Discordant rearrangement of primary and anamnestic CD8+ T cell responses to influenza A viral epitopes upon exposure to bacterial superantigens: Implications for prophylactic vaccination, heterosubtypic immunity and superinfections

Author summary Exposure to bacterial superantigens (SAgs) is often a consequence of infection with common Gram-positive bacteria causing septic and toxic shock or food poisoning. How SAgs affect the magnitude, breadth and quality of infection/vaccine-elicited CD8(+) T cell (T-CD8) responses to respiratory viral pathogens, including influenza A viruses (IAVs), is far from clear. Also importantly, superinfections with IAVs and SAg-producing bacteria are serious clinical occurrences during seasonal and pandemic flu and require urgent attention. We demonstrate that two structurally distinct SAgs, including staphylococcal enterotoxin B (SEB), unexpectedly enhance primary T-CD8 responses to 'select' IAV-derived epitopes depending on the TCR makeup of the responding clones. Intriguingly, the timing of exposure to SEB dictates the outcome of prime-boost immunization. Seeing a SAg before priming raises memory precursor frequencies and augments anamnestic T-CD8 responses. Conversely, a SAg encounter before boosting renders T-CD8 prone to death or exhaustion and impedes recall responses, thus likely compromising heterosubtypic immunity to IAVs. Finally, local exposure to SEB increases the pulmonary response of immunodominant IAV-specific T-CD8. These findings shed new light on how bacterial infections and SAgs influence the effectiveness of anti-IAV T-CD8 responses, and have, as such, wide-ranging implications for preventative vaccination and infection control. Infection with (SAg)-producing bacteria may precede or follow infection with or vaccination against influenza A viruses (IAVs). However, how SAgs alter the breadth of IAV-specific CD8(+) T cell (T-CD8) responses is unknown. Moreover, whether recall responses mediating heterosubtypic immunity to IAVs are manipulated by SAgs remains unexplored. We employed wild-type (WT) and mutant bacterial SAgs, SAg-sufficient/deficient Staphylococcus aureus strains, and WT, mouse-adapted and reassortant IAV strains in multiple in vivo settings to address the above questions. Contrary to the popular view that SAgs delete or anergize T cells, systemic administration of staphylococcal enterotoxin B (SEB) or Mycoplasma arthritidis mitogen before intraperitoneal IAV immunization enlarged the clonal size of 'select' IAV-specific T-CD8 and reshuffled the hierarchical pattern of primary T-CD8 responses. This was mechanistically linked to the TCR V beta makeup of the impacted clones rather than their immunodominance status. Importantly, SAg-expanded T-CD8 retained their IFN-gamma production and cognate cytolytic capacities. The enhancing effect of SEB on immunodominant T-CD8 was also evident in primary responses to vaccination with heat-inactivated and live attenuated IAV strains administered intramuscularly and intranasally, respectively. Interestingly, in prime-boost immunization settings, the outcome of SEB administration depended strictly upon the time point at which this SAg was introduced. Accordingly, SEB injection before priming raised CD127(high)KLRG1(low) memory precursor frequencies and augmented the anamnestic responses of SEB-binding T-CD8. By comparison, introducing SEB before boosting diminished recall responses to IAV-derived epitopes drastically and indiscriminately. This was accompanied by lower Ki67 and higher Fas, LAG-3 and PD-1 levels consistent with a pro-apoptotic and/or exhausted phenotype. Therefore, SAgs can have contrasting impacts on anti-IAV immunity depending on the naive/memory status and the TCR composition of exposed T-CD8. Finally, local administration of SEB or infection with SEB-producing S. aureus enhanced pulmonary T-CD8 responses to IAV. Our findings have clear implications for superinfections and prophylactic vaccination.