title: The Resistome: A Comprehensive Database of Escherichia coli Resistance Phenotypes.
abstract: The microbial ability to resist stressful environmental conditions and chemical inhibitors is of great industrial and medical interest. Much of the data related to mutation-based stress resistance, however, is scattered through the academic literature, making it difficult to apply systematic analyses to this wealth of information. To address this issue, we introduce the Resistome database: a literature-curated collection of Escherichia coli genotypes-phenotypes containing over 5,000 mutants that resist hundreds of compounds and environmental conditions. We use the Resistome to understand our current state of knowledge regarding resistance and to detect potential synergy or antagonism between resistance phenotypes. Our data set represents one of the most comprehensive collections of genomic data related to resistance currently available. Future development will focus on the construction of a combined genomic-transcriptomic-proteomic framework for understanding E. coli's resistance biology. The Resistome can be downloaded at https://bitbucket.org/jdwinkler/resistome_release/overview .
authors.affiliation: Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80303, United States.
authors.forename: James D
authors.initials: JD
authors.lastname: Winkler
authors.affiliation: Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80303, United States.
authors.forename: Andrea L
authors.initials: AL
authors.lastname: Halweg-Edwards
authors.affiliation: Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80303, United States.
authors.forename: Keesha E
authors.initials: KE
authors.lastname: Erickson
authors.affiliation: Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80303, United States.
authors.forename: Alaksh
authors.initials: A
authors.lastname: Choudhury
authors.affiliation: Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80303, United States.
authors.forename: Gur
authors.initials: G
authors.lastname: Pines
authors.affiliation: Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80303, United States.
authors.forename: Ryan T
authors.initials: RT
authors.lastname: Gill
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics / Q000502:physiology; D016208:Databases, Factual; D024881:Drug Resistance, Bacterial; D004843:Epistasis, Genetic; D004926:Escherichia coli / Q000235:genetics / Q000502:physiology; D005838:Genotype; D000069550:Machine Learning; D009154:Mutation; D009997:Osmotic Pressure; D010641:Phenotype
keywords: adaptive evolution; genomics; standardization; synthetic biology