Our hypothesis is that S. aureus skin decolonization in atopic dermatitis reduces disease severity and favorably alters the function and gene expression of epidermal and immune skin cells that contribute to disease severity.

Patients will sign an informed consent and assent to participate. Skin and both nares will be cultured for S aureus. A blood sample and two 2 mm skin biopsies will be obtained one from non-lesional skin and another one from lesional skin). The patients will be instructed in the use of the three-week S. aureus decolonization regimen and provided with the medications (sulfamethoxazole/trimethoprim and Mupirocin ointment) and Chlorhexidine. The second visit will take place immediately at the end of the three-week S. aureus skin decolonization regimen. Disease severity will be assessed, the skin and nares will be re-cultured, and skin biopsies and blood will be obtained.

Inclusion Criteria:

1. Male or female participants ≥6 yrs of age
2. Meet atopic dermatitis Standard Diagnostic Criteria
3. SCORAD > 40.

Exclusion Criteria:

1. . Enrollment in another clinical trial
2. Hypersensitivity to an agent used for the skin decolonization protocol
3. Use within 4 weeks of systemic treatment with immunosuppressive/immunomodulating drugs (corticosteroids, cyclosporine, mycophenolate, azathioprine, methotrexate)
4. Phototherapy for AD within 4 weeks
5. Treatment with biologics (dupilumab, omalizumab, benralizumab, etc) within sixteen weeks
6. Use of topical steroids, topical calcineurin inhibitors within 7 days
7. Bleach baths within 7 days of the first Visit
8. Use of oral or topical antibiotics within 21 days of the beginning of the study
9. Asthmatics receiving more than 500 μg per day of inhaled corticosteroids
10. History of (HIV, hepatitis B, hepatitis C, tuberculosis malignancy
11. Skin comorbidities that may interfere with assessments: psoriasis, cutaneous T Cell lymphoma,,
12. Severe ongoing medical illnesses e.g. cardiovascular, renal disease, autoimmune disease.
13. Febrile illness at time of visits
14. Suspected immune deficiency or family history of primary immunodeficiency
15. Pregnancy