The infection of macrophages with MtbΔdosS but not Mtb resulted in overrepresentation of genes involved in the following processes: ‘immune response’ (e.g., IL1B, TNF, TNFAIP2, TNFAIP3, TNFSF13B, TNFRSF21); ‘apoptosis and cell death’ (e.g., CASP3, CASP8, DDIT4, DDIT4L CASP9, BCL2L14, and TNF itself); ‘oxidative and DNA damage response’ (e.g., DDITL4, GADD45)13; and IFN gamma-inducible signature (GBP1, IFI44, IFIH1, IFIT1, IFIT1B, IFIT2, IFIT3, IDO1, CXCL10, CCL20, etc.)(Fig. 2a, b and Supplementary data 1). Here, IFIT3 is linked to infection.