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Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries.

  • Munk P Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
  • Knudsen BE Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
  • Lukjancenko O Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
  • Duarte ASR Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
  • Van Gompel L Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands.
  • Luiken REC Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands.
  • Smit LAM Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands.
  • Schmitt H Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands.
  • Garcia AD Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands.
  • Hansen RB Intomics A/S. Diplomvej 377, Kongens Lyngby, Denmark.
  • Petersen TN Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
  • Bossers A Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands.
  • Ruppé E Genomic Research Laboratory, Hôpitaux Universitaires de Genève, Geneva, Switzerland.
  • Lund O Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
  • Hald T Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
  • Pamp SJ Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
  • Vigre H Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands.
  • Heederik D Wageningen Bioveterinary Research, Lelystad, the Netherlands.
  • Wagenaar JA Wageningen Bioveterinary Research, Lelystad, the Netherlands.
  • Mevius D Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark. fmaa@food.dtu.dk.
  • Aarestrup FM
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  • 2018-07-25
Published in:
  • Nature microbiology. - 2018
Animals
Bacteria
Bacterial Proteins
Biodiversity
Chickens
Drug Resistance, Bacterial
Europe
Feces
Gene Expression Profiling
Metagenomics
Sequence Analysis, DNA
Species Specificity
Swine
English Antimicrobial 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
Open access status
green
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Persistent URL
https://sonar.ch/global/documents/170400
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