# Metagenomic Insights into Antimicrobial Resistance in Small-Scale Poultry and Cattle Farms

## TL;DR

This study explores antimicrobial resistance in small poultry and cattle farms, finding high levels of resistance genes and potential health risks.

## Contribution

The study provides new insights into the prevalence of antimicrobial resistance genes in small-scale animal farms using metagenomic analysis.

## Key findings

- Tetracycline and beta-lactam resistance genes were most abundant in farm samples.
- Proteobacteria was the dominant bacterial phylum across all sampled environments.
- The presence of virulence factors alongside resistance genes indicates potential pathogenic risks.

## Abstract

Antimicrobial resistance (AMR) poses a critical challenge to global health, with food animal production systems recognized as significant reservoirs of antimicrobial-resistant bacteria. This study evaluated the prevalence and distribution of antimicrobial resistance genes (ARGs) and virulence factors (VFs) across small-scale poultry and cattle farms. A total of 468 samples (soil, feces, water, and natural land soil) were collected from four farms and analyzed using shotgun metagenomics. Proteobacteria (34.91%) were the dominant phylum across environments, followed by Cyanobacteria (15.67%), Actinobacteria (14.95%), Firmicutes (10.57%), and Bacteroidetes (8.69%). Tetracycline (33.41%) and beta-lactam (30.30%) resistance genes were the most abundant, with macrolide (9.32%) and aminoglycoside (8.39%) resistance also detected. Both tetracycline and beta-lactam resistance genes were significantly enriched across sample types (p < 0.05). The detection of diverse VFs alongside ARGs highlights the pathogenic potential of bacterial communities in these production systems. Collectively, the findings reveal that small-scale animal farms are reservoirs of AMR with implications for public health through foodborne transmission. Targeted surveillance and control measures are necessary to prevent the dissemination of ARGs into the broader food chain and to safeguard both human and animal health.