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

Patrick Munk, Berith Elkær Knudsen, Oksana Lukjacenko, Ana Sofia Ribeiro Duarte, Liese Van Gompel, Roosmarijn E.C. Luiken, Lidwien A.M. Smit, Heike Schmitt, Alejandro Dorado Garcia, Rasmus Borup Hansen, Thomas Nordahl Petersen, Alex Bossers, Etienne Ruppé, Haitske Graveland, Alieda van Essen, Bruno Gonzalez-Zorn, Gabriel Moyano, Pascal Sanders, Claire Chauvin, Julie DavidAntonio Battisti, Andrea Caprioli, Jeroen Dewulf, Thomas Blaha, Katharina Wadepohl, Maximiliane Brandt, Dariusz Wasyl, Magdalena Skarzyńska, Magdalena Zajac, Hristo Daskalov, Helmut W. Saatkamp, Katharina D.C. Stärk, Ole Lund, Tine Hald, Sünje Johanna Pamp, Håkan Vigre, Dick Heederik, Jaap A. Wagenaar, Dik Mevius, Frank M. Aarestrup*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

211 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)898-908
JournalNature Microbiology
Issue number8
Publication statusPublished - 23 Jul 2018


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