Antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals

The misuse of antimicrobials has contributed to the alarming rise of antimicrobial resistance (AMR), posing a significant global health threat. Effective AMR control necessitates a One Health approach, integrating human, veterinary, and environmental health efforts. The presence of AMR in the environment poses challenges for wildlife conservation, as treatment options are limited and resistance may diminish treatment success. This study investigates the impact of antimicrobial treatment on the gut microbiome and resistome of harbour seals (Phoca vitulina) undergoing rehabilitation at the Sealcentre Pieterburen, the Netherlands. A longitudinal cohort study was conducted with 200 seals, from which 127 were treated with antimicrobials and 73 were not treated. Samples were collected before and during rehabilitation, including before and after treatment and analysed using 16S sequencing, shotgun metagenomics, and targeted qPCR. We observe a significant but transient decrease in gut microbiome alpha diversity following antimicrobial treatment, with a recovery observed by the time of release. Beta diversity analysis indicated persistent changes in microbial composition post-treatment. An increase in antimicrobial resistance gene load was observed in treated seals, with some resistance genes remaining elevated at release. Untreated seals cohabiting with treated seals also exhibited increased resistance gene loads, suggesting environmental transmission. Antimicrobial treatments in rehabilitation settings alter the gut microbiome and enhance AMR gene persistence in seals. Future research should focus on long-term impacts of antimicrobial use and develop methods to minimize AMR transmission within and beyond rehabilitation environments.