Journal article
Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries
Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark1
Experimental Zooprophylactic Institute of Lazio and Toscana2
Ghent University3
University of Veterinary Medicine Hannover, Foundation4
National Veterinary Research Institute5
National Diagnostic and Research Veterinary Medical Institute6
SAFOSO7
Department of Bio and Health Informatics, Technical University of Denmark8
Genomic Epidemiology, Department of Bio and Health Informatics, Technical University of Denmark9
EFFORT Group10
National Food Institute, Technical University of Denmark11
Technical University of Denmark12
Utrecht University13
Intomics A/S14
Wageningen University & Research15
University of Geneva16
Complutense University17
Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail18
...and 8 moreAntimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. The use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock and in humans. We quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, sequencing more than 5,000 Gb of DNA using shotgun metagenomics.
We quantified acquired AMR using the ResFinder database and a second database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than in poultry.
We found higher AMR loads in pigs, whereas poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and between countries. We found that the total acquired AMR level was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes.
However, functionally determined AMR genes were not associated with total drug use.
Language: | English |
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Publisher: | Nature Publishing Group UK |
Year: | 2018 |
Pages: | 898-908 |
ISSN: | 20585276 |
Types: | Journal article |
DOI: | 10.1038/s41564-018-0192-9 |
ORCIDs: | Munk, Patrick , Knudsen, Berith Elkær , Duarte, Ana Sofia Ribeiro , Petersen, Thomas Nordahl , Lund, Ole , Hald, Tine , Pamp, Sünje Johanna , Vigre, Håkan , Møller Aarestrup, Frank and 0000-0002-6586-717X |