Parasitism perturbs the mucosal microbiome of Atlantic Salmon

Interactions between parasite, host and host-associated microbiota are increasingly understood as important determinants of disease progression and morbidity. Salmon lice, including the parasitic copepod Lepeophtheirus salmonis and related species, are perhaps the most important problem facing Atlantic Salmon aquaculture after feed sustainability. Salmon lice parasitize the surface of the fish, feeding off mucus, scales and underlying tissue. Secondary bacterial infections are a major source of associated morbidity. In this study we tracked the diversity and composition of Salmo salar skin surface microbiota throughout a complete L. salmonis infection cycle among 800 post-smolts as compared to healthy controls. Among infected fish we observed a significant reduction in microbial richness (Chao1, P = 0.0136), raised diversity (Shannon, P < 7.86e-06) as well as highly significant destabilisation of microbial community composition (Pairwise Unifrac, beta-diversity, P < 1.86e-05; P = 0.0132) by comparison to controls. While undetectable on an individual level, network analysis of microbial taxa on infected fish revealed the association of multiple pathogenic genera (Vibrio, Flavobacterium, Tenacibaculum, Pseudomonas) with high louse burdens. We discuss our findings in the context of ecological theory and colonisation resistance, in addition to the role microbiota in driving primary and secondary pathology in the host.

Transcriptional response of Atlantic salmon (Salmo salar) after primary versus secondary exposure to infectious salmon anemia virus (ISAV)

Following an infection with a specific pathogen, the acquired immune system of many teleostean fish, including salmonids, is known to retain a specific memory of the infectious agent, which protects the host against subsequent infections. For example, Atlantic salmon (Salmo salar) that have survived an infection with a low-virulence infectious salmon anemia virus (ISAV) isolate are less susceptible to subsequent ISAV infections. A greater understanding of the mechanisms and immunological components involved in this acquired protection against ISAV is fundamental for the development of efficacious vaccines and treatments against this pathogen. To better understand the immunity components involved in this observed resistance, we have used an Atlantic salmon DNA microarray to study the global gene expression responses of preexposed Atlantic salmon (fish having survived an infection with a low-virulence ISAV isolate) during the course of a secondary infection, 18 months later, with a high-virulence ISAV isolate. We present global gene expression patterns in both preexposed and naïve fish, following exposure by either cohabitation with infected fish or by direct intra-peritoneal injection of a high-virulence ISAV isolate. Our results show a clear reduction of ISAV viral loads in head-kidney of secondary infected fish compared to primary infected fish. Further, we note a lower-expression of many antiviral innate immunity genes in the secondary infected fish, such as the interferon induced GTP-binding protein Mx, CC-chemokine 19 and signal transducer and activator of transcription 1 (STAT 1), as well as MHC class I antigen presentation involved genes. Potential acquired immunity genes such as GILT, leukocyte antigen transcript CD37 and Ig mu chain C region membrane-bound form were observed to be over-expressed in secondary infected fish. The observed differential gene expression profile in secondary and primary infected fish head-kidney provides great insight into immunity components involved during primary and secondary ISAV infection.

Mapping of quantitative trait loci associated with size, shape, and parr mark traits using first- and second-generation backcrosses between European and North American Atlantic salmon (Salmo salar)

Little is known about the genetic architecture of traits important for salmonid restoration ecology. We mapped quantitative trait loci (QTL) using single nucleotide polymorphisms (SNPs) for juvenile body length, weight, shape, and vertical skin pigmentation patterns (parr marks) within three hybrid backcross families between European and North American subspecies of Atlantic salmon. Amounts of variation in skin colour and pattern quantified in the two second-generation transAtlantic families exceeded the ranges seen in purebred populations. GridQTL analyses using low-density female-specific linkage maps detected QTL showing experiment-wide significance on Ssa02, Ssa03, Ssa09, Ssa11, Ssa19, and Ssa26/28 for both length and weight; on Ssa04 and Ssa23 for parr mark number; on Ssa09 and Ssa13 for parr mark contrast; and on Ssa05, Ssa07, Ssa10, Ssa11, Ssa18, Ssa23, and Ssa26/28 for geometric morphometric shape coordinates. Pleiotrophic QTL on Ssa11 affected length, weight, and shape. No QTL was found that explained more than 10% of the phenotypic variance in pigmentation or shape traits. Each QTL was approximately positioned on the physical map of the Atlantic salmon genome. Some QTL locations confirmed previous studies but many were new. Studies like ours may increase the success of salmon restoration projects by enabling better phenotypic and genetic matching between introduced and extirpated strains.

In vivo virulence and genomic comparison of infectious Salmon Anaemia Virus isolates from Atlantic Canada

The infectious salmon anaemia virus (ISAV) is capable of causing a significant disease in Atlantic salmon, which has resulted in considerable financial losses for salmon farmers around the world. Since the first detection of ISAV in Canada in 1996, it has been a high priority for aquatic animal health management and surveillance programmes have led to the identification of many genetically distinct ISAV isolates of variable virulence. In this study, we evaluated the virulence of three ISAV isolates detected in Atlantic Canada in 2012 by doing in vivo-controlled disease challenges with two sources of Atlantic salmon. We measured viral loads in fish tissues during the course of infection. Sequences of the full viral RNA genomes of these three ISAV isolates were obtained and compared to a high-virulence and previously characterized isolate detected in the Bay of Fundy in 2004, as well as a newly identified ISAV NA-HPR0 isolate. All three ISAV isolates studied were shown to be of low to mid-virulence with fish from source A having a lower mortality rate than fish from source B. Viral load estimation using an RT-qPCR assay targeting viral segment 8 showed a high degree of similarity between tissues. Through genomic comparison, we identified various amino acid substitutions unique to some isolates, including a stop codon in the segment 8 ORF2 not previously reported in ISAV, present in the isolate with the lowest observed virulence.

A pilot study on the effects of in-feed probiotic Lactobacillus rhamnosus ATCC 53103 (LGG) on vaccinated Atlantic salmon (Salmo salar): microbiomes and Aeromonas salmonicida challenge resilience

The use of probiotics is an alternative approach to mitigate the proliferation of antimicrobial resistance in aquaculture. In our study, we examined the effects of Lactobacillus rhamnosus GG (ATCC 53103, LGG) delivered in-feed on the weight, length, skin mucus, and faecal microbiomes of Atlantic salmon. We also challenged the salmon with Aeromonas salmonicida 2004-05MF26 (Asal2004) and assessed the mortality. Our results showed no significant change (P > 0.05) in weight or length of Atlantic salmon or their resilience to Asal2004 infection after LGG feeding. Infection changed significantly the skin mucus and faecal microbiomes: Clostridium sensu stricto increased from 3.14% to 9.20% in skin mucus and 1.39% to 3.74% in faeces (P < 0.05). Aeromonas increased from 0.02% to 0.60% in faeces (P < 0.05). Photobacterium increased from not detected (0%) to 52.16% (P < 0.01) and Aliivibrio decreased from 67.21% to 0.71% in faeces (P < 0.01). After infection, Lactococcus (9.93%) and Lactobacillus (2.11%) in skin mucus of the LGG group were significantly higher (P < 0.05) than in the skin mucus from the rest of the groups (4.14% and 1.08%, respectively). In conclusion, LGG feeding did not further increase the resilience of vaccinated Atlantic salmon. Asal2004 infection had much greater impact on skin mucus and faecal microbiomes than LGG feeding.