Optimization of routine identification of clinically relevant gram-negative bacteria by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry and the bruker biotyper

Journal of Clinical Microbiology

Volumn 51, Issue 5, 2013, Pages 1412-1420

  Ford, Bradley A ^a,b   Burnham, Carey Ann D ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF IOWA HOSPITALS AND CLINICS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FORMIC ACID; RNA 16S; STAINLESS STEEL; BACTERIAL DNA;

ANALYTICAL EQUIPMENT; ARTICLE; BACTERIAL GROWTH; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BIOTYPER; CLINICAL LABORATORY; CONTROLLED STUDY; CULTURE MEDIUM; DENSITY; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; INCUBATION TEMPERATURE; INTERMETHOD COMPARISON; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SMEAR; SPECIES IDENTIFICATION; CLASSIFICATION; DNA SEQUENCE; GENETICS; GRAM-NEGATIVE BACTERIAL INFECTIONS; HUMAN; ISOLATION AND PURIFICATION; MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE;

NEGIBACTERIA;

BACTERIAL TYPING TECHNIQUES; BASE SEQUENCE; DNA, BACTERIAL; GRAM-NEGATIVE BACTERIA; GRAM-NEGATIVE BACTERIAL INFECTIONS; HUMANS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84876772502     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.01803-12     Document Type: Article

References (35)

1. Beavis RC, Chait BT. 1989. Cinnamic acid derivatives as matrices for ultraviolet laser desorption mass spectrometry of proteins. Rapid Commun. Mass Spectrom. 3:432-435.
2. Lay JO, Jr. 2001. MALDI-TOF mass spectrometry of bacteria. Mass Spectrom. Rev. 20:172-194.
3. Stevenson LG, Drake SK, Murray PR. 2010. Rapid identification of bacteria in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 48: 444-447.
4. Tan KE, Ellis BC, Lee R, Stamper PD, Zhang SX, Carroll KC. 2012. Prospective evaluation of a matrix-assisted laser desorption ionizationtime of flight mass spectrometry system in a hospital clinical microbiology laboratory for identification of bacteria and yeasts: a bench-by-bench study for assessing the impact on time to identification and costeffectiveness. J. Clin. Microbiol. 50:3301-3308.
5. Alatoom AA, Cunningham SA, Ihde SM, Mandrekar J, Patel R. 2011. Comparison of direct colony method versus extraction method for identification of gram-positive cocci by use of Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 49:2868-2873.
6. McElvania TeKippe E, Shuey S, Winkler DW, Butler MA, Burnham CAD. 2013. Optimizing identification of clinically relevant Gram-positive organisms by use of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system. J. Clin. Microbiol. 51:1421-1427.
7. 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.
8. Watson ME, Jr, Estabrook MM, Burnham CAD. 2011. Catheterassociated Nocardia higoensis bacteremia in a child with acute lymphocytic leukemia. J. Clin. Microbiol. 49:469-471.
9. Clinical and Laboratory Standards Institute. 2008. Interpretive criteria for identification of bacteria and fungi by DNA target sequencing; approved guideline. CLSI document MM18-A (ISBN 1-56238-664-6). Clinical and Laboratory Standards Institute, Wayne, PA.
10. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2005. GenBank. Nucleic Acids Res. 33:D34-D38. doi:10.1093/nar/gkq1079.
11. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145. doi:10.1093/nar /gkn879.
12. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. 2006. Greengenes, a chimerachecked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:5069-5072.
13. Saffert RT, Cunningham SA, Ihde SM, Jobe KE, Mandrekar J, Patel R. 2011. Comparison of Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometer to BD Phoenix automated microbiology system for identification of gram-negative bacilli. J. Clin. Microbiol. 49:887-892.
14. Drancourt M, Bollet C, Carta A, Rousselier P. 2001. Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov. Int. J. Syst. Evol. Microbiol. 51:925-932.
15. Ferreira L, Vega S, Sánchez-Juanes F, González M, Herrero A, Muñiz MC, González-Buitrago JM, Muñoz JL. 2010. Identifying bacteria using a matrix-assisted laser desorption ionization time-of-flight (MALDITOF) mass spectrometer. Comparison with routine methods used in clinical microbiology laboratories. Enferm. Infecc. Microbiol. Clin. 28:492-497. (In Spanish.)
16. Paauw A, Caspers MPM, Schuren FHJ, Leverstein-van Hall MA, Delétoile A, Montijn RC, Verhoef J, Fluit AC. 2008. Genomic diversity within the Enterobacter cloacae complex. PLoS One 3:e3018. doi:10.1371/journal .pone.0003018.
17. Bosshard PP, Zbinden R, Abels S, Böddinghaus B, Altwegg M, Böttger EC. 2006. 16S rRNA gene sequencing versus the API 20 NE system and the VITEK 2 ID-GNB card for identification of nonfermenting Gramnegative bacteria in the clinical laboratory. J. Clin. Microbiol. 44:1359-1366.
18. Kiska DL, Kerr A, Jones MC, Caracciolo JA, Eskridge B, Jordan M, Miller S, Hughes D, King N, Gilligan PH. 1996. Accuracy of four commercial systems for identification of Burkholderia cepacia and other gram-negative nonfermenting bacilli recovered from patients with cystic fibrosis. J. Clin. Microbiol. 34:886-891.
19. Funke G, Funke-Kissling P. 2004. Evaluation of the new VITEK 2 card for identification of clinically relevant gram-negative rods. J. Clin. Microbiol. 42:4067-4071.
20. He Y, Li H, Lu X, Stratton CW, Tang YW. 2010. Mass spectrometry Biotyper system identifies enteric bacterial pathogens directly from colonies grown on selective stool culture media. J. Clin. Microbiol. 48:3888-3892.
21. Neville SA, Lecordier A, Ziochos H, Chater MJ, Gosbell IB, Maley MW, van Hal SJ. 2011. Utility of matrix-assisted laser desorption ionizationtime of flight mass spectrometry following introduction for routine laboratory bacterial identification. J. Clin. Microbiol. 49:2980-2984.
22. Marko DC, Saffert RT, Cunningham SA, Hyman J, Walsh J, Arbefeville S, Howard W, Pruessner J, Safwat N, Cockerill FR, Bossler AD, Patel R, Richter SS. 2012. Evaluation of the Bruker Biotyper and Vitek MS matrixassisted laser desorption ionization-time of flight mass spectrometry systems for identification of nonfermenting gram-negative bacilli isolated from cultures from cystic fibrosis patients. J. Clin. Microbiol. 50:2034-2039.
23. Bessède E, Angla-Gre M, Delagarde Y, Sep Hieng S, Ménard A, Mégraud F. 2010. Matrix-assisted laser-desorption/ionization biotyper: experience in the routine of a University hospital. Clin. Microbiol. Infect. 17:533-538.
24. Carbonnelle E, Grohs P, Jacquier H, Day N, Tenza S, Dewailly A, Vissouarn O, Rottman M, Herrmann JL, Podglajen I, Raskine L. 2012. Robustness of two MALDI-TOF mass spectrometry systems for bacterial identification. J. Microbiol. Methods 89:133-136.
25. Cloud JL, Harmsen D, Iwen PC, Dunn JJ, Hall G, Lasala PR, Hoggan K, Wilson D, Woods GL, Mellmann A. 2010. Comparison of traditional phenotypic identification methods with partial 5= 16S rRNA gene sequencing for species-level identification of nonfermenting Gram-negative bacilli. J. Clin. Microbiol. 48:1442-1444.
26. Anderson NW, Buchan BW, Riebe KM, Parsons LN, Gnacinski S, Ledeboer NA. 2012. Effects of solid-medium type on routine identification of bacterial isolates by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 50:1008-1013.
27. Haigh J, Degun A, Eydmann M, Millar M, Wilks M. 2011. Improved performance of bacterium and yeast identification by a commercial matrix-assisted laser desorption ionization-time of flight mass spectrometry system in the clinical microbiology laboratory. J. Clin. Microbiol. 49:3441.
28. Walker J, Fox AJ, Edwards-Jones V, Gordon DB. 2002. Intact cell mass spectrometry (ICMS) used to type methicillin-resistant Staphylococcus aureus: media effects and inter-laboratory reproducibility. J. Microbiol. Methods 48:117-126.
29. Valentine N, Wunschel S, Wunschel D, Petersen C, Wahl K. 2005. Effect of culture conditions on microorganism identification by matrix-assisted laser desorption ionization mass spectrometry. Appl. Environ. Microbiol. 71:58-64.
30. 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.
31. 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.
32. Eigner U, Holfelder M, Oberdorfer K, Betz-Wild U, Bertsch D, Fahr AM. 2009. Performance of a matrix-assisted laser desorption ionizationtime-of-flight mass spectrometry system for the identification of bacterial isolates in the clinical routine laboratory. Clin. Lab. 55:289-296.
33. Peng J, Yang J, Jin Q. 2009. The molecular evolutionary history of Shigella spp. and enteroinvasive Escherichia coli. Infect. Genet. Evol. 9:147-152.
34. Desai AP, Stanley T, Atuan M, McKey J, Lipuma JJ, Rogers B, Jerris R. 2012. Use of matrix assisted laser desorption ionisation-time of flight mass spectrometry in a paediatric clinical laboratory for identification of bacteria commonly isolated from cystic fibrosis patients. J. Clin. Pathol. 65: 835-838.
35. Valenza G, Ruoff C, Vogel U, Frosch M, Abele-Horn M. 2007. Microbiological evaluation of the new VITEK 2 Neisseria-Haemophilus identification card. J. Clin. Microbiol. 45:3493-3497.