RT Journal Article
SR Electronic
T1 Abundance and diversity of the fecal resistome in slaughter pigs and broilers in nine European countries
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 194647
DO 10.1101/194647
A1 Patrick Munk
A1 Berith Elkær Knudsen
A1 Oksana Lukjacenko
A1 Ana Sofia Ribeiro Duarte
A1 Roosmarjin E. C. Luiken
A1 Liese Van Gompel
A1 Lidwien A. M. Smit
A1 Heike Schmitt
A1 Alejandro Dorado Garcia
A1 Rasmus Borup Hansen
A1 Thomas Nordahl Petersen
A1 Alex Bossers
A1 Etienne Ruppé
A1 Ole Lund
A1 Hald Tine
A1 Sünje Johanna Pamp
A1 Håkan Vigre
A1 Dick Heederik
A1 Jaap A. Wagenaar
A1 Dik Mevius
A1 Frank M. Aarestrup
YR 2017
UL http://biorxiv.org/content/early/2017/09/28/194647.abstract
AB EFFORT group Haitske Graveland, Alieda van Essen, Bruno Gonzalez-Zorn, Gabriel Moyano, Pascal Sanders, Claire Chauvin, Julie David, Antonio Battisti, Andrea Caprioli, Jeroen Dewulf, Thomas Blaha, Katharina Wadepohl, Maximiliane Brandt, Dariusz Wasyl, Magdalena Skarzyñska, Magdalena Zajac, Hristo Daskalov, Helmut W Saatkamp, Katharina D.C. Stärk.Abstract Antimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. 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 as well as in humans. As part of the EFFORT project (www.effort-against-amr.eu), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 gigabases of DNA sequence, using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a 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 poultry. We found higher AMR loads in pigs, while 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 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. Novel, functionally-determined AMR genes were, however, not associated with total drug use.