Streptococcus pneumoniae colonization modulates human nasal epithelial responses to respiratory syncytial virus infection

ABSTRACT Respiratory syncytial virus (RSV) is a major cause of morbidity and mortality in infants globally. Specific nasal bacterial genera are differentially associated with RSV severity in infants: Haemophilus and Streptococcus with more severe disease and Dolosigranulum with healthy controls or milder outcomes. We hypothesized these differential bacterial effects begin at the epithelial level. Therefore, we established human nasal epithelial organoids differentiated at air-liquid interface (HNO-ALI) as a model system to assess effects of individual nasal microbionts on the epithelial response to subsequent RSV infection and of RSV on those microbionts. Infant-derived HNO-ALI were monocolonized with either Streptococcus pneumoniae, nontypeable Haemophilus influenzae, or Dolosigranulum pigrum one day before viral infection. RSV reduced colonizing S. pneumoniae and D. pigrum levels without affecting H. influenzae. S. pneumoniae precolonization uniquely reduced RSV levels during infection. S. pneumoniae precolonization also modulated the epithelial transcriptional response to RSV infection more so than H. influenzae or D. pigrum, with a pronounced effect on genes involved in immune response, cell cycle, stress, and growth signaling. Gene set enrichment analysis showed S. pneumoniae precolonization blunted RSV-induced increase in inflammatory and immune responses, consistent with S. pneumoniae also modulating RSV-induced cytokine production. Furthermore, S. pneumoniae precolonization blocked RSV-mediated dysregulation of cell-cycle genes, consistent with preventing arrest. Bacterial rescue of cell-cycle progression is a potential mechanism for reduced infectious virion production, since cell-cycle arrest enhances RSV replication. HNO-ALI facilitated elucidation of bacterial-viral-epithelial interplay at a frequent site of viral infection, directly linking nasal bacterial colonization to RSV infection dynamics. IMPORTANCE Most RSV-related hospitalizations occur in healthy young children, yet predictors of RSV severity in this population are limited. The nasal passages are a major microbiota site exposed to frequent respiratory viral infections. Specific nasal bacterial genera/species correlate with RSV clinical outcomes; however, the biological basis of these associations is poorly defined. Here, we established human nasal epithelial organoids differentiated at air-liquid interface (HNO-ALI) as a tractable experimental system for defining the interplay between bacteria, virus, and epithelial cells in the human nasal passages, enabling mechanistic insight into how the nasal microbiota contribute to RSV disease severity. Using this approach, we found that precolonization with each of the common nasal bacteria S. pneumoniae, H. influenzae, or D. pigrum differentially affected the nasal epithelial response to RSV infection. This work highlights that the nasal epithelium actively integrates microbial and viral signals and that variation in bacterial colonization can shape viral infection trajectories.