Fig. 3: Genes responsible for entry into and survival in host cells are grouped into functional groups.

a The genes involved in intracellular survival are grouped by their functions, and the selected pathways are presented in a diagram. Genes that were not substantially depleted but are needed as part of the functional group are marked with dotted lines. MQ, menaquinone. Image created in BioRender (Lee, W. (2025) https://BioRender.com/sfrjhgv). The mutants of selected genes were obtained from the Nebraska Tn library and were confirmed for their role in (b) intracellular entry or (c) both entry and post-entry survival by the infection assay (\(\%\;{\rm{entry}}=\,\frac{{\rm{CFU}}\; {\rm{recovered}}\; {\rm{at\;}}0\;{\rm{h}}}{{\rm{input}}\; {\rm{CFU}}}\times 100\); \(\%\;{\rm{recovery}}=\,\frac{{\rm{CFU}}\; {\rm{recovered}}\; {\rm{from}}\; {\rm{cells}}}{{\rm{input}}\; {\rm{CFU}}}\times 100\)). d USA300 pre-exposed to 120 μM of oligomycin A (oligo A), an ATPase inhibitor, was examined for the extent of infection into and proliferation inside the host A549 cells in the presence of 120 μM oligomycin A (\(\%\;{\rm{recovery}}=\,\frac{{\rm{CFU}}\; {\rm{recovered}}\; {\rm{from}}\; {\rm{cells}}}{{\rm{input}}\; {\rm{CFU}}}\times 100\)). Data in b–d are presented as the mean ± SD (n = 3 biological replicates), and the P values are calculated by a two-sided, unpaired Student’s t-test. The source data for b–d are available in the Source data file.