Assessment Tool Combination Reveals Higher AD Risk and Atopic March Progression

Key Takeaways

• Culture and metagenomic shotgun sequencing (MSS) methods detect non-overlapping cases of Staphylococcus aureus (SA) on atopic dermatitis (AD) skin.

• Children with SA detected by both methods had more severe AD and a higher risk of allergic rhinitis.

• Culture-based detection was linked with biologically relevant SA exposure.

Children with Staphylococcus aureus (SA) detected by metagenomic sequencing, as well as culture-based methods, had worse atopic dermatitis (AD) outcomes, new study results suggest.

Despite metagenomic shotgun sequencing (MSS)'s wide usage for assessing skin microbiota, its clinical relevance and ability to detect SA had not been compared to single-assay detection, the researchers said. Study authors followed 328 children with AD using skin tape-based MSS and contact agar plate culture. Patients reported for five annual visits. SA detection was categorized as double negative, sequencing-only positive, culture-only positive, or double positive.

According to the results, culture missed nearly 70% of SA-positive samples identified by MSS, while MSS missed 54% of culture-positive samples. Despite this discordance, the subset of children with SA detected by both methods (double positive) had the highest SCORAD scores, greater allergen sensitization, higher total serum IgE, and higher incidence of allergic rhinitis.

Sensitivity analyses controlling for anatomical sampling site confirmed that the associations between dual detection and adverse clinical outcomes held steady, suggesting the results were not artifacts of sampling location. Furthermore, among non-Black children, being double positive was associated with a significantly elevated Pediatric Asthma Risk Score, indicating a link between dual SA detection and atopic march progression.

“Our novel findings suggest that detecting SA via multiple methodologies may be essential in determining AD and atopic march outcomes, irrespective of SA load," the authors wrote in the study. "Furthermore, while MSS may be suitable for comprehensive microbial analysis, detecting SA on contact agar plates and other culture-dependent assays may be more practical and yields important insight on biologically and clinically relevant bacteria that influence the atopic disease course and outcomes.”

Source: Dahal A, et al. Sci Rep. 2025;15:17606. doi:10.1038/s41598-025-16479-2