TY - JOUR
T1 - Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries
AU - Munk, Patrick
AU - Knudsen, Berith Elkær
AU - Lukjacenko, Oksana
AU - Duarte, Ana Sofia Ribeiro
AU - Van Gompel, Liese
AU - Luiken, Roosmarijn E.C.
AU - Smit, Lidwien A.M.
AU - Schmitt, Heike
AU - Garcia, Alejandro Dorado
AU - Hansen, Rasmus Borup
AU - Petersen, Thomas Nordahl
AU - Bossers, Alex
AU - Ruppé, Etienne
AU - Graveland, Haitske
AU - van Essen, Alieda
AU - Gonzalez-Zorn, Bruno
AU - Moyano, Gabriel
AU - Sanders, Pascal
AU - Chauvin, Claire
AU - David, Julie
AU - Battisti, Antonio
AU - Caprioli, Andrea
AU - Dewulf, Jeroen
AU - Blaha, Thomas
AU - Wadepohl, Katharina
AU - Brandt, Maximiliane
AU - Wasyl, Dariusz
AU - Skarzyńska, Magdalena
AU - Zajac, Magdalena
AU - Daskalov, Hristo
AU - Saatkamp, Helmut W.
AU - Stärk, Katharina D.C.
AU - Lund, Ole
AU - Hald, Tine
AU - Pamp, Sünje Johanna
AU - Vigre, Håkan
AU - Heederik, Dick
AU - Wagenaar, Jaap A.
AU - Mevius, Dik
AU - Aarestrup, Frank M.
PY - 2018/8/1
Y1 - 2018/8/1
N2 - 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.
AB - 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.
U2 - 10.1038/s41564-018-0192-9
DO - 10.1038/s41564-018-0192-9
M3 - Article
C2 - 30038308
SN - 1740-1526
VL - 3
SP - 898
EP - 908
JO - Nature Microbiology
JF - Nature Microbiology
IS - 8
ER -
