Reprint of "Identification of staphylococcal species based on variations in protein sequences (mass spectrometry) and DNA sequence (sodA microarray)".
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.
Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC 29208, USA.
Jennifer
J
Kooken
Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC 29208, USA.
Karen
K
Fox
Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC 29208, USA. Electronic address: alvin.fox@uscmed.sc.edu.
Alvin
A
Fox
Department of Pharmaceutical and Biomedical Sciences, School of Pharmacy, University of South Carolina, Columbia, SC 29209, USA.
Diego
D
Altomare
Department of Pharmaceutical and Biomedical Sciences, School of Pharmacy, University of South Carolina, Columbia, SC 29209, USA.
Kim
K
Creek
Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, PO Box 999 MS P7-50, Richland, WA 99354, USA.
David
D
Wunschel
Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain.
Sara
S
Pajares-Merino
Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain.
Ilargi
I
Martínez-Ballesteros
Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz 01006, Spain.
Javier
J
Garaizar
Poultry Division, Institute for Environmental Health, Inc, 15300 Bothell Way NE, Lake Forest Park, WA 98155, USA.
Omar
O
Oyarzabal
Poultry Division, Institute for Environmental Health, Inc, 15300 Bothell Way NE, Lake Forest Park, WA 98155, USA.
Mansour
M
Samadpour
D000154:Aconitate Hydratase / Q000737:chemistry / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics*; D002853:Chromatography, Liquid; D004269:DNA, Bacterial / Q000032:analysis / Q000737:chemistry; D019143:Evolution, Molecular; D005819:Genetic Markers; D014644:Genetic Variation; D006801:Humans; D007655:Ketoglutarate Dehydrogenase Complex / Q000737:chemistry / Q000235:genetics; D008297:Male; D013058:Mass Spectrometry / Q000379:methods; D058889:Molecular Typing / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D010802:Phylogeny; D040901:Proteomics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012984:Software; D013210:Staphylococcus / Q000145:classification* / Q000235:genetics; D013482:Superoxide Dismutase / Q000737:chemistry / Q000235:genetics*
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D005819:Genetic Markers; D010455:Peptides; D012336:RNA, Ribosomal, 16S; C095500:SodA protein, Bacteria; D013482:Superoxide Dismutase; D007655:Ketoglutarate Dehydrogenase Complex; D000154:Aconitate Hydratase
Liquid chromatography-tandem mass spectrometry; Mass spectrometry; Peptide sequence; Soda microarray