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The European brown shrimpCrangon crangonis an abundant and commercially important species in the North Sea. Currently, there is interest in landing live shrimp to provide fresh animals for a growing market in live brown shrimp. During 4 survival studies between 2014 and 2016, shrimp were collected from commercial trawlers and maintained alive in off-shore facilities. From Day 1 onwards, a minority of shrimp (~2.24%) developed a white discoloration of the abdominal muscles and a depigmentation of the distal part of the abdomen, along with paralysis of the affected tissues and appendages. As the symptoms progressed, a circumferential blackish delineation appeared, creating a distinct boundary between healthy and necrotic tissue. Affected shrimp survived up to 3 wk, although in several animals the distal part of the tail was completely lost. Histological and electron microscopical examination confirmed the myonecrosis. A secondary bacterial invasion of the necrotic muscle was observed in some animals. RT-PCR for infectious myonecrosis virus was negative. The condition appears not to be contagious, based on the feeding of healthy shrimp with necrotic tissue of affected shrimp. Based on these observations, a mechanical cause inflicted during the catching process is proposed.

Additional file 3: Overview of the existing research and reported values of scale and plasma cortisol concentrations and the methods used.

Additional file 2: Detailed overview of the effects on fish health correlated with plasma (PCC) and scale cortisol concentrations (SCC).

Additional file 1: Mean fish characteristics before the experiment of the control group (CONT) and fish that were fed with feed supplemented with cortisol (CORT). Length (p = 0.6211), weight (p = 0.8491) and body condition (p = 0.1810) of the common dab were not significantly different between CORT and CONT fish. Fish of both groups did not differ in age (p = 0.4582). The sex ratio of both groups were similar with 6 (33 %) females and 12 (67 %) males in the CONT group and 7 (39 %) females and 11 (61 %) males in the CORT group (p = 0.4582).

Additional file 4. Unique protein-encoding genes in the highly virulent trout isolate genome. 374 genes were identified in the genome of the highly virulent F. columnare JIP P11/91 isolate while being absent in that of the non-virulent F. columnare ATCC 49512. Of these 374 genes, the 263 hypothetical genes were left out in the representation above. Genes marked in bold are also predicted to be involved in virulence when identifying them via Virulence Factor Database. *Gene locations are formatted as NODEn:s-e where n is a unique scaffold number, s and e are the gene’s start and end position respectively.

Additional file 2. Protein-encoding genes present only in the virulent F. columnare genomes. The latter 42 genes are only present in genomes of the highly virulent carp (04017018) and trout (JIPP11/91) and low virulent carp (CDI-A) F. columnare isolates that could cause tissue damage and mortality. These genes are not present in the genome of the non-virulent F. columnare trout isolate ATCC49512. Hypothetical genes (114) were not included here. Genes marked in bold are also predicted to be involved in virulence when identifying them via Virulence Factor Database.

This study reports the comparative analyses of four Flavobacterium columnare isolates that have different virulence and antimicrobial resistance patterns. The main research goal was to reveal new insights into possible virulence genes by comparing the genomes of bacterial isolates that could induce tissue damage and mortality versus the genome of a non-virulent isolate. The results indicated that only the genomes of the virulent isolates possessed unique genes encoding amongst others a methyl-accepting chemotaxis protein possibly involved in the initial colonization of tissue, and several VgrG proteins engaged in interbacterial competition. Furthermore, comparisons of genes unique for the genomes of the highly virulent (HV) carp and trout isolates versus the, respectively, low and non-virulent carp and trout isolates were performed. An important part of the identified unique virulence genes of the HV-trout isolate was located in one particular gene region identified as a genomic island. This region contained araC and nodT genes, both linked to pathogenic and multidrug-resistance, and a luxR-gene, functional in bacterial cell-to-cell communication. Furthermore, the genome of the HV-trout isolate possessed unique sugar-transferases possibly important in bacterial adhesion. The second research goal was to obtain insights into the genetic basis of acquired antimicrobial resistance. Several point-mutations were discovered in gyrase-genes of an isolate showing phenotypic resistance towards first and second-generation quinolones, which were absent in isolates susceptible to quinolones. Tetracycline-resistance gene tetA was found in an isolate displaying acquired phenotypic resistance towards oxytetracycline. Although not localized on a prophage, several flanking genes were indicative of the gene’s mobile character.

Additional file 7. Characteristics of prophage regions in the four Flavobacterium columnare isolates. The prophage regions were identified in the genome of the reference isolate (ATCC49512) and the three newly assembled F. columnare isolates 04017018, CDI-A and JIP P11/91 via PHASTER. Prophage regions with scores less than 70 are incomplete.

Additional file 3. Unique protein-encoding genes in the highly virulent carp isolate genome. 80 genes were identified to be present in the genome of the highly virulent carp isolate 04017018 while absent in that of the low virulent carp isolate CDI-A. Of these 80 genes, the 62 hypothetical genes were left out in the representation above. Genes marked in bold are also predicted to be involved in virulence when identifying them via Virulence Factor Database. *Gene locations are formatted as NODEn:s-e where n is a unique scaffold number, s and e are the gene’s start and end position respectively.

Additional file 6. Unique single nucleotide variants (SNVs) present in gyrA of isolate CDI-A. The impact of the SNP (single nucleotide polymorphism) on protein activity/stability was predicted by comparison of amino acid characteristics, by using PredictSNP and I-Mutant Suite 3.0 tools, and by investigating which amino acids were present in the reference strain of F. columnare and of HV carp isolate 04017018, both of the latter not displaying acquired resistance towards fluoroquinolones, using BLAST and ConSurf.

Additional file 5. Single nucleotide variants (SNVs) in gyrase genes of Flavobacterium columnare isolates. This table shows the SNVs present in the gyrase genes of F. columnare isolates CDI-A and 04017018 when compared to gyrase genes of the reference genome ATCC 49512. However, as only isolate CDI-A displayed phenotypic antimicrobial resistance towards both first- and second-generation quinolones, the unique SNVs in the gyrase genes of the latter isolate are highlighted in grey background. No SNVs were encountered in DNA gyrase subunit B (EC 5.99.1.3). Average read quality score of the bases supporting a variant was higher than 35 (which is considered very good quality).

Environmental changes or stressors can result in the development of diseases. Through regular fish disease surveys in the Belgian part of the North Sea, attention was drawn to a sudden increase of skin ulceration prevalence between 2011 and 2014 in common dab (Limanda limanda). Information on prevalence, ulceration, bacteriology, fish-related (e.g., length, age, and sex) and (spatial and temporal) environmental factors, and fishing intensity were gathered. This detailed investigation was framed within a long-term monitoring program, executed every spring-autumn from 2000 to present. Ulcerations were observed in 1.3% of fish (n=3,999). Spatial and temporal differences were evident, and highest prevalence was found in summer. Vibrio was the dominant cultivated bacterial genus present in the lesions. Skin ulcerations appeared to be correlated with length and body condition of the fish, as well as with temperature and pH of the seawater and fishing vessel density. Our research suggested the involvement of multiple factors in the development of skin ulcerations in common dab and endorsed the effects of changing environment and human influence on the marine ecosystem through activities such as fishing.

European brown shrimp (Crangon crangon) have great commercial value. Recently, an increasing demand for fresh shrimp has led fishermen to land part of their catch alive. In the present study, the effects of various parameters on the post-catch survival of brown shrimp were investigated by housing them in natural seawater and monitoring survival for two weeks. In a first experiment shrimp survival was tested under high population densities at different temperature settings ranging between 8 degrees C and 21 degrees C. A second experiment investigated the effect of a sand layer in the holding tanks when shrimp were housed at low population densities. Finally, the impact of onboard sorting with a rotary sorting riddle on subsequent survival was assessed. A higher survival rate was found at lower water temperatures. The use of a sand substrate did not significantly improve survival but did result in a more even distribution of shrimp across the bottom of the holding tanks. Onboard sorting with a mechanical rotary sorting riddle did not significantly affect the survival of brown shrimp during the first four days of holding although injuries sustained during onboard handling resulted in high mortality at the time of landing.

Plasma cortisol is the classical parameter to assess acute stress in vertebrates, while in fish larvae whole body cortisol is used. Immuno assays are commonly adopted for cortisol determination in a pool of fish larvae. At present no method exists for quantification of a full glucocorticoid profile of a single fish larva providing a detailed snap-shot of hypothalamic-pituitary-interrenal (HPI) axis activity. To date, a substantial amount of studies has confirmed the potential of probiotics to positively impact fish welfare by alleviating the general stress response. However, no study investigated how probiotics impact the glucocorticoid profile in an individual fish larva. In this respect, this study assessed the effect of the administration of the probiotic candidate Vibrio lentus, previously shown to protect European sea bass (Dicentrarchus labrax) larvae, on the HPI axis activity. Therefore, V. lentus was administered to germ-free European sea bass larvae and a ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) method for quantifying cortisol, its precursors (17α-hydroxyprogesterone and 11-deoxycortisol) and phase I metabolites (cortisone, 20β-dihydrocortisone, tetrahydrocortisol and tetrahydrocortisone) in the whole body of a single fish larva was developed in an EN ISO/IEC 17025 regulated environment and validated according the requirements of the Commission Decision No. 2002/657/EC and applied, making this the first study in its kind. In the supplemented larvae, the administration of the probiotic candidate V. lentus significantly decreased glucocorticoid baseline levels. This study provides a better insight into the effect of the probiotic candidate V. lentus on the HPI axis activity in European sea bass larvae.

Despite electric pulse fishing being regarded as a promising environmentally friendly fishing method, very little is known about possible negative effects on early life stages of bottom-dwelling species such as Sole Solea solea. Electrotrawling for brown shrimp Crangon crangon is increasingly used in shallow coastal zones and estuaries of the southern North Sea. As these fishing grounds are often important nurseries and spawning areas for various marine species, electrotrawling could therefore harm inhabiting fishes during their early life stages. Hence, this research aims to investigate the effect of electric pulses used to catch brown shrimp on the survival and development of Sole embryos and larvae. Exposure of Sole embryos at 2d postfertilization and larvae at 11d posthatching to pulsed DC used to catch brown shrimp did not result in a lower survival 8d after exposure. Additionally, no differences in yolk sac resorption and morphometric length measurements of the notochord, muscle, eye, and head were observed in the developing larvae.

Electrotrawling using electric pulse stimulation is a promising alternative to beam trawling in the brown shrimp Crangon crangon and Dover Sole Solea solea (also known as Solea vulgaris) fisheries of the North Sea. In the sole fishery, a 40-80-Hz pulse stimulation induces tetany in the muscles, which may result in injuries. Whereas no injuries have been reported in flatfish or selachian sharks and rays, electrically induced spinal injuries have been observed in gadoids such as Atlantic Cod Gadus morhua and Whiting (also known as European Whiting) Merlangius merlangus. This may indicate that fish species with a fusiform shape are more susceptible to electric pulses. Similar variation among species in electrically induced spinal injuries has been observed in freshwater electrofishing, although large variability in vulnerability has been reported among different freshwater fusiform species. Therefore, we aimed to assess the vulnerability of another, nongadoid, fusiform osteichthyan: Sea Bass Dicentrarchus labrax (also known as European Bass Morone labrax). Two length groups of Sea Bass (31.3 +/- 2.2 and 42.1 +/- 2.5cm) were exposed to electric pulses as used in commercial electrotrawls targeting Sole (80 bipolar pulses per second, 2% duty cycle). Thereafter, the fish were monitored daily and then euthanized 14d after exposure for gross, radiographic, and histologic examination. No injuries were found in fish exposed to the electrical pulses. Differences in vertebral morphology among fusiform species may result in varying vulnerabilities to electrically induced spinal injuries. As a result, electrically induced spinal injuries and/or their variability in both marine and freshwater species may be determined by similar morphological parameters.