Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 540570
Title Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries
Author(s) Munk, Patrick; Knudsen, Berith Elkær; Lukjacenko, Oksana; Duarte, Ana Sofia Ribeiro; Gompel, Liese Van; Luiken, Roosmarijn E.C.; Smit, Lidwien A.M.; Schmitt, Heike; Garcia, Alejandro Dorado; Hansen, Rasmus Borup; Petersen, Thomas Nordahl; Bossers, Alex; Ruppé, Etienne; Graveland, Haitske; Essen, Alieda van; Gonzalez-Zorn, Bruno; Moyano, Gabriel; Sanders, Pascal; Chauvin, Claire; David, Julie; Battisti, Antonio; Caprioli, Andrea; Dewulf, Jeroen; Blaha, Thomas; Wadepohl, Katharina; Brandt, Maximiliane; Wasyl, Dariusz; Skarzyńska, Magdalena; Zajac, Magdalena; Daskalov, Hristo; Saatkamp, Helmut W.; Stärk, Katharina D.C.; Lund, Ole; Hald, Tine; Pamp, Sünje Johanna; Vigre, Håkan; Heederik, Dick; Wagenaar, Jaap A.; Mevius, Dik; Aarestrup, Frank M.
Source Nature Microbiology 3 (2018)8. - ISSN 2058-5276 - p. 898 - 908.
DOI https://doi.org/10.1038/s41564-018-0192-9
Department(s) CVI Infection Biology
CVI Bacteriology and Epidemiology
Business Economics
WASS
Publication type Refereed Article in a scientific journal
Publication year 2018
Abstract

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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