---
title: "Immunoinformatics Design of a Multi-Epitope Vaccine and mRNA Construct Against Multidrug-Resistant"
id: "pubmed-42663966"
canonical_url: "https://medichelpline.com/clinical-feed/pubmed-42663966"
content_type: "clinical_feed_article"
specialty: "Critical Care"
source_name: "PubMed / NCBI"
source_url: "https://pubmed.ncbi.nlm.nih.gov/42663966/"
doi: "10.1007/s12602-026-11188-3"
published_at: "2026-08-28T00:00:00.000Z"
evidence_level: "Journal Article"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Immunoinformatics Design of a Multi-Epitope Vaccine and mRNA Construct Against Multidrug-Resistant
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/pubmed-42663966
- **Specialty:** [Critical Care](https://medichelpline.com/clinical-feed/critical-care.md)
- **Primary Source:** PubMed / NCBI
- **Source URL:** [Original Journal Publication](https://pubmed.ncbi.nlm.nih.gov/42663966/)
- **DOI:** [10.1007/s12602-026-11188-3](https://doi.org/10.1007%2Fs12602-026-11188-3)
- **Published At:** 2026-08-28T00:00:00.000Z
- **Evidence Rating:** Journal Article
## Executive GIST (TL;DR)
- Elizabethkingia anophelis is a multidrug-resistant opportunistic pathogen linked to neonatal meningitis, sepsis, hospital outbreaks, and high mortality with limited treatment options. - Researchers used a comprehensive **immunoinformatics** and reverse vaccinology pipeline to design a hybrid **multi-epitope vaccine (MEV)** and an mRNA construct targeting four outer membrane and secretion-associated proteins. - Predicted and screened epitopes included highly antigenic B-cell, MHC-I, and MHC-II candidates; selections were filtered for antigenicity, allergenicity, toxicity, cytokine induction potential, binding affinity, and population coverage. - The final MEV combined eight MHC-I, eight MHC-II, and eight B-cell epitopes, linked with appropriate linkers, adjuvanted with Human Beta Defensin-3, and appended with a 6×His tag. - Global population coverage for the selected T-cell epitopes was 99.38%. - Structural modeling used **AlphaFold2** with subsequent refinement; the 3D model showed 98.0% Ramachandran favored residues, ERRAT 98.621 score, and a ProSA Z-score of −4.68 indicating high-quality structure. - Molecular docking indicated strong binding between the MEV and **TLR-2**; 200 ns molecular dynamics simulations demonstrated a stable vaccine–receptor complex. - In silico immune simulations predicted a robust Th1-biased response, high antibody production with IgG class switching, and generation of long-term memory B and T cells. - Codon optimization for Escherichia coli K12 yielded CAI 0.982; the construct was in silico cloned into pET-28a(+) supporting efficient recombinant expression. - mRNA secondary structure analysis suggested high stability for the mRNA construct. - The authors conclude the computationally designed MEV is a promising preventive strategy against E. anophelis, but state that further experimental validation is required to confirm immunogenicity and protective efficacy.
## Clinical Analysis & Structured Key Points
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Online ahead of print. # Toward a Vaccine Against Multidrug-Resistant Elizabethkingia anophelis: Comprehensive Immunoinformatics-Based Design of a Multi-Epitope Vaccine and mRNA Construct [Muhammad Hanzala](https://pubmed.ncbi.nlm.nih.gov/?term=Hanzala+M&cauthor_id=42663966)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#full-view-affiliation-1 "School of Engineering, Ulster University, York Street, Belfast, BT15 1AP, United Kingdom."), [Rana Zohaib Abbas](https://pubmed.ncbi.nlm.nih.gov/?term=Abbas+RZ&cauthor_id=42663966)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#full-view-affiliation-1 "School of Engineering, Ulster University, York Street, Belfast, BT15 1AP, United Kingdom."), [Mahnoor Habib](https://pubmed.ncbi.nlm.nih.gov/?term=Habib+M&cauthor_id=42663966)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#full-view-affiliation-2 "School of Biological Sciences \(SBS\), University of the Punjab, Quaid-E-Azam Campus, Lahore, 54590, Pakistan."), [Allah Rakha Yaseen](https://pubmed.ncbi.nlm.nih.gov/?term=Yaseen+AR&cauthor_id=42663966)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#full-view-affiliation-3 "School of Biological Sciences \(SBS\), University of the Punjab, Quaid-E-Azam Campus, Lahore, 54590, Pakistan. 123allah.rakha@gmail.com."), [Muhammad Suleman](https://pubmed.ncbi.nlm.nih.gov/?term=Suleman+M&cauthor_id=42663966)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#full-view-affiliation-2 "School of Biological Sciences \(SBS\), University of the Punjab, Quaid-E-Azam Campus, Lahore, 54590, Pakistan."), [Khalid J Alzahrani](https://pubmed.ncbi.nlm.nih.gov/?term=Alzahrani+KJ&cauthor_id=42663966)[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#full-view-affiliation-4 "Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia.")[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#full-view-affiliation-5 "Research Center of Basic Sciences, Engineering and High Altitude, Taif University, Taif, Saudi Arabia."), [Khalaf F Alsharif](https://pubmed.ncbi.nlm.nih.gov/?term=Alsharif+KF&cauthor_id=42663966)[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#full-view-affiliation-4 "Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia.")[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#full-view-affiliation-5 "Research Center of Basic Sciences, Engineering and High Altitude, Taif University, Taif, Saudi Arabia."), [Fuad M Alzahrani](https://pubmed.ncbi.nlm.nih.gov/?term=Alzahrani+FM&cauthor_id=42663966)[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#full-view-affiliation-4 "Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia.")[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#full-view-affiliation-5 "Research Center of Basic Sciences, Engineering and High Altitude, Taif University, Taif, Saudi Arabia."), [Sehrish Firyal](https://pubmed.ncbi.nlm.nih.gov/?term=Firyal+S&cauthor_id=42663966)[ 6 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#full-view-affiliation-6 "Institute of Biochemistry and Biotechnology \(IBBT\), University of Veterinary & Animal Sciences, Lahore, 54000, Pakistan.") Affiliations Expand ### Affiliations * 1 School of Engineering, Ulster University, York Street, Belfast, BT15 1AP, United Kingdom. * 2 School of Biological Sciences (SBS), University of the Punjab, Quaid-E-Azam Campus, Lahore, 54590, Pakistan. * 3 School of Biological Sciences (SBS), University of the Punjab, Quaid-E-Azam Campus, Lahore, 54590, Pakistan. 123allah.rakha@gmail.com. * 4 Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia. * 5 Research Center of Basic Sciences, Engineering and High Altitude, Taif University, Taif, Saudi Arabia. * 6 Institute of Biochemistry and Biotechnology (IBBT), University of Veterinary & Animal Sciences, Lahore, 54000, Pakistan. * PMID: **42663966** * DOI: [ 10.1007/s12602-026-11188-3 ](https://doi.org/10.1007/s12602-026-11188-3) Item in Clipboard # Toward a Vaccine Against Multidrug-Resistant Elizabethkingia anophelis: Comprehensive Immunoinformatics-Based Design of a Multi-Epitope Vaccine and mRNA Construct Muhammad Hanzala et al. Probiotics Antimicrob Proteins. 2026. Show details Display options Display options Format Abstract PubMed PMID Probiotics Antimicrob Proteins Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Probiotics+Antimicrob+Proteins%22%5Bjour%5D&sort=date&sort_order=desc) * [ Search in NLM Catalog ](https://www.ncbi.nlm.nih.gov/nlmcatalog?term=%22Probiotics+Antimicrob+Proteins%22%5BTitle+Abbreviation%5D) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42663966/) . 2026 Aug 28. doi: 10.1007/s12602-026-11188-3. Online ahead of print. ### Authors [Muhammad Hanzala](https://pubmed.ncbi.nlm.nih.gov/?term=Hanzala+M&cauthor_id=42663966)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#short-view-affiliation-1 "School of Engineering, Ulster University, York Street, Belfast, BT15 1AP, United Kingdom."), [Rana Zohaib Abbas](https://pubmed.ncbi.nlm.nih.gov/?term=Abbas+RZ&cauthor_id=42663966)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#short-view-affiliation-1 "School of Engineering, Ulster University, York Street, Belfast, BT15 1AP, United Kingdom."), [Mahnoor Habib](https://pubmed.ncbi.nlm.nih.gov/?term=Habib+M&cauthor_id=42663966)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#short-view-affiliation-2 "School of Biological Sciences \(SBS\), University of the Punjab, Quaid-E-Azam Campus, Lahore, 54590, Pakistan."), [Allah Rakha Yaseen](https://pubmed.ncbi.nlm.nih.gov/?term=Yaseen+AR&cauthor_id=42663966)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#short-view-affiliation-3 "School of Biological Sciences \(SBS\), University of the Punjab, Quaid-E-Azam Campus, Lahore, 54590, Pakistan. 123allah.rakha@gmail.com."), [Muhammad Suleman](https://pubmed.ncbi.nlm.nih.gov/?term=Suleman+M&cauthor_id=42663966)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#short-view-affiliation-2 "School of Biological Sciences \(SBS\), University of the Punjab, Quaid-E-Azam Campus, Lahore, 54590, Pakistan."), [Khalid J Alzahrani](https://pubmed.ncbi.nlm.nih.gov/?term=Alzahrani+KJ&cauthor_id=42663966)[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#short-view-affiliation-4 "Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia.")[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#short-view-affiliation-5 "Research Center of Basic Sciences, Engineering and High Altitude, Taif University, Taif, Saudi Arabia."), [Khalaf F Alsharif](https://pubmed.ncbi.nlm.nih.gov/?term=Alsharif+KF&cauthor_id=42663966)[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#short-view-affiliation-4 "Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia.")[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#short-view-affiliation-5 "Research Center of Basic Sciences, Engineering and High Altitude, Taif University, Taif, Saudi Arabia."), [Fuad M Alzahrani](https://pubmed.ncbi.nlm.nih.gov/?term=Alzahrani+FM&cauthor_id=42663966)[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#short-view-affiliation-4 "Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia.")[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#short-view-affiliation-5 "Research Center of Basic Sciences, Engineering and High Altitude, Taif University, Taif, Saudi Arabia."), [Sehrish Firyal](https://pubmed.ncbi.nlm.nih.gov/?term=Firyal+S&cauthor_id=42663966)[ 6 ](https://pubmed.ncbi.nlm.nih.gov/42663966/#short-view-affiliation-6 "Institute of Biochemistry and Biotechnology \(IBBT\), University of Veterinary & Animal Sciences, Lahore, 54000, Pakistan.") ### Affiliations * 1 School of Engineering, Ulster University, York Street, Belfast, BT15 1AP, United Kingdom. * 2 School of Biological Sciences (SBS), University of the Punjab, Quaid-E-Azam Campus, Lahore, 54590, Pakistan. * 3 School of Biological Sciences (SBS), University of the Punjab, Quaid-E-Azam Campus, Lahore, 54590, Pakistan. 123allah.rakha@gmail.com. * 4 Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia. * 5 Research Center of Basic Sciences, Engineering and High Altitude, Taif University, Taif, Saudi Arabia. * 6 Institute of Biochemistry and Biotechnology (IBBT), University of Veterinary & Animal Sciences, Lahore, 54000, Pakistan. * PMID: **42663966** * DOI: [ 10.1007/s12602-026-11188-3 ](https://doi.org/10.1007/s12602-026-11188-3) Item in Clipboard Cite Display options Display options Format Abstract PubMed PMID ## Abstract Elizabethkingia anophelis is a multidrug-resistant opportunistic pathogen associated with severe neonatal meningitis, sepsis, and hospital outbreaks, with high mortality rates and limited treatment options. In this study, a hybrid multi-epitope vaccine (MEV) was designed using an extensive immunoinformatics approach targeting four key outer membrane and secretion-associated proteins. Highly antigenic B-cell and T-cell (MHC-I and MHC-II) epitopes were predicted, rigorously screened for antigenicity, allergenicity, toxicity, and cytokine induction potential, and selected based on binding affinity and population coverage. The final MEV construct incorporated eight MHC-I, eight MHC-II, and eight B-cell epitopes linked with appropriate linkers, adjuvanted with Human Beta Defensin-3, and tagged with a 6 × His sequence. Population coverage analysis revealed 99.38% global coverage. Structural modeling using AlphaFold2 followed by refinement yielded a high-quality 3D model (98.0% Ramachandran favored residues, ERRAT 98.621, ProSA Z-score - 4.68). Molecular docking demonstrated strong binding of the MEV to TLR-2, while 200 ns molecular dynamics simulations confirmed the stability of the vaccine-receptor complex. Immune simulations predicted robust Th1-biased responses, high antibody production (IgG class switching), and generation of long-term memory B and T cells. Codon optimization for E. coli K12 (CAI 0.982) and in silico cloning into pET-28a( +) vector supported efficient recombinant expression, while mRNA secondary structure analysis indicated high stability. This computationally designed MEV offers a promising preventive strategy against E. anophelis infections. Further experimental validation is warranted to confirm its immunogenicity and protective efficacy. **Keywords:** Elizabethkingia anopheles; Immunoinformatics; Meningitis; Molecular dynamics simulation, Reverse vaccinology; Multi-epitope vaccine; Multidrug-resistant (MDR). © 2026. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature. [PubMed Disclaimer](https://pubmed.ncbi.nlm.nih.gov/disclaimer/) ## Conflict of interest statement Declarations. Ethical Approval: Not applicable. Informed Consent: Not applicable. Competing interests: The authors declare no competing interests. ## References 1. 1. Abby SS, Cury J, Guglielmini J, Néron B, Touchon M, Rocha EPC (2016) Identification of protein secretion systems in bacterial genomes. Sci Rep 6(1):23080. - [DOI](https://doi.org/10.1038/srep23080) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/26979785/) - [PMC](https://pmc.ncbi.nlm.nih.gov/articles/4793230/) 2. 1. Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, Lindahl E (2015) GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2:19–25. - [DOI](https://doi.org/10.1016/j.softx.2015.06.001) 3. 1. Albutti A (2024) An integrated approach to develop a potent vaccine candidate construct against prostate cancer by utilizing machine learning and bioinformatics. Cancer Reports 7(12):e70079. - [DOI](https://doi.org/10.1002/cnr2.70079) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/39651594/) - [PMC](https://pmc.ncbi.nlm.nih.gov/articles/11626413/) 4. 1. Ali S, Shah A, Khan S, Suleman M, Islam Z, Aleem MT (2026) Immunoinformatics-guided design of a universal chimeric multi-epitope subunit vaccine against Marburg virus disease and Ravn virus co-infection. Sci Rep 16(1):6984. - [DOI](https://doi.org/10.1038/s41598-026-37178-7) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/41629588/) - [PMC](https://pmc.ncbi.nlm.nih.gov/articles/12921230/) 5. 1. Allemailem KS (2025) In silico development of a chimeric multi-epitope vaccine targeting Helcococcus kunzii: coupling subtractive proteomics and reverse vaccinology for vaccine target discovery. Pharmaceuticals (Basel) 18(9):1258 - [DOI](https://doi.org/10.3390/ph18091258) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/41011130/) - [PMC](https://pmc.ncbi.nlm.nih.gov/articles/12472865/) Show all 162 references [x] Cite Copy Download .nbib .nbib Format: AMA APA MLA NLM **Send To** * [Clipboard](https://pubmed.ncbi.nlm.nih.gov/42663966/) * [Email](https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F42663966%2F%23open-email-panel) * [Save](https://pubmed.ncbi.nlm.nih.gov/42663966/) * [My Bibliography](https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F42663966%2F%23open-bibliography-panel) * [Collections](https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F42663966%2F%23open-collections-panel) * [Citation Manager](https://pubmed.ncbi.nlm.nih.gov/42663966/) [x] NCBI Literature Resources [MeSH](https://www.ncbi.nlm.nih.gov/mesh/) [PMC](https://www.ncbi.nlm.nih.gov/pmc/) [Bookshelf](https://www.ncbi.nlm.nih.gov/book
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