Long-term antimicrobial resistance monitoring by phenotypic methods and metagenomics

The Danish Integrated Antimicrobial Resistance Monitoring and Research Programme (DANMAP), established in 1995, encompasses annual estimates of antimicrobial -use (AMU) and -resistance (AMR), with isolates of indicator bacteria collected from animals at slaughter and tested for antimicrobial susceptibility. Recently, novel monitoring possibilities emerged, including metagenomics shotgun-sequencing. Here we compare the monitoring of AMR using phenotypic resistance in indicator bacteria with metagenomics, and investigate the correlation of both with AMU. The aim of this study was to assess the relevance of indicator bacteria and the future utility of metagenomics in AMR surveillance. Both measures of resistance were equally positively correlated to AMU. Metagenomics further allowed to rank abundance of different resistances and individual antimicrobial resistance genes and to identify significant cross-correlations between trends over time. We validated the long-term usefulness of indicator bacteria and also showed that metagenomics is a promising and potentially preferable option for future improved AMR surveillance.