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PROTEOTYPING: Tandem Mass Spectrometry Proteomics and Whole Genome Sequence-Based Diagnostics of Infectious Bacteria is Depedent upon a Reliable and Comprehensive Systematic Framework

Conference contribution
Authors Edward R.B. Moore
Lucia Gonzales-Siles
Francisco Salvà-Serra
Hedvig E Jakobsson
Fredrik Boulund
Erik Kristiansson
Roger Karlsson
Published in Third Meeting on “Microbial Systematics and Metagenomics”. Bergey’s International Society for Microbial Systematics (BISMiS). September 12 - 15, 2016, Pune, India
Publication year 2016
Published at Department of Mathematical Sciences, Mathematical Statistics
Institute of Biomedicine, Department of Infectious Medicine
Language en
Links bismis.org/?cm=body_bismis2016
Subject categories Biological Systematics, Functional genomics, Microbiology

Abstract

The global expansion of anti-microbial resistance (AMR) in bacteria, including human pathogens, presents major challenges for treatment and preventing the spread of infection. The World Health Organisation (WHO) has predicted the advent of infectious diseases for which no antibiotic treatment will be available [1]. With this outlook in the escalation of AMR, combined with continuing decline in new antibiotic discovery, development of innovative, reliable, rapid and costefficient analytical techniques for effective diagnostics and characterisations of infectious microorganisms is increasingly essential to prevent rising mortality and to reduce the costs associated with antibiotic-resistant infections. However, the routine methodologies used today for diagnosing infectious bacteria depend upon protocols that require prior cultivation from samples. Faced with patients exhibiting symptoms of infection, physicians typically resort to prescribing broad-spectrum antibiotics while they wait days or weeks for results from the laboratory. With increasing whole-genome DNA sequence data becoming available, MS-based proteomics also have increasingly been applied to biological studies. Proteomic analyses of bacterial cells may be considered indirect analyses of the genomes of bacteria. The ‘proteome’ comprises the entire set of proteins expressed by a cell, an organism or a biological system. ‘Proteotyping’ [2], using state-ofthe-art LC-MS/MS analyses of generated cellular peptides, enables identification of the most closely related bacterial species and sub-species-level strain discrimination, AMR- and virulence-factors, from single MS analyses. Comprehensive and accurate genome sequence data is the key to obtaining accurate peptide matching and to be able to discriminate between the most closely related species. In this study, genome sequences were analysed, using Average Nucleotide Identity Blast (ANIb) and taxon-specific MLSA to assess their reliabilities. Critically, significant numbers of sequenced genomes in the public databases exhibited questionable identifications. Characterisations and identifications of responsible agents of infectious disease have relied heavily upon established systematic frameworks and the documented features of well-described microbial species. As methodologies, such as whole-genome sequencing and MS proteomics are developed to enable more comprehensive, detailed and complex analyses, comprehensive databases derived from a reliable systematic framework are essential. References [1] World Health Organization (WHO). (2014) Antimicrobial Resistance: Global Report on Surveillance. ISBN: 978-92-4-15674-8. [2] Karlsson et al. [2015) Proteotyping: Proteomic characterization, classification and identification of microorganisms – A prospectus. Syst. Appl. Microbiol. 38: 246-257.

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