Temporal changes in the nasal microbiota and host antimicrobial responses to intranasal mupirocin decolonisation: Observations in healthy staphylococcal carriers

Background How intranasal mupirocin decolonisation affects the human nasal microbiota remains unknown. To characterize the temporal dynamics of the nasal microbial community in healthy staphylococcal carriers in response to intranasal mupirocin decolonisation, we serially sampled the anterior nares of four healthy carriers to determine the nasal microbial profile via sequencing of bacterial 16S ribosomal DNA.

Results Before decolonisation, the nasal microbiota differed by the initial, culture-based staphylococcal carriage status, with Firmicutes (54.1%) and Proteobacteria (75.8%) dominating the microbial community in the carriers and the noncarrier, separately. The nasal microbiota lost its diversity immediately after decolonisation (Shannon diversity: 1.33, 95% confidence interval [CI]: 1.06-1.54) as compared to before decolonisation (1.78, 95%CI: 0.58-1.93). The initial staphylococcal carriage status, expression levels of human neutrophil peptide 1, and sampling times were major contributors to the between-community dissimilarities (P for marginal permutation test: .014) though of borderline significance when considering data correlation (P for blocked permutation test: .047) in both nonmetric multidimensional scaling and constrained correspondence analysis. Results of univariable and multivariable differential abundance analysis further showed that, in addition to Staphylococci, multiple genera of Actinobacteria and Proteobacteria were differentially enriched or depleted by mupirocin use.

Conclusions Mupirocin could affect both Gram-positive and Gram-negative commensals along with altered host antimicrobial responses. How the nasal microbiome recovered after short-term antibiotic perturbation depended on the initial staphylococcal carriage status. The potential risks associated with loss of colonisation resistance need to be considered in high-risk populations receiving targeted decolonisation.