Conserved and context-dependent changes in pathogen and host cell gene expression during Staphylococcus aureus intracellular infection

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BACKGROUND: The opportunistic intracellular lifestyle of Staphylococcus aureus contributes to its ability to maintain chronic infective states. However, knowledge of pathogen-encoded factors that enable S. aureus to invade and persist within human cells, host cell responses to infection, and how such features vary across different bacterial strains and host cell types remains incomplete. Here, we used dual RNA-seq to examine alterations in S. aureus and host cell transcription following bacterial invasion, comparing results from two different S. aureus strains (JE2 and ATCC29213) and human cell lines (THP-1-derived macrophages and CCL-185 lung epithelial cells) over time. RESULTS: The fates of bacteria and host cells, and their changes in gene expression were dependent on the combination of strain and cell type examined. Transcriptional changes largely occurred early in infection (by 3 h), with subtler changes over longer timescales (24 h). Some bacterial alterations, including upregulation of metal ion homeostasis and pyrimidine biosynthesis and downregulation of anaerobic respiration and certain virulence factors, were consistent across infections, indicating general importance to intracellular pathogenesis. Other changes occurred only in particular S. aureus strains or during infection of specific host cell lines. Host cell analysis revealed marked differences in transcriptional response between infected cell types, and specific alterations dependent on the infecting S. aureus strain. Phenotypic contributions of bacterial genes with the most significant expression changes during infection were evaluated using CRISPRi knockdown experiments, most of which confirmed significant alterations in host cell invasion phenotypes under the conditions tested (26 of 32, 81%). CONCLUSIONS: This work identifies a limited number of conserved transcriptional changes occurring during S. aureus intracellular pathogenesis that were common to all host cell-pathogen combinations examined, suggesting these are key to the infection process. However, most transcriptional changes were contingent and specific to the strain of bacteria, type of human cell, or combination of the two, indicating significant variation in context-dependent responses.

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