UNDERSTANDING the factors that determine Staphylococcus aureus nasal carriage is clinically important, particularly given its role as a reservoir for invasive disease and transmission in both community and healthcare settings. A new large-scale study involving approximately 1,100 adults provides the most comprehensive assessment to date of how nasal microbial community structures influence S. aureus colonisation status, and how these profiles may support future targeted prevention strategies.
Nasal Microbiome Community Structure and Staph Status
Using metagenomic sequencing and culture-based assessment, researchers identified seven distinct nasal community state types (CSTs). One CST was dominated by S. aureus and accounted for roughly 70% of persistent carriers. Non-carriers were distributed across CSTs characterised by higher bacterial diversity and the presence of organisms associated with reduced S. aureus abundance.
Key taxa negatively associated with S. aureus included three Corynebacterium species, Dolosigranulum pigrum, Staphylococcus epidermidis, and Moraxella catarrhalis. Previous in vitro and clinical studies have suggested inhibitory activity from these organisms, supporting the concept of bacterial interference as a determinant of colonisation resistance. Two CSTs enriched among female participants may also help explain observed sex-based differences in persistence.
Predictive Modelling and Reclassification of “Intermittent Carriers”
Machine learning models incorporating microbiome composition and culture data demonstrated high accuracy in predicting persistent carriage, particularly in identifying true non-carriers. These findings highlight the potential for microbiome-informed risk stratification, which may complement or refine decolonisation strategies in high-risk populations.
The study further challenges the traditional “intermittent carrier” category. Individuals previously labelled as intermittent carriers did not exhibit a unique microbial signature; rather, their CSTs resembled either persistent carriers, when S. aureus abundance was high, or non-carriers. This suggests that many intermittent carriers may transiently acquire S. aureus from environmental or interpersonal exposure.
Finally, certain S. aureus lineages were shown to achieve higher abundance and were more strongly associated with persistent colonisation, underscoring the role of bacterial genotype in host-microbe dynamics.
Collectively, these findings broaden current understanding of the nasal microbiome’s role in colonisation and may inform future preventive or therapeutic approaches, including microbiome modulation and targeted biotherapeutics.
Reference
Aggarwal D et al. Large-scale characterisation of the nasal microbiome redefines Staphylococcus aureus colonisation status. Nat Commun. 2025;16(1):10415.
