Towards an understanding of genetic resistance to Flavobacterium psychrophilum in Atlantic salmon (Salmo salar L.) and rainbow trout (Oncorhynchus mykiss (Walbaum, 1792))

Abstract

Flavobacteriosis is a widespread challenge for the aquaculture sector, with infections reported in salmonids farmed in Scotland, Chile, Norway, and Canada, causing major welfare, environmental and economic concerns. A better understanding of the interactions between the host immune system and the pathogens are required for the development of new methods to control or prevent disease outbreaks. The current treatment and prevention programmes are limited to antimicrobial therapy and vaccines (ALPHA JECT® IPNV-Flavo) delivered by injection and therefore not suitable for fry, which is when the fish are most vulnerable to this pathogen. As the sector continues to move away from antibiotic treatments, a genetic breakthrough could be the key to preventing Flavobacterium psychrophilum infections in Atlantic salmon and rainbow trout. The selection of families of fish with resistance or decreased susceptibility to this pathogen offers another possibility for addressing the problems posed by F. psychrophilum. Therefore, the aim of this thesis was to study F. psychrophilum infection in rainbow trout, Oncorhynchus mykiss (Walbaum, 1792), and Atlantic salmon (Salmo salar L.) resistant and susceptible families, and to uncover the genetic underpinnings of resistance to F. psychrophilum. To achieve this, a successful immersion challenge model for F. psychrophilum in Atlantic salmon and rainbow trout, which mimics the natural infection route, was developed. Rainbow trout and Atlantic salmon were challenged using this newly developed challenge model, and a genome wide association study (GWAS) was conducted in both species, which identified genetic markers for disease resistance. In rainbow trout resistance to F. psychrophilum is a polygenic trait, while in Atlantic salmon the trait is oligogenic, which suggests that the trait is influenced by few genes with large effects (Chapter 2). A SYBR Green quantitative polymerase chain reaction (qPCR) was developed, validated, and used to quantify F. psychrophilum load in Atlantic salmon and rainbow trout head kidney tissues at different time points post challenge. However, there was not a clear relationship between fish genotype and bacterial load in head kidney tissues (Chapter 3). Since F. psychrophilum infection was not solely localised to the head kidney, and low bacterial load was determined in this tissue, the mucosal immune response of Atlantic salmon and rainbow trout was investigated by immunohistochemistry (IHC) by detecting and quantifying F. psychrophilum in different tissues (gills, head kidney, and gut), and the IHC supported the qPCR results of low bacterial load in the head kidney. Similarly, immunoglobulin T (IgT) positive cells were detected in all mucosal tissues, with the highest detection in the secondary lamellae of the gills, suggesting the importance of this immunoglobulin (Ig) in teleosts (Chapter 4). Finally, for the first time the transcriptomic response to F. psychrophilum infection in Atlantic salmon head kidney was investigated to unravel genes and pathways that take part in disease resistance. Genes and pathways up regulated in infected Atlantic salmon head kidney included those related to the immune response, cell chemotaxis and iron homeostasis; pattern recognition receptors (PRRs), complement molecules, inflammatory cytokines, chemokines, and iron-related genes, which indicated these genes participate in the response of Atlantic salmon to F. psychrophilum challenge (Chapter 5). This present study is the first to describe a F. psychrophilum immersion challenge model that can be used to study host-pathogen interactions, and molecular and immunological techniques that allow for the rapid detection of this bacterium in infected fish tissues. Moreover, the transcriptomic study provided an insight into the immune system and the defence mechanisms of Atlantic salmon against F. psychrophilum, which is an important step forward towards preventing infections by this bacterium in farmed Atlantic salmon.