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

PhD thesis of Nicolas Helsens (2017-2020)

Nicolas Helsens
Characterization of bacterial communities and antibiotic resistance genes in farmed fish - Application to the control of microbial and environmental contaminations in the smoked salmon production chain (Director: Catherine Magras, Co-supervisor: Hervé Prévost and co-supervisor: Ségolène Calvès)

Nicolas Helsens's PhD thesis is a project between SECALIM and BioEPAR research units of Oniris. It is called Food Resistome.

Foods of animal origin are thought to play a role in the spread of antibiotic resistance. Fresh fillet of farmed fish, the consumption of which is on the rise, is subject to contamination from the farming and processing environments that can influence its resistance profile. This first characterization of the resistance profile of the rainbow trout fillet microbiota takes into account different situations that can influence the exposure of the fillets. The bacterial microbiota and its antibiotic resistance profile of a panel of 56 samples collected at the sites were described after the extraction methods suitable for this complex matrix and a low contamination level were calibrated. If the constituent microbiota of rainbow trout is similar between samples, the filleting process appears to be a factor of community diversity. Resistance genes were detected in low numbers in fresh fillets with a prevalence of 20% or more in the fish population of the basin. Their nature seems to be influenced by previous antibiotic treatments whose residues have been detected. Strains of Pseudomonas have been isolated, some of which exhibited multidrug resistance. The aging of the nets increases the number of genes detected and the abundance of bacteria of the genus Pseudomonas. This raises the question of the risk presented by these genes present but not detected in fresh fillets, and of the transmission of determinants of antibiotic resistance to other environments such as the consumer's gut microbiota.


  •   Helsens, N., S. Calvez, H. Prevost, 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.
  •   Helsens, N., S. Calvez, A. Bouju-Albert, A. Rossero, H. Prevost and C. Magras 2020. Comparison of stomaching versus rinsing, for recovering bacterial communities from rainbow trout (Oncorhynchus mykiss) fillets. Journal of Food Protection. JCR Ranking: Q3 (JCR® 2019).