Skin Staphylococcus aureus detection and relationship to atopic dermatitis outcomes using culture and metagenomic sequencing.

Staphylococcus aureus (SA) skin colonization in pediatric atopic dermatitis (AD) increases risk for severe AD and development of other allergic diseases. Despite this, there is no consensus regarding the optimal method to detect SA. Studies comparing metagenomic shotgun sequencing (MSS) and culture-based methods in SA detection and relationships to AD outcomes are lacking. In the Mechanisms of Progression of Atopic Dermatitis to Asthma in Children (MPAACH) cohort, we defined SA colonization categories by contact agar plate sampling/culture and skin tape sampling/MSS: double negative, sequencing only positive, contact plate only positive, and double positive (n = 759). We assessed AD severity, sensitization, total IgE, and atopic outcomes across categories. Culture missed 69% of samples detected by MSS and MSS missed 54% of samples detected by culture. The double positive group exhibited higher AD severity, sensitization load, and total serum IgE, and was more likely to develop allergic rhinitis (AR) compared to other groups. Detection of SA by MSS or culture missed over half of the SA detected by the other method. Importantly, detection via both methods correlated with increased AD severity, sensitization, total IgE, and AR. Thus, these methods are complementary and both may be necessary for comprehensive evaluation of SA and its clinical and biologic impact.