Combined metagenomic- and culture-based approaches to investigate bacterial strain-level associations with medication-controlled mild-moderate atopic dermatitis

Abstract

ABSTRACTBackgroundThe skin microbiome is disrupted in atopic dermatitis (AD). Existing research focuses on moderate-severe, unmedicated disease.ObjectiveInvestigate metagenomic- and culture-based bacterial strain-level differences in mild, medicated AD, and the effects these have on human keratinocytes (HK).MethodsSkin swabs from anterior forearms were collected from 20 pediatric participants; 11 participants with AD sampled at lesional and nonlesional sites and 9 age- and sex-matched controls). Participants had primarily mild-moderate AD and maintained medication use. Samples were processed for microbial metagenomic sequencing and bacterial isolation. Isolates identified asS. aureuswere tested for enterotoxin production. HK cultures were treated with cell free conditioned media from representativeStaphylococcusspecies to measure barrier effects.ResultsMetagenomic sequencing identified significant differences in microbiome composition between AD and control groups. Differences were seen at the species- and strain-levels forStaphylococci, withS. aureusonly found in AD participants and differences inS. epidermidisstrains between control and AD swabs. These strains showed differences in toxin gene presence, which was confirmedin vitroforS. aureusenterotoxins. The strain from the most severe AD participant produced enterotoxin B levels >100-fold higher than the other strains (p<0.001). Strains also displayed differential effects on HK metabolism and barrier function.ConclusionsStrain level differences in toxin genes fromStaphylococcusstrains may explain varying effects on HK, withS. aureusandnon-aureusstrains negatively impacting viability and barrier function. These differences are likely important in AD pathogenesis.KEY MESSAGESStaphylococcal strain effects, more so than species effects, impact keratinocyte barrier function and metabolism, suggesting that strain level differences, and not species-level, may be critical in AD pathogenesis.The microbiome from mild, medicated atopic dermatitis patients harborStaphylococcusstrains with detrimental effects on skin barrier, and may not only be mediated byS. aureus.CAPSULE SUMMARYPatients with mild atopic dermatitis controlled by medication may still harbor strains ofStaphylococcus spp.that carry toxins that negatively impact skin barrier function.