Novel T cell based vaccines against ESKAPE pathogens globally

Abstract

Antibiotic resistance poses a significant global health threat, necessitating innovative strategies to combat the rise of multi-drug resistant pathogens. Among these strategies, vaccination stands out as a promising approach capable of reducing infection rates, minimizing antibiotic usage, and curtailing the spread of resistance. Our hypothesis focuses on T cell-epitope-based prediction to pinpoint potential protective candidates against bacterial pathogens like Acinetobacter baumannii, Klebsiella pneumoniae and Enterobacter spp., three members of the ESKAPE pathogens. To validate our hypothesis, we adopted a reverse vaccinology approach. Utilizing bioinformatic tools, we constructed core pan-proteomes for A. baumannii, K. pneumoniae and Enterobacter spp. A rigorous filtration process was implemented to determine antigen probability, homology to mammalian hosts, and protein size, and prediction of T-cell epitopes. At the final stage of our pipeline, 229 predicted antigens were identified for A. baumannii and 248 predicted antigens were identified to be shared between K. pneumoniae and Enterobacter spp, demonstrating potential for cross-protection. Proteins with the highest probability of being antigens were prioritized for molecular cloning. Through screening over 60 candidates in a murine in vitro splenocyte restimulation model, we identified top antigenic candidates based on their IFNγ responses. We show that our top candidate proteins are immunogenic and cross-protective against K. pneumoniae and E. bugandensis challenge in a sepsis infection model with increased survival and significantly reduced bacterial burden and inflammation. Notably, this protection extends from mother to offspring, safeguarding pups from E. bugandensis infection in a neonatal sepsis setting. Further investigation of two antigens revealed that adoptive or passive transfer from immunized animals to naïve mice can significantly reduce mortality and bacterial burden in E. bugandensis sepsis. Analysis of the lymphocyte population show that the protection in response to E. bugandensis is associated with increased CD8+ and γδ T cells, and NK cells. This was further supported by demonstrating increased amounts of transcription factors that upregulate the proliferation of these cells, such as T-bet, GATA3, RORγt and AHR levels. We have established a pipeline based on T-cell epitope prediction, which is successful at identifying protective antigens, thus validating our hypothesis and paving the way for the development of T-cell-based vaccines against ESKAPE pathogens.

Thesis is embargoed until 31 December 2029.

Date of Award	Dec 2024
Original language	English
Awarding Institution	Queen's University Belfast
Sponsors	BactiVax International Training Network
Supervisor	Miguel A. Valvano (Supervisor) & Beckie Ingram (Supervisor)