Skin Bacteriome and Systemic Therapies in Atopic Dermatitis

Abstract Background: Atopic dermatitis (AD) is a multifactorial disorder, the treatment of which should aim not only to control inflammation but also to restore microbial balance. Objective: We aimed to elucidate how different therapeutic interventions affect the skin bacteriome and clinical outcomes in AD patients, comparing modern targeted systemic therapies such as Janus kinase inhibitors (JAKi) and dupilumab (DUPI) with traditional systemic immunosuppressant cyclosporine A (CyA) and topical corticosteroids (TCS). Methods: This pilot prospective observational study included 60 AD patients divided into four subgroups based on their treatment JAKi, DUPI, CyA, or TCS. Evaluation of clinical parameters and bacteriome analysis of skin swabs from the affected area was performed at three time points (before – TP1, three months – TP2, and six months after the initiation of the systemic therapy – TP3). Microbiological examination, targeted quantification obtained by qPCR, and 16S rRNA amplicon sequencing with species-level classification were used. Results:In all study groups, a significant improvement in the Eczema Area and Severity Index (EASI) was detected in TP2. However, IgE levels significantly decreased only in the DUPI group, in which also the presence of Staphylococcus aureus on skin (negatively correlated with EASI improvement) dropped under detection limit in TP2. In TP3, relative quantity of S. aureuswas significantly lower in the DUPI group than in CyA and TCS groups. While alpha diversity was similar among groups, the ratio of the genus Staphylococcusto commensals (Corynebacteriumand Cutibacterium)was significantly lower in both the JAKi (TP3) and DUPI (TP2 and TP3) groups than in the CyA and TCS groups. The best clinical microbiological outcomes were observed in the DUPI group, followed by JAKi, CyA, and TCS groups. A significant shift towards commensal bacteria and almost total depletion of S. aureus was observed with DUPI at TP2. While in JAKi, the shift was observed later at TP3 and the relative quantity of S. aureus decreased at both TP2 and TP3 compared to the initial condition, but it was not statistically significant. No differences in the relative quantity of S. aureus among time points were detected for CyA and TCS throughout the study.While alpha diversity was similar among groups, the ratio of the genus Staphylococcusto commensals (Corynebacteriumand Cutibacterium)was significantly lower in both the JAKi (TP3) and DUPI (TP2 and TP3) groups than in the CyA and TCS groups. Conclusions:Three-month DUPI treatment led to improvement in clinical parameters and shift in the skin bacteriome composition in AD patients. Given that S. aureus was initially present on the skin in all study groups, its decline during the DUPI therapy likely explains the observed changes in skin bacteriome and may be related to the clinical response on the therapy. We confirmed that specific targeting of type 2 inflammation helps to restore healthy skin bacteriome in patients with AD. The DUPI therapy was the most effective, followed by JAKi therapy. Most subjects in the DUPI group achieved eradication of S. aureuswithin 3 months and significant reduction of serum IgE levels.Traditional anti-inflammatory therapy with CyA and intermittent use of TCS (methylprednisolone aceponate) did not produce a significant shift in bacteriome composition. Mock spike-in Samples were spiked with internal MOCK standard of Allobacillus and Imtechella.