We designated ([LC3-positive pneumococci-containing vacuoles containing cells] − [NDP52-positive pneumococci-containing vacuoles containing cells]) as a putative population of PcAV-containing cells (Supplementary Fig. 6A), showing that PcAV was gradually induced after 90 min of infection and proceeded until 180 min after infection (Supplementary Fig. 6B). This evidence concerns the gene MAP1LC3A and infection.