As part of the EFFORT project, we sampled feces from pig and poultry livestock in nine European countries (BE, BG, DK, FR, ES, GE, NL, PL, SP). More than 9000 animals were sampled, across 181 pig and 178 poultry herds to generate herd-level composite fecal samples. Using shotgun metagenomics, we have quantified and characterized the antimicrobial resistance gene pools (resistomes) in Europe’s two most intensively raised livestock species.. Gut microbiomes from 359 European pig and poultry herds (EFFORT)

Antimicrobial resistance (AMR) in bacteria and associated morbidity and mortality is increasing. Use of antimicrobials for livestock selects for AMR that can subsequently be transferred to the human reservoir. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (http://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. 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 newly described, critical AMR genes, including mcr-1 and optrA, which differed both between host species and countries. We found that the total AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns have similar resistomes.