Understanding the Risks Associated With Recirculating Aquaculture Systems: Identification of Enterococcus Species, Persistence, and Antimicrobial Resistance Phenotypes

Enterococci are considered indicators of fecal contamination from mammals and birds and of antimicrobial resistance (AMR) from the environment. This longitudinal observational study assessed the persistence of Enterococcus spp. in a recirculating aquaculture system (RAS), determined AMR phenotypes and compared them with isolates recovered from human infections. Over five monthly sampling events, 95 samples were collected from all compartments of the RAS rearing rainbow trout at a French experimental facility: water ( n = 33), biofilm ( n = 23), sediment ( n = 5), fish feces ( n = 30) and commercial fish feed ( n = 4). Enterococcus isolates from feed and RAS, in addition to 15 E. faecium from human infections retrieved at Nantes University Hospital, were tested using broth microdilution method against 12 antibiotics of importance for human or animal health. Minimum inhibitory concentrations (MICs) were interpreted using epidemiological cutoff (ECOFF) values and clinical breakpoints reported by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Clinically important species ( E. faecium , E. gallinarum , and E. casseliflavus ) were found in commercial fish feed (3/4). However, only environmental Enterococcus species were isolated within the RAS, and at a low overall rate (7/91). The isolation rate of Enterococcus spp. within the RAS was significantly higher ( p < 0.05) in May, probably due to both warmer water temperature and higher biomass. For four antibiotics, E. faecium isolates from human infections showed higher resistance rates than E. faecium from fish feed ( p < 0.01). Although clinically important enterococci introduced via feed do not appear to persist within a RAS, the potential risk of AMR‐gene transfer to environmental Enterococcus spp. and its spread via effluents needs further investigation.