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The aquaculture sector is an interesting model because it can be considered as an interface between the environment (water treatment plant effluents, crops, fish farms, river water, etc.) and the fish net. However, few studies have made it possible to describe the diversity of bacterial communities in fresh fish fillets, from the farm environment to the plant environment.

In this study, the bacterial microbiota and its antibiotic resistance profile of a panel of 56 fillets were described using extraction methods adapted to this matrix with a low level of natural flora, and methods of sequencing by amplicon of the 16S RNAr gene, by high-throughput qPCR using Smartchip Realtime PCR technology, and by the determination of antibiotic residues by liquid chromatography coupled with mass spectrometry. The fillets were derived from trout reared on two farms located upstream and downstream of the same river, either in the factory or under sterile laboratory conditions. The microbiota of the fillets (muscle and skin) is dominated by the bacterial genera Pseudomonas, Escherichia-Shigella, Chryseobacterium and Carnobacterium.

Variations within the microbiota were observed for the less abundant bacterial communities depending on the location of the farm or the filleting conditions. Of the 73 antibiotic residues tested, only oxytetracycline residues were detected in 23% of the fillets, but all at a dose below the maximum permitted limit in the European Union. Of the 248 resistance genes sought, 17 were present in at least 20% of the trout population but at very low concentrations (resistance to tetracycline, b-lactams, macrolides and vancomycin, etc.). On the scale of this study, the fish fillets studied carried little or no elements that could contribute to antibiotic resistance (residues, genes and bacteria).

Partners: this study was carried out by the following units INRAE-Oniris SECALIM and BIOEPAR, with the financial support of RFI Food For Tomorrow (Pays de la Loire Region).

Related publication : Helsens, N., S. Calvez, H. Prévost, A. Bouju-Albert, A. Maillet, A. Rossero, D. Hurtaud-Pessel, M. Zagorec and C. Magras 2020. Antibiotic resistance genes and bacterial communities of farmed rainbow trout fillets (Oncorhynchus mykiss). Frontiers in Microbiology 11(3070). https://doi.org10.3389/fmicb.2020.590902.

Research projects carried out on antibiotic resistance in fish :

• Alter for fish (A2F) - Efficacy and safety of alternative(s) to antibiotics for farmed fish (Ecoantibio 2 project: 2018 - 2020)

Due to the location of fish production in open environments (rivers, ponds), the use of antibiotics in this sector contributes to the development of antibiotic-resistant (ABR) ichthyopathogenic bacteria and the diffusion in the environment of bacteria and ABR genes and antibiotic residues that can have an impact on public health. The reduction in the use of antibiotics and the prevention of antibiotic resistance are national and international issues which require research work relating to the sanitary, zootechnical and medical prevention of infectious diseases and in particular the development of biocontrol methods. The objective of the A2F project is to i) identify possibilities for "alternative" practices and treatments that aim to reduce the use of antibiotics and the conditions for their adoption in the field through qualitative research interviews with rainbow trout breeders and aquaculture veterinarians, (ii) to determine their efficacy and safety against furunculosis in rainbow trout under experimental conditions and to evaluate the impact of their administration on the use of antibiotics and the risk of development of SAB bacteria in fish and their environment under natural exposure conditions in fish farming.

Contacts (BIOEPAR Unit) : Ségolène Calvez, Emmanuelle Moreau

• ANTIBIOFISH - evolution of antibiotic resistance of Aeromonas and Yersinia ruckerii strains isolated from diseased fish over the last 40 years

The use of antibiotics in intensive animal husbandry contributes to the emergence of bacteria resistant to these molecules, limiting the effectiveness of treatments available in both veterinary and human medicine. In this context, the phenomena of antibiotic resistance observed in recent years are a major concern for human and animal public health. There is no monitoring plan for the fish farming industry to assess the prevalence of resistant bacteria at the fish farm level or in filleting or processing workshops.

The ANTIBIOFISH project aims to
- Build up a database by pooling the partners' collections.
- Cultivate, identify and characterize antibiotic resistance profiles of strains
- Creating a common library

Contact BIOEPAR : Ségolène Calvez