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Byadgi OV, Rahmawaty A, Wang PC, Chen SC. Comparative genomics of Edwardsiella anguillarum and Edwardsiella piscicida isolated in Taiwan enables the identification of distinctive features and potential virulence factors using Oxford-Nanopore MinION® sequencing. JOURNAL OF FISH DISEASES 2023; 46:287-297. [PMID: 36571326 DOI: 10.1111/jfd.13743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Edwardsiella tarda (ET) and Edwardsiella anguillarum (EA) are the most harmful bacterial fish pathogens in Taiwan. However, there is confusion regarding the genotypic identification of E. tarda and E. piscicida (EP). Therefore, we used a novel Nanopore MinION MK1C platform to sequence and compare the complete genomes of E. piscicida and E. anguillarum. The number of coding genes, rRNA, and tRNA recorded for E. anguillarum and E. piscicida were 8322, 25, and 98, and 5458, 25, and 98, respectively. Ribosomal multilocus sequence typing (rMLST) for E. piscicida indicated 35 rps. The shared clusters between E. anguillarum and E. piscicida indicated several unique clusters for the individual genomes. The phylogenetic tree analysis for all complete genomes indicated that E. anguillarum and E. piscicida were placed into two species-specific genotypes. Distribution of subsystems for annotated genomes found that genes related to virulence, defence, and disease for E. anguillarum were 103 and those for E. piscicida were 60 and pathogenic islands (PI) were 498 and 225, respectively. Vaccine candidates were identified in silico from the core genes using high antigenic, solubility, and secretion probabilities. Altogether, the genome data revealed distinctive features between E. anguillarum and E. piscicida, which suggest different pathogenicity and thus the need for separate preventive strategies.
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Affiliation(s)
- Omkar Vijay Byadgi
- International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Atiek Rahmawaty
- International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Pei-Chi Wang
- International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shih-Chu Chen
- International College, International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Centre for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, Taiwan
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Li L, Song M, Peng B, Peng XX, Li H. Identification and innate immunity mechanism of protective immunogens from extracellular proteins of Edwardsiella tarda. FISH & SHELLFISH IMMUNOLOGY 2020; 97:41-45. [PMID: 31830569 DOI: 10.1016/j.fsi.2019.12.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
One of the most important emerging pathogens in the aquaculture industry is Edwardsiella tarda, and it causes extensive losses in farmed fish globally. The identification of protective immunogens against E. tarda is increasingly valued. We previously investigated 20 recombinant proteins of 38 E. tarda extracellular secretory proteins and identified 10 as protective immunogens in a zebrafish model. Here, we clone 10 of the remaining 18 genes, and the resulting recombinant proteins are used for evaluation of immune protection. ETAE_2147 (FliK), ETAE_0654 (PpdD), and ETAE_3259 (DamX) are identified as protective immunogens. Furthermore, their protection mechanism is explored by the detection of innate immunity genes encoding IL-1b, IL-6, IL-8, C3b, and NF-κB. The three protective immunogens stimulate zebrafish to produce higher and more lasting expression of the five immunity genes than non-protective immunogens during the first 48 h of infection. In addition, these protective immunogens are prone to be regulated by host products, which is helpful for cross-talk between host and pathogen, and thus they become vaccine candidates. These results highlight the way to understand the working mechanisms of protective immunogens.
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Affiliation(s)
- Lu Li
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, 510006, People's Republic of China
| | - Ming Song
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, 510006, People's Republic of China
| | - Bo Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, 510006, People's Republic of China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Xuan-Xian Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, 510006, People's Republic of China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Hui Li
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, University City, Guangzhou, 510006, People's Republic of China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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Gene Cloning, Recombinant Expression, Characterization, and Molecular Modeling of the Glycolytic Enzyme Triosephosphate Isomerase from Fusarium oxysporum. Microorganisms 2019; 8:microorganisms8010040. [PMID: 31878282 PMCID: PMC7022633 DOI: 10.3390/microorganisms8010040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/16/2019] [Accepted: 12/23/2019] [Indexed: 12/17/2022] Open
Abstract
Triosephosphate isomerase (TPI) is a glycolysis enzyme, which catalyzes the reversible isomerization between dihydroxyactetone-3-phosphate (DHAP) and glyceraldehyde-3-phosphate (GAP). In pathogenic organisms, TPI is essential to obtain the energy used to survive and infect. Fusarium oxisporum (Fox) is a fungus of biotechnological importance due to its pathogenicity in different organisms, that is why the relevance of also biochemically analyzing its TPI, being the first report of its kind in a Fusarium. Moreover, the kinetic characteristics or structural determinants related to its function remain unknown. Here, the Tpi gene from F. oxysporum was isolated, cloned, and overexpressed. The recombinant protein named FoxTPI was purified (97% purity) showing a molecular mass of 27 kDa, with optimal activity at pH 8.0 and and temperature of 37 °C. The values obtained for Km and Vmax using the substrate GAP were 0.47 ± 0.1 mM, and 5331 μmol min−1 mg−1, respectively. Furthemore, a protein structural modeling showed that FoxTPI has the classical topology of TPIs conserved in other organisms, including the catalytic residues conserved in the active site (Lys12, His94 and Glu164). Finally, when FoxTPI was analyzed with inhibitors, it was found that one of them inhibits its activity, which gives us the perspective of future studies and its potential use against this pathogen.
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Buján N, Toranzo AE, Magariños B. Edwardsiella piscicida: a significant bacterial pathogen of cultured fish. DISEASES OF AQUATIC ORGANISMS 2018; 131:59-71. [PMID: 30324915 DOI: 10.3354/dao03281] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Edwardsiella piscicida, a Gram-negative, facultative aerobic pathogen belonging to the Enterobacteriaceae family, is the etiological agent of edwardsiellosis in fish and a significant problem in global aquaculture. E. piscicida has been reported from a broad geographical range and has been isolated from more than 20 fish host species to date, but this is likely to be an underestimation, because misidentification of E. piscicida as other species within the genus remains to be resolved. Common clinical signs associated with edwardsiellosis include, but are not limited to, exophthalmia, haemorrhages of the skin and in several internal organs, mild to moderate dermal ulcerations, abdominal distension, discoloration in the fish surface, and erratic swimming. Many antibiotics are currently effective against E. piscicida, although legal restrictions and the cost of medicated feeds have encouraged significant research investment in vaccination for the management of edwardsiellosis in commercial aquaculture. Here we summarise the current understanding of E. piscicida and highlight the difficulties with species assignment and the need for further research on epidemiology and strain variability.
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Affiliation(s)
- N Buján
- Departamento de Microbioloxía y Parasitoloxía, Facultade de Bioloxía-Edif, CIBUS, and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain
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Nagpal G, Usmani SS, Raghava GPS. A Web Resource for Designing Subunit Vaccine Against Major Pathogenic Species of Bacteria. Front Immunol 2018; 9:2280. [PMID: 30356876 PMCID: PMC6190870 DOI: 10.3389/fimmu.2018.02280] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/13/2018] [Indexed: 01/02/2023] Open
Abstract
Evolution has led to the expansion of survival strategies in pathogens including bacteria and emergence of drug resistant strains proved to be a major global threat. Vaccination is a promising strategy to protect human population. Reverse vaccinology is a more robust vaccine development approach especially with the availability of large-scale sequencing data and rapidly dropping cost of the techniques for acquiring such data from various organisms. The present study implements an immunoinformatic approach for screening the possible antigenic proteins among various pathogenic bacteria to systemically arrive at epitope-based vaccine candidates against 14 pathogenic bacteria. Thousand four hundred and fifty nine virulence factors and Five hundred and forty six products of essential genes were appraised as target proteins to predict potential epitopes with potential to stimulate different arms of the immune system. To address the self-tolerance, self-epitopes were identified by mapping on 1000 human proteome and were removed. Our analysis revealed that 21proteins from 5 bacterial species were found as virulent as well as essential to their survival, proved to be most suitable vaccine target against these species. In addition to the prediction of MHC-II binders, B cell and T cell epitopes as well as adjuvants individually from proteins of all 14 bacterial species, a stringent criteria lead us to identify 252 unique epitopes, which are predicted to be T-cell epitopes, B-cell epitopes, MHC II binders and Vaccine Adjuvants. In order to provide service to scientific community, we developed a web server VacTarBac for designing of vaccines against above species of bacteria. This platform integrates a number of tools that includes visualization tools to present antigenicity/epitopes density on an antigenic sequence. These tools will help users to identify most promiscuous vaccine candidates in a pathogenic antigen. This server VacTarBac is available from URL (http://webs.iiitd.edu.in/raghava/vactarbac/).
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Affiliation(s)
- Gandharva Nagpal
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India.,Centre for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Salman Sadullah Usmani
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India.,Center for Computational Biology, Indraprastha Institute of Information Technology, Okhla, India
| | - Gajendra P S Raghava
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India.,Center for Computational Biology, Indraprastha Institute of Information Technology, Okhla, India
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