title: Identification of staphylococcal species based on variations in protein sequences (mass spectrometry) and DNA sequence (sodA microarray).
abstract: This report is among the first using sequence variation in newly discovered protein markers for staphylococcal (or indeed any other bacterial) speciation. Variation, at the DNA sequence level, in the sodA gene (commonly used for staphylococcal speciation) provided excellent correlation. Relatedness among strains was also assessed using protein profiling using microcapillary electrophoresis and pulsed field electrophoresis. A total of 64 strains were analyzed including reference strains representing the 11 staphylococcal species most commonly isolated from man (Staphylococcus aureus and 10 coagulase negative species [CoNS]). Matrix assisted time of flight ionization/ionization mass spectrometry (MALDI TOF MS) and liquid chromatography-electrospray ionization tandem mass spectrometry (LC ESI MS/MS) were used for peptide analysis of proteins isolated from gel bands. Comparison of experimental spectra of unknowns versus spectra of peptides derived from reference strains allowed bacterial identification after MALDI TOF MS analysis. After LC-MS/MS analysis of gel bands bacterial speciation was performed by comparing experimental spectra versus virtual spectra using the software X!Tandem. Finally LC-MS/MS was performed on whole proteomes and data analysis also employing X!tandem. Aconitate hydratase and oxoglutarate dehydrogenase served as marker proteins on focused analysis after gel separation. Alternatively on full proteomics analysis elongation factor Tu generally provided the highest confidence in staphylococcal speciation.
authors.affiliation: Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC 29208, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Kooken
authors.forename: Karen
authors.initials: K
authors.lastname: Fox
authors.forename: Alvin
authors.initials: A
authors.lastname: Fox
authors.forename: Diego
authors.initials: D
authors.lastname: Altomare
authors.forename: Kim
authors.initials: K
authors.lastname: Creek
authors.forename: David
authors.initials: D
authors.lastname: Wunschel
authors.forename: Sara
authors.initials: S
authors.lastname: Pajares-Merino
authors.forename: Ilargi
authors.initials: I
authors.lastname: Martínez-Ballesteros
authors.forename: Javier
authors.initials: J
authors.lastname: Garaizar
authors.forename: Omar
authors.initials: O
authors.lastname: Oyarzabal
authors.forename: Mansour
authors.initials: M
authors.lastname: Samadpour
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics*; D001483:Base Sequence; D015415:Biomarkers; D002853:Chromatography, Liquid / Q000379:methods*; D014644:Genetic Variation; D006801:Humans; D008297:Male; D058889:Molecular Typing / Q000379:methods*; D010444:Peptide Elongation Factor Tu / Q000235:genetics; D010455:Peptides / Q000032:analysis; D010802:Phylogeny; D020543:Proteome; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012984:Software; D021241:Spectrometry, Mass, Electrospray Ionization; D013210:Staphylococcus / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D013482:Superoxide Dismutase / Q000737:chemistry / Q000235:genetics*; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins; D015415:Biomarkers; D010455:Peptides; D020543:Proteome; D012336:RNA, Ribosomal, 16S; C095500:SodA protein, Bacteria; D013482:Superoxide Dismutase; D010444:Peptide Elongation Factor Tu
keywords: Liquid chromatography-tandem mass spectrometry; Mass spectrometry; Peptide sequence; Soda microarray