Antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals (Phoca vitulina)
Abstract 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...
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BMC
2025-07-01
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| Series: | Animal Microbiome |
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| Online Access: | https://doi.org/10.1186/s42523-025-00449-1 |
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| author | Ana Rubio-Garcia Roosmarijn E. C. Luiken Inês Marcelino John W. A. Rossen Jan H. van Zeijl Jaap A. Wagenaar Aldert L. Zomer |
| author_facet | Ana Rubio-Garcia Roosmarijn E. C. Luiken Inês Marcelino John W. A. Rossen Jan H. van Zeijl Jaap A. Wagenaar Aldert L. Zomer |
| author_sort | Ana Rubio-Garcia |
| collection | DOAJ |
| description | Abstract 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 (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 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. |
| format | Article |
| id | doaj-art-567c479ccca844e2bc02d4a4e0c2e2a8 |
| institution | Kabale University |
| issn | 2524-4671 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Animal Microbiome |
| spelling | doaj-art-567c479ccca844e2bc02d4a4e0c2e2a82025-08-20T03:46:12ZengBMCAnimal Microbiome2524-46712025-07-017111410.1186/s42523-025-00449-1Antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals (Phoca vitulina)Ana Rubio-Garcia0Roosmarijn E. C. Luiken1Inês Marcelino2John W. A. Rossen3Jan H. van Zeijl4Jaap A. Wagenaar5Aldert L. Zomer6Veterinary and Research Department, Sealcentre PieterburenDivision of Infectious Diseases and Immunology, Utrecht University Faculty of Veterinary MedicineDivision of Infectious Diseases and Immunology, Utrecht University Faculty of Veterinary MedicineDepartment of Medical Microbiology and Infection Prevention, University Medical Center GroningenWageningen Bioveterinary ResearchDivision of Infectious Diseases and Immunology, Utrecht University Faculty of Veterinary MedicineDivision of Infectious Diseases and Immunology, Utrecht University Faculty of Veterinary MedicineAbstract 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 (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 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.https://doi.org/10.1186/s42523-025-00449-1Harbour sealCommon sealMicrobiomeResistomeAntimicrobialRehabilitation |
| spellingShingle | Ana Rubio-Garcia Roosmarijn E. C. Luiken Inês Marcelino John W. A. Rossen Jan H. van Zeijl Jaap A. Wagenaar Aldert L. Zomer Antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals (Phoca vitulina) Animal Microbiome Harbour seal Common seal Microbiome Resistome Antimicrobial Rehabilitation |
| title | Antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals (Phoca vitulina) |
| title_full | Antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals (Phoca vitulina) |
| title_fullStr | Antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals (Phoca vitulina) |
| title_full_unstemmed | Antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals (Phoca vitulina) |
| title_short | Antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals (Phoca vitulina) |
| title_sort | antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals phoca vitulina |
| topic | Harbour seal Common seal Microbiome Resistome Antimicrobial Rehabilitation |
| url | https://doi.org/10.1186/s42523-025-00449-1 |
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