Intracellular bacteria showed elevated expression of infection-associated genes, encoding for Salmonella Pathogenicity Island (SPI)-2 and SPI-3 effector proteins as well as the typhoidal toxin hlyE, but downregulated expression of genes encoding for SPI-1 factors, flagella and capsule’s biosynthesis (Fig. 2a and Supplementary Data 2). This evidence concerns the gene SPI1 and infection.