1. Associations between antimicrobial use and the faecal resistome on broiler farms from nine European countries
- Author
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Luiken, Roosmarijn, van Gompel, Liese, Munk, Patrick, Sarrazin, Steven, Joosten, Philip, Dorado-García, Alejandro, Borup Hansen, Rasmus, Knudsen, Berith, Bossers, Alex, Wagenaar, Jaap, Aarestrup, Frank, Dewulf, Jeroen, Mevius, Dik, Heederik, Dick, Smit, Lidwien, Schmitt, Heike, Graveland, Haitske, Vanessen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Hald, Tine, Ribeiro Duarte, Ana Sofia, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut, Stärk, Katharina, One Health Microbieel, dI&I I&I-4, Dep IRAS, dIRAS RA-I&I RA, Part of Wageningen UR, Central Veterinary Institute, Obstetrics, Reproduction and Herd Health, Universiteit Gent = Ghent University (UGENT), Environmental and Occupational Health Group, Wageningen University and Research [Wageningen] (WUR), Division of Environmental Epidemiology [Utrecht, The Netherlands], Utrecht University [Utrecht]- Institute of Risk Assessment Sciences [Utrecht, The Netherlands] (IRAS), Institute for Risk Assessment Sciences [Utrecht, The Netherlands] (IRAS), Utrecht University [Utrecht], Facultad de Veterinaria, Dpto. de Sanidad Animal - VISAVET, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Pharmacoepidemiologie et évaluation de l'impact des produits de santé sur les populations, Université Bordeaux Segalen - Bordeaux 2-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Istituto Zooprofilattico Sperimentale del Lazio e della Toscana (IZSLT), Department of Microbiology, National Veterinary Research Institute [Pulawy, Pologne] (NVRI), European Project: 613754,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,EFFORT(2013), Universiteit Gent = Ghent University [Belgium] (UGENT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Bordeaux Segalen - Bordeaux 2-Université de Rouen Normandie (UNIROUEN), and Normandie Université (NU)-Normandie Université (NU)
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Veterinary medicine ,antibiotic resistance ,Epidemiology ,animal diseases ,Biosecurity ,Drug resistance ,veterinary drug ,antibiotique ,Anti-Infective Agents ,Risk Factors ,Pharmacology (medical) ,Veterinary drug ,bacteria ,Original Research ,agriculture ,2. Zero hunger ,bactérie ,0303 health sciences ,Lincosamides ,Microbiota ,poultry ,Bacteriologie ,Bacteriology, Host Pathogen Interaction & Diagnostics ,Antimicrobial ,usage ,médicamentvétérinaire ,Europe ,Infectious Diseases ,farm ,Microbiology (medical) ,Farms ,medicine.drug_class ,Bioinformatica & Diermodellen ,Biology ,03 medical and health sciences ,Antibiotic resistance ,Drug Resistance, Bacterial ,Bio-informatics & Animal models ,medicine ,Animals ,Life Science ,Epidemiology, Bio-informatics & Animal models ,antimicrobial resistance ,microbiologie ,030304 developmental biology ,Pharmacology ,Host Pathogen Interaction & Diagnostics ,Epidemiologie ,[SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health ,030306 microbiology ,microbiology ,Computational Biology ,Bacteriology ,antimicrobial use ,Host Pathogen Interactie & Diagnostiek ,Resistome ,volaille ,Cross-Sectional Studies ,feces ,Epidemiologie, Bioinformatica & Diermodellen ,Bacteriologie, Host Pathogen Interactie & Diagnostiek ,Flock ,Metagenomics ,antimicrobien ,Chickens - Abstract
Objectives To determine associations between farm- and flock-level antimicrobial usage (AMU), farm biosecurity status and the abundance of faecal antimicrobial resistance genes (ARGs) on broiler farms. Methods In the cross-sectional pan-European EFFORT study, conventional broiler farms were visited and faeces, AMU information and biosecurity records were collected. The resistomes of pooled faecal samples were determined by metagenomic analysis for 176 farms. A meta-analysis approach was used to relate total and class-specific ARGs (expressed as fragments per kb reference per million bacterial fragments, FPKM) to AMU (treatment incidence per DDD, TIDDDvet) per country and subsequently across all countries. In a similar way, the association between biosecurity status (Biocheck.UGent) and the resistome was explored. Results Sixty-six (38%) flocks did not report group treatments but showed a similar resistome composition and roughly similar ARG levels to antimicrobial-treated flocks. Nevertheless, we found significant positive associations between β-lactam, tetracycline, macrolide and lincosamide, trimethoprim and aminoglycoside antimicrobial flock treatments and ARG clusters conferring resistance to the same class. Similar associations were found with purchased products. In gene-level analysis for β-lactams and macrolides, lincosamides and streptogramins, a significant positive association was found with the most abundant gene clusters blaTEM and erm(B). Little evidence was found for associations with biosecurity. Conclusions The faecal microbiome in European broilers contains a high diversity of ARGs, even in the absence of current antimicrobial selection pressure. Despite this, the relative abundance of genes and the composition of the resistome is positively related to AMU in European broiler farms for several antimicrobial classes.
- Published
- 2019