Proteômica subtrativa integrativa baseada no genoma e vacinologia reversa identificam potenciais candidatos a vacinas contra Klebsiella oxytoca

Abstract

Antimicrobial resistance in Klebsiella oxytoca compromises the therapeutic efficacy of available antibiotics and limits treatment options, highlighting the urgent need for effective preventive strategies. This study describes the in silico development of a multi-epitope vaccine against K. oxytoca through an integrated approach combining reverse vaccinology and subtractive proteomics. Analysis of the pan-genome of 34 strains associated with human hosts identified a core proteome composed of 4.201 conserved proteins. The application of criteria related to essentiality, virulence, antimicrobial resistance, and the absence of homology with human and gut microbiota proteins allowed for the identification of 10 surface proteins with high antigenic potential. These proteins were then subjected to immunogenic epitope prediction, resulting in the identification of 11 MHC class I epitopes, five MHC class II epitopes, and five B-cell epitopes. The selected epitopes were subsequently organized into five multi-epitope vaccine constructs (KOV1–KOV5), containing different adjuvants and the PADRE sequence. All constructs exhibited a favorable antigenic profile, absence of allergenic potential, and adequate solubility. Among them, the KOV4 construct, associated with the L7/L12 ribosomal protein adjuvant, stood out for its superior structural parameters and higher binding affinity for the TLR4-MD2 and TLR1-TLR2 complexes in molecular docking analyses. The stability of these complexes was corroborated by normal mode analysis. Furthermore, immunological simulations indicated the induction of robust humoral and cellular responses, characterized by class switching to IgG, expansion of memory B cells, and cytokine production with a predominantly Th1 profile. Codon adaptation demonstrated potential for efficient expression of the KOV4 vaccine in Escherichia coli, with a CAI index of 0.82 and a GC content of 58.69%. Taken together, these findings highlight KOV4 as a promising vaccine candidate against K. oxytoca, although in vivo and in vitro experimental studies will be necessary to validate its immunogenicity, protective efficacy, and biological safety.