title: Application of whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry for rapid identification and clustering analysis of pantoea species.
abstract: Pantoea agglomerans is an ecologically diverse taxon that includes commercially important plant-beneficial strains and opportunistic clinical isolates. Standard biochemical identification methods in diagnostic laboratories were repeatedly shown to run into false-positive identifications of P. agglomerans, a fact which is also reflected by the high number of 16S rRNA gene sequences in public databases that are incorrectly assigned to this species. More reliable methods for rapid identification are required to ascertain the prevalence of this species in clinical samples and to evaluate the biosafety of beneficial isolates. Whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) methods and reference spectra (SuperSpectrum) were developed for accurate identification of P. agglomerans and related bacteria and used to detect differences in the protein profile within variants of the same strain, including a ribosomal point mutation conferring streptomycin resistance. MALDI-TOF MS-based clustering was shown to generally agree with classification based on gyrB sequencing, allowing rapid and reliable identification at the species level.
authors.affiliation: Agroscope Changins-Wädenswil ACW, Postfach, Schloss, CH-8820 Wädenswil, Switzerland.
authors.forename: Fabio
authors.initials: F
authors.lastname: Rezzonico
authors.forename: Guido
authors.initials: G
authors.lastname: Vogel
authors.forename: Brion
authors.initials: B
authors.lastname: Duffy
authors.forename: Mauro
authors.initials: M
authors.lastname: Tonolla
mesh_terms: D015373:Bacterial Typing Techniques; D016000:Cluster Analysis; D027081:DNA Gyrase / Q000235:genetics; D008969:Molecular Sequence Data; D020636:Pantoea / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D013997:Time Factors
chemical_list: D027081:DNA Gyrase
references.citation: Acta Pathol Microbiol Immunol Scand B. 1986 Aug;94(4):205-13
references.pmid: 3751575
references.citation: FEMS Microbiol Lett. 2010 Jul 1;308(1):48-54
references.pmid: 20487014
references.citation: Appl Environ Microbiol. 2001 Jan;67(1):284-92
references.pmid: 11133457
references.citation: Int J Syst Bacteriol. 1999 Apr;49 Pt 2:377-83
references.pmid: 10319458
references.citation: Phytopathology. 2000 Apr;90(4):368-75
references.pmid: 18944586
references.citation: J Clin Microbiol. 1997 Dec;35(12):3269-73
references.pmid: 9399532
references.citation: J Bacteriol. 1992 May;174(9):2785-96
references.pmid: 1314801
references.citation: Extremophiles. 2004 Aug;8(4):259-68
references.pmid: 15042434
references.citation: Phytopathology. 2008 Oct;98(10):1136-43
references.pmid: 18943460
references.citation: J Clin Microbiol. 2006 Mar;44(3):928-33
references.pmid: 16517878
references.citation: Rapid Commun Mass Spectrom. 2004;18(18):2013-9
references.pmid: 15378711
references.citation: Int J Syst Bacteriol. 1997 Oct;47(4):1061-7
references.pmid: 9336906
references.citation: Appl Environ Microbiol. 1998 May;64(5):1837-44
references.pmid: 9572960
references.citation: Int J Syst Bacteriol. 1990 Oct;40(4):379-83
references.pmid: 2275853
references.citation: J Virol Methods. 2000 Mar;85(1-2):93-9
references.pmid: 10716342
references.citation: Rapid Commun Mass Spectrom. 2005;19(11):1454-60
references.pmid: 15880621
references.citation: J Clin Microbiol. 2009 Sep;47(9):2912-7
references.pmid: 19571014
references.citation: Int J Syst Evol Microbiol. 2010 Mar;60(Pt 3):484-494
references.pmid: 19654354
references.citation: J Clin Microbiol. 1993 Dec;31(12):3165-9
references.pmid: 8308108
references.citation: Anal Chem. 2001 Feb 15;73(4):746-50
references.pmid: 11248887
references.citation: Int J Syst Evol Microbiol. 2002 Mar;52(Pt 2):531-47
references.pmid: 11931166
references.citation: J Clin Microbiol. 2007 Jun;45(6):1989-92
references.pmid: 17442803
references.citation: BMC Microbiol. 2009 Sep 22;9:204
references.pmid: 19772624
references.citation: Orthopedics. 1988 Mar;11(3):465-7
references.pmid: 3368414
references.citation: Mass Spectrom Rev. 2001 Jul-Aug;20(4):172-94
references.pmid: 11835305
references.citation: J Appl Microbiol. 2002;92(2):247-55
references.pmid: 11849352
references.citation: Appl Environ Microbiol. 2008 Sep;74(17):5402-7
references.pmid: 18606788
references.citation: Mol Plant Pathol. 2003 Sep 1;4(5):307-14
references.pmid: 20569391
references.citation: J Clin Microbiol. 2006 Oct;44(10):3506-9
references.pmid: 17021074
references.citation: J Appl Microbiol. 2007 Jan;102(1):134-43
references.pmid: 17184328
references.citation: Annu Rev Phytopathol. 1998;36:227-48
references.pmid: 15012499
references.citation: Syst Appl Microbiol. 2007 Jul;30(5):413-7
references.pmid: 17321713
references.citation: Mol Biol Evol. 2007 Aug;24(8):1596-9
references.pmid: 17488738
references.citation: Appl Environ Microbiol. 2008 Dec;74(24):7767-78
references.pmid: 18952875
references.citation: Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8596-601
references.pmid: 9671723
references.citation: Int J Hyg Environ Health. 2008 Jul;211(3-4):374-84
references.pmid: 17870668
references.citation: Jpn J Infect Dis. 2006 Apr;59(2):120-1
references.pmid: 16632913
references.citation: J Clin Microbiol. 2000 Jan;38(1):460-1
references.pmid: 10618144
references.citation: Int J Food Microbiol. 2003 Jul 15;84(1):93-104
references.pmid: 12781959
references.citation: Int J Syst Evol Microbiol. 2010 Oct;60(Pt 10):2430-2440
references.pmid: 19946052
references.citation: Syst Appl Microbiol. 2008 Dec;31(6-8):447-60
references.pmid: 19008066
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: Int J Syst Evol Microbiol. 2009 Sep;59(Pt 9):2339-45
references.pmid: 19620357