Antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals (Phoca vitulina).

BACKGROUND

Antimicrobial use has contributed to the alarming rise of antimicrobial resistance (AMR), posing a significant global health threat. Effective AMR control requires a One Health approach. The presence of AMR in the environment can challenge wildlife conservation, as resistance may reduce treatment success. This study investigates the impact of antimicrobial treatment on the gut microbiome and resistome of harbour seals () 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 16 S rRNA gene sequencing, shotgun metagenomics, and targeted qPCR.

RESULTS

We observed 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 high at release. Untreated seals cohabiting with treated seals also exhibited increased resistance gene loads, suggesting exposure through environmental transmission.

CONCLUSIONS

Antimicrobial treatments in rehabilitation settings alter the gut microbiome and enhance AMR gene persistence in seals. The potential risk of antimicrobial resistance transmission among rehabilitating seals suggests the need for antimicrobial stewardship as the risk of antimicrobial resistance contamination by seals returning to the wild is currently unknown.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s42523-025-00449-1.