Investigation published in Nature microbiology

August 3^rd, 2018

EFFORT Group
Haitske Graveland2 , Alieda van Essen4, Bruno Gonzalez-Zorn8, Gabriel Moyano8, Pascal Sanders9, Claire Chauvin9, Julie David9, Antonio Battisti10, Andrea Caprioli10, Jeroen Dewulf11, Thomas Blaha12, Katharina Wadepohl12, Maximiliane Brandt12, Dariusz Wasyl13, Magdalena Skarzyńska13, Magdalena Zajac13, Hristo Daskalov14, Helmut W. Saatkamp4 and Katharina D. C. Stärk15
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

Munk P., Knudsen BE., Lukjacenko O., Ribeiro-Duarte AS., Van Gompel L., Luiken REC., Smit LAM., Schmitt H., Dorado Garcia A., Borup-Hansen R., Nordahl-Petersen T., Bossers A., Ruppe E., EFFORT Group., Lund O., Hald T., Pamp SJ., Vigre H., Heederik D., Wagenaar J., Mevius D. and Aarestrup FM.

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

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

	Research Group for Genomic Epidemiology. National Food Institute (DTU Food). Technical University of Denmark (DTU).
	Institute for Risk Assessment Sciences. Utrecht University (UU).
	INTOMICS AS.
	Wageningen Bioveterinary Research.
	Genomic Research Laboratory. Hôpitaux Universitaires de Genève.
	Department of Infectious Diseases and Immunology. Faculty of Veterinary Medicine. Utrecht University (UU).
	Servicio de Zoonosis de Transmisión Alimentaria y Resistencia a Antimicrobianos (ZTA). Centro de Vigilancia Sanitaria Veterinaria (VISAVET). Universidad Complutense (UCM).