Co-occurrence patterns of bacterial communities and resistance genes: A comprehensive fecal microbiome and resistome study from multiple dairy cattle farms

Antimicrobial resistance (AMR) poses a critical public health threat, with rising multidrug resistance cases compromising treatment effectiveness. Knowledge about the resistome in dairy production systems remains limited, particularly regarding lactating cows. This study investigated the microbiome and resistome variations across the hospital, fresh, and mid-lactation pens on 18 conventional dairy farms in California and Ohio using shotgun metagenomic sequencing of pooled fecal samples. Findings from this study suggest that antimicrobial drug use may not be the primary driver of resistome composition in dairy cattle, highlighting the need to investigate other factors influencing AMR dynamics in livestock systems.