Micro-epidemiology of S. aureus colonisation in atopic eczema disease flares.

Staphylococcus aureus colonisation is a characteristic feature of atopic eczema (AE). Despite this the colonisation dynamics of S. aureus during disease flare eczema are poorly understood. To interrogate flare-associated populations we sampled children with moderate to severe AE across multiple body sites. Healthy children asymptomatically carrying S. aureus nasally were assessed as a controls. Whole genome sequencing (WGS) of multiple S. aureus colonies per eczema case and control was then used to genetically characterise the colonising populations. Case and control populations demonstrate varying degrees of within host heterogeneity in the colonising population. Colonisation of eczema skin differed with respects to genetic backgrounds observed in the S. aureus populations compared to controls. Evidence of clinically relevant adaptive mutations were identified in cases, linked to survival during prolonged periods of carriage, including examples affecting a global regulatory of virulence and antimicrobial resistance. The deep sequencing of AE patients has generated an unprecedented view into the population dynamics of S. aureus, revealing heterogeneity in the colonising population that has implications for clinical interventions and the management of disease.