Large-Scale Metagenomic-Based Study of Antibiotic Resistance in the Environment

• Published in: Current Biology
• Main Authors: Nesme, Joseph, Cecillon, Sébastien, Delmont, Tom, Monier, Jean-Michel, Vogel, Timothy, M., Simonet, Pascal
• Other Authors: Ampère, Département Bioingénierie (BioIng), Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was financed by grants from the French Agency for the Environment and Energy Management (ADEME, project Générique) and from French Agency for Food, Environmental and Occupational Health and Safety (ANSES, project Impactance, convention number EST-2012/2/28). The French Ministry of Higher Education and Research funded J.N. T.O.D. was supported by a doctoral fellowship from the Rhône Alpes Région.
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2014
• Subjects: [SDE]Environmental Sciences; permafrost
• Online Access: https://hal.science/hal-00988678; https://doi.org/10.1016/j.cub.2014.03.036

International audience Antibiotic resistance, including multiresistance acquisition and dissemination by pathogens, is a critical healthcare issue threatening our management of infectious diseases [ 1-3 ]. Rapid accumulation of resistance phenotypes implies a reservoir of transferable antibiotic resistance gene determinants (ARGDs) selected in response to inhibition of antibiotic concentrations, as found in hospitals [ 1, 3-5 ]. Antibiotic resistance genes were found in environmental isolates, soil DNA [ 4-6 ], secluded caves [ 6, 7 ], and permafrost DNA [ 7, 8 ]. Antibiotics target essential and ubiquitous cell functions, and resistance is a common characteristic of environmental bacteria [ 8-11 ]. Environmental ARGDs are an abundant reservoir of potentially transferable resistance for pathogens [ 9-12 ]. Using metagenomic sequences, we show that ARGDs can be detected in all (n = 71) environments analyzed. Soil metagenomes had the most diverse pool of ARGDs. The most common types of resistances found in environmental metagenomes were efflux pumps and genes conferring resistance to vancomycin, tetracycline, or β-lactam antibiotics used in veterinary and human healthcare. Our study describes the diverse and abundant antibiotic resistance genes in nonclinical environments and shows that these genes are not randomly distributed among different environments (e.g., soil, oceans or human feces).