Dataset - Nasal microbiome disruption and recovery after mupirocin treatment in Staphylococcus aureus carriers and noncarriers

<strong>Background. </strong>Nasal decolonization procedures against the opportunistic pathogen <em>Staphylococcus aureus</em> rely on topical antimicrobial drug usage, whose impact on the nasal microbiota is poorly understood. We examined this impact in healthy <em>S. aureus </em>carriers and noncarriers. <strong>Methods. </strong>This is a prospective interventional cohort study of 8 <em>S. aureus </em>carriers and 8 noncarriers treated with nasal mupirocin and chlorhexidine bath. Sequential nasal swabs were taken over 6 months. <em>S. aureus</em> was detected by quantitative culture and genotyped using <em>spa</em> typing. RNA-based 16S species-level metabarcoding was used to assess the living microbial diversity. <strong>Results. </strong>The species <em>Dolosigranulum pigrum, Moraxella nonliquefaciens </em>and<em> Corynebacterium propinquum </em>correlated negatively with <em>S. aureus</em> carriage. Mupirocin treatment effectively eliminated <em>S. aureus, D. pigrum </em>and<em> M. nonliquefaciens, </em>but not corynebacteria. <em>S. aureus</em> recolonization in carriers occurred more rapidly than recolonization by the dominant species in noncarriers (median 3 vs. 6 months, respectively). Recolonizing <em>S. aureus</em> isolates had the same <em>spa</em> type as the initial isolate. <strong>Conclusions. </strong>Mupirocin-chlorhexidine treatment had a long-lasting impact on the nasal microbiota. <em>S. aureus</em> recolonization predated microbiota recovery, emphasizing the strong adaptation of this pathogen to the nasal niche and the transient efficacy of the decolonization procedure.