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Background   Coxiella burnetii  is the Gram-negative bacterium responsible for Q fever in humans and coxiellosis in domesticated agricultural animals. Previous vaccination efforts with whole cell inactivated bacteria or surface isolated proteins confer protection but can produce a reactogenic immune responses. Thereby a protective vaccine that does not cause aberrant immune reactions is required. The critical role of T-cell immunity in control of  C. burnetii  has been made clear, since either CD8 +  or CD4 +  T cells can empower clearance. The purpose of this study was to identify  C. burnetii  proteins bearing epitopes that interact with major histocompatibility complexes (MHC) from multiple host species (human, mouse, and cattle).    Results  Of the annotated 1815 proteins from the Nine Mile Phase I (RSA 493) assembly, 402 proteins were removed from analysis due to a lack of inter-isolate conservation. An additional 391 proteins were eliminated from assessment to avoid potential autoimmune responses due to the presence of host homology. We analyzed the remaining 1022 proteins for their ability to produce peptides that bind MHCI or MHCII. MHCI and MHCII predicted epitopes were filtered and compared between species yielding 777 MHCI epitopes and 453 MHCII epitopes. These epitopes were further examined for presentation by both MHCI and MHCII, and for proteins that contained multiple epitopes. There were 31 epitopes that overlapped positionally between MHCI and MHCII across host species. Of these, there were 9 epitopes represented within proteins containing ≥ 5 total epitopes, where an additional 24 proteins were also epitope dense. In all, 55 proteins were found to contain high scoring T-cell epitopes. Besides the well-studied protein Com1, most identified proteins were novel when compared to previously studied vaccine candidates.    Conclusion  These data represent the first proteome-wide evaluation of  C. burnetii  peptide epitopes. Furthermore, the inclusion of human, mouse, and bovine data capture a range of hosts for this zoonotic pathogen plus an important model organism. This work provides new vaccine targets for future vaccination efforts and enhances opportunities for selecting multiple T-cell epitope types to include within a vaccine.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12859-021-04181-w.

Proteome-wide analysis of Coxiella burnetii for conserved T-cell epitopes with presentation across multiple host species