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

Antibiotic resistance, an investigation from breeding to food

Antibiotic resistance
Do Rainbow Trout Fillets Host Determinants of Antibiotic Resistance?

The growing acquisition of resistance to antibiotics by bacteria poses a new question, that of the place of food as a potential source of transmission of determinants of antibiotic resistance: antibiotic residues, resistance genes and resistant bacteria. These determinants are linked to the natural bacterial flora of the food, the composition of which can be impacted by its production 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, which has a low level of natural flora, and methods of amplicon sequencing of the 16S rRNA gene, by high throughput qPCR by Smartchip Realtime PCR technology, and by the determination of antibiotic residues by liquid chromatography coupled with mass spectrometry. The fillets were obtained from trout reared on two farms located upstream and downstream of the same river, raised 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 least abundant bacterial communities depending on the location of the farm or the filleting conditions. Of the 73 antibiotic residues investigated, only oxytetracycline residues were detected in 23% of the fillets, but all at a dose below the maximum limit authorized 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, beta-lactams, macrolides and vancomycin, etc.). At the scale of this study, the fish fillets studied had little or no carriers of elements that could participate in antibiotic resistance (residues, genes and bacteria).

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

Associated 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.