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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.