Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping
Journal article, 2020

Mass spectrometry (MS) and proteomics offer comprehensive characterization and identification of microorganisms and discovery of protein biomarkers that are applicable for diagnostics of infectious diseases. The use of biomarkers for diagnostics is widely applied in the clinic and the use of peptide biomarkers is increasingly being investigated for applications in the clinical laboratory. Respiratory-tract infections are a predominant cause for medical treatment, although, clinical assessments and standard clinical laboratory protocols are time-consuming and often inadequate for reliable diagnoses. Novel methods, preferably applied directly to clinical samples, excluding cultivation steps, are needed to improve diagnostics of infectious diseases, provide adequate treatment and reduce the use of antibiotics and associated development of antibiotic resistance. This study applied nano-liquid chromatography (LC) coupled with tandem MS, with a bioinformatics pipeline and an in-house database of curated high-quality reference genome sequences to identify species-unique peptides as potential biomarkers for four bacterial pathogens commonly found in respiratory tract infections (RTIs): Staphylococcus aureus; Moraxella catarrhalis; Haemophilus influenzae and Streptococcus pneumoniae. The species-unique peptides were initially identified in pure cultures of bacterial reference strains, reflecting the genomic variation in the four species and, furthermore, in clinical respiratory tract samples, without prior cultivation, elucidating proteins expressed in clinical conditions of infection. For each of the four bacterial pathogens, the peptide biomarker candidates most predominantly found in clinical samples, are presented. Data are available via ProteomeXchange with identifier PXD014522. As proof-of-principle, the most promising species-unique peptides were applied in targeted tandem MS-analyses of clinical samples and their relevance for identifications of the pathogens, i.e. proteotyping, was validated, thus demonstrating their potential as peptide biomarker candidates for diagnostics of infectious diseases.

Author

Roger Karlsson

Nanoxis Consulting AB

University of Gothenburg

Annika Thorsell

University of Gothenburg

Margarita Gomila

University of the Balearic Islands

Francisco Salva-Serra

University of the Balearic Islands

University of Gothenburg

Hedvig E. Jakobsson

University of Gothenburg

Lucia Gonzales-Siles

University of Gothenburg

Daniel Jaen-Luchoro

University of Gothenburg

Susann Skovbjerg

University of Gothenburg

Johannes Fuchs

University of Gothenburg

Anders Karlsson

Nanoxis Consulting AB

Fredrik Boulund

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

Karolinska Institutet

Anna Johnning

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

University of Gothenburg

Fraunhofer-Chalmers Centre

Erik Kristiansson

University of Gothenburg

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

Edward R. B. Moore

University of Gothenburg

Molecular and Cellular Proteomics

1535-9476 (ISSN) 1535-9484 (eISSN)

Vol. 19 3 518-528

Subject Categories

Infectious Medicine

Microbiology

Microbiology in the medical area

DOI

10.1074/mcp.RA119.001667

PubMed

31941798

More information

Latest update

4/23/2020