Fish immune responses to parasitic copepod (namely sea lice) infection

Immunoprotective role of fish mucus against the ectoparasitic flatworm Sparicotyle chrysophrii

The gill ectoparasite, Sparicotyle chrysophrii, has a significant impact on gilthead seabream farming in the Mediterranean. Yet, it remains unclear whether gilthead seabream develops immunological memory and protection following exposure to the parasite, which causes severe anaemia by feeding on the host's blood. This study compared recovered gilthead seabream (RE), which had overcome sparicotylosis, and naïve fish (NAI), never exposureed to the parasite. Both groups were exposed to S. chrysophrii eggs, and parasitic burdens, biometric and haematological parameters were monitored over 62 days post-exposure (dpe). Total and specific IgM and IgT titers were measured in plasma and gill mucus by ELISA, binding specificity of specific immunoglobulins were determined by immunohistochemistry, and immunoglobulin-expressing cells were quantified in spleens and gills of RE and NAI fish. Infection outcome, haematological parameters and fish fitness were worse in NAI than in RE fish. Results showed a strong mucosal immune response in RE gills, with high local secretion of parasite-specific immunoglobulins, particularly IgT, which were absent in NAI and undetectable in plasma of all recipient fish. Five months after the initial exposure, RE gill mucus still had significantly higher specific IgM and IgT titers than NAI. However, after the secondary exposure, these titres gradually decreased in RE, eventually becoming significantly lower than in NAI by the end of the trial. Immunohistochemistry confirmed the binding specificity of anti-S. chrysophrii IgT in RE gill mucus and IgM in plasma. Additionally, RE showed a higher number of IgT-expressing cells in the gills and IgM-expressing cells in the spleen.

Mucosal epithelial homeostasis: Reference intervals for skin, gill lamellae and filament for Atlantic salmon and other fish species

Mucosal barriers are gatekeepers of health and exhibit homeostatic variation in relation to habitat and disease. Mucosal Mapping technology provides an in-depth examination of the dynamic mucous cells (MCs) in fish mucosal barriers on tangential sections, about 90° from the view of traditional histology. The method was originally developed and standardized in academia prior to the establishment of QuantiDoc AS to apply mucosal mapping, now trademarked as Veribarr™ for the analysis of skin, gills and gastrointestinal tracts. Veribarr™ uses design-based stereology for the selection and measurement of cell area (size) (μm2), the volumetric density of MCs in the epithelium (MCD, amount of the epithelia occupied by MCs, in %) and the calculated abundance of the MCs (barrier status or defence activity). MC production was mapped across the skin and gill epithelia in 12 species, discovering that gills consistently have two distinct groups of MCs, one on the lamellae where MCs are few and small and one on the filament where MCs are larger and more abundant. MCs were usually much larger in the skin than in the gills, with the latter requiring fewer and smaller cells for adequate respiration. The difference observed between MCs in gill lamella and gill filament is likely a result of functional demands. In addition, our findings also highlight a variation in the mucosal parameters between the species skin, which cannot be explained by the weight differences, and a potential link between MC distribution and species-specific lifestyles in the gill lamella. This diversity necessitates the development of species and tissue site-specific reference intervals for mucosal health evaluation. Mucosal bivariate reference intervals were developed for MC production, including size (trophy) and calculated defence activity (plasia) in the skin and gills of Atlantic salmon, to contrast new measurements against historical data patterns. The application of mucosal reference intervals demonstrates that stress from parasites and treatments can manifest as changes in mucosal architecture, as evidenced by MC hypertrophy and hyperplasia within the gill lamellae. These reference intervals also facilitate comparisons with wild Atlantic salmon, revealing a somewhat higher MC level in farmed salmon gill lamellae. These findings suggest that MC hyperplasia and hypertrophy in the gills are stress/environmental responses in aquaculture. They also advocate for developing specific mucosal bivariate homeostatic reference intervals in aquaculture to improve fish health and welfare across all farmed species.

The skin mucosal barrier of lumpfish (Cyclopterus lumpus L.) is weakened by exposure to potential aquaculture production-related stressors

Various cleaner fish species, such as the lumpfish (Cyclopterus lumpus L.), are used in the sea cage production of Atlantic salmon (Salmo salar L.) as a control measure against the ectoparasitic salmon louse (Lepeophtheirus salmonis). Nonetheless, during severe lice infestation, alternative treatments are required to control parasitic burden. The aim of this study was to gain insight into how lumpfish skin responds to different chemicals used to treat parasites. The authors collected skin from lumpfish from both research facilities (tank-reared fish) and commercial production (cage-reared fish) and used operational welfare indicators, in vitro models, histology and transcriptomics to study how the skin responded to two anti-parasitic oxidative chemicals, hydrogen peroxide (H2O2) and peracetic acid. Lumpfish sampled from the farm were classified as clinically healthy or weak based on their morbidity status, and fish from each category were used to gain insight into how the therapeutics affect the skin barrier. Differences between healthy and weakened (moribund) fish, and between treated fish from each of the two groups, were observed. Histological examination showed an overall reduced skin quality in fish characterized as moribund, including different grades of exposed bony plates. In vitro oxidant-treated lumpfish skin had reduced the migration capacity of keratocytes, a weakened epidermal barrier, and altered gene transcription, changes that are known predisposing factors to secondary infections. Skin from non-treated, healthy fish sampled from commercial farms exhibited similar features and attributes to oxidant-exposed tank-reared fish from a research facility, suggesting that apparently healthy cage-held lumpfish exhibited stress responses in the epidermal barrier. The results of the study outline the risks and consequences lumpfish can face if accidentally subjected to potential anti-parasitic oxidant treatments aimed at Atlantic salmon. It also strengthens the evidence behind the requirement that lumpfish should be removed from the cages before being potentially exposed to this type of treatment and outlines the potential risks of differing husbandry practices upon lumpfish health, welfare and resilience.

Comprehensive review of Argulus infestations in aquaculture: Biological impacts and advanced management strategies

The aquaculture industry is hindered by various factors. One of the most noticeable factors is infection by parasites and pathogens. Argulus stands out as a prominent and economically significant ectoparasite in freshwater aquaculture. Argulus infestation causes severe immunomodulatory effects on its hosts by promoting argulosis, causing inflammation, extensive tissue damage, and death. Indian aquaculture sector faced a loss of 62.5 million USD due to Argulus infection. However, current control methods, such as pesticides, cause serious environmental damage. Herbal treatment methods are ineffective and have limitations. Hence, a more efficient and cost-effective control method is needed. In recent years, vaccine development has emerged as a promising avenue of research. Understanding the effect of the host-parasite relationship in the host immune system is essential to develop strategies for prevention, control, and management of argulosis. These interactions provide insights into the co-evolutionary dynamics between hosts and parasites. This review provides an overview of the current knowledge on the host-searching behaviour of Argulus, host-parasite interaction and control strategies. This review also highlights the need for further research and the development of sustainable control measures for Argulus infection.

Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon

BACKGROUND

Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown.

RESULTS

We characterized the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12 h, 24 h, 36 h, 48 h, and 60 h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite.

CONCLUSIONS

Our results highlight the key role of keratinocytes in coho salmon's sea lice resistance and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.

A comparative analysis of alternative splicing patterns in Atlantic salmon (Salmo salar) in response to Moritella viscosa and sea lice (Lepeophtheirus salmonis) infection

Moritella viscosa (M. viscosa) and sea lice (Lepeophtheirus salmonis) are severe pathogens that primarily infect the skin of Atlantic salmon (Salmo salar), which cause significant economic losses in the farming industry. However, the pathogenesis and molecular mechanisms underlying the host's immune defence at the post-transcriptional level remain unclear. Alternative splicing (AS) is an evolutionarily conserved post-transcriptional mechanism that can greatly increase the richness of the transcriptome and proteome. In this study, transcriptomic data derived from skin tissues of Atlantic salmon after M. viscosa and sea lice infections were used to examine the AS profiles and their differential expression patterns. In total, we identified 33,044 AS events (involving 13,718 genes) in the control (CON) group, 35,147 AS events (involving 14,340 genes) in the M. viscosa infection (MV) group, and 30,364 AS events (involving 13,142 genes) in the sea lice infection (LC) group, respectively. Among the five types of AS identified in our study (i.e., SE, A5SS, A3SS, MXE, and RI), SE was the most prevalent type in all three groups (i.e., CON, MV, and LC groups). Decreased percent-spliced-in (PSI) levels were observed in SE events under both MV- and LC-infected conditions, suggesting that MV or LC infection elevated exon-skipping isoforms and promoted the selection of shorter transcripts in numerous DAS genes. In addition, most of the differential AS genes were found to be associated with pathways related to mRNA regulation, epithelial or muscle development, and immune response. These findings provide novel insights into the role of AS in host-pathogen interactions and represent the first comparative analysis of AS in response to bacterial and parasitic infections in fish.

Vegetable omega-3 and omega-6 fatty acids differentially modulate the antiviral and antibacterial immune responses of Atlantic salmon

The immunomodulatory effects of omega-3 and omega-6 fatty acids are a crucial subject of investigation for sustainable fish aquaculture, as fish oil is increasingly replaced by terrestrial vegetable oils in aquafeeds. Unlike previous research focusing on fish oil replacement with vegetable alternatives, our study explored how the omega-6 to omega-3 polyunsaturated fatty acid (PUFA) ratio in low-fish oil aquafeeds influences Atlantic salmon's antiviral and antibacterial immune responses. Atlantic salmon were fed aquafeeds rich in soy oil (high in omega-6) or linseed oil (high in omega-3) for 12 weeks and then challenged with bacterial (formalin-killed Aeromonas salmonicida) or viral-like (polyriboinosinic polyribocytidylic acid) antigens. The head kidneys of salmon fed high dietary omega-3 levels exhibited a more anti-inflammatory fatty acid profile and a restrained induction of pro-inflammatory and neutrophil-related genes during the immune challenges. The high-omega-3 diet also promoted a higher expression of genes associated with the interferon-mediated signaling pathway, potentially enhancing antiviral immunity. This research highlights the capacity of vegetable oils with different omega-6 to omega-3 PUFA ratios to modulate specific components of fish immune responses, offering insights for future research on the intricate lipid nutrition-immunity interplay and the development of novel sustainable low-fish oil clinical aquaculture feeds.

A Proof-of-Concept Study to Develop a Peptide-Based Vaccine against Salmon Lice Infestation in Atlantic Salmon (Salmo salar L.)

Proteins present in blood samples from Atlantic salmon (Salmo salar) infected with salmon lice (Lepeophtheirus salmonis) were analyzed using liquid chromatography-high-resolution mass spectrometry. Bioinformatic analyses revealed 1820 proteins, of which 58 were assigned to lice. Among these, peroxiredoxin-2, an antioxidant protein, was found relevant with respect to blood feeding of the parasite. The three-dimensional structure analysis of the protein revealed a surface amino acid sequence of interest. A 13-amino-acid peptide was selected as a potential antigen due to its predicted solubility, antigenicity, probable non-allergenic, and non-toxic nature. This peroxiredoxin-2-derived peptide was synthesized, combined with a commercially available adjuvant, and used for vaccination. The test vaccine demonstrated a 60-70% protection rate against early-stage Lepeophtheirus salmonis infection in a challenge trial in Norway. Additionally, the vaccine was tested against salmon lice (Caligus rogercresseyi) in Chile, where a remarkable 92% reduction in the number of adult lice was observed. Thus, in combination with the selected adjuvant, the peptide showed antigenic potential, making it a suitable candidate for future vaccine development. The approach described holds promise for the development of peptide vaccines against various ectoparasites feeding on blood or skin secretions of their hosts.

Mucous cell histopathology and label-free quantitative proteomic analysis of skin mucus in fat greenling (Hexagrammos otakii) infected with Vibrio harveyi

Hexagrammos otakii is favored by consumers and aquaculture practitioners because of its strong adaptability and fast growth. However, recently, frequent outbreaks of diseases in the breeding of H. otakii have led to significant economic losses, especially due to bacterial diseases, which limit the healthy breeding of H. otakii. As a luminescent Gram-negative bacterium, Vibrio harveyi is the main pathogenic bacteria of H. otakii. In this study, the histopathology and label-free quantitative proteomics analysis were performed to reveal the changes of skin mucus proteins in H. otakii after infection with V. harveyi. The histopathological changes in the skin of H. otakii showed that when the bacteria were injected into the epithelial cells, it caused an increase in the number of mucous cells and a certain degree of damage and deformation in skin. Moreover, the quantitative proteomics analysis revealed a total of 364 differentially expressed proteins (DEPs), and these DEPs were found to be involved in environmental information processing, metabolism, infectious diseases: bacteria, replication and repair. More importantly, the enrichment analysis of the DEPs revealed that these different proteins were mainly targeted immune-related pathways. After infection of bacteria, the host's immune ability will be weakened, causing V. harveyi to enter the organism more easily, resulting in increased mucus in H. otakii, which will eventually lead to a decline in its physical function. These results provided an insight into a series of physiological changes after the bacterial infection of fish at the proteomic level and basic data for further exploration of the potential mechanism of skin mucus. Taken together, the results indicated more opportunities for the future designs and discoveries of effective antibacterial vaccines and antibacterial drugs for H. otakii.

Immune response induced by coinfection of the sea louse Caligus rogercresseyi and the intracellular bacteria Piscirickettsia salmonis in vaccinated Atlantic salmon

Recently, we showed that Atlantic salmon vaccinated against Piscirickettsia salmonis lose their protection upon coinfection with Caligus rogercresseyi (sea lice). However, the causes of the overriding effect of C. rogercresseyi infection have not been elucidated, and the molecular basis of the cellular and humoral immune responses upon C. rogercresseyi infection has not been described for vaccinated salmon. Therefore, we studied changes in the transcription of immune genes in vaccinated Atlantic salmon that were experimentally challenged by co-infecting them with C. rogercresseyi and P. salmonis. In general, coinfection treatments showed immune gene expression similar to treatments with a single P. salmonis infection, showing a decreased cellular response. However, a high variance was found between individual fish in the case of crucial cellular immune genes, with a few fish reacting overwhelmingly highly compared to the majority. This supports our previous findings on vaccination response variation and reinforces the idea that vaccination failures in the field might be caused by an overwhelming amount of vaccinated fish that display a deficient immune response to the infection.

Does Anisakis spp. infestation affect the proximate composition, fatty acids, and minerals contents of its host Merluccius merlucccius?

Fish play an important role in human nutrition. They are not only a great source of protein and healthy fats, but also a unique source of essential nutrients such as omega-3 fatty acids. Moreover, most fish are parasitized, and some of these parasites are able to influence the reallocation of resources in their favor and thus reduce the nutritional quality of the fish. The present study was conducted to investigate the impact of the third stage larvae (L3) of Anisakis spp. on the proximate composition, macro-minerals (potassium, calcium, and sodium), and fatty acids of European hake (Merluccius merluccius Linnaeus, 1758). In parasitized female group, our results revealed a decrease (p< 0.005) in the amount of carbohydrate by 6.5%, of calcium by 17%, and of 2 polyunsaturated fatty acids (arachidonic acid (C20: 4w-6), and eicosapentaenoic acid (C20: 5w-3) with 33% and 15% respectively. Simultaneously, an increase by 25% in the level of a single saturated fatty acid C10:0 was noticed. According to the principal component analysis, the parasitized female was wealthy of saturated fatty acids and monounsaturated fatty acids and contains less of polyunsaturated fatty acids, omega-3 fatty acids, and omega-6 fatty acids than the unparasitized female and male. No significant changes were observed in the biochemical composition of male hake, probably due to the low mean intensity of L3 larvae of Anisakis spp. in this group.

Applying genetic technologies to combat infectious diseases in aquaculture

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.

Characterization of the MMP9 Gene and Its Association with Cryptocaryon irritans Resistance Traits in Trachinotus ovatus (Linnaeus, 1758)

The MMPs are endogenous proteolytic enzymes that require zinc and calcium as cofactors. MMP9 is one of the most complex matrix metalloproteinases in the gelatinase family and has many biological functions. In mammals, mmp9 is thought to be closely associated with cancer. However, studies in fish have rarely been reported. In this study, to understand the expression pattern of the ToMMP9 gene and its association with the resistance of Trachinotus ovatus to Cryptocaryon irritans, the sequence of the MMP9 gene was obtained from the genome database. The expression profiles were measured by qRT-PCR, the SNPs were screened by direct sequencing, and genotyping was performed. The ToMMP9 gene contained a 2058 bp ORF encoding a putative amino acid sequence of 685 residues. The homology of the ToMMP9 in teleosts was more than 85%, and the genome structure of ToMMP9 was conserved in chordates. The ToMMP9 gene was expressed in different tissues of healthy individuals and was highly expressed in the fin, the gill, the liver and the skin tissues. The ToMMP9 expression in the skin of the infected site and its adjacent sites increased significantly after C. irritans infection. Two SNPs were identified in the ToMMP9 gene, and the SNP (+400A/G) located in the first intron was found to be significantly associated with the susceptibility/resistance to C. irritans. These findings suggest that ToMMP9 may play an important role in the immune response of T. ovatus against C. irritans.

Integrative analysis of miRNA and mRNA expression associated with the immune response in the intestine of rainbow trout (Oncorhynchus mykiss) infected with infectious hematopoietic necrosis virus

Rainbow trout (Oncorhynchus mykiss), an economically important cold-water fish cultured worldwide, suffers from infectious hematopoietic necrosis virus (IHNV) infection, resulting in huge financial losses. In order to understand the immune response of rainbow trout during virus infection, we explored trout intestine transcriptome profiles following IHNV challenge, and identified 3355 differentially expressed genes (DEGs) and 80 differentially expressed miRNAs (DEMs). Transcriptome analysis revealed numerous DEGs involved in immune responses, such as toll-like receptor 3 (TLR3), toll-like receptor 7/8 (TLR7/8), tripartite motif-containing 25 (TRIM25), DExH-Box helicase 58 (DHX58), interferon-induced with helicase C domain 1 (IFIH1), interferon regulatory factor 3 (IRF3/7), signal transducer and activator of transcription 1 (STAT1) and heat shock protein 90-alpha 1 (HSP90A1). Integrated analysis identified five key miRNAs (miR-19-y, miR-181-z, miR-203-y, miR-143-z and miR-206-y) targeting at least two important immune genes (TRIM25, DHX58, STAT1, TLR7/8 and HSP90A1). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that DEGs and target genes were significantly enriched in various immune-related terms including immune system process, binding, cell part and pathways of Toll-like receptor signalling, RIG-I-like receptor signalling, NOD-like receptor signalling, JAK-STAT signalling, PI3K-Akt signalling, NF-kappa B signalling, IL-17 signalling and AGE-RAGE signalling. In addition, protein-protein interaction networks (PPI) was used to display highly interactive DEG networks involving eight immune-related pathways. The expression trends of 12 DEGs and 10 DEMs were further verified by quantitative real-time PCR, which confirmed the reliability of the transcriptome sequencing results. This study expands our understanding of the immune response of rainbow trout infected with IHNV, and provides valuable resources for future studies on the immune molecular mechanism and disease resistance breeding.

Dual RNA-Seq Analysis Reveals Transcriptome Effects during the Salmon–Louse Interaction in Fish Immunized with Three Lice Vaccines

Due to the reduced efficacy of delousing drugs used for sea lice control in salmon aquaculture, fish vaccines have emerged as one of the most sustainable strategies in animal health. Herein, the availability of C. rogercresseyi and Salmo salar genomes increases the capability of identifying new candidate antigens for lice vaccines using RNA sequencing and computational tools. This study aimed to evaluate the effects of two recombinant antigens characterized as peritrophin and cathepsin proteins on the transcriptome profiling of Atlantic salmon during a sea lice infestation. Four experimental groups were used: Peritrophin, cathepsin, and peritrophin/cathepsin (P/C), and PBS as the control. C. rogercresseyi female, S. salar head kidney, and skin tissue samples were sampled at 25 days post-infestation (dpi) for Illumina sequencing and RNA-seq analysis. Differential gene expression, gene ontology, and chromosomal expression analyses were performed. Furthermore, the dual RNA-seq analysis approach was performed to simultaneously explore host and pathogen transcriptomes, identifying functional associations for vaccine design. The morphometry of female sea lice exposed to immunized fish was also evaluated. The RNA-Seq analysis exhibited prototype-dependent transcriptome modulation, showing a conspicuous competition for metal ions during the infestation. Moreover, Dual RNA-seq analysis revealed vaccine-dependent gene patterns in both the host and the pathogen. Notably, significant morphometric differences between lice collected from immunized and control fish were observed, where cathepsin and P/C showed 57% efficacy. This study showed the potential of two proteins as lice vaccines for the salmon industry, suggesting novel molecular mechanisms between host–parasite interactions.

Peritrophin-like Genes Are Associated with Delousing Drug Response and Sensitivity in the Sea Louse Caligus rogercresseyi

Caligus rogercresseyi is the main ectoparasite that affects the salmon industry in Chile. The mechanisms used by the parasite to support its life strategy are of great interest for developing control strategies. Due to the critical role of insect peritrophins in host–parasite interactions and response to pest control drugs, this study aimed to identify and characterize the peritrophin-like genes present in C. rogercresseyi. Moreover, the expression of peritrophin-like genes was evaluated on parasites exposed to delousing drugs such as pyrethroids and azamethiphos. Peritrophin genes were identified by homology analysis among the sea louse transcriptome database and arthropods peritrophin-protein database obtained from GenBank and UniProt. Moreover, the gene loci in the parasite genome were located. Furthermore, peritrophin gene expression levels were evaluated by RNA-Seq analysis in sea louse developmental stages and sea lice exposed to delousing drugs deltamethrin, cypermethrin, and azamethiphos. Seven putative peritrophin-like genes were identified in C. rogercresseyi with high homology with other crustacean peritrophins. Differences in the presence of signal peptides, the number of chitin-binding domains, and the position of conserved cysteines were found. In addition, seven peritrophin-like gene sequences were identified in the C. rogercresseyi genome. Gene expression analysis revealed a stage-dependent expression profile. Notably, differential regulation of peritrophin genes in resistant and susceptible populations to delousing drugs was found. These data are the first report and characterization of peritrophin genes in the sea louse C. rogercresseyi, representing valuable knowledge to understand sea louse biology. Moreover, this study provides evidence for a deeper understanding of the molecular basis of C. rogercresseyi response to delousing drugs.

Seasonal variations in the skin epidermal structure and mucosal immune parameters of rainbow trout skin (Oncorhynchus mykiss) at different stages of farming

The aim of this study was to investigate the seasonal changes in the epidermal structure and the innate immunity parameters of skin mucus in rainbow trout. The skin epidermis and mucus samples were collected over three consecutive seasons including winter, spring and late summer from three different weight groups i.e., 2-20 g (W1), 100-200 g (W2) and 400-600 g (W3) fish. The skin mucosal immunity analysis of rainbow trout showed that the haemagglutination activity increased significantly with increasing fish size from W1 to W3 in all three seasons, while no significant seasonal changes occurred in haemagglutination activity. Moreover, the bactericidal activity against fish pathogens increased significantly with increasing water bacterial load in late summer. The SDS-PAGE analysis of mucus showed a high amount of low molecular weight proteins (<35 kDa) in the late summer that was correlated with the increase in bactericidal activity. Histological analysis of the epidermis structure of rainbow trout skin showed that the density and size of goblet cells and consequently the mucus secretion significantly increased in W3 group in all seasons. In all three weight groups of fish, the density of goblet cells significantly increased from winter to spring and late summer along with increasing water temperature. Moreover, the goblet cell density showed a significant positive relationship with the soluble protein concentration and haemagglutination activity (p < 0.01). The results of this study demonstrated the more active immune role of the skin epidermal cells and mucus in rainbow trout during summer to protect fish against the pathogenic microorganisms. Given its potent bactericidal properties and the lack of haemolytic activity, the rainbow trout mucus might be used as a safe and inexpensive source for developing antimicrobial agents to prevent and treat some bacterial diseases in human and fish.

cMOS enhanced the mucosal immune function of skin and gill of goldfish (Carassius auratus Linnaeus) to improve the resistance to Ichthyophthirius multifiliis infection

of supporting mucosal immune barrier integrity and prevention of some pathogenic infections in aquatic species, are key areas of active study, often focusing on feed additives. The objectives of this study were to explore the effects of feeding cMOS (concentrated mannan oligosaccharide) on the gill and skin mucosal barriers of goldfish (Carassius auratus Linnaeus) and evaluate health status during Ichthyophthirius multifiliis infection. After feeding the cMOS-containing diet for 60 days, Hematoxylin and eosin (H&E) staining showed greater length of gill lamella and thicker dermal dense layer, while Alcian Blue and Periodic acid-Schiff (AB-PAS) staining showed higher numbers of mucin cells in cMOS fed fish. Chemical analysis showed that fish fed cMOS had greater enzyme activity of lysozyme (LZM) and alkaline phosphatase (AKP) in gill and skin tissues, while qRT-PCR revealed higher expression of Muc-2 and IL-1β, as well as lower expression of IL-10. After Ichthyophthirius multifiliis challenge, goldfish fed the cMOS diet had lower mortality and infection rates, as well as fewer visible white spots on the body surfaces. Histologically, the gill and skin of these fish presented less tissue damage and fewer parasites, and had a greater number of mucus cells. In addition, the expression of Muc-2 and IL-10 were notably higher while the expression of IL-1β was significantly lower in cMOS fed goldfish than control fed fish. In this study, cMOS fed goldfish had stronger immune barrier function of skin and gill mucous, and better survival following Ichthyophthirius multifiliis infection.

Exploring Sea Lice Vaccines against Early Stages of Infestation in Atlantic Salmon (Salmo salar)

The sea louse Caligus rogercresseyi genome has opened the opportunity to apply the reverse vaccinology strategy for identifying antigens with potential effects on lice development and its application in sea lice control. This study aimed to explore the efficacy of three sea lice vaccines against the early stage of infestation, assessing the transcriptome modulation of immunized Atlantic salmon. Therein, three experimental groups of Salmo salar (Atlantic salmon) were vaccinated with the recombinant proteins: Peritrophin (prototype A), Cathepsin (prototype B), and the mix of them (prototype C), respectively. Sea lice infestation was evaluated during chalimus I-II, the early-infective stages attached at 7-days post infestation. In parallel, head kidney and skin tissue samples were taken for mRNA Illumina sequencing. Relative expression analyses of genes were conducted to identify immune responses, iron transport, and stress responses associated with the tested vaccines during the early stages of sea lice infection. The vaccine prototypes A, B, and C reduced the parasite burden by 24, 44, and 52% compared with the control group. In addition, the RNA-Seq analysis exhibited a prototype-dependent transcriptome modulation. The high expression differences were observed in genes associated with metal ion binding, molecular processes, and energy production. The findings suggest a balance between the host’s inflammatory response and metabolic process in vaccinated fish, increasing their transcriptional activity, which can alter the early host–parasite interactions. This study uncovers molecular responses produced by three vaccine prototypes at the early stages of infestation, providing new knowledge for sea lice control in the salmon aquaculture.

Gill and Liver Transcript Expression Changes Associated With Gill Damage in Atlantic Salmon (Salmo salar)

Gill damage represents a significant challenge in the teleost fish aquaculture industry globally, due to the gill's involvement in several vital functions and direct contact with the surrounding environment. To examine the local and systemic effects accompanying gill damage (which is likely to negatively affect gill function) of Atlantic salmon, we performed a field sampling to collect gill and liver tissue after several environmental insults (e.g., harmful algal blooms). Before sampling, gills were visually inspected and gill damage was scored; gill scores were assigned from pristine [gill score 0 (GS0)] to severely damaged gills (GS3). Using a 44K salmonid microarray platform, we aimed to compare the transcriptomes of pristine and moderately damaged (i.e., GS2) gill tissue. Rank Products analysis (5% percentage of false-positives) identified 254 and 34 upregulated and downregulated probes, respectively, in GS2 compared with GS0. Differentially expressed probes represented genes associated with functions including gill remodeling, wound healing, and stress and immune responses. We performed gill and liver qPCR for all four gill damage scores using microarray-identified and other damage-associated biomarker genes. Transcripts related to wound healing (e.g., neb and klhl41b) were significantly upregulated in GS2 compared with GS0 in the gills. Also, transcripts associated with immune and stress-relevant pathways were dysregulated (e.g., downregulation of snaclec 1-like and upregulation of igkv3) in GS2 compared with GS0 gills. The livers of salmon with moderate gill damage (i.e., GS2) showed significant upregulation of transcripts related to wound healing (i.e., chtop), apoptosis (e.g., bnip3l), blood coagulation (e.g., f2 and serpind1b), transcription regulation (i.e., pparg), and stress-responses (e.g., cyp3a27) compared with livers of GS0 fish. We performed principal component analysis (PCA) using transcript levels for gill and liver separately. The gill PCA showed that PC1 significantly separated GS2 from all other gill scores. The genes contributing most to this separation were pgam2, des, neb, tnnt2, and myom1. The liver PCA showed that PC1 significantly separated GS2 from GS0; levels of hsp70, cyp3a27, pparg, chtop, and serpind1b were the highest contributors to this separation. Also, hepatic acute phase biomarkers (e.g., serpind1b and f2) were positively correlated to each other and to gill damage. Gill damage-responsive biomarker genes and associated qPCR assays arising from this study will be valuable in future research aimed at developing therapeutic diets to improve farmed salmon welfare.

Interacting Effects of Sea Louse (Lepeophtheirus salmonis) Infection and Formalin-Killed Aeromonas salmonicida on Atlantic Salmon Skin Transcriptome

Lepeophtheirus salmonis (sea lice) and bacterial co-infection threatens wild and farmed Atlantic salmon performance and welfare. In the present study, pre-adult L. salmonis-infected and non-infected salmon were intraperitoneally injected with either formalin-killed Aeromonas salmonicida bacterin (ASAL) or phosphate-buffered saline (PBS). Dorsal skin samples from each injection/infection group (PBS/no lice, PBS/lice, ASAL/no lice, and ASAL/lice) were collected at 24 h post-injection and used for transcriptome profiling using a 44K salmonid microarray platform. Microarray results showed no clear inflammation gene expression signatures and revealed extensive gene repression effects by pre-adult lice (2,189 down and 345 up-regulated probes) in the PBS-injected salmon (PBS/lice vs. PBS/no lice), which involved basic cellular (e.g., RNA and protein metabolism) processes. Lice repressive effects were not observed within the group of ASAL-injected salmon (ASAL/lice vs. ASAL/no lice); on the contrary, the observed skin transcriptome changes –albeit of lesser magnitude (82 up and 1 down-regulated probes)– suggested the activation in key immune and wound healing processes (e.g., neutrophil degranulation, keratinocyte differentiation). The molecular skin response to ASAL was more intense in the lice-infected (ASAL/lice vs. PBS/lice; 272 up and 11 down-regulated probes) than in the non-infected fish (ASAL/no lice vs. PBS/no lice; 27 up-regulated probes). Regardless of lice infection, the skin’s response to ASAL was characterized by the putative activation of both antibacterial and wound healing pathways. The transcriptomic changes prompted by ASAL+lice co-stimulation (ASAL/lice vs. PBS/no lice; 1878 up and 3120 down-regulated probes) confirmed partial mitigation of lice repressive effects on fundamental cellular processes and the activation of pathways involved in innate (e.g., neutrophil degranulation) and adaptive immunity (e.g., antibody formation), as well as endothelial cell migration. The qPCR analyses evidenced immune-relevant genes co-stimulated by ASAL and lice in an additive (e.g., mbl2b, bcl6) and synergistic (e.g., hampa, il4r) manner. These results provided insight on the physiological response of the skin of L. salmonis-infected salmon 24 h after ASAL stimulation, which revealed immunostimulatory properties by the bacterin with potential applications in anti-lice treatments for aquaculture. As a simulated co-infection model, the present study also serves as a source of candidate gene biomarkers for sea lice and bacterial co-infection.

Variation in volatile organic compounds in Atlantic salmon mucus is associated with resistance to salmon lice infection

Salmon lice are ectoparasites that threaten wild and farmed salmonids. Artificial selection of salmon for resistance to the infectious copepodid lice stage currently relies on in vivo challenge trials on thousands of salmon a year. We challenged 5750 salmon with salmon lice (Lepeophtheirus salmonis) from two distinct farmed strains of salmon in two separate trials. We found that volatile organic compounds (VOC), 1-penten-3-ol, 1-octen-3-ol and 6-methyl-5-hepten-2-one in the mucus of the salmon host after salmon lice infection, were significantly associated with lice infection numbers across a range of water temperatures (5 °C, 10 °C, 17 °C). Some VOCs (benzene, 1-octen-3-ol and 3,5,5-trimethyl-2-hexene) were significantly different between lines divergently selected for salmon lice resistance. In a combined population assessment, selected VOCs varied between families in the range of 47- 59% indicating a genetic component and were positively correlated to the salmon hosts estimated breeding values 0.59–0.74. Mucosal VOC phenotypes could supplement current breeding practices and have the potential to be a more direct and ethical proxy for salmon lice resistance provided they can be measured prior to lice infestation.

Transcriptome Analysis of Atlantic Salmon (Salmo salar) Skin in Response to Sea Lice and Infectious Salmon Anemia Virus Co-Infection Under Different Experimental Functional Diets

Sea lice (Lepeophtheirus salmonis) are ectoparasitic copepods that cause significant economic loss in marine salmoniculture. In commercial salmon farms, infestation with sea lice can enhance susceptibility to other significant pathogens, such as the highly contagious infectious salmon anemia virus (ISAv). In this study, transcriptomic analysis was used to evaluate the impact of four experimental functional feeds (i.e. 0.3% EPA/DHA+high-ω6, 0.3% EPA/DHA+high-ω6+immunostimulant (IS), 1% EPA/DHA+high-ω6, and 1% EPA/DHA+high-ω3) on Atlantic salmon (Salmo salar) during a single infection with sea lice (L. salmonis) and a co-infection with sea lice and ISAv. The overall objectives were to compare the transcriptomic profiles of skin between lice infection alone with co-infection groups and assess differences in gene expression response among animals with different experimental diets. Atlantic salmon smolts were challenged with L. salmonis following a 28-day feeding trial. Fish were then challenged with ISAv at 18 days post-sea lice infection (dpi), and maintained on individual diets, to establish a co-infection model. Skin tissues sampled at 33 dpi were subjected to RNA-seq analysis. The co-infection’s overall survival rates were between 37%-50%, while no mortality was observed in the single infection with lice. With regard to the infection status, 756 and 1303 consensus differentially expressed genes (DEGs) among the four diets were identified in “lice infection vs. pre-infection” and “co-infection vs. pre-infection” groups, respectively, that were shared between the four experimental diets. The co-infection groups (co-infection vs. pre-infection) included up-regulated genes associated with glycolysis, the interferon pathway, complement cascade activity, and heat shock protein family, while the down-regulated genes were related to antigen presentation and processing, T-cell activation, collagen formation, and extracellular matrix. Pathway enrichment analysis conducted between infected groups (lice infection vs. co-infection) resulted in several immune-related significant GO terms and pathways unique to this group, such as “autophagosome”, “cytosolic DNA-sensing pathway” and “response to type I interferons”. Understanding how experimental functional feeds can impact the host response and the trajectory of co-infections will be an essential step in identifying efficacious intervention strategies that account for the complexities of disease in open cage culture.

Lernaea cyprinacea Linnaeus, 1758 (Copepoda: Lernaeidae) infection on Betta rubra Perugia, 1893 (Anabantiformes: Osphronemidae) from Aceh Province, Indonesia

Betta rubra is an ornamental freshwater fish endemic to northern Sumatra, Indonesia. The B. rubra population has decreased in recent decades, and is classified as an endangered species in the IUCN Red List. This study aims to report for the first time infection by L. cyprinacea in B. rubra harvested from the Aceh Besar region of Indonesia. The fish samples were obtained from the Cot Bira tributaries, Aceh Besar District, Indonesia from January to December 2020. The results showed that the parasite infected 6 out of 499 samples in August and September, with a prevalence and intensity rate of 1% and 2 parasites/fish, respectively. The eyes and pectoral fins were the common infection sites. Despite B. rubra is not an optimal host (small size) for the parasite, this parasite might serve as additional threatening factors for the endangered B. rubra fish population.

Energetic costs of ectoparasite infection in Atlantic salmon

Parasites are widespread in nature where they affect energy budgets of hosts, and depending on the imposed pathogenic severity, this may reduce host fitness. However, the energetic costs of parasite infections are rarely quantified. In this study, we measured metabolic rates in recently seawater adapted Atlantic salmon (Salmo salar) infected with the ectoparasitic copepod Lepeophtheirus salmonis and used an aerobic scope framework to assess the potential ecological impact of this parasite-host interaction. The early chalimus stages of L. salmonis did not affect either standard or maximum metabolic rates. However, the later mobile pre-adult stages caused an increase in both standard and maximum metabolic rate yielding a preserved aerobic scope. Notably, standard metabolic rates were elevated by 26%, presumably caused by increased osmoregulatory burdens and costs of mobilizing immune responses. The positive impact on maximum metabolic rates was unexpected and suggests that fish are able to transiently overcompensate energy production to endure the burden of parasites and thus allow for continuation of normal activities. However, infected fish are known to suffer reduced growth, and this suggests that a trade-off exists in acquisition and assimilation of resources despite of an uncompromised aerobic scope. As such, when assessing impacts of environmental or biotic factors, we suggest that elevated routine costs may be a stronger predictor of reduced fitness than the available aerobic scope. Furthermore, studying effects on parasitized fish in an ecophysiological context deserves more attention, especially considering interacting effects of other stressors in the Anthropocene.

Estimating the dispersal of Lepeophtheirus salmonis sea lice within and among Atlantic salmon sites of the Bay of Fundy, New Brunswick

The objective of this study was to estimate the impact of infestation pressures on the abundance of the parasitic sea louse, Lepeophtheirus salmonis, in the Bay of Fundy, New Brunswick (NB), Canada, using the Fish-iTrends database for the years 2009-2018. Infestation pressures were calculated as time-lagged weighted averages of the abundance of adult female (AF) sea lice within a site (internal infestation pressure: IIP) and among sites (external infestation pressure: EIP). The EIP weights were calculated from seaway distances among sites and a Gaussian kernel density for bandwidths of 5 to 60 km. The EIP with a bandwidth of 10 km had the best fit, as determined with Akaike's information criterion, and historical AF sea lice abundance. This estimated dispersal distance of 10 km was similar to previous studies in Norway, Scotland and in New Brunswick. The infestation pressures estimated from empirical AF sea lice abundance within and among sites significantly increased the abundance of AF sea lice (p < .001). This study concludes that sea lice burdens within Atlantic salmon farms in the Bay of Fundy, NB, are affected by within site management and could be improved by synchronizing treatments between sites.

To React or Not to React: The Dilemma of Fish Immune Systems Facing Myxozoan Infections

Myxozoans are microscopic, metazoan, obligate parasites, belonging to the phylum Cnidaria. In contrast to the free-living lifestyle of most members of this taxon, myxozoans have complex life cycles alternating between vertebrate and invertebrate hosts. Vertebrate hosts are primarily fish, although they are also reported from amphibians, reptiles, trematodes, mollusks, birds and mammals. Invertebrate hosts include annelids and bryozoans. Most myxozoans are not overtly pathogenic to fish hosts, but some are responsible for severe economic losses in fisheries and aquaculture. In both scenarios, the interaction between the parasite and the host immune system is key to explain such different outcomes of this relationship. Innate immune responses contribute to the resistance of certain fish strains and species, and the absence or low levels of some innate and regulatory factors explain the high pathogenicity of some infections. In many cases, immune evasion explains the absence of a host response and allows the parasite to proliferate covertly during the first stages of the infection. In some infections, the lack of an appropriate regulatory response results in an excessive inflammatory response, causing immunopathological consequences that are worse than inflicted by the parasite itself. This review will update the available information about the immune responses against Myxozoa, with special focus on T and B lymphocyte and immunoglobulin responses, how these immune effectors are modulated by different biotic and abiotic factors, and on the mechanisms of immune evasion targeting specific immune effectors. The current and future design of control strategies for myxozoan diseases is based on understanding this myxozoan-fish interaction, and immune-based strategies such as improvement of innate and specific factors through diets and additives, host genetic selection, passive immunization and vaccination, are starting to be considered.

Oral Immunization of Larvae and Juvenile of Lumpfish (Cyclopterus lumpus) against Vibrio anguillarum Does Not Influence Systemic Immunity

Vibrio anguillarum, a marine bacterial pathogen that causes vibriosis, is a recurrent pathogen of lumpfish (Cyclopterus lumpus). Lumpfish is utilized as a cleaner fish in the Atlantic salmon (Salmo salar) aquaculture in the North Atlantic region because of its ability to visualize and prey on the ectoparasite sea lice (Lepeophtheirus salmonis) on the skin of Atlantic salmon, and its performance in cold environments. Lumpfish immunity is critical for optimal performance and sea lice removal. Oral vaccine delivery at a young age is the desired method for fish immunization because is easy to use, reduces fish stress during immunization, and can be applied on a large scale while the fish are at a young age. However, the efficacy of orally delivered inactivated vaccines is controversial. In this study, we evaluated the effectiveness of a V. anguillarum bacterin orally delivered to cultured lumpfish and contrasted it to an intraperitoneal (i.p.) boost delivery. We bio-encapsulated V. anguillarum bacterin in Artemia salina live-feed and orally immunized lumpfish larvae. Vaccine intake and immune response were evaluated by microscopy and quantitative polymerase chain reaction (qPCR) analysis, respectively. qPCR analyses showed that the oral immunization of lumpfish larvae resulted in a subtle stimulation of canonical immune transcripts such as il8b, il10, igha, ighmc, ighb, ccl19, ccl20, cd8a, cd74, ifng, and lgp2. Nine months after oral immunization, one group was orally boosted, and a second group was both orally and i.p. boosted. Two months after boost immunization, lumpfish were challenged with V. anguillarum (7.8 × 10⁵ CFU dose⁻¹). Orally boosted fish showed a relative percentage of survival (RPS) of 2%. In contrast, the oral and i.p. boosted group showed a RPS of 75.5% (p < 0.0001). V. anguillarum bacterin that had been orally delivered was not effective in lumpfish, which is in contrast to the i.p. delivered bacterin that protected the lumpfish against vibriosis. This suggests that orally administered V. anguillarum bacterin did not reach the deep lymphoid tissues, either in the larvae or juvenile fish, therefore oral immunization was not effective. Oral vaccines that are capable of crossing the epithelium and reach deep lymphoid tissues are required to confer an effective protection to lumpfish against V. anguillarum

Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout

Sea lice (Caligus rogercresseyi) is an ectoparasite which causes major production losses in the salmon aquaculture industry worldwide. Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) are two of the most susceptible salmonid species to sea lice infestation. The objectives of this study were to: (1) identify genomic regions associated with resistance to Caligus rogercresseyi in Atlantic salmon and rainbow trout by performing single-step Genome-Wide Association studies (ssGWAS), and (2) identify candidate genes related to trait variation based on exploring orthologous genes within the associated regions across species. A total of 2626 Atlantic salmon and 2643 rainbow trout were challenged and genotyped with 50 K and 57 K SNP panels, respectively. We ran two independent ssGWAS for sea lice resistance on each species and identified 7 and 13 regions explaining more than 1% of the genetic variance for the trait, with the most important regions explaining 3% and 2.7% for Atlantic salmon and rainbow trout, respectively. We identified genes associated with immune response, cytoskeleton function, and cell migration when focusing on important genomic regions for each species. Moreover, we found 15 common orthogroups which were present in more than one associated genomic region, within- or between-species; however, only one orthogroup showed a clear potential biological relevance in the response against sea lice. For instance, dual-specificity protein phosphatase 10-like (dusp10) and dual-specificity protein phosphatase 8 (dusp8) were found in genomic regions associated with lice density in Atlantic salmon and rainbow trout, respectively. Dusp10 and dusp8 are modulators of the MAPK pathway and might be involved in the differences of the inflammation response between lice resistant and susceptible fish from both species. Our results provide further knowledge on candidate genes related to sea lice resistance and may help establish better control for sea lice in fish populations.

Caligus coryphaenae infection from the Osumi strait, Southern Japan: A new record on wild yellowtail (Seriola quinqueradiata)

The caligid parasite Caligus coryphaenae has been reported in several marine fishes from Japan. In this study, a total of 223 wild yellowtail (Seriola quinqueradiata) were collected from Kagoshima fish market, separated into three groups according to total length (TL < 50 cm, TL: 50-70 cm, and TL > 70 cm), and examined for C. coryphaenae infection. A total of 518 specimens of C. coryphaenae were isolated giving an overall prevalence of infection and mean intensity of 24.2% and 4.7 ± 3.5, respectively. Body surface, fins and operculum of hosts TL > 50 cm were recorded as preferred sites for the attachment of C. coryphaenae. Of female specimens, 56.7% bore egg strings with various egg string lengths (7.1 ± 1.2 mm), carrying from 98 to 140 eggs (0.06 ± 0.005 mm in length) per each string. To our knowledge, this is the first report of C. coryphaenae infection from wild yellowtail in Japanese waters and globally. This parasite has not been reported in yellowtail culture to date, but the finding on wild specimens of yellowtail means that it poses a risk to their culture.

A Novel Marine Pathogen Isolated from Wild Cunners (Tautogolabrus adspersus): Comparative Genomics and Transcriptome Profiling of Pseudomonas sp. Strain J380

Cunner (Tautogolabrus adspersus) is a cleaner fish being considered for utilized in the North Atlantic salmon (Salmo salar) aquaculture industry to biocontrol sea lice infestations. However, bacterial diseases due to natural infections in wild cunners have yet to be described. This study reports the isolation of Pseudomonas sp. J380 from infected wild cunners and its phenotypic, genomic, and transcriptomic characterization. This Gram-negative motile rod-shaped bacterium showed a mesophilic (4-28 °C) and halotolerant growth. Under iron-limited conditions, Pseudomonas sp. J380 produced pyoverdine-type fluorescent siderophore. Koch's postulates were verified in wild cunners by intraperitoneally (i.p.) injecting Pseudomonas sp. J380 at 4 × 103, 4 × 105, and 4 × 107 colony forming units (CFU)/dose. Host-range and comparative virulence were also investigated in lumpfish and Atlantic salmon i.p. injected with ~106 CFU/dose. Lumpfish were more susceptible compared to cunners, and Atlantic salmon was resistant to Pseudomonas sp. J380 infection. Cunner tissues were heavily colonized by Pseudomonas sp. J380 compared to lumpfish and Atlantic salmon suggesting that it might be an opportunistic pathogen in cunners. The genome of Pseudomonas sp. J380 was 6.26 megabases (Mb) with a guanine-cytosine (GC) content of 59.7%. Biochemical profiles, as well as comparative and phylogenomic analyses, suggested that Pseudomonas sp. J380 belongs to the P. fluorescens species complex. Transcriptome profiling under iron-limited vs. iron-enriched conditions identified 1159 differentially expressed genes (DEGs). Cellular metabolic processes, such as ribosomal and energy production, and protein synthesis, were impeded by iron limitation. In contrast, genes involved in environmental adaptation mechanisms including two-component systems, histidine catabolism, and redox balance were transcriptionally up-regulated. Furthermore, iron limitation triggered the differential expression of genes encoding proteins associated with iron homeostasis. As the first report on a bacterial infection in cunners, the current study provides an overview of a new marine pathogen, Pseudomonas sp. J380.

Development of Fish Parasite Vaccines in the OMICs Era: Progress and Opportunities

Globally, parasites are increasingly being recognized as catastrophic agents in both aquaculture sector and in the wild aquatic habitats leading to an estimated annual loss between 1.05 billion and 9.58 billion USD. The currently available therapeutic and control measures are accompanied by many limitations. Hence, vaccines are recommended as the "only green and effective solution" to address these concerns and protect fish from pathogens. However, vaccine development warrants a better understanding of host-parasite interaction and parasite biology. Currently, only one commercial parasite vaccine is available against the ectoparasite sea lice. Additionally, only a few trials have reported potential vaccine candidates against endoparasites. Transcriptome, genome, and proteomic data at present are available only for a limited number of aquatic parasites. Omics-based interventions can be significant in the identification of suitable vaccine candidates, finally leading to the development of multivalent vaccines for significant protection against parasitic infections in fish. The present review highlights the progress in the immunobiology of pathogenic parasites and the prospects of vaccine development. Finally, an approach for developing a multivalent vaccine for parasitic diseases is presented. Data sources to prepare this review included Pubmed, google scholar, official reports, and websites.

Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis

Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecule real-time sequencing (SMRT) and proximity ligation (Hi-C) analysis. Coding RNAs and non-coding RNAs, and specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were identified through whole transcriptome sequencing from different life stages. A total of 23,686 protein-coding genes and 12,558 non-coding RNAs were annotated. In addition, 6,308 lncRNAs and 5,774 miRNAs were found to be transcriptionally active from larvae to adult stages. Taken together, this genomic resource for C. rogercresseyi represents a valuable tool to develop sustainable control strategies in the salmon aquaculture industry.

Sea Lice (Lepeophtheirus salmonis) Infestation Reduces the Ability of Peripheral Blood Monocytic Cells (PBMCs) to Respond to and Control Replication of Salmonid Alphavirus in Atlantic Salmon (Salmo salar L.)

Here we have studied the impact of lice (Lepeophtheirus salmonis) infestation of donor fish on the ability of isolated peripheral blood monocytes (PBMCs) to control the replication of salmonid alphavirus (SAV) ex vivo. PBMCs were collected by Percoll gradients at eight and nine weeks post copepodid infestation of Atlantic salmon post smolt. Uninfested fish were controls. PBMCs were then infected ex vivo with SAV (subtype 3), and samples were collected for analysis at two, four, and six days post virus infection. Virus titer in the supernatant was assayed in CHH-1 cells, and in addition, the relative expression of the virus structural protein E2 and selected host antiviral genes, IRF9, ISG15, Mx, and IFIT5, were assayed using real-time PCR. Significantly higher virus replication was detected in cells collected from lice-infested fish compared to controls. Higher virus titer coincided with an inability to upregulate the expression of different immune genes, IFIT5, IRF9, and Mx. These findings point towards compromised ability of PBMCs from lice-infested fish to control virus replication, and, to our knowledge, is the first report showing the direct effect of lice infestation on the interplay between viruses and immune cells. There is a possible impact on the dynamic spread of viral diseases in the aquatic environment.

Microhabitat distributions and species interactions of ectoparasites on the gills of cichlid fish in Lake Victoria, Tanzania

Heterogeneous exposure to parasites may contribute to host species differentiation. Hosts often harbour multiple parasite species which may interact and thus modify each other's effects on host fitness. Antagonistic or synergistic interactions between parasites may be detectable as niche segregation within hosts. Consequently, the within-host distribution of different parasite taxa may constitute an important axis of infection variation among host populations and species. We investigated the microhabitat distributions and species interactions of gill parasites (four genera) infecting 14 sympatric cichlid species in Lake Victoria, Tanzania. We found that the two most abundant ectoparasite genera (the monogenean Cichlidogyrus spp. and the copepod Lamproglena monodi) were non-randomly distributed across the host gills and their spatial distribution differed between host species. This may indicate microhabitat selection by the parasites and cryptic differences in the host-parasite interaction among host species. Relationships among ectoparasite genera were synergistic: the abundances of Cichlidogyrus spp. and the copepods L. monodi and Ergasilus lamellifer tended to be positively correlated. In contrast, relationships among morphospecies of Cichlidogyrus were antagonistic: the abundances of morphospecies were negatively correlated. Together with niche overlap, this suggests competition among morphospecies of Cichlidogyrus. We also assessed the reproductive activity of the copepod species (the proportion of individuals carrying egg clutches), as it may be affected by the presence of other parasites and provide another indicator of the species specificity of the host-parasite relationship. Copepod reproductive activity did not differ between host species and was not associated with the presence or abundance of other parasites, suggesting that these are generalist parasites, thriving in all cichlid species examined from Lake Victoria.

Impact of a candidate vaccine on the dynamics of salmon lice (Lepeophtheirus salmonis) infestation and immune response in Atlantic salmon (Salmo salar L.)

Infection with parasitic copepod salmon louse Lepeophtheirus salmonis, represents one of the most important limitations to sustainable Atlantic salmon (Salmo salar L.) farming today in the North Atlantic region. The parasite exerts negative impact on health, growth and welfare of farmed fish as well as impact on wild salmonid populations. It is therefore central to ensure continuous low level of salmon lice with the least possible handling of the salmon and drug use. To address this, vaccination is a cost-effective and environmentally friendly control approach. In this study, efficacy of a vaccine candidate, containing a peptide derived from ribosomal protein P0, was validated post infestation with L. salmonis, at the lab-scale. The sampling results showed good potential of the vaccine candidate when administered intraperitoneally in the host, in reducing the ectoparasite load, through reduction of adult female lice counts and fecundity and with greater presumptive effect in F1 lice generation. The sampling results correlated well with the differential modulation of pro-inflammatory, Th1, Th2 and T regulatory mediators at the transcript level at different lice stages. Overall, the results supports approximately 56% efficacy when administered by intraperitoneal injection. However, additional validation is necessary under large-scale laboratory trial for further application under field conditions.

Tackling the Molecular Drug Sensitivity in the Sea Louse Caligus rogercresseyi Based on mRNA and lncRNA Interactions

Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. This pathogen is mainly controlled by immersion baths with delousing drugs, which can lead to resistant traits selection in lice populations. Bioassays are commonly used to assess louse drug sensitivity, but the current procedures may mask relevant molecular responses. This study aimed to discover novel coding genes and non-coding RNAs that could evidence drug sensitivity at the genomic level. Sea lice samples from populations with contrasting sensitivity to delousing drugs were collected. Bioassays using azamethiphos, cypermethrin, and deltamethrin drugs were conducted to evaluate the sensitivity and to collect samples for RNA-sequencing. Transcriptome sequencing was conducted on samples exposed to each drug to evaluate the presence of coding and non-coding RNAs associated with the response of these compounds. The results revealed specific transcriptome patterns in lice exposed to azamethiphos, deltamethrin, and cypermethrin drugs. Enrichment analyses of Gene Ontology terms showed specific biological processes and molecular functions associated with each delousing drug analyzed. Furthermore, novel long non-coding RNAs (lncRNAs) were identified in C. rogercresseyi and tightly linked to differentially expressed coding genes. A significant correlation between gene transcription patterns and phenotypic effects was found in lice collected from different salmon farms with contrasting drug treatment efficacies. The significant correlation among gene transcription patterns with the historical background of drug sensitivity suggests novel molecular mechanisms of pharmacological resistance in lice populations.

Salmon immunological defence and interplay with the modulatory capabilities of its ectoparasite Lepeophtheirus salmonis

The salmon louse Lepeophtheirus salmonis (Lsal) is an ectoparasitic copepod that exerts immunomodulatory and physiological effects on its host Atlantic salmon. Over 30 years of research on louse biology, control, host responses and the host-parasite relationship has provided a plethora of information on the intricacies of host resistance and parasite adaptation. Atlantic salmon exhibit temporal and spatial impairment of the immune system and wound healing ability during infection. This immunosuppression may render Atlantic salmon less tolerant to stress and other confounders associated with current management strategies. Contrasting susceptibility of salmonid hosts exists, and early pro-inflammatory Th1 type responses are associated with resistance. Rapid cellular responses to larvae appear to tip the balance of the host-parasite relationship in favour of the host, preventing severe immune-physiological impacts of the more invasive adults. Immunological, transcriptomic, genomic and proteomic evidence suggests pathological impacts occur in susceptible hosts through modulation of host immunity and physiology via pharmacologically active molecules. Co-evolutionary and farming selection pressures may have incurred preference of Atlantic salmon as a host for Lsal reflected in their interactome. Here, we review host-parasite interactions at the primary attachment/feeding site, and the complex life stage-dependent molecular mechanisms employed to subvert host physiology and immune responses.

Impact of co-infection with Lepeophtheirus salmonis and Moritella viscosa on inflammatory and immune responses of Atlantic salmon (Salmo salar)

This study was conducted to determine the effects of a co-infection with Moritella viscosa at different exposure levels of sea lice Lepeophtheirus salmonis in Atlantic salmon (Salmo salar). M. viscosa (1.14 × 10⁶  cfu/ml) was introduced to all experimental tanks at 10 days post-lice infection (dpLs). Mean lice counts decreased over time in both the medium lice co-infection (31.5 ± 19.0 at 7 dpLs; 16.9 ± 9.3 at 46 dpLs) and high lice co-infection (62.0 ± 10.8 at 7 dpLs; 37.6 ± 11.3 at 46 dpLs). There were significantly higher mortalities and more severe skin lesions in the high lice co-infected group compared to medium lice co-infected group or M. viscosa-only infection. Quantitative gene expression analysis detected a significant upregulation of genes in skin from the high lice co-infection group consistent with severe inflammation (il-8, mmp-9, hep, saa). Skin lesions retrieved throughout the study were positive for M. viscosa growth, but these were rarely located in regions associated with lice. These results suggest that while M. viscosa infection itself may induce skin lesion development in salmon, co-infection with high numbers of lice can enhance this impact and significantly reduce the ability of these lesions to resolve, resulting in increased mortality.

Integrated analysis of mRNA-miRNA expression in Tilapia infected with Tilapia lake virus (TiLV) and identifies primarily immuneresponse genes

We investigated differential gene expression in Tilapia infected with the Tilapia Lake virus (TiLV).We used high-throughput sequencing to identify mRNAs and miRNAs involved in TiLV infection progression We identified 25,359 differentially expressed genes that included 863 new genes. We identified 1770, 4142 and 4947 differently expressed genes comparing non-infected controls with 24 and 120 h infections and between the infected groups, respectively. These genes were enriched to 291 GO terms and 62 KEGG pathways and included immune system progress and virion genes. High-throughput miRNA sequencing identified 316 conserved miRNAs, 525 known miRNAs and 592 novel miRNAs. Furthermore, 138, 198 and 153 differently expressed miRNAs were found between the 3 groups listed above, respectively. Target prediction revealed numerous genes including erythropoietin isoform X2, double-stranded RNA-specific adenosine deaminase isoform X1, bone morphogenetic protein 4 and tapasin-related protein that are involved in immune responsiveness. Moreover, these target genes overlapped with differentially expressed mRNAs obtained from RNA-seq. These target genes were significantly enriched to GO terms and KEGG pathways including immune system progress, virion and Wnt signaling pathways. Expression patterns of differentially expressed mRNA and miRNAs were validated in 20 mRNA and 19 miRNAs by qRT-PCR. We also were able to construct a miRNA-mRNA target network that can further understand the molecular mechanisms on the pathogenesis of TiLV and guide future research in developing effective agents and strategies to combat TiLV infections in Tilapia.

Transcriptomic Profiling in Fins of Atlantic Salmon Parasitized with Sea Lice: Evidence for an Early Imbalance Between Chalimus-Induced Immunomodulation and the Host's Defense Response

Parasitic sea lice (e.g., Lepeophtheirus salmonis) cause costly outbreaks in salmon farming. Molecular insights into parasite-induced host responses will provide the basis for improved management strategies. We investigated the early transcriptomic responses in pelvic fins of Atlantic salmon parasitized with chalimus I stage sea lice. Fin samples collected from non-infected (i.e. pre-infected) control (PRE) and at chalimus-attachment sites (ATT) and adjacent to chalimus-attachment sites (ADJ) from infected fish were used in profiling global gene expression using 44 K microarrays. We identified 6568 differentially expressed probes (DEPs, FDR < 5%) that included 1928 shared DEPs between ATT and ADJ compared to PRE. The ATT versus ADJ comparison revealed 90 DEPs, all of which were upregulated in ATT samples. Gene ontology/pathway term network analyses revealed profound changes in physiological processes, including extracellular matrix (ECM) degradation, tissue repair/remodeling and wound healing, immunity and defense, chemotaxis and signaling, antiviral response, and redox homeostasis in infected fins. The QPCR analysis of 37 microarray-identified transcripts representing these functional themes served to confirm the microarray results with a significant positive correlation (p < 0.0001). Most immune/defense-relevant transcripts were downregulated in both ATT and ADJ sites compared to PRE, suggesting that chalimus exerts immunosuppressive effects in the salmon's fins. The comparison between ATT and ADJ sites demonstrated the upregulation of a suite of immune-relevant transcripts, evidencing the salmon's attempt to mount an anti-lice response. We hypothesize that an imbalance between immunomodulation caused by chalimus during the early phase of infection and weak defense response manifested by Atlantic salmon makes it a susceptible host for L. salmonis.

Allergic Reactions and Immunity in Response to Tick Salivary Biogenic Substances and Red Meat Consumption in the Zebrafish Model

Ticks are arthropod ectoparasite vectors of pathogens and the cause of allergic reactions affecting human health worldwide. In humans, tick bites can induce high levels of immunoglobulin E antibodies against the carbohydrate Galα1-3Galβ1-(3)4GlcNAc-R (α-Gal) present in glycoproteins and glycolipids from tick saliva that mediate anaphylactic reactions known as the alpha-Gal syndrome (AGS) or red meat allergy. In this study, a new animal model was developed using zebrafish for the study of allergic reactions and the immune mechanisms in response to tick salivary biogenic substances and red meat consumption. The results showed allergic hemorrhagic anaphylactic-type reactions and abnormal behavior patterns likely in response to tick salivary toxic and anticoagulant biogenic compounds different from α-Gal. However, the results showed that only zebrafish previously exposed to tick saliva developed allergic reactions to red meat consumption with rapid desensitization and tolerance. These allergic reactions were associated with tissue-specific Toll-like receptor-mediated responses in types 1 and 2 T helper cells (T_H1 and T_H2) with a possible role for basophils in response to tick saliva. These results support previously proposed immune mechanisms triggering the AGS and provided evidence for new mechanisms also potentially involved in the AGS. These results support the use of the zebrafish animal model for the study of the AGS and other tick-borne allergies.

Identification of proteins from the secretory/excretory products (SEPs) of the branchiuran ectoparasite Argulus foliaceus (Linnaeus, 1758) reveals unique secreted proteins amongst haematophagous ecdysozoa

BACKGROUND

It is hypothesised that being a blood-feeding ectoparasite, Argulus foliaceus (Linnaeus, 1758), uses similar mechanisms for digestion and host immune evasion to those used by other haematophagous ecdysozoa, including caligid copepods (e.g. sea louse). We recently described and characterised glands associated with the feeding appendages of A. foliaceus using histological techniques. The work described in the present study is the first undertaken with the objective of identifying and partially characterising the components secreted from these glands using a proteomic approach.

METHODS

Argulus foliaceus parasites were sampled from the skin of rainbow trout (Oncorhynchus mykiss), from Loch Fad on the Isle of Bute, Scotland, UK. The proteins from A. foliaceus secretory/excretory products (SEPs) were collected from the supernatant of artificial freshwater conditioned with active adult parasites (n = 5-9 per ml; n = 560 total). Proteins within the SEPs were identified and characterised using LC-ESI-MS/MS analysis. Data are available via ProteomeXchange with identifier PXD016226.

RESULTS

Data mining of a protein database translated from an A. foliaceus dataset using ProteinScape allowed identification of 27 predicted protein sequences from the A. foliaceus SEPs, each protein matching the criteria of 2 peptides with at least 4 contiguous amino acids. Nine proteins had no matching sequence through OmicsBox (Blast2GO) analysis searches suggesting that Argulus spp. may additionally have unique proteins present in their SEPs. SignalP 5.0 software, identified 13 proteins with a signal sequence suggestive of signal peptides and supportive of secreted proteins being identified. Notably, the functional characteristics of identified A. foliaceus proteins/domains have also been described from the salivary glands and saliva of other blood-feeding arthropods such as ticks. Identified proteins included: transporters, peroxidases, metalloproteases, proteases and serine protease inhibitors which are known to play roles in parasite immune evasion/induction (e.g. astacin), immunomodulation (e.g. serpin) and digestion (e.g. trypsin).

CONCLUSIONS

To our knowledge, the present study represents the first proteomic analysis undertaken for SEPs from any branchiuran fish louse. Here we reveal possible functional roles of A. foliaceus SEPs in digestion and immunomodulation, with a number of protein families shared with other haematophagous ectoparasites. A number of apparently unique secreted proteins were identified compared to other haematophagous ecdysozoa.

Behavioural mechanisms underlying parasite-mediated competition for refuges in a coral reef fish

Parasites have been increasingly recognized as participants in indirect ecological interactions, including those mediated by parasite-induced changes to host behaviour (trait-mediated indirect interactions or TMIIs). In most documented examples, host behaviours altered by parasites increase susceptibility to predation because the predator is also a host (host-manipulation). Here, we test for a TMII in which a parasitic copepod modifies the predator-prey interaction between a small goby host and several larger predatory fish. Gobies compete for crevices in the reef to avoid predation and goby mortality increases more rapidly with increasing refuge shortage for parasitized gobies than for those free of parasites. We found interactive effects of refuge shortage and parasitism on two behaviours we predicted might be associated with parasite-mediated competition for refuges. First, as refuge-shortage increases, the rate of aggression among gobies increases and parasitism intensifies this interaction. Second, goby proximity to refuges increases as refuges become scarce, but parasitism nullifies this increase. In combination, these parasite-induced changes in behaviour may explain why parasitized gobies are poor competitors for refuges. Because the parasite is not trophically transmitted via host manipulation, these altered behaviours in parasitized gobies are likely coincidental to infection.

Histological and hematological alterations of silver catfish Rhamdia quelen highly parasitized by Lernaea cyprinacea

The main objective of this study was to evaluate the histological and hematological alterations of silver catfish Rhamdia quelen (Quoy & Gaimard, 1824) against intense parasitism by anchor worm Lernaea cyprinacea Linnaeus, 1758. Thirteen fish specimens were collected at the Fish Genetic Improvement Unit (EPAGRI/CEDAP), Brazil. After acclimatization, the fish were anesthetized for blood collection, and the samples were used for counting thrombocytes, total leukocytes, differential leukocytes and for quantification of total erythrocytes. Afterwards, the animals were euthanized, the parasites removed and quantified, and the portions of the affected tegument fixed in 10% buffered formalin. All the analyzed animals were parasitized by L. cyprinacea with mean intensity of 192 specimens per fish. The hematological profile of the animals was different from that reported for healthy fish. Immature leukocytes were the most abundant cells, followed by monocytes, lymphocytes, neutrophils, and periodic acid-Schiff-positive granular leukocytes. A small number of neutrophils were present in the bloodstream of parasitized fish, while histological examination evidenced the accumulation of this cell type near the place of infection by the parasite. Total leukocytes correlated significantly and positively (r = 0.6, p = 0.030) with the intensity of L. cyprinacea infection and the fish weight. Histological changes included hemorrhage, liquefactive necrosis and connective tissue disarrangement, necrosis, granulomatous inflammation, mononuclear and polynuclear inflammation, as well as hyperplasia and hypertrophy of the alarm and mucous cells. The L. cyprinacea infection intensity caused deleterious changes both in the hematological profile and the integument of R. quelen, confirming the pathogenic potential of this parasite to the affected fish species.

Modulation of the Expression of Immune-related Gene in Atlantic and Coho Salmon during Infestation with the Sea lice Caligus rogercresseyi

Caligus rogercresseyi, a marine ectoparasite, causes notable economic losses for the Chilean salmonid industry. Nevertheless, the immunological responses of infected fish remain poorly understood, including proinflammatory cytokine generation and the respective modulatory effects of various cytokine receptors. This study evaluated mRNA expression of the NLRC5, major histocompatibility complex (MHC) class II, I-kappa-B-alpha, a regulatory that inhibits NF-kappa-B, and proinflammatory cytokines (IL-1β and IL-18) in the liver and muscle of Atlantic salmon (Salmo salar) and Coho salmon (Oncorhynchus kisutch) during a time-course C. rogercresseyi infestation trial. All assessed mRNA were strongly regulated during infestation, but S. salar showed up-regulated expression, possibly accounting for the high infestation vulnerability of this salmonid. In conclusion, this work helps to understand the modulation of the expression of different transcripts involved over short periods of C. rogercresseyi infestation in two salmonid species (S. salar and O. kisutch).

Potential of Genome Editing to Improve Aquaculture Breeding and Production

Aquaculture is the fastest growing food production sector and is rapidly becoming the primary source of seafood for human diets. Selective breeding programs are enabling genetic improvement of production traits, such as disease resistance, but progress is limited by the heritability of the trait and generation interval of the species. New breeding technologies, such as genome editing using CRISPR/Cas9 have the potential to expedite sustainable genetic improvement in aquaculture. Genome editing can rapidly introduce favorable changes to the genome, such as fixing alleles at existing trait loci, creating de novo alleles, or introducing alleles from other strains or species. The high fecundity and external fertilization of most aquaculture species can facilitate genome editing for research and application at a scale that is not possible in farmed terrestrial animals.

Catching the complexity of salmon-louse interactions

The study of host-parasite relationships is an integral part of the immunology of aquatic species, where the complexity of both organisms has to be overlayed with the lifecycle stages of the parasite and immunological status of the host. A deep understanding of how the parasite survives in its host and how they display molecular mechanisms to face the immune system can be applied for novel parasite control strategies. This review highlights current knowledge about salmon and sea louse, two key aquatic animals for aquaculture research worldwide. With the aim to catch the complexity of the salmon-louse interactions, molecular information gleaned through genomic studies are presented. The host recognition system and the chemosensory receptors found in sea lice reveal complex molecular components, that in turn, can be disrupted through specific molecules such as non-coding RNAs.