title: FARME DB: a functional antibiotic resistance element database.
abstract: Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria. In addition, existing AR databases provide no information about flanking sequences containing regulatory or mobile genetic elements. To help address this issue, we created an annotated database of DNA and protein sequences derived exclusively from environmental metagenomic sequences showing AR in laboratory experiments. Our Functional Antibiotic Resistant Metagenomic Element (FARME) database is a compilation of publically available DNA sequences and predicted protein sequences conferring AR as well as regulatory elements, mobile genetic elements and predicted proteins flanking antibiotic resistant genes. FARME is the first database to focus on functional metagenomic AR gene elements and provides a resource to better understand AR in the 99% of bacteria which cannot be cultured and the relationship between environmental AR sequences and antibiotic resistant genes derived from cultured isolates.Database URL: http://staff.washington.edu/jwallace/farme.
authors.affiliation: Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA.
authors.forename: James C
authors.initials: JC
authors.lastname: Wallace
authors.affiliation: Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA.
authors.forename: Jesse A
authors.initials: JA
authors.lastname: Port
authors.affiliation: Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA.
authors.forename: Marissa N
authors.initials: MN
authors.lastname: Smith
authors.affiliation: Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA.
authors.forename: Elaine M
authors.initials: EM
authors.lastname: Faustman
mesh_terms: D000900:Anti-Bacterial Agents; D001419:Bacteria / Q000235:genetics*; D030561:Databases, Nucleic Acid; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D054892:Metagenome
chemical_list: D000900:Anti-Bacterial Agents