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Typing and Characte...
Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics
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- Boulund, Fredrik, 1985 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,Department of Mathematical Sciences,University of Gothenburg,Chalmers tekniska högskola,Chalmers University of Technology
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- Karlsson, Roger, 1975 (author)
- Sahlgrenska universitetssjukhuset,Sahlgrenska University Hospital,Göteborgs universitet,University of Gothenburg
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- Gonzales-Siles, L. (author)
- Göteborgs universitet,University of Gothenburg
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- Johnning, Anna, 1985 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,Department of Mathematical Sciences,Chalmers tekniska högskola,Chalmers University of Technology,University of Gothenburg
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- Karami, N. (author)
- Göteborgs universitet,University of Gothenburg
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- Al-Bayati, O. (author)
- Sahlgrenska universitetssjukhuset,Sahlgrenska University Hospital
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- Ahren, C. (author)
- Göteborgs universitet,University of Gothenburg
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- Moore, Edward R.B. 1954 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,Department of Mathematical Sciences,Sahlgrenska universitetssjukhuset,Sahlgrenska University Hospital,University of Gothenburg
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- Kristiansson, Erik, 1978 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,Department of Mathematical Sciences,University of Gothenburg,Chalmers tekniska högskola,Chalmers University of Technology
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(creator_code:org_t)
- 2017
- 2017
- English.
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In: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 16:6, s. 1052-1063
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Abstract
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- Methods for rapid and reliable microbial identification are essential in modern healthcare. The ability to detect and correctly identify pathogenic species and their resistance phenotype is necessary for accurate diagnosis and efficient treatment of infectious diseases. Bottom-up tandem mass spectrometry (MS) proteomics enables rapid characterization of large parts of the expressed genes of microorganisms. However, the generated data are highly fragmented, making downstream analyses complex. Here we present TCUP, a new computational method for typing and characterizing bacteria using proteomics data from bottom-up tandem MS. TCUP compares the generated protein sequence data to reference databases and automatically finds peptides suitable for characterization of taxonomic composition and identification of expressed antimicrobial resistance genes. TCUP was evaluated using several clinically relevant bacterial species (Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae), using both simulated data generated by in silico peptide digestion and experimental proteomics data generated by liquid chromatography-tandem mass spectrometry (MS/MS). The results showed that TCUP performs correct peptide classifications at rates between 90.3 and 98.5% at the species level. The method was also able to estimate the relative abundances of individual species in mixed cultures. Furthermore, TCUP could identify expressed beta-lactamases in an extended spectrum beta-lactamase-producing (ESBL) E.coli strain, even when the strain was cultivated in the absence of antibiotics. Finally, TCUP is computationally efficient, easy to integrate in existing bioinformatics workflows, and freely available under an open source license for both Windows and Linux environments.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine (hsv//eng)
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
Keyword
- searching sequence databases
- antimicrobial resistance
- pseudomonas-aeruginosa
- escherichia-coli
- protein database
- identification
- classification
- spectra
- genomes
- genes
- Biochemistry & Molecular Biology
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Boulund, Fredrik ...
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Karlsson, Roger, ...
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Gonzales-Siles, ...
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Johnning, Anna, ...
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Karami, N.
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Al-Bayati, O.
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show more...
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Ahren, C.
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Moore, Edward R. ...
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Kristiansson, Er ...
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- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Microbiology
- Articles in the publication
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Molecular & Cell ...
- By the university
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University of Gothenburg
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Chalmers University of Technology