OHEJP-RaDAR-D-JRP3-5.2 A proposal for a new paradigm for AMR surveillance

SUMMARY

In this study we recovered and shotgun-sequenced caecal samples collected from pigs under the Danish monitoring of antimicrobial resistance (AMR) over two time periods (1999-2004 and 2015-2018), and compared this to gathered phenotypic results and antimicrobial use (AMU) data for the same time periods. The aim was to compare findings obtained with the present methods employed in AMR surveillance (phenotypic testing of indicator- and pathogenic-bacteria), with a new surveillance paradigm - a metagenomics-based surveillance of AMR determinants. We showed that metagenomic surveillance is a suitable methodology for population based surveillance of AMR and observed that AMU and AMR are in general correlated both at phenotypic and genotypic levels, but also that other factors play a role in the abundances of AMR.