Bacteriome interactions in pediatric atopic dermatitis in a rural and urban South African cohort

Doctoral Thesis


Permanent link to this Item
Journal Title
Link to Journal
Journal ISSN
Volume Title
Skin and nasal bacterial dysbiosis is common in children with atopic dermatitis (AD). However, there is limited data of these bacterial changes in sub-Saharan children with AD. Therefore, this study investigated the bacterial alterations in skin and nasal bacterial communities in AD compared to healthy children in rural and urban South African settings. Staphylococcus aureus was more common in children with AD (cases) than healthy children (controls). S. aureus carriage was also associated with increased disease severity. Using spa typing, we also showed that cases and controls were colonised by distinct spa types. This led us to comprehensively explore genomic differences of S. aureus in cases and controls using whole-genome sequencing. Here, we showed that S. aureus strains from cases and controls had distinct genomic features, with cases harbouring genes associated with antibiotic resistance, DNA damage repair and virulence while controls had genes associated with adhesion. Recent reports indicate the potential role of coagulase-negative Staphylococcus (CoNS) in AD pathology. This study found that CoNS and S. aureus were commonly co-carried on nonlesional skin among cases (regardless of location) and anterior nares among urban cases than the control group. The carriage of S. capitis on nonlesional skin and anterior nares was positively associated with more severe disease in both rural and urban cases. 16S rDNA amplicon sequencing analysis revealed that bacterial diversity was higher on the nonlesional skin and anterior nares of controls. Bacterial community structure differed on lesional skin, nonlesional skin and anterior nares based on AD disease status. The relative abundance of Streptococcus, Granulicatela, Veillonella and Prevotella was high in lesional skin specimens, Anoxybacillus and Cutibacterium on nonlesional skin, and Staphylococcus, Veillonella and Sphingomonas in the anterior nares among cases Overall, the findings presented in this thesis indicate that S. aureus and other CoNS, particularly S. capitis, may predominate among cases and are associated with increased disease severity. However, the increased relative abundance of genera such as Streptococcus, especially among skin samples, indicates that other bacterial genera may be contributing to disease activity on lesional skin in AD than the traditionally reported Staphylococcus.