| description |
Reliable methods for monitoring antimicrobial resistance (AMR) in livestock and other reservoirs are essential to understand the trends, transmission and importance of agricultural resistance. Quantification of AMR is mostly done using culture-based techniques, but metagenomic read mapping shows promise for quantitative resistance monitoring. Here, we present a workflow, from sampling to interpretation, showing how resistance monitoring can be carried out in swine herds using a metagenomic approach. We show that metagenomics outperform traditional MIC and CFU counting in terms of predicting expected resistance based on antimicrobial consumption and demonstrate that composite pen floor samples are suited to approximate the in-animal resistomes. Finally, we show the method is sensitive enough to detect subtle differences in antimicrobial-induced resistome changes and can identify genes whose abundances are affected by antimicrobial usage. We propose metagenomic sequencing should be part of routine livestock resistance monitoring programs and potentially of integrated One Health monitoring in all reservoirs. |