Assessing antimicrobial resistance in pasture-based dairy farms: a 15-month surveillance study in New Zealand

Antimicrobial resistance is a global public and animal health concern. Antimicrobial resistance genes (ARGs) have been detected in dairy farm environments globally; however, few longitudinal studies have utilized shotgun metagenomics for ARG surveillance in pasture-based systems. This 15-month study aimed to undertake a baseline survey using shotgun metagenomics to assess the relative abundance and diversity of ARGs in two pasture-based dairy farm environments in New Zealand with different management practices. There was no statistically significant difference in overall ARG relative abundance between the two dairy farms (<i>P</i> = 0.321) during the study period. Compared with overseas data, the relative abundance of ARG copies per 16S rRNA gene in feces (0.08–0.17), effluent (0.03–0.37), soil (0.20–0.63), and bulk tank milk (0.0–0.12) samples was low. Models comparing the presence or absence of resistance classes found in &gt;10% of all feces, effluent, and soil samples demonstrated no statistically significant associations (<i>P</i> &gt; 0.05) with “season,” and only multi-metal (<i>P</i> = 0.020) and tetracycline (<i>P</i> = 0.0003) resistance were significant at the “farm” level. Effluent samples harbored the most diverse ARGs, some with a recognized public health risk, whereas soil samples had the highest ARG relative abundance but without recognized health risks. This highlights the importance of considering the genomic context and risk of ARGs in metagenomic data sets. This study suggests that antimicrobial resistance on pasture-based dairy farms is low and provides essential baseline ARG surveillance data for such farming systems.