Fig. 1

The early infection model. A confluent monolayer of alveolar epithelial cells (A549) was co-incubated with S. pneumoniae strain D39 at an MOI of 10 (ten pneumococci per epithelial cell). a Five infection time points were interrogated: 0, 30, 60, 120, and 240 minutes post-infection (mpi). b Since adherence is a hallmark of infection, we used an unencapsulated S. pneumoniae strain (∆cps2E), which adheres more readily to epithelial cells than its encapsulated parental strain. c At 30 mpi, ∆cps2E (orange bar) showed significantly (p < 0.001) more adherent cells than the wild-type (wt) parental strain (cyan bar). Data are presented as mean ± standard error of the mean. d At 240 mpi, both strains multiplied significantly (p < 0.01) with no significant difference between them. e The setup with the encapsulated strain contains more free-floating than adherent bacteria while ∆cps2E has a higher fraction of adherent bacteria. f After quality control (QC), low-quality reads were trimmed and aligned to a synthetic chimeric genome. Aligned reads were counted and classified as epithelial or pneumococcal counts. We removed three gene fractions and performed clustering and functional enrichment of the working libraries