The severe bronchiolitis endotype characterized by a high abundance of H. influenzae, high proportion of RV-A and RV-C infections, and high asthma genetic risk had a significantly higher risk for developing asthma. Background Infants with bronchiolitis are at increased risk for developing asthma. Growing evidence suggests bronchiolitis is a heterogeneous condition. However, little is known about its biologically distinct subgroups based on the integrated metagenome and asthma genetic risk signature and their longitudinal relationships with asthma development. Methods In a multi-center prospective cohort study of infants with severe bronchiolitis ( i.e. , bronchiolitis requiring hospitalization), we profiled nasopharyngeal airway metagenome and virus at hospitalization, and calculated the polygenic risk score of asthma. Using similarity network fusion clustering approach, we identified integrated metagenome-asthma genetic risk endotypes. We also examined their longitudinal association with the risk of developing asthma by age six years. Results Of 450 infants with bronchiolitis (median age, 3 months), we identified five distinct endotypes—characterized by their nasopharyngeal metagenome, virus, and asthma genetic risk profiles. Compared with endotype A infants (who clinically resembled “classic” bronchiolitis), endotype E infants (characterized by a high abundance of H. influenzae , high proportion of RV-A and RV-C infections, and high asthma genetic risk) had a significantly higher risk for developing asthma (35.9% versus 16.7%; OR adj , 2.24; 95%CI, 1.02–4.97; p=0.046). The pathway analysis showed that endotype E had enriched microbial pathways ( e.g. , glycolysis, L-lysine, arginine metabolism) and host pathways ( e.g. , IFNs, IL-6/JAK/STAT3, fatty acids, MHC, and immunoglobin-related) (FDR&lt;0.05). Additionally, endotype E had a significantly higher proportion of neutrophils (FDR&lt;0.05). Conclusion In this multi-center prospective cohort study of infant bronchiolitis, the clustering analysis of integrated-omics data identified biologically distinct endotypes with differential risks for developing asthma.

Integrated nasopharyngeal airway metagenome and asthma genetic risk endotyping of severe bronchiolitis in infancy and risk of childhood asthma