Environmental Spread and Persistence of Antibiotic REsistances in aquatic Systems Exposed to oyster Aquaculture

Aquaculture plays a crucial role in food production, but it has also been identified as a potential gateway for the spread of antibiotic resistance. However, our understanding of antibiotic resistance within bivalve aquaculture remains limited. The Pacific oyster (Crassostrea gigas) is a key species in the largest oyster aquaculture industry and represents the optimal proxy for the determination of antibiotics, resistance genes, and resistant bacteria, along with other pollutants in water. Further, their consumption as raw leads to a direct risk for human health. We assessed the first comprehensive microbiome of oysters aquaculture systems, by defining the microbial community, the resistome and the pathobiome of oyster farms with a different degree of productivity in Europe. The farms, from diffuse natural to intensive systems are located in the Thau Lagoon (France), in the Ebro Delta (Spain), in the Bay of Brest (France), and in the Island of Sylt (Germany). We recovered and compared microbial data from water and sediments, from the oysters, from other animals in the area of the farms (tunicates, crabs, mussels, clams, other mollusks) and from the stools of birds and fish feeding in the area. Our data allow a first assessment of the impact of oyster farms in coastal areas in Europe, the impact of anthropogenic pollution on the bacteriological risks related to the farmed oysters, and overall the comprehensive assessment of the disturbance of coastal environments exposed to oyster farming, in areas where the impact of other anthropogenic activities is high.