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

Background The intracellular persistence of Staphylococcus aureus remains a major therapeutic challenge, enabling immune evasion and reducing the efficacy of antibiotics with limited intracellular activity. Host-directed therapies, particularly those based on microRNAs (miRNAs), represent a promising strategy to overcome these limitations. Methods We performed a high-throughput screen of 2,469 human miRNA mimics in A549 epithelial cells infected with S. aureus USA300. Candidate miRNAs were prioritised using network centrality analysis and validated across different S. aureus strains and epithelial cell lines. RNA-seq profiling was conducted to examine host responses. Results From this screen, ten candidates were identified, of which miR-4430, miR-1249-5p, and miR-147a consistently reduced intracellular bacterial burden and protected host cells. Transcriptomic analysis revealed complementary pathway-level programs: miR-4430 enhanced innate immune pathways, including STAT1- and PTAFR-associated signalling programs, while miR-1249-5p and miR-147a modulated extracellular matrix organisation and integrin-mediated adhesion, thereby interfering with bacterial entry. Discussion These findings highlight a coordinated host defence strategy in which miR-4430 calibrates immune responses, while miR-1249-5p and miR-147a remodel host adhesion machinery. Together, they elicit complementary pressures that transiently reduce S. aureus intracellular proliferation and promote bacterial clearance. Our results underscore the therapeutic potential of miRNA-based host-directed interventions, which may be combined with conventional antibiotics to limit infection and resistance development.