An in vivo atlas of host-pathogen transcriptomes during colonization and disease.

() colonizes the nasopharynx and can cause pneumonia. From the lungs it spreads to the bloodstream and causes organ damage. We characterized the in vivo and mouse transcriptomes within the nasopharynx, lungs, blood, heart, and kidneys using three strains. We identified genes highly expressed at all anatomical sites and in an organ-specific manner; highly expressed genes were shown to have vital roles with knockout mutants. The in vivo bacterial transcriptome during colonization/disease was distinct from previously reported in vitro transcriptomes. Distinct and host gene-expression profiles were observed during colonization and disease states, revealing specific genes/operons whereby adapts to and influences host sites in vivo. We identified and experimentally verified host-defense pathways induced by during invasive disease, including proinflammatory responses and the interferon response. These results shed light on the pathogenesis of and identify therapeutic targets.