To confirm the CRISPR–Cas activity in the CAPs, we measured the cas3 transcripts in samples obtained at 5, 15 and 30 min following a synchronized infection with the equal multiplicity of infection (MOI) of CAP α15.2 in comparison to WT α15 using RT-qPCR and observed increasing levels of cas3 RNA only upon CAP α15.2 infection (Supplementary Fig. 4). Here, EFS is linked to infection.