Title:

Shotgun metagenomic virulence factor detection for food safety screening of aquaponic culture water

Aquaponics combines two well-studied food production models—recirculating aquaculture and hydroponics—into a complex controlled-environment agricultural system. The unique nature of aquaponics, with plants and fish in close proximity and shared culture water, brings new food safety challenges and questions to bear. Current industry standards and produce safety regulations are based on the assumption that aquaponic produce is unsafe to eat raw if the edible portion of the crop comes into contact with the culture water. This research seeks to investigate the food safety risk posed by aquaponic culture water utilizing replicated, large-scale aquaponic systems that were operated under normal commercial production conditions following current industry good agricultural practices (GAPs). After a year of continuous operation, we spent 8 weeks collecting weekly water samples from several sites within each aquaponic system. These samples were screened for E. coli, Salmonella, and Listeria using culture-based and biochemical methods. We also extracted and sequenced DNA from each water sample using whole genome sequencing, and are developing a bioinformatic analysis tool to screen the WGS sequence data for known virulence factors associated with human pathogens.

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