Host-directed microRNA-based intervention against intracellular Staphylococcus aureus: High-throughput screening identifies miR-4430, miR-147a, and miR-1249-5p as multifunctional antimicrobial candidates

The intracellular persistence of Staphylococcus aureus represents a major therapeutic challenge, as it facilitates immune evasion and limits the efficacy of antibiotics with poor intracellular activity. Host-directed therapies based on microRNAs (miRNAs) offer a promising alternative to overcome these limitations. We performed a high-throughput screen of 2,469 human miRNA mimics in S. aureus USA300–infected A549 epithelial cells, followed by network centrality–based prioritization and validation across multiple S. aureus strains and epithelial cell lines. This approach identified ten candidate miRNAs, among which miR-4430, miR-1249-5p, and miR-147a consistently reduced intracellular bacterial burden and improved host cell viability. Host transcriptomic profiling revealed distinct yet complementary mechanisms of action: miR-4430 enhanced innate immune responses, including STAT1- and PTAFR-associated signaling, whereas miR-1249-5p and miR-147a modulated extracellular matrix organization and integrin-mediated adhesion, thereby impairing bacterial entry. Collectively, these miRNAs impose convergent host-driven pressures that restrict intracellular S. aureus proliferation. Our findings highlight the therapeutic potential of miRNA-based host-directed interventions, which could be combined with conventional antibiotics to improve infection control and reduce the emergence of resistance. Overall design: RNA-seq profiling of A549 cells transfected with cel-miR-231 (negative control) or with hsa-miR-4430, hsa-miR-147a, and hsa-miR-1249-5p (candidate treatments) to investigate host transcriptional responses associated with the control of intracellular Staphylococcus aureus.