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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #385305

Research Project: Improving Salmonid Health through Breeding, Vaccination and Microbiome Modulation

Location: Cool and Cold Water Aquaculture Research

Title: Detecting Flavobacterial Fish Pathogens in the Environment Using High-Throughput 2 Community Analysis

item TESTERMAN, TODD - University Of Connecticut
item BEKA, LIDIA - University Of Connecticut
item MCCLURE, EMILY - University Of Connecticut
item REICHLEY, STEPHEN - Clear Springs Foods, Inc
item KING, STACY - Clear Springs Foods, Inc
item Welch, Timothy - Tim
item GRAF, JOERG - University Of Connecticut

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/17/2021
Publication Date: 6/21/2021
Citation: Testerman, T., Beka, L., Mcclure, E.A., Reichley, S., King, S., Welch, T.J., Graf, J. 2021. Detecting flavobacterial fish pathogens in the environment using high-throughput 2 community analysis. Applied and Environmental Microbiology. 6(21):447745.

Interpretive Summary: Early detection of a deadly disease outbreak in a population can be the difference between mass fatality or mitigated effects. In this study, we present and compare two techniques for detecting economically impactful aquaculture pathogens. We demonstrate that one of these techniques, 16S rRNA gene sequencing using Illumina technology, provides the ability to accurately detect two impactful fish pathogens, Flavobacterium columnare and Flavobacterium psychrophilum, while simultaneously profiling the native microbial community. The second technique, droplet digital PCR, is a more standard approach for pathogen detection and the results provided by the assays we designed with this method served to validate the results provided by the Illumina method. These two methods offer distinct advantages. The Illumina method pairs pathogen detection and microbial community profiling to answer immediate and long-term fish health concerns. The droplet digital PCR method provides fast and highly sensitive detection useful for surveillance and rapid clinical responses.

Technical Abstract: Disease caused by the fish pathogens Flavobacterium columnare and Flavobacterium psychrophilum are a major contributor of preventable losses in the aquaculture industry. Persistent and difficult to control infections make timely intervention and eliminating the pathogen’s reservoirs important mechanisms to combat these disease agents. In this study, we present two independent assays for detecting these pathogens from a range of environmental samples. Natural water samples were inoculated with F. columnare and F. psychrophilum cells and pathogen levels were detected using Illumina sequencing and droplet digital PCR. Both detection methods accurately identified pathogen-positive samples and showed good agreement in quantifying each pathogen. The real-world application of these approaches was demonstrated using environmental samples collected at a rainbow trout aquaculture facility. These methods can serve as useful tools for surveillance efforts in aquaculture facilities and provide early detection of these flavobacterial pathogens so that preventative measures can be taken.