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Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics

Journal article
Authors Roger Karlsson
Lucia Gonzales-Siles
M. Gomila
A. Busquets
Francisco Salvà-Serra
Daniel Jaen-Luchoro
Hedvig E Jakobsson
A. Karlsson
Fredrik Boulund
Erik Kristiansson
Edward R.B. Moore
Published in Plos One
Volume 13
Issue 12
ISSN 1932-6203
Publication year 2018
Published at Department of Mathematical Sciences
Centre for antibiotic resistance research, CARe
Institute of Biomedicine, Department of Infectious Medicine
Language en
Links dx.doi.org/10.1371/journal.pone.020...
Keywords acinetobacter-baumannii, genomics, taxonomy, pneumoniae, annotation, resistance, influenza, parallel, insights, database
Subject categories Microbiology in the medical area, Infectious Medicine

Abstract

A range of methodologies may be used for analyzing bacteria, depending on the purpose and the level of resolution needed. The capability for recognition of species distinctions within the complex spectrum of bacterial diversity is necessary for progress in microbiological research. In clinical settings, accurate, rapid and cost-effective methods are essential for early and efficient treatment of infections. Characterization and identification of microorganisms, using, bottom-up proteomics, or "proteotyping", relies on recognition of species-unique or associated peptides, by tandem mass spectrometry analyses, dependent upon an accurate and comprehensive foundation of genome sequence data, allowing for differentiation of species, at amino acid-level resolution. In this study, the high resolution and accuracy of MS/MS-based proteotyping was demonstrated, through analyses of the three phylogenetically and taxonomically most closely-related species of the Mitis Group of the genus Streptococcus: i.e., the pathogenic species, Streptococcus pneumoniae (pneumococcus), and the commensal species, Streptococcus pseudopneumoniae and Streptococcus mitis. To achieve high accuracy, a genome sequence database used for matching peptides was created and carefully curated. Here, MS-based, bottom-up proteotyping was observed and confirmed to attain the level of resolution necessary for differentiating and identifying the most-closely related bacterial species, as demonstrated by analyses of species of the Streptococcus Mitis Group, even when S. pneumoniae were mixed with S. pseudopneumoniae and S. mitis, by matching and identifying more than 200 unique peptides for each species.

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