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

An Author Correction to this article was published on 21 August 2018


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.

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Fig. 1: Overview of AMR abundance and composition.
Fig. 2: Resistome clustering is influenced by both host animal and country.
Fig. 3: AMR genes differ in abundance between countries.
Fig. 4: Resistome alpha diversity and richness differ between animal host and countries.
Fig. 5: Taxonomic variation explains resistome variation.
Fig. 6: National veterinary AMU is associated with total metagenomic AMR.


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We thank all of the anonymous pig and poultry herd owners who agreed to participate in the study and especially everyone involved in sampling and laboratory work: M. Schlepers (Belgium); T. Ivanova, N. Cholakov, E. Gurova-Mehmedova and K. Penchev (Bulgaria); F. Nienhaus (Germany); C. L. Nielsen, P. Ryt-Hansen, B. Hølstad, B. Rasmussen and K. Nielsen (Denmark); C. Jenna, D. Virginie, E. Florent, E. Eric, S. Le Bouquin, L. Denis and T. Rodolphe (France); M. Gherpelli, M. Pegoraro and V. Carfora (Italy); D. de Vries (the Netherlands); B. Gawlik, D. Krasucka and A. Hoszowski (Poland). The EFFORT project ( and the work presented here is supported by the European Union, FP7-KBBE-2013-7, grant agreement 613754.

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Authors and Affiliations




F.M.A., D.H., J.A.W., T.H., D.M. and the EFFORT group designed the study. F.M.A. and B.E.K. detailed the sampling and sequencing. A.S.R.D. and the EFFORT group carried out the sampling. B.E.K. and S.J.P. conducted the DNA purification and, with P.M., organized the sequencing. R.B.H., O.Lund. and T.N.P. created the read-mapping pipeline. E.R. created the FRD. P.M., O.Lukjacenko., R.E.C.L., L.V.G., L.A.M.S., H.S., A.B., A.D.G. and H.V. carried out the bioinformatics and statistical analysis. P.M. created the figures and drafted the manuscript. All authors helped review, edit and complete the manuscript.

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Correspondence to Frank M. Aarestrup.

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Supplementary Figures 1–17, Supplementary Table legends and Supplementary Methods.

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Munk, P., Knudsen, B.E., Lukjancenko, O. et al. Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries. Nat Microbiol 3, 898–908 (2018).

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