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In an aquaponic system, fish and plants are cultivated together in a symbiotic environment where they mutually benefit, using significantly less water than traditional farming methods. The main aim of this study was to investigate the occurrence of antimicrobial resistance in two aquaponic systems implemented in two Chilean high schools using rainbow trout and lettuce cultures. When water samples (fish tank, biofilter, and plant raft) were analyzed over a three-month period, no resistance to oxytetracycline was detected, whereas the occurrence of resistance to florfenicol was rather small, ranging from 0.01% to 3.1% of bacterial culturable counts. Eighteen isolates were recovered from various sources as representatives of the florfenicol-resistant population, and all of them belonged to the Pseudomonas genus, showing a multi-drug-resistance phenotype and exhibiting simultaneous resistance to 7–13 antimicrobials. All isolates exhibited resistance to amoxicillin, chloramphenicol, florfenicol, and furazolidone and susceptibility to meropenem, oxytetracycline, oxolinic acid, flumequine, ciprofloxacin, and enrofloxacin. Five and two isolates carried the amphenicol-resistance-encoding genes floR and cmlA, respectively, whereas no carriage of integrons or the fexA, fexB, pexA, optrA, and cfr genes encoding for florfenicol resistance was detected. Eleven isolates carried plasmids, but only two of them were able to transfer their plasmid content by conjugation. The knowledge of the microbiome associated with aquaponic systems is still scarce, and their role as potential reservoirs of antimicrobial-resistant bacteria and related genes of these systems must be elucidated. [ABSTRACT FROM AUTHOR]

Simple Summary: The culture of the marine fish red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture but low larval survival rates have prompted the need for the continuous use of antibiotics, mainly florfenicol. In this study, the role of live prey (rotifers and the brine shrimp Artemia franciscana) used to feed fish larvae as a source of antibacterial-resistant bacteria in a commercial culture of G. chilensis was investigated. Samples of live feeds were collected during the larval growth period and their bacterial contents were determined. High levels of potentially opportunistic pathogens, such as Vibrio spp., as well as florfenicol-resistant bacteria, were detected. Sixty-five florfenicol-resistant isolates were recovered from these cultures and identified as Vibrio (81.5%) and Pseudoalteromonas (15.4%), which exhibited a high incidence of co-resistance to the antibiotics streptomycin, oxytetracycline, co-trimoxazole, and kanamycin. The majority of them carried the florfenicol-resistance encoding genes floR and fexA. The high prevalence of antibiotic-resistant bacteria and the associated genetic elements in live feed administered to reared fish larvae requires the prompt implementation of efficient management strategies to prevent future therapy failures in fish larval cultures and the spread of antibiotic-resistant bacteria to associated aquatic environments. The culture of red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture but low larval survival rates have prompted the need for the continuous use of antibacterials. The main aim of this study was to evaluate the role of live feed as a source of antibacterial-resistant bacteria in a commercial culture of G. chilensis. Samples of rotifer and Artemia cultures used as live feed were collected during the larval growth period and culturable bacterial counts were performed using a spread plate method. Rotifer and Artemia cultures exhibited high levels of resistant bacteria (8.03 × 104 to 1.79 × 107 CFU/g and 1.47 × 106 to 3.50 × 108 CFU/g, respectively). Sixty-five florfenicol-resistant isolates were identified as Vibrio (81.5%) and Pseudoalteromonas (15.4%) using 16S rRNA gene sequence analysis. A high incidence of resistance to streptomycin (93.8%), oxytetracycline (89.2%), co-trimoxazole (84.6%), and kanamycin (73.8%) was exhibited by resistant isolates. A high proportion of isolates (76.9%) carried the florfenicol-resistance encoding genes floR and fexA, as well as plasmid DNA (75.0%). The high prevalence of multiresistant bacteria in live feed increases the incidence of the resistant microbiota in reared fish larvae, thus proper monitoring and management strategies for live feed cultures appear to be a priority for preventing future therapy failures in fish larval cultures. [ABSTRACT FROM AUTHOR]