Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms.

Microbiome
Oscar Mencía-AresHéctor Argüello

Abstract

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. 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 l...Continue Reading

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Citations

Apr 4, 2021·Medicina·Sarah Humboldt-Dachroeden, Alberto Mantovani
Jun 29, 2021·EFSA Journal·UNKNOWN EFSA Panel on Biological Hazards (BIOHAZ)Luisa Peixe

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Methods Mentioned

BETA
DNA assay
Illumina sequencing

Software Mentioned

Inkscape
BLASTn
ggpubr package
Finder
VSEARCH
Kraken2
Integron
PRINSEQ
Bowtie2
UD

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