Molecular approaches for pathogen assessment in remote aquaculture settings

Abstract

Aquaculture is a growing industry with an important role in providing a growing human population with protein. This thesis explores the use of a number of modern molecular biology techniques and technologies for detection of seven bacterial pathogens of aquaculture: Aeromonas salmoncida, Flavobacterium branchiophilum, Flavobacterium psychrophilum, Moritella viscosa, Renibacterium salmoninarum, Tenacibaculum maritimum and Yersinia ruckeri. It starts with a comparative genomics study, focused on A. salmonicida; the high genomic diversity of this bacterium highlights the value of sequencing pathogen genomes on a case-by-case basis. Nanopore sequencing was then employed to assemble the genomes of the seven bacteria, and although it has some advantages, such as low computational requirements, it performs worse several parameters than hybrid assemblies (which combine long and short read data). There was also an interest in providing a means of detecting these bacteria pre-emptively in aquaculture water by using a naïve surveillance system based on the detection of their DNA with nanopore sequencing. This led to an optimised method of obtaining DNA from river and seawater, consisting in centrifugation of the water and DNA extraction with a PowerSoil kit. Because this method did not yield enough DNA for a true metagenomic approach, other approaches to detection were considered. Loop-mediated isothermal amplification (LAMP) assays that could detect DNA of specific bacterial pathogens were developed for each of the bacteria mentioned above, with the exception of A. salmonicida. A proof of concept was also developed for a broad-range assay that combined LAMP and nanopore sequencing, the former to amplify DNA from a range of bacteria, the latter to discern the species of origin of the amplicons. Overall, this thesis could contribute to bring the advantages of molecular biology as close as possible to the fish farmer and improve monitoring and management of aquaculture pathogens.

Date of Award	2022
Original language	English
Awarding Institution	Aberystwyth University
Sponsors	Knowledge Economy Skills Scholarships
Supervisor	Arwyn Edwards (Supervisor) & Russ Morphew (Supervisor)