{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T11:46:10Z","timestamp":1777463170662,"version":"3.51.4"},"reference-count":32,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2019,5,23]],"date-time":"2019-05-23T00:00:00Z","timestamp":1558569600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Medicina"],"abstract":"<jats:p>Background and Objective: Vibrio cholerae continues to emerge as a dangerous pathogen because of increasing resistance to a number of antibiotics. This paper provides a solution to emerging antibiotic resistance by introducing novel proteins as vaccine candidates against cholera. Materials and Methods: Vibrio cholerae genome versatility is a hurdle for developing a vaccine to combat diarrhoeal infection, so its core gene information was used to determine a potential vaccine candidate. Whole genome sequence data of more than 100 Vibrio cholerae strains were used simultaneously to get core genome information. The VacSol pipeline based on reverse vaccinology was selected to address the problem of safe, cheap, temperature-stable, and effective vaccine candidates which can be used for vaccine development against Vibrio cholerae. VacSol screens vaccine candidates using integrated, well-known, and robust algorithms\/tools for proteome analysis. The proteomes of the pathogens were initially screened to predict homology using BLASTp. Proteomes that are non-homologous to humans are then subjected to a predictor for localization. Helicer predicts transmembrane helices for the protein. Proteins failing to comply with the set parameters were filtered at each step, and finally, 11 proteins were filtered as vaccine candidates. Results: This selected group of vaccine candidates consists of proteins from almost all structural parts of Vibrio cholerae. Their blast results show that this filtered group includes flagellin A protein, a protein from the Zn transporter system, a lipocarrier outer membrane protein, a peptidoglycan-associated protein, a DNA-binding protein, a chemotaxis protein, a tRNA Pseuriudine synthase A, and two selected proteins, which were beta lactamases. The last two uncharacterized proteins possess 100% similarity to V. albensis and Enterobacter, respectively. Tertiary structure and active site determination show a large number of pockets on each protein. Conclusions: The most interesting finding of this study is that 10 proteins out of 11 filtered proteins are introduced as novel potential vaccine candidates. These novel vaccine candidates can result in the development of cost-effective and broad-spectrum vaccines which can be used in countries where cholera is a major contributor to diarrheal disease.<\/jats:p>","DOI":"10.3390\/medicina55050195","type":"journal-article","created":{"date-parts":[[2019,5,24]],"date-time":"2019-05-24T02:22:00Z","timestamp":1558664520000},"page":"195","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Preliminary Work Towards Finding Proteins as Potential Vaccine Candidates for Vibrio cholerae Pakistani Isolates through Reverse Vaccinology"],"prefix":"10.3390","volume":"55","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1131-1691","authenticated-orcid":false,"given":"Samia","family":"Zeb","sequence":"first","affiliation":[{"name":"Department of Bio-Sciences, COMSATS University Islamabad, Islamabad 45550, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0486-4661","authenticated-orcid":false,"given":"Amjad","family":"Ali","sequence":"additional","affiliation":[{"name":"Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences &amp; Technology (NUST), Islamabad 44000, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8921-8636","authenticated-orcid":false,"given":"Sardar Muhammad","family":"Gulfam","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering, COMSATS University Islamabad, Islamabad 45550, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Habib","family":"Bokhari","sequence":"additional","affiliation":[{"name":"Department of Bio-Sciences, COMSATS University Islamabad, Islamabad 45550, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,5,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Almagro-Moreno, S., and Taylor, R.K. (2012). Cholera: Environmental Reservoirs and Impact on Disease Transmission. Microbiol. Spectr., 1.","DOI":"10.1128\/microbiolspec.OH-0003-2012"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1128\/MMBR.62.4.1301-1314.1998","article-title":"Epidemiology, Genetics, and Ecology of Toxigenic Vibrio cholerae","volume":"62","author":"Faruque","year":"1998","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1111\/j.1574-6976.2002.tb00605.x","article-title":"Vibrio cholerae and cholera: Out of the water and into the host","volume":"26","author":"Reidl","year":"2002","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1016\/j.genrep.2016.07.002","article-title":"In silico identification of receptor specific epitopes as potential vaccine candidates from Vibrio cholerae strains","volume":"4","author":"Noureen","year":"2016","journal-title":"Gene Rep."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1128\/iai.24.1.111-116.1979","article-title":"In vivo and in vitro characterization of virulence-deficient mutants of Vibrio cholerae","volume":"24","author":"Baselski","year":"1979","journal-title":"Infect. Immun."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1020","DOI":"10.1128\/IAI.71.2.1020-1025.2003","article-title":"Pathogenic potential of environmental Vibrio cholerae strains carrying genetic variants of the toxin-coregulated pilus pathogenicity island","volume":"71","author":"Faruque","year":"2003","journal-title":"Infect. Immun."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"4157","DOI":"10.1128\/jb.178.14.4157-4165.1996","article-title":"A new type of conjugative transposon encodes resistance to sulfamethoxazole, trimethoprim, and streptomycin in Vibrio cholerae O139","volume":"178","author":"Waldor","year":"1996","journal-title":"J. Bacteriol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"3134","DOI":"10.1073\/pnas.95.6.3134","article-title":"A Vibrio cholerae pathogenicity island associated with epidemic and pandemic strains","volume":"95","author":"Karaolis","year":"1998","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1016\/j.ijantimicag.2012.10.008","article-title":"LysR family activator-regulated major facilitator superfamily transporters are involved in Vibrio cholerae antimicrobial compound resistance and intestinal colonisation","volume":"41","author":"Chen","year":"2013","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1086\/500953","article-title":"An improved technique for isolation of environmental Vibrio cholerae with epidemic potential: Monitoring the emergence of a multiple-antibiotic\u2013resistant epidemic strain in Bangladesh","volume":"193","author":"Faruque","year":"2006","journal-title":"J. Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1128\/AAC.01045-09","article-title":"Transferable quinolone resistance in Vibrio cholerae","volume":"54","author":"Kim","year":"2010","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Tarca, A.L., Carey, V.J., Chen, X.W., Romero, R., and Dr\u0103ghici, S. (2007). Machine learning and its applications to biology. PLoS Comput. Biol., 3.","DOI":"10.1371\/journal.pcbi.0030116"},{"key":"ref_13","first-page":"17","article-title":"The genome revolution in vaccine research","volume":"6","author":"Capecchi","year":"2004","journal-title":"Curr. Issues Mol. Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1080\/01652176.1992.9694344","article-title":"Risks connected with the use of conventional and genetically engineerd vaccines","volume":"14","author":"Kimman","year":"1992","journal-title":"Vet. Q."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/S1369-5274(00)00119-3","article-title":"Reverse vaccinology","volume":"3","author":"Rappuoli","year":"2000","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1016\/j.immuni.2010.09.017","article-title":"Reverse vaccinology: Developing vaccines in the era of genomics","volume":"33","author":"Sette","year":"2010","journal-title":"Immunity"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1816","DOI":"10.1126\/science.287.5459.1816","article-title":"Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing","volume":"287","author":"Pizza","year":"2000","journal-title":"Science"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1002\/ddr.20413","article-title":"In silico subtractive genomics for target identification in human bacterial pathogens","volume":"72","author":"Barh","year":"2011","journal-title":"Drug Dev. Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1126\/science.1109869","article-title":"Identification of a universal Group B streptococcus vaccine by multiple genome screen","volume":"309","author":"Maione","year":"2005","journal-title":"Science"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"10834","DOI":"10.1073\/pnas.0603940103","article-title":"A universal vaccine for serogroup B meningococcus","volume":"103","author":"Giuliani","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2252","DOI":"10.1016\/j.vaccine.2006.12.003","article-title":"Discovery of a vaccine antigen that protects mice from Chlamydia pneumoniae infection","volume":"25","author":"Thorpe","year":"2007","journal-title":"Vaccine"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"4554","DOI":"10.1128\/IAI.00532-08","article-title":"Immunization with Vibrio cholerae outer membrane vesicles induces protective immunity in mice","volume":"76","author":"Schild","year":"2008","journal-title":"Infect. Immun."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"13","DOI":"10.3201\/eid2001.130428","article-title":"Genomic epidemiology of Vibrio cholerae O1 associated with floods, Pakistan, 2010","volume":"20","author":"Shah","year":"2014","journal-title":"Emerg. Infect. Dis."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Rizwan, M., Naz, A., Ahmad, J., Naz, K., Obaid, A., Parveen, T., Ahsan, M., and Ali, A. (2017). VacSol: A high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology. BMC Bioinform., 18.","DOI":"10.1186\/s12859-017-1540-0"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"12105","DOI":"10.1073\/pnas.1831973100","article-title":"Coupled prediction of protein secondary and tertiary structure","volume":"100","author":"Meiler","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1093\/bioinformatics\/bti315","article-title":"Q-SiteFinder: An energy-based method for the prediction of protein\u2013ligand binding sites","volume":"21","author":"Laurie","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Ryan, E.T. (2011). The cholera pandemic, still with us after half a century: Time to rethink. PLoS Negl. Trop. Dis., 5.","DOI":"10.1371\/journal.pntd.0001003"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1111\/j.1745-7254.2007.00600.x","article-title":"Enhanced efficacy of CTLA-4 fusion anti-caries DNA vaccines in gnotobiotic hamsters","volume":"28","author":"Zhang","year":"2007","journal-title":"Acta Pharmacol. Sin."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1111\/j.1574-695X.1999.tb01384.x","article-title":"Purification and characterization of outer membrane protein P6, a vaccine antigen of non-typeable Haemophilus influenzae","volume":"26","author":"Karalus","year":"1999","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1111\/j.1472-765X.2009.02768.x","article-title":"Expression, purification and antibody preparation of flagellin FlaA from Vibrio alginolyticus strain HY9901","volume":"50","author":"Liang","year":"2010","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1006\/jmbi.2001.4992","article-title":"Changing the direction of flagellar rotation in bacteria by modulating the ratio between the rotational states of the switch protein FliM1","volume":"312","author":"Bren","year":"2001","journal-title":"J. Mol. Biol."},{"key":"ref_32","first-page":"1434","article-title":"Combination vaccines against diarrheal diseases","volume":"11","author":"Venkatesan","year":"2015","journal-title":"Hum. Vaccines Immunother."}],"container-title":["Medicina"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1648-9144\/55\/5\/195\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T12:54:32Z","timestamp":1760187272000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1648-9144\/55\/5\/195"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,23]]},"references-count":32,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2019,5]]}},"alternative-id":["medicina55050195"],"URL":"https:\/\/doi.org\/10.3390\/medicina55050195","relation":{},"ISSN":["1648-9144"],"issn-type":[{"value":"1648-9144","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,23]]}}}