Fish Pathology Research and Diagnosis in Aquaculture of Farmed Fish; a Proteomics Perspective
Abstract
:Simple Summary
Abstract
1. Introduction
2. Fish Health, Stress and Welfare
3. Disease Diagnostics
3.1. Pathogen Identification
3.2. Symptomatology
4. Tools for the Study of Host-Pathogen Interactions
4.1. The “Holobiome” Approach: Metagenomics and Metaproteomics
4.2. Omics-Based Strategies and Protein-Protein Interaction (PPI) Networks
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Pathogen | Disease | Pathogen ID | Metabolic Process | Proteomic Method | Reference |
---|---|---|---|---|---|
Vírus | |||||
Singapore grouper iridovirus (SGIV) | Sistemic diseases | Vírus proteín characterization | - | SDS-PAGE MALDI-TOF-MS | [99] |
Singapore grouper iridovirus (SGIV) | Sistemic diseases | Vírus envelope proteín analysis and characterization | - | 1-DE MALDI-TOF/TOF-MS/MS and LC-MALDI-TOF/TOF-MS/MS | [100] |
Cyprinid herpesvirus 3 (CyHV-3) | Koi herpesvirus (KHV) disease | Functional analyses of the virion transmembrane proteome | - | SDS-PAGE LC-MS/MS | [101] |
Bacteria | |||||
Photobacterium damselaesubsp. piscicida | Pasteurellosis | - | Importance of outer membrane proteins in osmotic adaptations and bacterial virulence | 2-DE LC-nano ESI-Q-TOF MS/MS | [102] |
Photobacterium damselaesubsp. damselae | Vibriosis | - | Importance of iron in virulence | 2-DE MALDI-TOF/TOF-MS | [103] |
Photobacterium damselae | Pasteurellosis | Differentiation of Photobacterium damselae subspecies | - | MALDI-TOF-MS | [104] |
Edwardsiella tarda | Haemorrhagic septicaemia | Identification of proteins associated with virulent and avirulent strains | - | 2-DE MALDI-TOF MS | [105,106] |
Edwardsiella tarda | Haemorrhagic septicaemia | - | Virulence determinants | 2-DE ESI MS/MS | [92] |
Yersinia ruckeri | Enteric redmouth disease | Identification and characterization of biotype 1 and biotype 2 strains | - | Nano LC-MS/MS | [107] |
Yersinia ruckeri | Enteric redmouth disease | - | Importance of iron in virulence | Nano LC-MS/MS | [108] |
Yersinia ruckeri | Enteric redmouth disease | - | Importance of outer membrane proteins in bacterial virulence | Gell free and 1-D nLC-ESI-MS/MS | [109] |
Flavobacterium columnare | Columnaris disease | - | Virulence determinants | 2-D LC ESI MS/MS and 2-DE MALDI TOF/TOF MS | [110] |
Flavobacterium psychrophilum | Bacterial coldwater disease | Proteomic profiling of strains, the importance of iron in virulence | - | 2-DE LC-MS/MS | [111] |
Flavobacterium psychrophilum | Bacterial coldwater disease | Differentiation of Flavobacterium psychrophilum from Flavobacterium psychrophilum-like species | - | MALDI-TOF MS | [112] |
Vibrio parahaemolyticus | Vibriosis | - | Identify proteins regulating antimicrobial peptide resistance | 2-DE LC-ESI-Q-TOF MS/MS | [113] |
Streptococcus agalactiae | Streptococcosis | - | Temperature effects on bacterial virulence | NanoUPLC-HDMSE | [114] |
Streptococcus iniaeand Streptococcus parauberis | Streptococcosis | Identification and molecular fingerprinting | - | MALDI-TOF-MS | [115] |
Streptococcus parauberis | Streptococcosis | Identification of bacterial strains | - | MALDI-TOF-MS | [116] |
Vagococcus salmoninarum | Cold-water streptococcosis | Typing and characterization of bacterial strains | - | MALDI-TOF-MS | [117] |
Streptococcus iniae | Streptococcosis | Proteomic profile of a pathogenic strain | - | 2-DE MALDI-TOF-MS | [118] |
Piscirickettsia salmonis | Salmonid rickettsial syndrome | Detection and identification | Virulence determinants | MALDI-TOF-MS | [119] |
Tenacibaculum sp. | Tenacibaculosis | Identification of Tenacibaculum species | - | MALDI-TOF-MS | [120,121] |
Mycobacterium marinum | Mycobacteriosis | Identification of Mycobacterium marinum subspecies | - | MALDI-TOF-MS | [122] |
Several bacterial species | - | Differentiate several gram-negative fish pathogenic bacteria | - | MALDI-TOF-MS | [123] |
Fungus | |||||
Saprolegnia parasitica | Saprolegniasis | Identification and characterization of developmental stages | - | iTRAQ SDS-PAGE Nano-LC-MS/MS | [124] |
Parasites | |||||
Caligus rogercresseyi | Sea lice | Detection and identification | Virulence determinants | MALDI-TOF-MS | [119] |
Disease | Pathogen | Host | Clinical Signs/Pathology | References |
---|---|---|---|---|
Virus | ||||
Epizootic haematopoietic necrosis (EHN) | Epizootic haematopoietic necrosis virus | Redfin perch (Perca fluviatilis), Rainbow trout (Oncorhynchus mykiss) | Erratic swimming, darkened skin, skin ulcers, exophthalmia, swollen spleen and kidney, petechial haemorrhages on fins, ascites, abdominal distension | [131] |
Infectious haematopoietic necrosis (IHN) | Infectious haematopoietic necrosis virus | Salmonids | Lethargy, darkened skin, exophthalmia, eye haemorrhage, pale gills, swollen abdomen, opaque faecal casts, petechial haemorrhage on fins, visceral pallor | [132,133] |
Infectious Pancreatic Necrosis (IPN) | Infectious pancreatic necrosis virus | Salmonids | Irregular swimming, loss of appetite, darkening of the skin, distended abdomen, exophthalmia, pale gills petechial haemorrhages, visceral ascites, intestine with catarrhal exudate and pale liver | [134,135,136] |
Infectious salmon Anaemia (ISA) | Infectious Salmon Anaemia virus | Atlantic salmon (Salmo salar) | Lethargy, anaemia, exophthalmia, pale gills and internal organs, ascites, oedemas, petechiae in visceral fat, liver and spleen congestion | [137,138] |
Lymphocystis disease | Lymphocystis disease virus | Broadly infectious | Nodular lesions on the skin, fins and internally | [137] |
Pancreatic disease (PD) | Salmonid alphaviruses (SAV) | Rainbow trout (Oncorhynchus mykiss), Atlantic salmon (Salmo salar) | Lethargy, hang in the corners of the cage or rest in the bottom, loss of appetite, yellow faecal casts, ascites, petechial haemorrhages in pyloric caecal fat, lesions in pancreas and skeletal and cardiac muscle | [139,140] |
Viral haemorrhagic septicaemia (VHS) | Viral haemorrhagic septicaemia virus | Broadly infectious | Aberrant swimming (spiral, leaping, flashing), exophthalmia, darkened skin, anaemia, pale gills and liver, internal haemorrhages, ascites leading to a swollen abdomen, swollen and hyperaemic kidney | [137,141] |
Viral nervous necrosis (VNN) | Betanodaviruses | Broadly infectious | Lethargy, abnormal swimming; anorexia, skin darkening, abdominal distension, hyperinflation of the swim bladder | [142,143] |
Bacteria | ||||
Vibriosis | Vibrio anguillarum | Broadly infectious | Lethargy, cease feeding, darkened skin, exophthalmia and corneal opacity, pale gills, petechiae at fin bases and skin, ulcers, generalized septicaemia | [127,144,145] |
Pasteurellosis | Photobacterium damselae subsp. piscicida | White perch (Morone americanus) yellowtail (Seriola quinqueradiata) gilthead seabream (Sparus aurata) | Darkened skin, swollen spleen, white-spotted lesions in spleen and kidney, bacterial accumulations on the tissues of internal organs | [146,147] |
Furunculosis | Aeromonas salmonicida subsp. salmonicida | Broadly infectious | Lethargy, cease feeding, darkened skin, exophthalmia, haemorrhages at the base of the fins, enlarged spleen, lesions on the skin (furuncles), ulcers, pale liver, general septicaemia | [148,149] |
Tenacibaculosis | Tenacibaculum maritimum | Broadly infectious | Flashing swimming behaviour, anorexic, erosion on the skin, fins (tail rot), head and gills, petechial haemorrhage on the abdominal peritoneum, ulcers | [150] |
Bacterial gill disease (BGD) | Flavobacterium branchiophilum | Coldwater fish (mainly salmonids) | Loss of appetite, gill infestation, increased opercular movements, gasping at the water surface, respiratory distress | [151] |
Rainbow Trout Fry Syndrom (RFTS) | Flavobacterium psychrophilum | Salmonids | Lethargy, anorexia, distended abdomen, darkened skin in caudal peduncle area, skin ulceration, swollen spleen, pale organs | [152] |
Red spot disease (Winter disease) | Pseudomonas anguilliseptica | Eels, salmonids, gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax), European cod (Gadus morhua) | Erratic swimming, petechial haemorrhages in the skin and liver, distended abdomen, ascitic fluid in the peritoneal cavity, pale liver, haemorrhaged kidney, intestine with yellowish exudate | [144,153] |
Disease | Pathogen | Host | Clinical Signs/Pathology | References |
Lactococcosis | Lactococcus garvieae | Broadly infectious | Lethargy, anorexia, exophthalmia, distended abdomen, ascitic fluid in the peritoneal cavity, congestion and haemorrhages of liver, intestine, spleen and kidney, haemorrhagic septicaemia | [154] |
Parasites | ||||
Amoebic gill disease (AGD) | Neoparamoeba perurans | Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss) | Lethargy, respiratory distress, increased opercular movements, whitish patches on gills and excessive mucus | [155,156] |
White spot disease/Ichthyophthiriasis | Ichthyophthirius multifiliis | Freshwater fish | Hyperactive (initially), lethargic; pale gills, darkened skin, white spots in the skin, increase of mucus production, skin ulcers, frayed fins, pale liver, enlarged spleen and kidney | [128,157,158] |
White spot disease/Cryptocaryoniasis | Cryptocaryon irritans | Saltwater fish | Hyperactive (initially), lethargic, numerous small whitish spots on the skin surface, petechial haemorrhages on the skin, excessive mucus production, skin ulcers, corneal clouding and blindness | [128,159] |
Amyloodiniosis | Amyloodinium ocellatum | Broadly infectious | Cease feeding, scratch against the bottom, infested gills and skin, excessive mucus production, epithelial erosion on attachment sites | [160,161,162] |
Trichodinosis | Trichodina sp. | Broadly infectious | Lethargy, cease feeding, infested gills, skin and fins, Greyish colour due to excessive mucus production, skin lesions in attachment sites, frayed fins | [163,164] |
Gyrodactilosis | Gyrodactylus salaris | Salmonids | Infest mainly fins and skin, lethargy, anorexia, emaciated fins, darkened skin, epithelium lesions | [165,166] |
Sea lice | Lepeophtheirus salmonis | Salmonids | Skin lesions, especially on the head, haemorrhages, scale loss, oedema, hyperplasia and cellular inflammations | [167] |
Aetiological Agent | Species | Tissue | Modified Protein Groups | Reference |
---|---|---|---|---|
Vírus | ||||
Infectious spleen and kidney necrosis virus (ISKNV) (Megalocytivirus) | Zebrafish (Danio rerio) | Spleen | Cytoskeletal proteins, stress response, lipoprotein and carbohydrate metabolism, signal transduction, proteolysis, metabolic and catabolic processes | [89] |
Megalocytivirus | Turbot (Scophtalmus maximus) | Spleen | Cytoskeleton proteins, molecular biosynthesis, cellular signal transduction and chaperone proteins | [187] |
Salmonid alphavirus subtype 3 (SAV3) | Atlantic salmon (Salmo salar) | Serum | Humoral components of immunity | [94] |
Rhabdovirus | Zebrafish (Danio rerio) | Fins | Proteins of the glycolytic pathway and cytoskeleton components | [188] |
Spring viremia of carp virus | Zebrafish (Danio rerio) | Plasma | Vitellogenin and Gig2 | [189] |
Viral septicemia hemorrhagic virus | Rainbow trout (Oncorhynchus mykiss) | Red blood cells from blood and head kidney | Proteins related to viral transcription | [190] |
Cyprinid herpesvirus-2 | Crucian carp (Carassius carassius) | Head kidney | Cytoskeleton, transport, immunologic, intracellular and physiologic proteins | [191] |
Bacteria | ||||
Aeromonas salmonicida | Rainbow trout (Oncorhynchus mykiss) | Liver | Complement system and acute phase response proteins | [192] |
Aeromonas salmonicida | Rainbow trout (Oncorhynchus mykiss) | Spleen | Immune system, signaling molecules and interaction | [193] |
Aeromonas hydrophila | Common carp (Cyprinus carpio) | Intestinal mucosa | Proteins involved in stress and immune response | [194] |
Aeromonas hydrophila | Zebrafish (Danio rerio) | Gills | Stress and immune response | [91] |
Edwardsiella ictaluri | Channel catfish (Ictalurus punctatus) | Head kidney | Macrophage function, cellular stress response, cellular energy production and metabolism | [195] |
Yersinia ruckeri | Rainbow trout (Oncorhynchus mykiss) | Head kidney and spleen | Immune system, cellular, metabolic, developmental, multicellular, adhesion, regulation and response to stimulus | [95] |
Yersinia ruckeri | Rainbow trout (Oncorhynchus mykiss) | Intestine | Metabolic process biological regulation, cellular processes and component organization | [196] |
Vibrio anguillarum | Atlantic cod (Gadus morhua) | Mucus | Proteins involved in the immune system | [83] |
Streptococcus parauberis | Olive flounder (Paralichthys olivaceus) | Kidney | Proteins involved in immune response, cellular recovery and glycoprotein synthesis | [197] |
Moraxella sp. | Gilthead seabream (Sparus aurata) | Kidney | Mitochondrial proteins, cellular response to oxidative stress, infection and inflammation | [198] |
Parasites | ||||
Ichthyophthirius multifiliis | Common carp (Cyprinus carpio) | Mucus | Proteins involved in the immune and inflammatory response | [199] |
Lepeophtheirus salmonis | Atlantic salmon (Salmo salar) | Mucus | Proteins involved in glycolysis, peptide synthesis, immune and defence response | [82] |
Amyloodinium ocellatum | Gilthead seabream (Sparus aurata) | Plasma | Proteins involved in the acute-phase response, inflammation, lipid transport, homeostasis and wound healing | [88] |
Neoparamoeba perurans | Atlantic salmon (Salmo salar) | Gill and skin mucus | Proteins involved in cell to cell signalling and inflammation pathway | [189] |
Neoparamoeba perurans | Atlantic salmon (Salmo salar) | Gill and skin mucus | Proteins involved in cell cycle regulation, cytoskeletal regulation, oxidative metabolism and immunity | [201] |
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Moreira, M.; Schrama, D.; Farinha, A.P.; Cerqueira, M.; Raposo de Magalhães, C.; Carrilho, R.; Rodrigues, P. Fish Pathology Research and Diagnosis in Aquaculture of Farmed Fish; a Proteomics Perspective. Animals 2021, 11, 125. https://doi.org/10.3390/ani11010125
Moreira M, Schrama D, Farinha AP, Cerqueira M, Raposo de Magalhães C, Carrilho R, Rodrigues P. Fish Pathology Research and Diagnosis in Aquaculture of Farmed Fish; a Proteomics Perspective. Animals. 2021; 11(1):125. https://doi.org/10.3390/ani11010125
Chicago/Turabian StyleMoreira, Márcio, Denise Schrama, Ana Paula Farinha, Marco Cerqueira, Cláudia Raposo de Magalhães, Raquel Carrilho, and Pedro Rodrigues. 2021. "Fish Pathology Research and Diagnosis in Aquaculture of Farmed Fish; a Proteomics Perspective" Animals 11, no. 1: 125. https://doi.org/10.3390/ani11010125
APA StyleMoreira, M., Schrama, D., Farinha, A. P., Cerqueira, M., Raposo de Magalhães, C., Carrilho, R., & Rodrigues, P. (2021). Fish Pathology Research and Diagnosis in Aquaculture of Farmed Fish; a Proteomics Perspective. Animals, 11(1), 125. https://doi.org/10.3390/ani11010125