title: What is a resistance gene? Ranking risk in resistomes.
abstract: Metagenomic studies have shown that antibiotic resistance genes are ubiquitous in the environment, which has led to the suggestion that there is a high risk that these genes will spread to bacteria that cause human infections. If this is true, estimating the real risk of dissemination of resistance genes from environmental reservoirs to human pathogens is therefore very difficult. In this Opinion article, we analyse the current definitions of antibiotic resistance and antibiotic resistance genes, and we describe the bottlenecks that affect the transfer of antibiotic resistance genes to human pathogens. We propose rules for estimating the risks associated with genes that are present in environmental resistomes by evaluating the likelihood of their introduction into human pathogens, and the consequences of such events for the treatment of infections.
authors.affiliation: Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Cantoblanco,Madrid 28049, Spain; and the Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
authors.forename: José L
authors.initials: JL
authors.lastname: Martínez
authors.affiliation: Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain; and the Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid 28034, Spain.
authors.forename: Teresa M
authors.initials: TM
authors.lastname: Coque
authors.affiliation: Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain; and the Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid 28034, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: Baquero
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001419:Bacteria / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism*; D001424:Bacterial Infections / Q000453:epidemiology / Q000382:microbiology; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D004783:Environmental Microbiology; D015964:Gene Expression Regulation, Bacterial; D022761:Gene Transfer, Horizontal; D006801:Humans
chemical_list: D000900:Anti-Bacterial Agents