Identification of <i>Streptococcus pneumoniae</i> <i>-</i> Specific Proteins by Surface-Shaving Proteomics

<i>Streptococcus pneumoniae</i> (pneumococcus) is a prominent cause of bacterial pneumonia, meningitis, and septicemia, causing high morbidity and high mortality, particularly in children and the elderly. In this study, proteomics- and genomics-based approaches were used for the identification of pneumococcal protein and peptide biomarkers of <i>S</i>. <i>pneumoniae</i> for diagnostics and prospective targets for treatment. Through a pan-genome analysis, 11 <i>S</i>. <i>pneumoniae</i> strains, demonstrating genetic variation within the species, were selected for proteomic characterization. Mass spectrometry-based proteomics, in combination with bacterial surface<i>-</i>shaving, were used to study the cell-surface proteome of <i>S</i>. <i>pneumoniae</i>. The data obtained from three biological replicates per strain were analyzed to identify and rank the proteins and peptides according to their presence in the strains, as well as their presence in all available <i>S</i>. <i>pneumoniae</i> proteomes (8,892) archived in public databases. Several highly ranked proteins have been described as "species-specific" for <i>S</i>. <i>pneumoniae</i> and as surface-associated virulence factors or demonstrate highly antigenic properties. Proteins (34) previously not recognized as <i>S</i>. <i>pneumoniae</i>-specific were proposed to be novel biomarkers, demonstrating high degrees of prevalence in all analyzed proteomes, with little or no sequence similarities to closely related species but common among the genetically diverse strains included in this study.