Ahmad T.A., Eweida A.E. and El-Sayed L.H. 2016. T-cell epitope mapping for the design of powerful vaccines. Vaccine Reports, 6: 13–22.
Alberts B., Johnson A., Lewis J., Raff M., Roberts K. and Walter P. 2002. Molecular Biology of the Cell. Garland Science, USA. 1464P.
Armenteros J.J.A., Tsirigos K.D., Sønderby C.K., Petersen T.N., Winther O., Brunak S., Von Heijne G. and Nielsen H. 2019. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nature Biotechnology, 37(4): 420–423.
Awasthi S.P., Asakura M., Chowdhury N., Neogi S.B., Hinenoya A., Golbar H.M., Yamate J., Arakawa E., Tada T. and Ramamurthy T. 2013. Novel cholix toxin variants, ADP-ribosylating toxins in Vibrio cholerae non-O1/non-O139 strains, and their pathogenicity. Infection and Immunity, 81(2): 531–541.
Barh D., Tiwari S., Jain N., Ali A., Santos A.R., Misra A.N., Azevedo V. and Kumar A. 2011. In silico subtractive genomics for target identification in human bacterial pathogens. Drug Development Research, 72(2): 162–177.
Cao Z. and Klebba P.E. 2002. Mechanisms of colicin binding and transport through outer membrane porins. Biochimie, 84(5): 399–412.
Chiang M.H., Sung W.C., Lien S.P., Chen Y.Z., Lo A.F.Y., Huang J.H., Kuo S.C. and Chong P. 2015. Identification of novel vaccine candidates against Acinetobacter baumannii using reverse vaccinology. Human vaccines and Immunotherapeutics, 11(4): 1065–1073.
Colmer J.A., Fralick J.A. and Hamood A.N. 1998. Isolation and characterization of a putative multidrug resistance pump from Vibrio cholerae. Molecular Microbiology, 27(1): 63–72.
Colwell R. and Huq A. 2001. Marine ecosystems and cholera. P: 141–145. In: Porter J.W. (Ed.). The Ecology and Etiology of Newly Emerging Marine Diseases. Springer, Netherlands.
Colwell R.R. 2002. A voyage of discovery: Cholera, climate and complexity. Environmental Microbiology, 4(2): 67–69.
Deshayes S., Daurel C., Cattoir V., Parienti J.J., Quilici M.L. and De La Blanchardiere A. 2015. Non-O1, non-O139 Vibrio cholerae bacteraemia: Case report and literature review. Springerplus, 4(1): 1–9.
Drasar B.S. and Forrest B.D. 1996. Cholera and the Ecology of Vibrio cholerae. Springer, Netherlands 376P.
El-Gebali S., Mistry J., Bateman A., Eddy S.R., Luciani A., Potter S.C., Qureshi M., Richardson L.J., Salazar G.A. and Smart A. 2019. The Pfam protein families database in 2019. Nucleic Acids Research, 47: 427–432.
Elluri S., Enow C., Vdovikova S., Rompikuntal P.K., Dongre M., Carlsson S., Pal A., Uhlin B.E. and Wai S.N. 2014. Outer membrane vesicles mediate transport of biologically active Vibrio cholerae cytolysin (VCC) from V. cholerae strains. PLOS One, 9(9): 1–13 (e106731).
Federici L., Du D., Walas F., Matsumura H., Fernandez-Recio J., McKeegan K.S., Borges-Walmsley M.I., Luisi B.F. and Walmsley A.R. 2005. The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 Å resolution. Journal of Biological Chemistry, 280(15): 15307–15314.
Feghali R. and Adib S. 2011. Two cases of Vibrio cholerae non-O1/non-O139 septicaemia with favourable outcome in Lebanon. Eastern Mediterranean Health Journal, 17(8): 722–724.
Finco O. and Rappuoli R. 2014. Designing vaccines for the twenty-first century society. Frontiers in Immunology, 5(12): 1–6.
Garg A. and Gupta D. 2008. VirulentPred: A SVM based prediction method for virulent proteins in bacterial pathogens. BMC Bioinformatics, 9(1): 1–12.
Gasteiger E., Hoogland C., Gattiker A., Duvaud S.E., Wilkins M.R., Appel R.D. and Bairoch A. 2005. Protein identification and analysis tools on the ExPASy server. P: 571–607. In: Walker J.M. (Ed.). The Proteomics Protocols Handbook. Springer, Germany.
Gershoni J.M., Roitburd-Berman A., Siman-Tov D.D., Freund N.T. and Weiss Y. 2007. Epitope mapping. BioDrugs, 21(3): 145–156.
Gil F., Ipinza F., Fuentes J., Fumeron R., Villarreal J.M., Aspee A., Mora G.C., Vasquez C.C. and Saavedra C. 2007. The ompW (porin) gene mediates methyl viologen (paraquat) efflux in Salmonella enterica serovar typhimurium. Research in Microbiology, 158(6): 529–536.
Gourlay L.J., Peri C., Ferrer-Navarro M., Conchillo-Sole O., Gor A., Rinchai D., Thomas R.J., Champion O.L., Michell S.L. and Kewcharoenwong C. 2013. Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for structure-based epitope discovery/design in structural vaccinology. Chemistry and Biology, 20(9): 1147–1156.
Grote A., Hiller K., Scheer M., Munch R., Nortemann B., Hempel D.C. and Jahn D. 2005. JCat: A novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Research, 33: 526–531.
Gupta S., Kapoor P., Chaudhary K., Gautam A., Kumar R., Raghava G.P. and Consortium O.S.D.D. 2013. In silico approach for predicting toxicity of peptides and proteins. PLOS One, 8(9): 1–10 (e73957).
Hailemichael Y. and Overwijk W.W. 2013. Peptide-based anticancer vaccines: The making and unmaking of a T-cell graveyard. Oncoimmunology, 2(7): 1–4 (e24743).
Halpern M. and Izhaki I. 2017. Fish as hosts of Vibrio cholerae. Frontiers in Microbiology, 8: 1–7 (282).
Harris J.F. Ryan E.T. and Calderwood S.B. 2012. Cholera. Lancet, 379: 2466–2476.
Hattotuwagama C.K., Guan P., Doytchinova I.A., Zygouri C. and Flower D.R. 2004. Quantitative online prediction of peptide binding to the major histo-compatibility complex. Journal of Molecular Graphics and Modelling, 22(3): 195–207.
Hong H., Patel D.R., Tamm L.K. and Van Den Berg B. 2006. The outer membrane protein OmpW forms an eight-stranded β-barrel with a hydrophobic channel. Journal of Biological Chemistry, 281(11): 7568–7577.
Ikai A. 1980. Thermostability and aliphatic index of globular proteins. The Journal of Biochemistry, 88(6): 1895–1898.
Islam M., Drasar B. and Bradley D. 1988. Survival and attachment of toxigenic Vibrio cholerae O1 in association with four marine algae. Bangladesh Journal of Microbiology, 5(2): 41–48.
Jenuth J.P. 1999. The NCBI: Publicly available tools and resources on the web. Bioinformatics Methods and Protocols, 132: 301–312.
Jertborn M., Svennerholm A.M. and Holmgren J. 1992. Safety and immunogenicity of an oral recombinant cholera B subunit-whole cell vaccine in Swedish volunteers. Vaccine, 10(2): 130–132.
Jertborn M., Svennerholm A.M. and Holmgren J. 1993. Evaluation of different immunization schedules for oral cholera B subunit-whole cell vaccine in Swedish volunteers. Vaccine, 11(10): 1007–1012.
Jespersen M.C., Peters B., Nielsen M. and Marcatili P. 2017. BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Research, 45: 24–29.
Juncker A.S., Willenbrock H., Von Heijne G., Brunak S., Nielsen H. and Krogh A. 2003. Prediction of lipoprotein signal peptides in Gram‐negative bacteria. Protein Science, 12(8): 1652–1662.
Kaper J.B., Morris J.G. and Levine M.M. 1995. Cholera. Clinical Microbiology Reviews, 8(1): 48–86.
Kringelum J.V., Lundegaard C., Lund O. and Nielsen M. 2012. Reliable B cell epitope predictions: Impacts of method development and improved benchmarking. PLoS Computational Biology, 8(12): 1–10 (e1002829).
Larsen J.E., Lund O. and Nielsen M. 2006. Improved method for predicting linear B-cell epitopes. Immunome Research, 2(1): 1–7.
Lehner P.J. and Cresswell P. 1996. Processing and delivery of peptides presented by MHC class I molecules. Current Opinion in Immunology, 8(1): 59–67.
Levine M.M. 2010. Immunogenicity and efficacy of oral vaccines in developing countries: Lessons from a live cholera vaccine. BMC Biology, 8(1): 1–10.
Lim J. 2015. The characterization of the lipoprotein VacJ in Burkholderia pseudomallei and Burkholderia thailandensis. Ph.D. Thesis, London School of Hygiene and Tropical Medicine, UK. 190P.
Lu S., Wang J., Chitsaz F., Derbyshire M.K., Geer R.C., Gonzales N.R., Gwadz M., Hurwitz D.I., Marchler G.H. and Song J.S. 2020. CDD/Sparcle: The conserved domain database in 2020. Nucleic Acids Research, 48: 265–268.
Madej T., Lanczycki C.J., Zhang D., Thiessen P.A., Geer R.C., Marchler-Bauer A. and Bryant S.H. 2014. MMDB and VAST+: Tracking structural similarities between macromolecular complexes. Nucleic Acids Research, 42: 297–303.
Magnan C.N., Randall A. and Baldi P. 2009. SOLpro: Accurate sequence-based prediction of protein solubility. Bioinformatics, 25(17): 2200–2207.
Marchler-Bauer A., Bo Y., Han L., He J., Lanczycki C.J., Lu S., Chitsaz F., Derbyshire M.K., Geer R.C. and Gonzales N.R. 2016. CDD/SPARCLE: Functional classification of proteins via subfamily domain architectures. Nucleic Acids Research, 45: 200–203.
McClelland M., Sanderson K.E., Spieth J. and Clifton S.W. 2001. Complete genome sequence of Salmonella enterica serovar typhimurium LT2. Nature, 413(6858): 852–856.
Mookerjee S., Batabyal P., Sarkar M.H. and Palit A. 2015. Seasonal prevalence of enteropathogenic Vibrio and their phages in the riverine estuarine ecosystem of South Bengal. PLOS One, 10(9): 1–13 (e0137338).
Murphy K. and Weaver C. 2016. Janeway's Immunobiology. Garland Science, USA. 904P.
Mwansa J., Mwaba J., Lukwesa C., Bhuiyan N., Ansaruzzaman M., Ramamurthy T., Alam M. and Nair G.B. 2007. Multiply antibiotic-resistant Vibrio cholerae O1 biotype El Tor strains emerge during cholera outbreaks in Zambia. Epidemiology and Infection, 135(5): 847–853.
Naz A., Awan F.M., Obaid A., Muhammad S.A., Paracha R.Z., Ahmad J. and Ali A. 2015. Identification of putative vaccine candidates against Helicobacter pylori exploiting exoproteome and secretome: A reverse vaccinology based approach. Infection, Genetics and Evolution, 32: 280–291.
Naz R.K. and Dabir P. 2007. Peptide vaccines against cancer, infectious diseases, and conception. Frontiers Bioscience, 12(12): 1833–1844.
Nelson E.J., Harris J.B., Morris J.G., Calderwood S.B. and Camilli A. 2009. Cholera transmission: The host, pathogen and bacteriophage dynamic. Nature Reviews Microbiology, 7(10): 693–702.
Pastor M., Pedraz J. and Esquisabel A. 2013. The state-of-the-art of approved and under-development cholera vaccines. Vaccine, 31(38): 4069–4078.
Patronov A. and Doytchinova I. 2013. T-cell epitope vaccine design by immunoinformatics. Open Biology, 3(1): 1–13 (120139).
Petsaris O., Nousbaum J., Quilici M., Le Coadou G., Payan C. and Abalain M. 2010. Non-O1, non-O139 Vibrio cholerae bacteraemia in a cirrhotic patient. Journal of Medical Microbiology, 59(10): 1260–1262.
Ponomarenko J., Bui H.H., Li W., Fusseder N., Bourne P.E., Sette A. and Peters B. 2008. ElliPro: A new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics, 9(1): 1–8.
Rauta P.R., Ashe S., Nayak D. and Nayak B. 2016. In silico identification of outer membrane protein (Omp) and subunit vaccine design against pathogenic Vibrio cholerae. Computational Biology and Chemistry, 65: 61–68.
Rehulka J., Petras P., Marejkova M. and Aldova E. 2015. Vibrio cholerae non-O1/non-O139 infection in fish in the Czech Republic. Veterinarni Medicina, 60(1): 16–22.
Reise S.P. and Waller N.G. 2009. Item response theory and clinical measurement. Annual Review of Clinical Psychology, 5: 27–48.
Resende J.A., Godon J.J., Bonnafous A., Arcuri P.B., Silva V.L., Otenio M.H. and Diniz C.G. 2016. Seasonal variation on microbial community and methane production during anaerobic digestion of cattle manure in Brazil. Microbial Ecology, 71(3): 735–746.
Richie E., Punjabi N.H., Sidharta Y., Peetosutan K., Sukandar M., Wasserman S.S., Lesmana M., Wangsasaputra F., Pandam S. and Levine M.M. 2000. Efficacy trial of single-dose live oral cholera vaccine CVD 103-HgR in North Jakarta, Indonesia, a cholera-endemic area. Vaccine, 18(22): 2399–2410.
Schulz G.E. 2002. The structure of bacterial outer membrane proteins. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1565(2): 308–317.
Sharma A., Singla D., Rashid M. and Raghava G.P.S. 2014. Designing of peptides with desired half-life in intestine-like environment. BMC Bioinformatics, 15(282): 1–8.
Sharma N., Patiyal S., Dhall A., Pande A., Arora C. and Raghava G.P. 2020. AlgPred 2.0: An improved method for predicting allergenic proteins and mapping of IgE epitopes. Briefings in Bioinformatics, 22(4): 1–12.
Shen H.B. and Chou K.C. 2010. Gneg-mPLoc: A top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins. Journal of Theoretical Biology, 264(2): 326–333.
Sigal L.J., Crotty S., Andino R. and Rock K.L. 1999. Cytotoxic T-cell immunity to virus-infected non-haematopoietic cells requires presentation of exogenous antigen. Nature, 398(6722): 25–29.
Thompson D.K., Beliaev A.S., Giometti C.S., Tollaksen S.L., Khare T., Lies D.P., Nealson K.H., Lim H., Yates J. and Brandt C.C. 2002. Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: Possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress. Applied and Environmental Microbiology, 68(2): 881–892.
Thompson F.L., Iida T. and Swings J. 2004. Biodiversity of vibrios. Microbiology and Molecular Biology Reviews, 68(3): 403–431.
Thungapathra M., Sinha K.K., Chaudhuri S.R., Garg P., Ramamurthy T., Nair G.B. and Ghosh A. 2002. Occurrence of antibiotic resistance gene cassettes aac (6′)-Ib, dfrA5, dfrA12, and ereA2 in class I integrons in non-O1, non-O139 Vibrio cholerae strains in India. Antimicrobial Agents and Chemotherapy, 46(9): 2948–2955.
Trach D.D., Cam P., Ke N., Rao M., Dinh D., Hang P., Hung N., Canh D., Thiem V. and Naficy A. 2002. Investigations into the safety and immunogenicity of a killed oral cholera vaccine developed in Viet Nam. Bulletin of the World Health Organization, 80: 2–8.
Uchiyama H. 2000. Distribution of Vibrio species isolated from aquatic environments with TCBS agar. Environmental Health and Preventive Medicine, 4(4): 199–204.
Umamaheswari A., Pradhan D. and Hemanthkumar M. 2012. Computer aided subunit vaccine design against pathogenic Leptospira serovars. Interdisciplinary Sciences: Computational Life Sciences, 4(1): 38–45.
Viret J.F., Dietrich G. and Favre D. 2004. Biosafety aspects of the recombinant live oral Vibrio cholerae vaccine strain CVD 103-HgR. Vaccine, 22(19): 2457–2469.
WHO. 2018. World Health Organization. Fourth annual Meeting of the Global Task Force on Cholera Control, South Africa. 30P.
Wimley W.C. 2002. Toward genomic identification of β‐barrel membrane proteins: Composition and architecture of known structures. Protein Science, 11(2): 301–312.
Yao B., Zhang L., Liang S. and Zhang C. 2012. SVMTriP: A method to predict antigenic epitopes using support vector machine to integrate tri-peptide similarity and propensity. PLOS One, 7(9): 1–5 (e45152).
Yosra M., Mahmoud M., Ebtsam S., Sabah I. and Elkamel A. 2016. Subclinical vibriosis in red swamp crayfish, Procambarus clarkii. International Journal of Fisheries and Aquatic Studies, 4(3): 119–123.
Yu C.S., Chen Y.C., Lu C.H. and Hwang J.K. 2006. Prediction of protein subcellular localization. Proteins: Structure, Function, and Bioinformatics, 64(3): 643–651.
Zhao L., Gao X., Liu C., Lv X., Jiang N. and Zheng S. 2017. Deletion of the vacJ gene affects the biology and virulence in Haemophilus parasuis serovar 5. Gene, 603: 42–53.