The Skin Microbiome of Patients With Atopic Dermatitis Normalizes Gradually During Treatment

Abstract

BackgroundAtopic dermatitis (AD) is characterized by an altered skin microbiome dominantly colonized by S. aureus. Standard treatment includes emollients, anti-inflammatory medications and antiseptics.ObjectivesTo characterize changes in the skin microbiome during treatment for AD.MethodsThe skin microbiomes of children with moderate-to-severe AD and healthy children were investigated in a longitudinal prospective study. Patients with AD were randomized to receive either standard treatment with emollients and topical corticosteroids or standard treatment with the addition of dilute bleach baths (DBB) and sampled at four visits over a three-month period. At each visit, severity of AD was measured, swabs were taken from four body sites and the composition of the microbiome at those sites was assessed using 16S rRNA amplification.ResultsWe included 14 healthy controls and 28 patients. We found high relative abundances of S. aureus in patients, which correlated with AD severity and reduced apparent alpha diversity. As disease severity improved with treatment, the abundance of S. aureus decreased, gradually becoming more similar to the microbiomes of healthy controls. After treatment, patients who received DBB had a significantly lower abundance of S. aureus than those who received only standard treatment.ConclusionsThere are clear differences in the skin microbiome of healthy controls and AD patients that diminish with treatment. After three months, the addition of DBB to standard treatment had significantly decreased the S. aureus burden, supporting its use as a therapeutic option. Further study in double-blinded trials is needed.

On-person adaptive evolution ofStaphylococcus aureusduring treatment for atopic dermatitis

“…The number of isolates analyzed per patient visit is variable and correlates with both disease severity and S. aureus relative abundance inferred from 16S rRNA sequencing 22 (0-68 isolates/visit; r 2 =0.41 and r 2 =0.21, respectively; Figure 1b and Extended Data Figure 2 ). While most patients provided isolates from intermittent or single timepoints, six patients suffering from severe AD throughout the study provided large numbers of isolates amenable to quantitative analyses (99-206 isolates/patient; Figure 1b ).…”

“…Linear least-square regression for the relative S. aureus frequency (16s rRNA; averaged across sites) and number of recovered S. aureus isolates per visit demonstrates a relationship between the relative abundance of S. aureus and the number of isolates recovered (r 2 =0.21). The 16S rRNA data was originally described in Khadka et al 22 . c .…”

A Pilot Study: Composition and Diversity of 16S rRNA Based Skin Bacterial Microbiome in Indonesian Atopic Dermatitis Population

“… 5 Higher S. aureus abundances in patients with AD relative to healthy subjects, in lesional sites, compared to non-lesional sites, and in patients with higher vs lower SCORAD also revealed in Khadka et al’s study. 30 …”

Cutaneous surgical wounds have distinct microbiomes from intact skin

“…To classify 16S amplicon sequence variants (ASVs) at the species level, we built a classifier using a cleaned up version of the SILVA database (version 132) and the first 180 base pairs of the V1-V3 region (Quast et al 2013). Staphylococcus species were filtered by the methods presented in Khadka et al (Khadka et al 2021), and the genuses Cutibacterium, Acidipropionibacterium, Pseudopropionibacterium and families Corynebacteriaceae and Neisseriaceae were cleaned in the database using the following filters: (i) sequences with inconsistent higher taxonomic classes were removed, (ii) sequences missing a species classification were removed, (iii) species with >60% of sequences that were identical to another taxa were relabeled as a specific “taxa cluster”, (iv) taxonomically mislabeled sequences identified using SATIVA using nomenclature code BAC (Kozlov et al 2016) with greater than 90% confidence were relabeled and sequences with below 90% confidence removed. To reduce computational load, each family or genus was run independently in SATIVA.…”