1128/AEM.01032-10.
23. Ghyselinck J, Van Hoorde K, Hoste B, Heylen K, De Vos P. 2011. Evaluation of MALDI-TOF MS as a tool for high-throughput dereplication. J. Microbiol. Methods 86:327-336. http://dx.doi.org/10.1016/j.mimet.2011.06.004.
24. Pavlovic M, Huber I, Konrad R, Busch U. 2013. Application of MALDITOF MS for the identification of food borne bacteria. Open Microbiol. J. 7:135-141. http://dx.doi.org/10.2174/1874285801307010135.
25. Reich M, Bosshard PP, Stark M, Beyser K, Borgmann S. 2013. Species identification of bacteria and fungi from solid and liquid culture media by MALDI-TOF mass spectrometry. J. Bacteriol. Parasitol. http://dx.doi.org /10.4172/2155-9597.S5-002.
26. Sparbier K, Weller U, Boogen C, Kostrzewa M. 2012. Rapid detection of Salmonella sp. by means of a combination of selective enrichment broth and MALDI-TOF MS. Eur. J. Clin. Microbiol. Infect. Dis. 31:767-773. http://dx.doi.org/10.1007/s10096-011-1373-0.
27. Brankatschk K, Blom J, Goesmann A, Smits THM, Duffy B. 2011. Genome of a European fresh-vegetable food safety outbreak strain of Salmonella enterica subsp. enterica serovar Weltevreden. J. Bacteriol. 193:2066. http://dx.doi.org/10.1128/JB.00123-11.
28. Madonna AJ, Basile F, Ferrer I, Meetani MA, Rees JC, Voorhees KJ. 2000. On-probe sample pretreatment for the detection of proteins above 15 KDa from whole cell bacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 14:2220-2229. http://dx.doi.org/10.1002/1097-0231(20001215)14:23<2220 ::AID-RCM155>3.0.CO;2-4.
29. Dieckmann R, Helmuth R, Erhard M, Malorny B. 2008. Rapid classification and identification of salmonellae at the species and subspecies levels by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl. Environ. Microbiol. 74:7767-7778. http://dx.doi.org/10.1128/AEM.01402-08.
30. Dieckmann R, Malorny B. 2011. Rapid screening of epidemiologically important Salmonella enterica subsp. enterica serovars by whole-cell ma-trix-assisted laser desorption ionization-time of flight mass spectrometry. Appl. Environ. Microbiol. 77:4136-4146. http://dx.doi.org/10.1128 /AEM.02418-10.
31. Fagerquist CK, Miller WG, Harden LA, Bates AH, Vensel WH, Wang G, Mandrell RE. 2005. Genomic and proteomic identification of a DNAbinding protein used in the "fingerprinting" of Campylobacter species and strains by MALDI-TOF-MS protein biomarker analysis. Anal. Chem. 77: 4897-4907. http://dx.doi.org/10.1021/ac040193z.
32. Fagerquist CK, Bates AH, Heath S, King BC, Garbus BR, Harden LA, Miller WG. 2006. Sub-speciating Campylobacter jejuni by proteomic analysis of its protein biomarkers and their post-translational modifications. J. Proteome Res. 5:2527-2538. http://dx.doi.org/10.1021/pr050485w.
33. Fagerquist CK, Garbus BR, Miller WG, Williams KE, Yee E, Bates AH, Boyle S, Harden LA, Cooley MB, Mandrell RE. 2010. Rapid identification of protein biomarkers of Escherichia coli O157:H7 by matrix-assisted laser desorption ionization-time-of-flight-time-of-flight mass spectrometry and top-down proteomics. Anal. Chem. 82:2717-2725. http://dx.doi.org/10.1021/ac902455d.
34. Syrmis MW, Moser RJ, Whiley DM, Vaska V, Coombs GW, Nissen MD, Sloots TP, Nimmo GR. 2011. Comparison of a multiplexed MassARRAY system with real-time allele-specific PCR technology for genotyping of methicillin-resistant Staphylococcus aureus. Clin. Microbiol. Infect. 17:1804-1810. http://dx.doi.org/10.1111/j.1469-0691.2011.03521.x.