Comparative Genomics of Typical and Atypical Aeromonas salmonicida Complete Genomes Revealed New Insights into Pathogenesis Evolution

Dual-seq transcriptomics of Aeromonas salmonicida infection in Atlantic salmon (Salmo salar) primary macrophages reveals lysosome and apoptosis impairments

A. salmonicida subsp. salmonicida is one of the oldest-known marine pathogens causing furunculosis in freshwater to marine fish species. A. salmonicida causes septicemia and fish death due to a systemic shock. Early stages of A. salmonicida infection, including intracellular macrophage infection, are not fully comprehended. Here, we conducted a dual RNA-seq study and functional analyses in Atlantic salmon primary macrophages infected with A. salmonicida to identify relevant genes for fish cellular immunity and A. salmonicida pathogenesis. At 1-h post-infection (hpi), A. salmonicida modulated the expression of genes associated with inflammation, fatty acids synthesis, and apoptosis. While at 2 hpi A. salmonicida hijacked pathways related to myeloid cell differentiation, cytoskeleton and actin filament organization, lysosome maturation, and apoptosis. In contrast, A. salmonicida upregulated genes encoding for hemolysin, aerolysin, type IVa pili, and T3SS effectors. In conclusion, these results suggest that A. salmonicida induces endocytosis, impairs lysosome maturation, and reduces apoptosis.

Susceptibility of Aeromonas salmonicida subsp. salmonicida bacteria from French farmed trout to antibiotics commonly used in fish farming, and attempt to set epidemiological cut-off values

Aeromonas salmonicida subsp. salmonicida (ASS) is a bacterium that can cause opportunistic infections in humans and animals. In farmed rainbow trout it causes furunculosis, with more frequent outbreaks when water temperatures are higher, an additional consequence of global warming. When infections occur, antibiotics are sometimes required. However, data on ASS susceptibility is limited. The aim of this study was to determine the distribution of Minimum Inhibitory Concentrations (MICs) of eight antibiotics commonly used in fish veterinary medicine in a population of pathogenic ASS, and to calculate provisional epidemiological cut-off values (called CO Epid ). To date, only four epidemiological cut-off values (ECV) have been established by CLSI, and none by EUCAST. In this study, 406 bacterial strains of ASS were collected exclusively from diseased French farmed trout over a 10-year period (2012-2021). A combination of PCR, MALDI-TOF and specific characteristics of the bacterial culture was used to identify each isolate to species level. All MIC data were obtained by the broth dilution method according to CLSI recommendations. Our CO Epid meets the CLSI defined ECV for florfenicol (4 mg/L) and oxytetracycline (1 mg/L). In the absence of a defined ECV, we proposed a CO Epid of 1 mg/L for doxycycline. For sulfadiazine alone, all strains tested were non-wild-type (NWT) with very high MICs. The CO Epid was calculated as 4.8/0.25 mg/L for sulfadiazine + trimethoprim (one two-fold dilution difference from the ECV established by CLSI for ormetoprim + sulfadimethoxine). For quinolones, CO Epid were 4 mg/L, 4 mg/L and 0.5 mg/L for oxolinic acid, flumequine and enrofloxacin, respectively, with a cross-resistance mechanism. This CO Epid for oxolinic acid far exceeds the CLSI defined ECV (0.125 mg/L). A total of 12 strains (3%) were classified as NWT for all antibiotics tested. Over the period studied, the proportion of bacteria susceptible to the different molecules remained stable, except for the tetracycline family. These data will be available to establish internationally agreed epidemiological cut-off values, which are lacking for some antibiotics. These cut-offs are essential to assess and monitor the emergence of bacterial populations with resistance traits, and to establish clinical breakpoints for better use of antimicrobials in fish.

Major antigenic differences in Aeromonas salmonicida isolates correlate with the emergence of a new strain causing furunculosis in Chilean salmon farms

Aeromonas salmonicida is the etiological agent of furunculosis, a septicemic disease with high mortality rates affecting salmonids and other teleost species worldwide. Reviewing molecular diagnostic protocols for routine diagnostics, we realized that the amplification of the vapA target gene failed in some cases of furunculosis. Therefore, we hypothesized that the emergence of a new strain may be involved in recent outbreaks. In this work, we demonstrate that the vapA locus is absent in the new strain, which explains why it lacks the major membrane component VapA protein, a critical virulence factor. In addition, we found that the vapA-absent strain differs from its counterparts in outer membrane protein and lipopolysaccharide profiles, suggesting profound changes at the membrane structure level and in antigenic properties. These features along with sequence analysis information allowed us to infer that a complex genomic rearrangement, probably an indel encompassing the entire vapA locus, gave rise to this membrane phenotype. Although the causes for pathogen evolution and emergence were not fully elucidated, our results strongly suggest that the vapA-absent strain is responsible for a raising proportion of recent furunculosis cases, and that it may be related to a less virulent disease and a low serological response upon vaccination with the A. salmonicida antigen formulation currently used in Chile.

Emergence of Aeromonas salmonicida subsp. masoucida MHJM250: unveiling pathological characteristics and antimicrobial susceptibility in golden mahseer, Tor putitora (Hamilton, 1822) in India

Aeromonas salmonicida subsp. masoucida, designated as laboratory strain MHJM250, was characterized from a naturally infected farmed golden mahseer, Tor putitora. The infected fish exhibited clinical signs of erosion at the caudal fin and hemorrhage onx the ventral body surface. Molecular identification through 16 S rDNA and phylogenetic analysis revealed 100% similarity with a known strain A. salmonicida subsp. masoucida (MT122821.1). MHJM250 exhibited positive reactions for oxidase, catalase, esculin, MR-VP, O/F and utilized arginine and lysine. It also demonstrated siderophore activity, thrived at various NaCl concentrations, hydrolyzed gelatinase, skimmed milk and casinase. In vitro studies exhibited its hemolytic nature, significant biofilm production in glucose-rich tryptone soya broth and beta-hemolysis. MHJM250 didn't produce slime and was non-precipitated upon boiling. It showed crystal violet binding characteristics and auto-agglutination with relatively weak hydrophobicity (25%). In the challenge assay, intraperitoneal administration of MHJM250 to T. pitutora fingerlings at 108 CFU mL-1 resulted in pathogenicity with 3% mortality and mild hemorrhagic symptoms. Histopathological analysis revealed degenerative changes in gill, kidney, liver, muscle, and intestine samples. The bacterium displayed resistance to several antibiotics (µg/disc); ampicillin (10 µg), ampicillin/ sulbactam (10/10 µg), clindamycin (2 µg), linezolid (30 µg), penicillin G (10 µg) and rifampicin (5 µg) and varied minimum inhibitory concentrations against oxytetracycline, erythromycin and florfenicol. Transmission electron microscopy showed its rod-shaped structure with single polar flagellum and lophotrichous flagella. An investigation on the molecular basis for virulence factors of A. salmonicida subsp. masoucida MHJM250 may offer crucial understandings to formulate disease prevention and control strategies in aquaculture.

Antibacterial and Antibiofilm Activity of Essential Oils Against Aeromonas spp. Isolated from Rainbow Trout

Aeromonas spp. is a major pathogen in aquaculture with a great negative economic impact. Essential oils (EOs) are compounds of the secondary metabolism of plants known for their antibacterial and antibiofilm activities. In this study, in vitro antibacterial activity of eight EOs: tea tree (extracted from Melaleuca alternifolia), eucalyptus (extracted from Eucalyptus globulus LABILL.), knee timber (extracted from Pini mungo L.), peppermint (extracted from Mentha piperita L.), oregano (extracted from Origanum vulgare L.), rosemary (extracted from Rosmarinus officinalis L.), thyme (extracted from Thymus vulgaris L.) and pine EO (extracted from Pinus silvestris L.), obtained from Calendula a.s., was evaluated. Their antibacterial activity was demonstrated against Aeromonas spp. isolates. Oregano and thyme EOs showed the strongest activity against all tested isolates at low concentrations, followed by tea tree and peppermint EOs. The MIC value ranged from 0.06 µL/mL to 1.0 µL/mL. The tested EOs showed a significant antibiofilm activity against biofilm-forming isolates with MBIC50 ranging from 0.015 µL/mL to 0.25 µL/mL. All tested isolates were obtained from rainbow trout free of clinical signs of infection. Twelve isolates of Aeromonas salmonicida subsp. masoucida, four Aeromonas hydrophila, and four isolates of Aeromonas veronii were identified. The results of the in vitro study showed a significant effect of EOs against Aeromonas spp., which confirmed their potential for use in aquaculture as a prevention against bacterial diseases and a way of reducing the use of antibiotics.

Complete genome sequence provides information on quorum sensing related spoilage and virulence of Aeromonas salmonicida GMT3 isolated from spoiled sturgeon

Foodborne bacteria can pose a threat to the public health due to their spoilage and virulence potential, which can be regulated by quorum sensing (QS) system. In the study, we isolated a spoilage bacteria strain Aeromonas salmonicida GMT3 from refrigerated sturgeon. The complete genome of A. salmonicida GMT3 was sequenced, and the QS related genes were assigned. QS signal molecules N-acyl-homoserine lactones (AHLs) and AI-2 were detected. Genes regulating the spoilage-related metabolic pathways, including protease and lipase secretion, amines metabolism, sulfur metabolism, motility and biofilm formation were analyzed. Furthermore, genes encoding for several virulence factors, e.g. hemolysin, aerolysin, type II secretion system (T2SS), type VI secretion system (T6SS), antibiotic and multidrug resistance were also identified. In addition, the spoilage and virulence phenotypes associated with QS including protease, swimming and swarming activity, biofilm and hemolytic activity were detected. This study provided new insights into spoilage and virulence mechanisms correlated with QS of A. salmonicida GMT3, which might promote development of new approaches for spoilage and virulence control based on QS target.

Role of cold shock proteins B and D in Aeromonas salmonicida subsp. salmonicida physiology and virulence in lumpfish (Cyclopterus lumpus)

Cold shock proteins (Csp) are pivotal nucleic acid binding proteins known for their crucial roles in the physiology and virulence of various bacterial pathogens affecting plant, insect, and mammalian hosts. However, their significance in bacterial pathogens of teleost fish remains unexplored. Aeromonas salmonicida subsp. salmonicida (hereafter A. salmonicida) is a psychrotrophic pathogen and the causative agent of furunculosis in marine and freshwater fish. Four csp genes (cspB, cspD, cspA, and cspC) have been identified in the genome of A. salmonicida J223 (wild type). Here, we evaluated the role of DNA binding proteins, CspB and CspD, in A. salmonicida physiology and virulence in lumpfish (Cyclopterus lumpus). A. salmonicida ΔcspB, ΔcspD, and the double ΔcspBΔcspD mutants were constructed and characterized. A. salmonicida ΔcspB and ΔcspBΔcspD mutants showed a faster growth at 28°C, and reduced virulence in lumpfish. A. salmonicida ΔcspD showed a slower growth at 28°C, biofilm formation, lower survival in low temperatures and freezing conditions (-20°C, 0°C, and 4°C), deficient in lipopolysaccharide synthesis, and low virulence in lumpfish. Additionally, ΔcspBΔcspD mutants showed less survival in the presence of bile compared to the wild type. Transcriptome analysis revealed that 200, 37, and 921 genes were differentially expressed in ΔcspB, ΔcspD, and ΔcspBΔcspD, respectively. In ΔcspB and ΔcspBΔcspD virulence genes in the chromosome and virulence plasmid were downregulated. Our analysis indicates that CspB and CspD mostly act as a transcriptional activator, influencing cell division (e.g., treB), virulence factors (e.g., aexT), and ultimately virulence.

Inactivated Aeromonas salmonicida impairs adaptive immunity in lumpfish (Cyclopterus lumpus)

Aeromonas salmonicida, a widely distributed aquatic pathogen causing furunculosis in fish, exhibits varied virulence, posing challenges in infectious disease and immunity studies, notably in vaccine efficacy assessment. Lumpfish (Cyclopterus lumpus) has become a valuable model for marine pathogenesis studies. This study evaluated several antigen preparations against A. salmonicida J223, a hypervirulent strain of teleost fish, including lumpfish. The potential immune protective effect of A. salmonicida bacterins in the presence and absence of the A-layer and extracellular products was tested in lumpfish. Also, we evaluated the impact of A. salmonicida outer membrane proteins (OMPs) and iron-regulated outer membrane proteins (IROMPs) on lumpfish immunity. The immunized lumpfish were intraperitoneally (i.p.) challenged with 104 A. salmonicida cells/dose at 8 weeks-post immunization (wpi). Immunized and non-immunized fish died within 2 weeks post-challenge. Our analyses showed that immunization with A. salmonicida J223 bacterins and antigen preparations did not increase IgM titres. In addition, adaptive immunity biomarker genes (e.g., igm, mhc-ii and cd4) were down-regulated. These findings suggest that A. salmonicida J223 antigen preparations hinder lumpfish immunity. Notably, many fish vaccines are bacterin-based, often lacking efficacy evaluation. This study offers crucial insights for finfish vaccine approval and regulations.

Genomics of Re-Emergent Aeromonas salmonicida in Atlantic Salmon Outbreaks

Furunculosis, caused by Aeromonas salmonicida, poses a significant threat to both salmonid and non-salmonid fish in diverse aquatic environments. This study explores the genomic intricacies of re-emergent A. salmonicida outbreaks in Atlantic salmon (Salmo salar). Previous clinical cases have exhibited pathological characteristics, such as periorbital hemorrhages and gastrointestinal abnormalities. Genomic sequencing of three Chilean isolates (ASA04, ASA05, and CIBA_5017) and 25 previously described genomes determined the pan-genome, phylogenomics, insertion sequences, and restriction-modification systems. Unique gene families have contributed to an improved understanding of the psychrophilic and mesophilic clades, while phylogenomic analysis has been used to identify mesophilic and psychrophilic strains, thereby further differentiating between typical and atypical psychrophilic isolates. Diverse insertion sequences and restriction-modification patterns have highlighted genomic structural differences, and virulence factor predictions can emphasize exotoxin disparities, especially between psychrophilic and mesophilic strains. Thus, a novel plasmid was characterized which emphasized the role of plasmids in virulence and antibiotic resistance. The analysis of antibiotic resistance factors revealed resistance against various drug classes in Chilean strains. Overall, this study elucidates the genomic dynamics of re-emergent A. salmonicida and provides novel insights into their virulence, antibiotic resistance, and population structure.

Genome sequence of the virulent Aeromonas salmonicida atypical strain T30 isolated from sablefish with furunculosis

Aeromonas salmonicida, a Gram-negative bacterium, causes the disease furunculosis in multiple fish species. We present the complete genome sequence of the atypical A. salmonicida strain T30, which was isolated from furunculosis in sablefish in Manchester, WA, USA. Analyzing this genome will help to identify the bacterium's role in marine aquaculture.

An Outbreak of Aeromonas salmonicida in Juvenile Siberian Sturgeons (Acipenser baerii)

Aeromonas salmonicida is one of the major threats to world aquaculture, causing fish furunculosis and high mortality rates in cultured fish, particularly salmonids. Although Aeromonas spp. is a thoroughly studied pathogen, little is known regarding aeromoniasis in sturgeons. After a mortality outbreak, four juvenile sturgeons (Acipenser baerii) were submitted for autopsy and tissue samples were collected for histopathological and microbiological studies. The external examination revealed size heterogenicity, skin hyperpigmentation and reduced body condition of sturgeons. Within the abdominal cavity, mild hepatomegaly and splenomegaly were observed, as well as generalized organic congestion. Histology revealed severe multifocal haemorrhagic and ulcerative dermatitis, mainly localized in the dorsal and latero-ventral areas of fish. The histological study also showed moderate to severe inflammation of gills and organic lesions compatible with septicaemia. Bacterial isolates were identified as Aeromonas salmonicida subsp. salmonicida using MALDI-TOF MS and PCR. Overall, the lesions first described here are consistent with those previously reported in other cultured fish species and contribute to a better understanding of the pathogenesis of Aeromonas salmonicida subsp. salmonicida in the Siberian sturgeon, aside from providing new diagnostic tools for bacterial diseases impacting the fast-growing industry of caviar.

Early Molecular Immune Responses of Turbot (Scophthalmus maximus L.) Following Infection with Aeromonas salmonicida subsp. salmonicida

Turbot aquaculture production is an important economic activity in several countries around the world; nonetheless, the incidence of diseases, such furunculosis, caused by the etiological agent A. salmonicida subsp. salmonicida, is responsible for important losses to this industry worldwide. Given this perspective, this study aimed to evaluate early immune responses in turbot (S. maximus L.) following infection with A. salmonicida subsp. salmonicida. For this, 72 fish were individually weighed and randomly distributed into 6 tanks in a circulating seawater system. For the bacterial challenge, half of the individuals (3 tanks with 36 individuals) were infected using a peritoneal injection with the bacterial suspension, while the other half of individuals were injected with PBS and kept as a control group. Several factors linked to the innate immune response were studied, including not only haematological (white blood cells, red blood cells, haematocrit, haemoglobin, mean corpuscular volume, mean cell haemoglobin, mean corpuscular haemoglobin concentration, neutrophils, monocytes, lymphocytes, thrombocytes) and oxidative stress parameters, but also the analyses of the expression of 13 key immune-related genes (tnf-α, il-1β, il-8, pparα-1, acox1, tgf-β1, nf-kB p65, srebp-1, il-10, c3, cpt1a, pcna, il-22). No significant differences were recorded in blood or innate humoral parameters (lysozyme, anti-protease, peroxidase) at the selected sampling points. There was neither any evidence of significant changes in the activity levels of the oxidative stress indicators (catalase, glutathione S-transferase, lipid peroxidation, superoxide dismutase). In contrast, pro-inflammatory (tnf-α, il-1β), anti-inflammatory (il-10), and innate immune-related genes (c3) were up-regulated, while another gene linked with the lipid metabolism (acox1) was down-regulated. The results showed new insights about early responses of turbot following infection with A. salmonicida subsp. salmonicida.

Characterization of atypical pathogenic Aeromonas salmonicida isolated from a diseased Siberian sturgeon (Acipenser baerii)

Acipenser baerii (Siberian sturgeon) is native to Kazakhstan and is currently endangered and is listed within the first class of protected animals. Sturgeon aquaculture is becoming an important tool for the recovery of this endangered species. Nonetheless, diseases involving typical symptoms of skin ulceration and systemic bacterial hemorrhagic septicemia have occurred in cultured A. baerii on a fish farm located in Western Kazakhstan. In this study, an infectious strain of bacteria isolated from an ulcer of diseased A. baerii was identified as Aeromonas salmonicida (strain AB001). This identification involved analyses of 16S rRNA, gyrB, rpoD, and flaA genes' sequences. Even though strain AB001 belongs to A. salmonicida, it exhibited noticeable mobility and growth at temperatures of ≥37 °C. Profiling of virulence genes uncovered the presence of seven such genes related to pathogenicity. Antibiotic sensitivity testing showed that the strain is sensitive to aminoglycosides, amphenicols, nitrofurans, quinolones, and tetracyclines. Half-lethal doses (LD₅₀) of strain AB001 for Oreochromis mossambicus and A. baerii were determined: respectively 1.7 × 10⁸ and 7.2 × 10⁷ colony-forming units per mL. The experimentally induced infection revealed that strain AB001 causes considerable histological lesions in O. mossambicus, including tissue degeneration, necrosis, and hemorrhages of varied severity.

Efficacy of bivalent vaccine against Aeromonas salmonicida and Edwardsiella tarda infections in turbot

In recent years, more than one pathogenic organism has usually been isolated from diseased turbot Scophthalmus maximus, creating a pressing need for the development of combination vaccines to prevent fish diseases brought on simultaneously by various infections. In this study, the inactivated bivalent vaccine of Aeromonas salmonicida and Edwardsiella tarda was prepared by the formalin inactivation method. After challenge with A. salmonicida and E. tarda at 4 weeks post-vaccination in turbot, the relative percentage survival (RPS) of the inactivated bivalent vaccine was 77.1%. In addition, we assessed the effects of the inactivated bivalent vaccine and evaluated the immunological processes after immunization in a turbot model. Serum antibody titer and lysozyme activity of the vaccinated group were both upregulated and higher than that in control group after vaccination. The expression levels of genes (TLR2, IL-1β, CD4, MHCI, MHCⅡ) that related to antigen recognition, processing and presentation were also studied in the liver, spleen and kidney tissues of vaccinated turbot. All the detected genes in the vaccinated group had a significant upward trend, and most of them reached the maximum value at 3-4 weeks, which had significant differences from the control group, suggesting that antigen recognition, processing and presentation pathway was activated by the inactivated bivalent vaccine. Our study provides a basis for further application of the killed bivalent vaccine against A. salmonicida and E. tarda in turbot, making it good potential that can be applied in aquaculture.

Aeromonas salmonicida: Genomics, Taxonomy, Diversity, Pathogenesis, Treatments and Beyond

For a long time, the bacterial species Aeromonas salmonicida seemed to be limited to a regrouping of psychrophilic subspecies that infect fish, particularly salmonids [...].

Comparative genomic analysis provides insights into taxonomy and temperature adaption of Aeromonas salmonicida

Aeromonas salmonicida has long been known as psychrophiles since it is mainly isolated from cold water fish, and recent reports have revealed the existence of mesophilic strains isolated from warm sources. However, the genetic differences between mesophilic and psychrophilic strains remain unclear due to few complete genomes of mesophilic strain are available. In this study, six A. salmonicida (2 mesophilic and 4 psychrophilic) were genome-sequenced, and comparative analyses of 25 A. salmonicida complete genomes were conducted. The ANI values and phylogenetic analysis revealed that 25 strains formed three independent clades, which were referred as typical psychrophilic, atypical psychrophilic and mesophilic groups. Comparative genomic analysis showed that two chromosomal gene clusters, related to lateral flagella and outer membrane proteins (A-layer and T2SS proteins), and insertion sequences (ISAs4, ISAs7 and ISAs29) were unique to the psychrophilic groups, while the complete MSH type IV pili were unique to the mesophilic group, all of which may be considered as lifestyle-related factors. The results of this study not only provide new insights into the classification, lifestyle adaption and pathogenic mechanism of different strains of A. salmonicida, but also contributes to the prevention and control of disease caused by psychrophilic and mesophilic A. salmonicida.

Comparative Genomics Revealed a Potential Threat of Aeromonas rivipollensis G87 Strain and Its Antibiotic Resistance

Aeromonas rivipollensis is an emerging pathogen linked to a broad range of infections in humans. Due to the inability to accurately differentiate Aeromonas species using conventional techniques, in-depth comparative genomics analysis is imperative to identify them. This study characterized 4 A. rivipollensis strains that were isolated from river water in Johannesburg, South Africa, by whole-genome sequencing (WGS). WGS was carried out, and taxonomic classification was employed to profile virulence and antibiotic resistance (AR). The AR profiles of the A. rivipollensis genomes consisted of betalactams and cephalosporin-resistance genes, while the tetracycline-resistance gene (tetE) was only determined to be in the G87 strain. A mobile genetic element (MGE), transposons TnC, was determined to be in this strain that mediates tetracycline resistance MFS efflux tetE. A pangenomic investigation revealed the G87 strain's unique characteristic, which included immunoglobulin A-binding proteins, extracellular polysialic acid, and exogenous sialic acid as virulence factors. The identified polysialic acid and sialic acid genes can be associated with antiphagocytic and antibactericidal properties, respectively. MGEs such as transposases introduce virulence and AR genes in the A. rivipollensis G87 genome. This study showed that A. rivipollensis is generally resistant to a class of beta-lactams and cephalosporins. MGEs pose a challenge in some of the Aeromonas species strains and are subjected to antibiotics resistance and the acquisition of virulence genes in the ecosystem.

Production of a monoclonal antibody specific to sablefish (Anoplopoma fimbria) IgM and its application in ELISA, western blotting, and immunofluorescent staining

Sablefish (Anoplopoma fimbria) are an emerging aquaculture species native to the continental shelf of the northern Pacific Ocean. There is limited information on both innate and adaptive immunity for this species and new tools are needed to determine antibody response following vaccination or disease outbreaks. In this paper, a monoclonal antibody, UI-25A, specific to sablefish IgM was produced in mice. Western blotting confirmed UI-25A recognizes the heavy chain of IgM and does not cross react to proteins or carbohydrates in serum of four other teleost species. An ELISA was developed to measure Aeromonas salmonicida specific IgM in the plasma of sablefish from a previous experiment where fish were immunized with a proprietary A. salmonicida vaccine. UI-25A was used in Western blot analyses to identify immunogenic regions of A. salmonicida recognized by this specific IgM from vaccinated sablefish. Immunofluorescent staining also demonstrated the ability of UI-25A to recognize membrane-bound IgM and identify IgM + cells in the head kidney. These results demonstrate the usefulness of UI-25A as a tool to improve the understanding of antibody-mediated immunity in sablefish as well as to provide valuable information for vaccine development and expansion of aquaculture efforts for this fish species.

Multi-Organ Transcriptome Response of Lumpfish (Cyclopterus lumpus) to Aeromonas salmonicida Subspecies salmonicida Systemic Infection

Lumpfish is utilized as a cleaner fish to biocontrol sealice infestations in Atlantic salmon farms. Aeromonas salmonicida, a Gram-negative facultative intracellular pathogen, is the causative agent of furunculosis in several fish species, including lumpfish. In this study, lumpfish were intraperitoneally injected with different doses of A. salmonicida to calculate the LD50. Samples of blood, head-kidney, spleen, and liver were collected at different time points to determine the infection kinetics. We determined that A. salmonicida LD50 is 102 CFU per dose. We found that the lumpfish head-kidney is the primary target organ of A. salmonicida. Triplicate biological samples were collected from head-kidney, spleen, and liver pre-infection and at 3- and 10-days post-infection for RNA-sequencing. The reference genome-guided transcriptome assembly resulted in 6246 differentially expressed genes. The de novo assembly resulted in 403,204 transcripts, which added 1307 novel genes not identified by the reference genome-guided transcriptome. Differential gene expression and gene ontology enrichment analyses suggested that A. salmonicida induces lethal infection in lumpfish by uncontrolled and detrimental blood coagulation, complement activation, inflammation, DNA damage, suppression of the adaptive immune system, and prevention of cytoskeleton formation.

Relative expression and validation of Aeromonas salmonicida subsp. salmonicida reference genes during ex vivo and in vivo fish infection

The genus Aeromonas is found worldwide in freshwater and marine environments and has been implicated in the etiology of human and animal diseases. In fish, among Aeromonas species, A. salmonicida causes massive mortality and great economic losses in marine and continental aquaculture species. Currently, several aspects of the clinical signs and pathogenesis of this Gram-negative bacterium have been described; however, determination of an appropriate reference gene is essential to normalize cellular mRNA data remain unknown. Here we evaluate the stability of seven candidate reference genes to be used for data normalization during ex vivo and in vivo experiments conducted in Atlantic cod, Atlantic salmon, and lumpfish. To assess this, raw Ct values obtained were evaluated by using geNorm, NormFinder, BestKeeper, Delta Ct comparison, and the comprehensive ranking, through the bioinformatic open-access portal RefFinder. We determined that fabD and era were most suitable reference genes in Atlantic cod primary macrophages, hfq and era in Atlantic salmon primary macrophages, rpoB and fabD in lumpfish head kidney samples, and hfq and era in lumpfish spleen. Our study demonstrates that use of multiple reference genes and its validation before measurements helps to minimize variability arising in qPCR studies that evaluate A. salmonicida gene expression in fish tissues. Overall, this study provided with an expanded list of reliable reference genes for A. salmonicida gene expression using qPCR during fish infection studies.