Know more

Our use of cookies

Cookies are a set of data stored on a user’s device when the user browses a web site. The data is in a file containing an ID number, the name of the server which deposited it and, in some cases, an expiry date. We use cookies to record information about your visit, language of preference, and other parameters on the site in order to optimise your next visit and make the site even more useful to you.

To improve your experience, we use cookies to store certain browsing information and provide secure navigation, and to collect statistics with a view to improve the site’s features. For a complete list of the cookies we use, download “Ghostery”, a free plug-in for browsers which can detect, and, in some cases, block cookies.

Ghostery is available here for free:

You can also visit the CNIL web site for instructions on how to configure your browser to manage cookie storage on your device.

In the case of third-party advertising cookies, you can also visit the following site:, offered by digital advertising professionals within the European Digital Advertising Alliance (EDAA). From the site, you can deny or accept the cookies used by advertising professionals who are members.

It is also possible to block certain third-party cookies directly via publishers:

Cookie type

Means of blocking

Analytical and performance cookies

Google Analytics

Targeted advertising cookies


The following types of cookies may be used on our websites:

Mandatory cookies

Functional cookies

Social media and advertising cookies

These cookies are needed to ensure the proper functioning of the site and cannot be disabled. They help ensure a secure connection and the basic availability of our website.

These cookies allow us to analyse site use in order to measure and optimise performance. They allow us to store your sign-in information and display the different components of our website in a more coherent way.

These cookies are used by advertising agencies such as Google and by social media sites such as LinkedIn and Facebook. Among other things, they allow pages to be shared on social media, the posting of comments, and the publication (on our site or elsewhere) of ads that reflect your centres of interest.

Our EZPublish content management system (CMS) uses CAS and PHP session cookies and the New Relic cookie for monitoring purposes (IP, response times).

These cookies are deleted at the end of the browsing session (when you log off or close your browser window)

Our EZPublish content management system (CMS) uses the XiTi cookie to measure traffic. Our service provider is AT Internet. This company stores data (IPs, date and time of access, length of the visit and pages viewed) for six months.

Our EZPublish content management system (CMS) does not use this type of cookie.

For more information about the cookies we use, contact INRA’s Data Protection Officer by email at or by post at:

24, chemin de Borde Rouge –Auzeville – CS52627
31326 Castanet Tolosan CEDEX - France

Dernière mise à jour : Mai 2018

Menu Logo Principal Oniris

Home page

Do rainbow trout fillets harbour determinants of antibiotic resistance?

Antibiotic resistance, an investigation from the farming to the food product

rainbow trout
The increasing acquisition of antibiotic resistance by bacteria raises a new question, that of the place of food as a potential source of transmission of antibiotic resistance determinants: antibiotic residues, resistance genes and resistant bacteria. These determinants are linked to the natural bacterial flora of the foodstuff whose composition may be impacted by its production environment.

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