title: Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance andE. colivirulence genes in bacteriophage and prophage nucleotide sequences.
abstract: Extensive research is currently being conducted on the use of bacteriophages for applications in human medicine, agriculture and food manufacturing. However, phages are important vehicles of horisontal gene transfer and play a significant role in bacterial evolution. As a result, concern has been raised that this increased use and dissemination of phages could result in spread of deleterious genes, e.g., antibiotic resistance and virulence genes. Meanwhile, in the wake of the genomic era, several tools have been developed for characterization of bacterial genomes. Here we describe how two of these tools, ResFinder and VirulenceFinder, can be used to identify acquired antibiotic resistance and virulence genes in phage genomes of interest. The general applicability of the tools is demonstrated on data sets of 1,642 phage genomes and 1,442 predicted prophages.
authors.affiliation: Center for Biological Sequence Analysis; Department of Systems Biology; Technical University of Denmark; Lyngby, Denmark.
authors.forename: Kortine Annina
authors.initials: KA
authors.lastname: Kleinheinz
authors.affiliation: National Food Institute; Division for Epidemiology and Microbial Genomics; Technical University of Denmark; Lyngby, Denmark ; Department of Microbiology and Infection Control; Statens Serum Institut; Copenhagen, Denmark.
authors.forename: Katrine Grimstrup
authors.initials: KG
authors.lastname: Joensen
authors.affiliation: Center for Biological Sequence Analysis; Department of Systems Biology; Technical University of Denmark; Lyngby, Denmark.
authors.forename: Mette Voldby
authors.initials: MV
authors.lastname: Larsen
keywords: antibiotic resistance genes; genomics; horizontal gene transfer; lysogenic conversion; prediction; virulence genes; web-services