Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments

These findings highlight small ruminant farm environments as potential reservoirs of clinically relevant ARGs, including WHO highest priority critically important antimicrobial (HPCIA) resistance genes for macrolides (<i>mph(c)</i>, <i>erm(f)</i>, <i>erm(b)</i>) and fluoroquinolones (<i>qnrD1</i>), as well as critically important antimicrobial (CIA) resistance genes for glycopeptides (<i>vanR-SC</i>, <i>vanR-O</i>) and aminoglycosides (<i>str</i>, <i>aadA</i>), supporting the need to incorporate these environments into surveillance strategies.