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Members of the jury :

• Reveiwers :
  • Sophie PAYOT-LACROIX Research Director, INRAE, Nancy, France
  • Nathalie WERY Directrice de Recherche, INRAE, Narbonne, France
• Examiners :
  • Sébastien LECLERCQ Researcher, INRAE, Nouzilly, France
  • Olivier GROVEL Professor, Université de Nantes, France
• Thesis Director : Catherine MAGRAS Professor, Oniris, Nantes
• Thesis co-supervisors :
  • Ségolène CALVEZ Lecturer, Oniris, Nantes
  • Hervé PRÉVOST Professor, Oniris, Nantes

Abstract :

Foods of animal origin are believed to play a role in the spread of antibiotic resistance. Fresh fillets of farmed fish, whose consumption is increasing rapidly, are subject to contamination by farming and processing environments that can influence their resistance profile. This initial characterization of the resistance profile of the rainbow trout fillet microbiota takes into account different situations that may cause variations in fillet exposure. The bacterial microbiota and its antibiotic resistance profile of a panel of 56 samples collected on site were described after the extraction methods adapted to this complex matrix and low level of contamination were calibrated. If the constituent microbiota of rainbow trout is similar between samples, the filleting process appears to be a factor in community diversity. Resistance genes were detected in low numbers in fresh fillets with a prevalence of 20% or more in the pond fish population. Their nature seems to be influenced by previous antibiotic treatments whose residues have been detected. Strains of Pseudomonas were isolated, some of which were multi-resistant. 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 posed by these genes present but not detected in fresh fillets, and the transmission of antibiotic resistance determinants to other environments such as the consumer's intestinal microbiota.