Synergistic Antibiotic Activity and Integrated Genomic-Metabolomic Profiling of Patch - and Plaque -Derived Staphylococcus aureus in Mycosis Fungoides

Mycosis fungoides (MF), the most common form of cutaneous T-cell lymphoma, is frequently accompanied by skin dysbiosis, with advanced lesions often dominated by multidrug-resistant Staphylococcus aureus. Increased S. aureus colonization is associated with clinical complications and accelerated disease progression, emphasizing the urgent need for effective antimicrobial strategies and a deeper understanding of bacterial adaptation to MF lesions. Here, we evaluated synergistic antibiotic combinations and performed integrated phenotypic, genomic, and metabolomic profiling of MF-associated S. aureus isolates derived from patch and plaque lesions to understand virulence and pathogenicity driving mechanisms in microbe-host interactions. Several antibiotic combinations, most notably carbenicillin with either gentamicin or levofloxacin, exhibited strong synergy and restored antimicrobial activity against highly resistant strains. Comparative genomic analyses revealed that plaque-derived isolates carried expanded resistomes and virulence repertoires, including increased enterotoxins, immune-evasion, and stress-response factors, whereas patch-derived isolates encoded more genes linked to interbacterial competition, such as accessory components of the T7SS. Metabolomic profiles further supported these findings: plaque isolates produced metabolites linked to host interaction, dysbiosis, and inflammation, whereas patch isolates showed profiles consistent with ecological competition. In summary, this work provides insight into the distinct adaptation strategies of S. aureus across MF disease stages. The differential virulence and resistance repertoires observed between patch- and plaque-derived isolates suggests progressive adaptation toward the host microenvironment, potentially influencing disease progression and patient outcomes. Additionally, our findings identify synergistic antibiotic combinations as promising therapeutic approaches for targeting multiresistant MF-associated S. aureus. Importance StatementThe role of multidrug-resistant Staphylococcus aureus in worsening clinical outcomes of mycosis fungoides remains poorly understood, despite its frequent dominance in advanced lesions. Bridging the gap between clinical observation and microbiological mechanisms is essential for clarifying how S. aureus (SA) persists within MF skin and for identifying therapeutic alternatives for SA-positive patients, where treatment options remain limited. This study sheds light on two major clinical needs: the lack of effective antibiotic strategies and the limited insight into bacterial factors that may accelerate MF progression. By integrating synergistic antibiotic testing with genomic, phenotypic, and metabolomic profiling, our work provides insight into stage-specific adaptation patterns of MF-associated S. aureus. These findings identify promising therapeutic directions and establish a framework for future studies to understand the role of S. aureus in MF pathogenesis and exploring how its effects may be therapeutically mitigated.