Heterogeneous early immune responses to the S. aureus EapH2 antigen induced by gastrointestinal tract colonisation impact the response to subsequent vaccination.

•Long-term S. aureus experimental gut colonisation can be established in two mouse strains.•Colonisation results in detectable serum IgG1 anti-S. aureus antibodies.•Responses to individual antigens induced by colonisation vary within genetically identical mice.•Immune responses against EapH2 are generated in some, but not other, colonised mice.•Natural priming modified the response to subsequent vaccination against EapH2.