NPTX2 and susceptibility to pneumonia measurement: One study of NTHi sputum samples from patients with pneumonia (similar to our NTHi_sup vs NTHi_wo comparison) showed downregulation of the tricarboxylic acid (TCA) cycle (NTHi_KEGG_Pathway_00020; see https://doi.org/10.6084/m9.figshare.27963945) and cytochrome c biogenesis genes (ccm genes, NarP regulon; Fig. S3C) (50), as well as upregulation of purine regulon genes (PurR regulon; see https://doi.org/10.6084/m9.figshare.27963945) (50, 51) when comparing NTHi during pneumonia vs in culture.