The host transcriptional response to superinfection by influenza virus and streptococcus pneumonia

Secondary bacterial challenges during influenza virus infection ( superinfection) cause excessive mortality and hospitalization. Here we present a longitudinal study of gene-expression changes in murine lungs during superinfection, with an initial influenza A virus (IAV) infection and a subsequent Streptococcus pneumonia (SP) infection. In addition to the well-characterized impairment of the innate immune response, we identified superinfection-specific alterations in endothelial-related genes, including a previously uncharacterized rapid downregulation of particular angiogenic and vascular markers. Superinfection-specific alterations were also evident in the analysis of cellular states related to the hosts immune resistance against pathogens. We found that superinfected mice manifested an excessive rapid induction of immune resistance starting only a few hours after the secondary bacterial challenge. In addition, there was a substantial rewiring of the resistance program: interferon-regulated genes were switched from positive to negative correlations with resistance, whereas genes of fatty-acid metabolism were switched from negative to positive correlations with resistance. Thus, the transcriptional resistance state in superinfection is reprogrammed toward repressed interferon signaling and induced fatty acid metabolism. Our findings suggest new insights into the remodeling of the host defense upon superinfection, providing promising targets for future therapeutic interventions.