Antimicrobial resistance monitoring in the Danish swine production by phenotypic methods and metagenomics from 1999 to 2018

Background: In Denmark, antimicrobial resistance (AMR) in pigs has been monitored since 1995 by phe-notypic approaches using the same indicator bacte-ria. Emerging methodologies, such as metagenomics, may allow novel surveillance ways. Aim: This study aimed to assess the relevance of indicator bacteria (Escherichia coli and Enterococcus faecalis) for AMR surveillance in pigs, and the utility of metagenomics. Methods: We collated existing data on AMR and anti-microbial use (AMU) from the Danish surveillance pro-gramme and performed metagenomics sequencing on caecal samples that had been collected/stored through the programme during 1999-2004 and 2015-2018. We compared phenotypic and metagenomics results regarding AMR, and the correlation of both with AMU. Results: Via the relative abundance of AMR genes, metagenomics allowed to rank these genes as well as the AMRs they contributed to, by their level of occur-rence. Across the two study periods, resistance to aminoglycosides, macrolides, tetracycline, and beta-lactams appeared prominent, while resistance to fos-fomycin and quinolones appeared low. In 2015-2018 sulfonamide resistance shifted from a low occurrence category to an intermediate one. Resistance to glyco-peptides consistently decreased during the entire study period. Outcomes of both phenotypic and metagenom-ics approaches appeared to positively correlate with AMU. Metagenomics further allowed to identify mul-tiple time-lagged correlations between AMU and AMR, the most evident being that increased macrolide use in sow/piglets or fatteners led to increased macrolide resistance with a lag of 3-6 months. Conclusion: We validated the long-term usefulness of indicator bac-teria and showed that metagenomics is a promising approach for AMR surveillance.

Automated summary

This study aimed to evaluate the relevance of indicator bacteria (Escherichia coli and Enterococcus faecalis) for AMR surveillance in pigs, and the utility of metagenomics. The results showed that metagenomics is a promising approach for AMR surveillance, as it allows for ranking of resistance genes and correlation analysis with antimicrobial use.