{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T09:47:09Z","timestamp":1762508829803,"version":"build-2065373602"},"reference-count":71,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2022,9,14]],"date-time":"2022-09-14T00:00:00Z","timestamp":1663113600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJERPH"],"abstract":"<jats:p>Helicobacter cinaedi is a Gram-negative bacterium from the family Helicobacteraceae and genus Helicobacter. The pathogen is a causative agent of gastroenteritis, cellulitis, and bacteremia. The increasing antibiotic resistance pattern of the pathogen prompts the efforts to develop a vaccine to prevent dissemination of the bacteria and stop the spread of antibiotic resistance (AR) determinants. Herein, a pan-genome analysis of the pathogen strains was performed to shed light on its core genome and its exploration for potential vaccine targets. In total, four vaccine candidates (TonB dependent receptor, flagellar hook protein FlgE, Hcp family type VI secretion system effector, flagellar motor protein MotB) were identified as promising vaccine candidates and subsequently subjected to an epitopes\u2019 mapping phase. These vaccine candidates are part of the pathogen core genome: they are essential, localized at the pathogen surface, and are antigenic. Immunoinformatics was further applied on the selected vaccine proteins to predict potential antigenic, non-allergic, non-toxic, virulent, and DRB*0101 epitopes. The selected epitopes were then fused using linkers to structure a multi-epitopes\u2019 vaccine construct. Molecular docking simulations were conducted to determine a designed vaccine binding stability with TLR5 innate immune receptor. Further, binding free energy by MMGB\/PBSA and WaterSwap was employed to examine atomic level interaction energies. The designed vaccine also stimulated strong humoral and cellular immune responses as well as interferon and cytokines\u2019 production. In a nutshell, the designed vaccine is promising in terms of immune responses\u2019 stimulation and could be an ideal candidate for experimental analysis due to favorable physicochemical properties.<\/jats:p>","DOI":"10.3390\/ijerph191811579","type":"journal-article","created":{"date-parts":[[2022,9,14]],"date-time":"2022-09-14T20:50:45Z","timestamp":1663188645000},"page":"11579","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Pan-Genome-Assisted Computational Design of a Multi-Epitopes-Based Vaccine Candidate against Helicobacter cinaedi"],"prefix":"10.3390","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8793-2972","authenticated-orcid":false,"given":"Saba","family":"Ismail","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Noorah","family":"Alsowayeh","sequence":"additional","affiliation":[{"name":"Department of Biology, College of Education (Majmaah), Majmaah University, Al-Majmaah 11952, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hyder Wajid","family":"Abbasi","sequence":"additional","affiliation":[{"name":"Pakistan Institute of Medical Sciences, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8697-5340","authenticated-orcid":false,"given":"Aqel","family":"Albutti","sequence":"additional","affiliation":[{"name":"Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4832-4250","authenticated-orcid":false,"given":"Muhammad","family":"Tahir ul Qamar","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0754-1742","authenticated-orcid":false,"given":"Sajjad","family":"Ahmad","sequence":"additional","affiliation":[{"name":"Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rabail Zehra","family":"Raza","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Khulah","family":"Sadia","sequence":"additional","affiliation":[{"name":"Department of Biosciences, COMSAT University, Islamabad 45550, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4998-937X","authenticated-orcid":false,"given":"Sumra Wajid","family":"Abbasi","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,9,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.tifs.2018.08.001","article-title":"Antibiotic Resistance in Foodborne Bacteria","volume":"84","author":"Manageiro","year":"2019","journal-title":"Trends Food Sci. 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