Synergistic antibiotic activity and integrated genomic–metabolomic profiling of patch- and plaque-derived Staphylococcus aureus in mycosis fungoides

ABSTRACT Mycosis fungoides (MF), the most common form of cutaneous T-cell lymphoma, is frequently associated with skin dysbiosis, and advanced lesions are often dominated by multidrug-resistant Staphylococcus aureus . To characterize microbiologically relevant properties of MF-associated S. aureus , we evaluated synergistic antibiotic combinations and performed integrated phenotypic, genomic, and metabolomic profiling. Several antibiotic combinations, most notably carbenicillin combined with either gentamicin or levofloxacin, exhibited pronounced synergistic activity and restored in vitro antimicrobial activity against highly resistant isolates. Comparative genomic analyses revealed substantial variability between isolates in resistomes and virulence repertoires, including enterotoxins, immune-evasion, and stress-response factors. Metabolomic profiling further revealed isolate-specific extracellular signatures, including putrescine and urocanic acid. In summary, this study identifies promising antibiotic combinations against multidrug-resistant S. aureus strains. Furthermore, this exploratory investigation demonstrates phenotypic and genomic heterogeneity among MF-associated S. aureus isolates, warranting further evaluation in larger longitudinal studies. IMPORTANCE Despite its predominance in advanced mycosis fungoides (MF) lesions, the role of multidrug‑resistant Staphylococcus aureus in adverse clinical outcomes remains poorly understood. Bridging the gap between clinical observations and microbiological mechanisms is essential to clarify how S. aureus persists in MF skin and to identify therapeutic alternatives for S. aureus ‑positive patients, for whom treatment options remain limited. This study addresses two major clinical needs: the lack of effective antibiotic strategies and the limited understanding of bacterial factors that may contribute to worsened clinical outcomes. By integrating synergistic antibiotic testing with genomic, phenotypic, and metabolomic profiling, our work highlights clinically relevant heterogeneity among MF-associated S. aureus isolates. These findings identify promising therapeutic directions and establish a framework for future large-scale longitudinal studies to better understand the role of diverse S. aureus strains in MF pathogenesis.