Genome‐Guided Discovery of Vaccine Targets for a Multi‐Epitope Construct Against Multidrug‐Resistant Enterobacter cloacae

ABSTRACT

Multidrug‐resistant (MDR) Enterobacter cloacae has emerged as a serious public health threat, particularly in hospital settings, due to its ability to cause severe infections and rapidly acquire antibiotic resistance. The limited effectiveness of current antibiotics highlights the urgent need for alternative preventive strategies such as vaccination. In this study an immunoinformatics‐based approach was employed to design a multi epitope vaccine (MEV) targeting the conserved and surface exposed outer membrane protein A (OmpA) of MDR E. cloacae . The entire proteome was screened to identify suitable vaccine targets based on antigenicity, allergenicity and homology analysis. Highly immunogenic B‐cell, MHC class I and MHC class II epitopes were predicted and selected for vaccine construction. The selected epitopes were linked using suitable linkers, while the 50S ribosomal L7/L12 protein was incorporated as an adjuvant. The designed MEV construct was evaluated through structural modelling, molecular docking with TLR4 receptor, immune simulation, population coverage analysis, codon optimization and in silico cloning. The vaccine candidate demonstrated strong antigenicity, non‐allergenicity, structural stability, and favourable physicochemical properties. Population coverage analysis indicated 99.92% global coverage. Molecular docking revealed stable and energetically favourable interactions with TLR4, while immune simulation predicted strong humoral and cellular immune responses, including memory cell formation and a Th1‐biased cytokine profile. Codon optimization indicated favorable expression potential in an E. coli . Overall, the proposed MEV predicted a promising, safe, stable and broadly protective vaccine candidate against MDR Enterobacter cloacae .