Nicolas Helsens

PhD thesis of Nicolas Helsens (2017-2020)

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

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.


  • Oberlé, K., A. Bouju‐Albert, N. Helsens, G. Pangga, H. Prevost, C. Magras and S. Calvez 2022. No evidence for a relationship between farm or transformation process locations and antibiotic resistance patterns of Pseudomonas population associated with rainbow trout (Oncorhynchus mykiss). Journal of Applied Microbiology 132(3): 1738-1750. 
  • 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).

Modification date: 21 November 2023 | Publication date: 17 May 2017 | By: SG