Identification of epitope-based peptide vaccine candidates against enterotoxigenic Escherichia coli: a comparative genomics and immunoinformatics approach

2016 ◽  
Vol 12 (3) ◽  
pp. 890-901 ◽  
Author(s):  
Kusum Mehla ◽  
Jayashree Ramana
Keyword(s):  
Escherichia Coli ◽  
Comparative Genomics ◽  
Peptide Vaccine ◽  
Enterotoxigenic Escherichia Coli ◽  
Vaccine Candidates ◽  
Integrated Omics ◽  
Potential Vaccine

In the present study, we have employed integrated omics approach to identify potential vaccine candidates against ETEC.

Comparative genomics and phylogeny of the IncI1 plasmids: A common plasmid type among porcine enterotoxigenic Escherichia coli

Plasmid ◽  
2011 ◽  
Vol 66 (3) ◽  
pp. 144-151 ◽  
Author(s):  
Timothy J. Johnson ◽  
Sara M. Shepard ◽  
Bernadette Rivet ◽  
Jessica L. Danzeisen ◽  
Alessandra Carattoli
Keyword(s):  
Escherichia Coli ◽  
Comparative Genomics ◽  
Enterotoxigenic Escherichia Coli

Comparative genomics of Edwardsiella ictaluri revealed four distinct host-specific genotypes and thirteen potential vaccine candidates

Genomics ◽  
2021 ◽  
Vol 113 (4) ◽  
pp. 1976-1987
Author(s):  
Vimbai Irene Machimbirike ◽  
Pichahpuk Uthaipaisanwong ◽  
Pongsak Khunrae ◽  
Ha Thanh Dong ◽  
Saengchan Senapin ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Edwardsiella Ictaluri ◽  
Vaccine Candidates ◽  
Potential Vaccine

scholarly journals A comparative genomics and immunoinformatics approach to identify epitope-based peptide vaccine candidates against bovine hemoplasmosis

2020 ◽  
Author(s):  
Rosa Estela Quiroz-Castañeda ◽  
Hugo Aguilar-Díaz ◽  
Diana Laura Flores-García ◽  
Fernando Martínez-Ocampo ◽  
Itzel Amaro-Estrada
Keyword(s):  
Comparative Genomics ◽  
Molecular Detection ◽  
Peptide Vaccine ◽  
Detection Methods ◽  
Cattle Production ◽  
Vaccine Candidates ◽  
Mycoplasma Wenyonii ◽  
Alignment Coverage ◽  
Genomic Characterization

AbstractMycoplasma wenyonii and ‘Candidatus Mycoplasma haemobos’ have been described as major hemoplasmas that infect cattle worldwide. Currently, three bovine hemoplasma genomes are known. The aim of this work was to know the main genomic characteristics and the evolutionary relationships between hemoplasmas, as well as to provide a list of epitopes identified by immunoinformatics that could be used as vaccine candidates against bovine hemoplasmosis. So far, there is not a vaccine to prevent this disease that impact economically in cattle production around the world.In this work, we used comparative genomics to analyze the genomes of the hemoplasmas so far reported. As a result, we confirm that ‘Ca. M haemobos’ INIFAP01 is a divergent species from M. wenyonii INIFAP02 and M. wenyonii Massachusetts. Although both strains of M. wenyonii have genomes with similar characteristics (length, G+C content, tRNAs and position of rRNAs) they have different structures (alignment coverage and identity of 51.58 and 79.37%, respectively).The correct genomic characterization of bovine hemoplasmas, never studied before, will allow to develop better molecular detection methods, to understand the possible pathogenic mechanisms of these bacteria and to identify epitopes sequences that could be used in the vaccine design.

Identification of Generalized Peptide Regions for Designing Vaccine Effective for All Significant Mutated Strains of SARS-CoV-2

2021 ◽  
Vol 24 ◽  
Author(s):  
Subhamoy Biswas ◽  
Smarajit Manna ◽  
Tathagata Dey ◽  
Shreyans Chatterjee ◽  
Sumanta Dey
Keyword(s):  
Comparative Study ◽  
Zika Virus ◽  
Peptide Vaccine ◽  
Vaccine Design ◽  
Current Approach ◽  
Polar Plot ◽  
Vaccine Candidates ◽  
The Future ◽  
Potential Vaccine ◽  
The Comparative Study

Background: Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has become a worldwide pandemic and created an utmost crisis across the globe. To mitigate the crisis, the design of vaccines is a crucial solution. The frequent mutation of the virus demands generalized vaccine candidates, which would be effective for all mutated strains at present and for the strains that would evolve due to further new mutations in the virus. Objective: The objective of this study is to identify more frequently occurring mutated variants of SARS-CoV-2 and to suggest peptide vaccine candidates effective in common against the viral strains considered. Method: In this study, we have identified all currently prevailing mutated strains of SARS-CoV-2 through 2D Polar plot and Quotient Radius〖(q〗_R) characterization descriptor. Then, by considering the top eight mutation strains, which are significant due to their frequency of occurrence, peptide regions suitable for vaccine design have been identified with the help of a mathematical model – 2D Polygon Representation, followed by the evaluation of epitope potential and ensuring that there is no case of any autoimmune threat. Lastly, in order to verify whether this entire approach is applicable for vaccine design against any other virus in general, we have made a comparative study between the peptide vaccine candidates prescribed for the Zika virus using the current approach and a list of potential vaccine candidates for the same already established in the past. Results: We have finally suggested three generalized peptide regions which would be suitable as sustainable peptide vaccine candidates against SARS-CoV-2 irrespective of its currently prevailing strains as well any other variant of the same that may appear in the future. We also observed that during the comparative study using the case of E protein of Zika virus, the peptide regions suggested using the new approach matched with the already established results. Conclusion: The study, therefore, illustrates an approach that would help in developing peptide vaccine against SARS-CoV-2 by suggesting those peptide regions which can be targeted irrespective of any mutated form of this virus. The consistency with which this entire approach was also able to figure out similar vaccine candidates for Zika virus with utmost accuracy proves that this protocol can be extended for peptide vaccine design against any other virus in the future.

scholarly journals Comparative Genomics and Immunoinformatics Approach for the Identification of Vaccine Candidates for Enterohemorrhagic Escherichia coli O157:H7

2014 ◽  
Vol 82 (5) ◽  
pp. 2016-2026 ◽  
Author(s):  
Víctor A. García-Angulo ◽  
Anjana Kalita ◽  
Mridul Kalita ◽  
Luis Lozano ◽  
Alfredo G. Torres
Keyword(s):  
Escherichia Coli ◽  
Comparative Genomics ◽  
Enterohemorrhagic Escherichia Coli ◽  
Th2 Cytokines ◽  
Structural Protein ◽  
Gene Encoding ◽  
Content Type ◽  
Vaccine Candidates ◽  
Genes Encoding ◽  
K 12

ABSTRACTEnterohemorrhagicEscherichia coli(EHEC) O157:H7 strains are major human food-borne pathogens, responsible for bloody diarrhea and hemolytic-uremic syndrome worldwide. Thus far, there is no vaccine for humans against EHEC infections. In this study, a comparative genomics analysis was performed to identify EHEC-specific antigens useful as potential vaccines. The genes present in both EHEC EDL933 and Sakai strains but absent in nonpathogenicE. coliK-12 and HS strains were subjected to anin silicoanalysis to identify secreted or surface-expressed proteins. We obtained a total of 65 gene-encoding protein candidates, which were subjected to immunoinformatics analysis. Our criteria of selection aided in categorizing the candidates as high, medium, and low priority. Three members of each group were randomly selected and cloned into pVAX-1.Candidates were pooled accordingly to their priority group and tested for immunogenicity against EHEC O157:H7 using a murine model of gastrointestinal infection. The high-priority (HP) pool, containing genes encoding a Lom-like protein (pVAX-31), a putative pilin subunit (pVAX-12), and a fragment of the type III secretion structural protein EscC (pVAX-56.2), was able to induce the production of EHEC IgG and sIgA in sera and feces. HP candidate-immunized mice displayed elevated levels of Th2 cytokines and diminished cecum colonization after wild-type challenge. Individually tested HP vaccine candidates showed that pVAX-12 and pVAX-56.2 significantly induced Th2 cytokines and production of fecal EHEC sIgA, with pVAX-56.2 reducing EHEC cecum colonization. We describe here a bioinformatics approach able to identify novel vaccine candidates potentially useful for preventing EHEC O157:H7 infections.

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