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Olymon K, Yadav M, Teronpi V, Kumar A. Unravelling the genomic secrets of bacterial fish pathogens: a roadmap to aquaculture sustainability. Mol Biol Rep 2024; 51:364. [PMID: 38407655 DOI: 10.1007/s11033-024-09331-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024]
Abstract
In the field of aquaculture, bacterial pathogens pose significant challenges to fish health and production. Advancements in genomic technologies have revolutionized our understanding of bacterial fish pathogens and their interactions with their host species. This review explores the application of genomic approaches in the identification, classification, and characterization of bacterial fish pathogens. Through an extensive analysis of the literature, we have compiled valuable data on 79 bacterial fish pathogens spanning 13 different phyla, encompassing their whole genome sequences. By leveraging high-throughput sequencing techniques, researchers have gained valuable insights into the genomic makeup of these pathogens, enabling a deeper understanding of their virulence factors and mechanisms of host interaction. Furthermore, genomic approaches have facilitated the discovery of potential vaccine and drug targets, opening up new avenues for the development of effective interventions against fish pathogens. Additionally, the utilization of genomics in fish disease resistance and control in aquaculture has shown promising results, enabling the identification of genetic markers associated with disease resistance traits. This review highlights the significant contributions of genomics to the field of fish pathogen research and underscores its potential for improving disease management strategies and enhancing the sustainability of aquaculture practices.
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Affiliation(s)
- Kaushika Olymon
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Mohit Yadav
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Valentina Teronpi
- Department, of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya, Behali, Biswanath, Assam, 784184, India.
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India.
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Godoy M, Montes de Oca M, Suarez R, Martinez A, Pontigo JP, Caro D, Kusch K, Coca Y, Bohle H, Bayliss S, Kibenge M, Kibenge F. Genomics of Re-Emergent Aeromonas salmonicida in Atlantic Salmon Outbreaks. Microorganisms 2023; 12:64. [PMID: 38257891 PMCID: PMC10819690 DOI: 10.3390/microorganisms12010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
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.
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Affiliation(s)
- Marcos Godoy
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Puerto Montt 5501842, Chile; (M.M.d.O.); (D.C.); (K.K.)
- Laboratorio de Biotecnología Aplicada, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Universidad San Sebastián, Sede de la Patagonia, Puerto Montt 5480000, Chile
| | - Marco Montes de Oca
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Puerto Montt 5501842, Chile; (M.M.d.O.); (D.C.); (K.K.)
| | - Rudy Suarez
- Programa de Magíster en Acuicultura, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo 1780000, Chile;
| | - Alexis Martinez
- ATC Patagonia S/N, Carretera Austral, Puerto Montt 5480000, Chile;
| | - Juan Pablo Pontigo
- Laboratorio Institucional, Facultad de Ciencias de la Naturaleza, Medicina Veterinaria, Universidad San Sebastián, Lago Panguipulli 1390, Puerto Montt 5501842, Chile;
| | - Diego Caro
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Puerto Montt 5501842, Chile; (M.M.d.O.); (D.C.); (K.K.)
| | - Karina Kusch
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Puerto Montt 5501842, Chile; (M.M.d.O.); (D.C.); (K.K.)
| | - Yoandy Coca
- Doctorado en Ciencias de la Ingeniería, Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago 7820436, Chile;
| | - Harry Bohle
- Laboratorio InnovoGen, Egaña 198 Piso 2, Puerto Montt 5502534, Chile;
| | - Sion Bayliss
- Bristol Veterinary School, University of Bristol, Bristol BS8 1QU, UK;
| | - Molly Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE C1A 4P3, Canada; (M.K.); (F.K.)
| | - Frederick Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE C1A 4P3, Canada; (M.K.); (F.K.)
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Cantillo Villa Y, Triga A, Katharios P. Polyinfection in Fish Aeromoniasis: A Study of Co-Isolated Aeromonas Species in Aeromonas veronii Outbreaks. Pathogens 2023; 12:1337. [PMID: 38003801 PMCID: PMC10674900 DOI: 10.3390/pathogens12111337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
We studied the phenotypic and genomic characteristics related to the virulence and antibiotic resistance of two Aeromonas strains, which were co-isolated before an outbreak of Aeromonas veronii among diseased seabass on Agathonisi Island, Greece, in April 2015. The first strain, AG2.13.2, is a potentially pathogenic mesophilic variant of Aeromonas salmonicida, and the second, AG2.13.5, corresponds to an Aeromonas rivipollensis related to A. rivipollensis KN-Mc-11N1 with an ANI value of 97.32%. AG2.13.2 lacks the type III secretion system just like other mesophilic strains of A. salmonicida. This characteristic has been associated with lower virulence. However, the genome of AG2.13.2 contains other important virulence factors such as type II and type VI secretion systems, and toxins such as rtxA, aerolysin aer/act, and different types of hemolysins. The strain also carries several genes associated with antibiotic resistance such as the tetE efflux pump, and exhibits resistance to tetracycline, ampicillin, and oxolinic acid. In an in vivo challenge test with gilthead seabream larvae, the A. veronii bv sobria strain AG5.28.6 exhibited the highest virulence among all tested strains. Conversely, both A. salmonicida and A. rivipollensis showed minimal virulence when administered alone. Interestingly, when A. veronii bv sobria AG5.28.6 was co-administered with A. rivipollensis, the larvae survival probability increased compared to those exposed to A. veronii bv sobria AG5.28.6 alone. This finding indicates an antagonistic interaction between A. veronii bv sobria AG5.28.6 and A. rivipollensis AG2.13.5. The co-administration of A. veronii bv sobria AG5.28.6 with Aeromonas salmonicida did not yield distinct survival probabilities. Our results validate that the primary pathogen responsible for European seabass aeromoniasis is Aeromonas veronii bv sobria.
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Affiliation(s)
- Yanelys Cantillo Villa
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), 71500 Gournes, Greece; (Y.C.V.); (A.T.)
- Department of Biology, University of Crete, 71110 Heraklion, Greece
| | - Adriana Triga
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), 71500 Gournes, Greece; (Y.C.V.); (A.T.)
- Department of Biology, University of Crete, 71110 Heraklion, Greece
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), 71500 Gournes, Greece; (Y.C.V.); (A.T.)
- Aquatic Biologicals, Thalassocosmos, 71500 Gournes, Greece
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Charette SJ. Aeromonas salmonicida: Genomics, Taxonomy, Diversity, Pathogenesis, Treatments and Beyond. Microorganisms 2023; 11:1189. [PMID: 37317163 DOI: 10.3390/microorganisms11051189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 06/16/2023] Open
Abstract
For a long time, the bacterial species Aeromonas salmonicida seemed to be limited to a regrouping of psychrophilic subspecies that infect fish, particularly salmonids [...].
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Affiliation(s)
- Steve J Charette
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada
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