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Journal Articles Journal of Antimicrobial Chemotherapy Year : 2019

Associations between antimicrobial use and the faecal resistome on broiler farms from nine European countries

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Roosmarijn Luiken
  • Function : Author
Liese van Gompel
Patrick Munk
Steven Sarrazin
  • Function : Author
Philip Joosten
Alejandro Dorado-García
  • Function : Author
Rasmus Borup Hansen
  • Function : Author
Berith Knudsen
  • Function : Author
Jaap Wagenaar
  • Function : Author
Frank Aarestrup
  • Function : Author
Jeroen Dewulf
  • Function : Author
  • PersonId : 883535
Dik Mevius
  • Function : Author
Haitske Graveland
  • Function : Author
Alieda Vanessen
  • Function : Author
Gabriel Moyano
  • Function : Author
Pascal Sanders
Andrea Caprioli
  • Function : Author
Thomas Blaha
  • Function : Author
Katharina Wadepohl
  • Function : Author
Maximiliane Brandt
  • Function : Author
Tine Hald
  • Function : Author
Ana Sofia Ribeiro Duarte
  • Function : Author
Magdalena Skarzyńska
  • Function : Author
Magdalena Zajac
  • Function : Author
Hristo Daskalov
  • Function : Author
Helmut Saatkamp
  • Function : Author
Katharina Stärk
  • Function : Author

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.

Dates and versions

anses-02335763 , version 1 (28-10-2019)

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Roosmarijn Luiken, Liese van Gompel, Patrick Munk, Steven Sarrazin, Philip Joosten, et al.. Associations between antimicrobial use and the faecal resistome on broiler farms from nine European countries. Journal of Antimicrobial Chemotherapy, 2019, 74 (9), pp.2596-2604. ⟨10.1093/jac/dkz235⟩. ⟨anses-02335763⟩
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