Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms
Background: The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by
antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a
more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how
sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment.
Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared
to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from
38 farms.
Results: Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive
farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome
across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those
from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were
defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences
between intensive and extensive farms could be linked to differences in the abundance of mobile genetic
elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs
between intensive and extensive herds, a significantly higher abundance of integrons in the environment and
plasmids, regardless of the sample type, was detected on intensive farms.
Conclusions: Overall, this study shows how AMU, production system, and sample type influence, mainly through
MGEs, the profile and dispersion of ARGs in pig production.
