title: Proteomics as the final step in the functional metagenomics study of antimicrobial resistance.
abstract: The majority of clinically applied antimicrobial agents are derived from natural products generated by soil microorganisms and therefore resistance is likely to be ubiquitous in such environments. This is supported by the fact that numerous clinically important resistance mechanisms are encoded within the genomes of such bacteria. Advances in genomic sequencing have enabled the in silico identification of putative resistance genes present in these microorganisms. However, it is not sufficient to rely on the identification of putative resistance genes, we must also determine if the resultant proteins confer a resistant phenotype. This will require an analysis pipeline that extends from the extraction of environmental DNA, to the identification and analysis of potential resistance genes and their resultant proteins and phenotypes. This review focuses on the application of functional metagenomics and proteomics to study antimicrobial resistance in diverse environments.
authors.affiliation: Teagasc - Moorepark Food Research Centre , Fermoy, Ireland.
authors.forename: Fiona
authors.initials: F
authors.lastname: Fouhy
authors.affiliation: Teagasc - Moorepark Food Research Centre , Fermoy, Ireland ; Alimentary Pharmabiotic Centre , Cork, Ireland.
authors.forename: Catherine
authors.initials: C
authors.lastname: Stanton
authors.affiliation: Teagasc - Moorepark Food Research Centre , Fermoy, Ireland ; Alimentary Pharmabiotic Centre , Cork, Ireland.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Cotter
authors.affiliation: Alimentary Pharmabiotic Centre , Cork, Ireland ; School of Microbiology, University College Cork , Cork, Ireland.
authors.forename: Colin
authors.initials: C
authors.lastname: Hill
authors.affiliation: Department of Biology, National University of Ireland Maynooth , Maynooth, Ireland.
authors.forename: Fiona
authors.initials: F
authors.lastname: Walsh
keywords: antibiotic resistance; functional metagenomics; microbiology; novel mechanisms; proteins