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 (Belgium, Bulgaria, Germany, Dernmark, Spain, France, Italy, The Netherlands and Poland), sequencing more than 5,000 Gb of ADN by using metagenomics. The study has identified the presence of 407 antibiotic resistance genes in the more than 9,000 animals tested.
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.
The homogeneity of the results obtained in the pig samples is also relevant: in most of them, tetracyclines, macrolides, beta-lactams and aminoglycosides resistance genes have been found. On the other hand, in the broiler samples the results obtained were very heterogeneous, with resistance genes against the same antibiotics having been found, but in very different amounts among the tested samples.
Patrick Munk, et al. Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries. Nature Microbiology 2018. DOI: 10.1038/s41564-018-0192-9.