The Association Between the Developing Nasal Microbiota of Hospitalized Neonates and Staphylococcus aureus Colonization

BACKGROUND: Hospitalized neonates are at high risk for invasive Staphylococcus aureus infections. S. aureus nasal colonization often precedes infection. The nasal microbiota may preclude or support colonization. We aimed to characterize and compare the nasal microbiota of hospitalized neonates who acquire S. aureus colonization (cases) and those who do not acquire S. aureus (controls). METHODS: We obtained residual nares samples from hospitalized neonates who were screened weekly for S. aureus nasal colonization and treated with intranasal mupirocin if colonized. Eight cases were matched based on chronologic age and systemic antibiotic exposure to 7 controls. We extracted DNA, sequenced the V3-V4 region of the 16s rRNA gene, and performed taxonomic assignments. The bacterial species richness, relative abundance, and in silico predicted gene content were compared between cases and controls at 7 days before S. aureus acquisition, at the time of acquisition, and 7 days after acquisition and treatment. RESULTS: Common commensals including nondiphtheriae corynebacteria were more abundant in the nares of controls and Rothia mucilaginosa was more abundant in cases 7 days after intranasal mupirocin treatment than in cases 7 days before S. aureus acquisition. Controls and treated cases had a higher predicted abundance of genes contributing to the synthesis of certain antimicrobial compounds than in cases before S. aureus acquisition. CONCLUSIONS: Neonates without S. aureus nasal colonization had a higher abundance of bacterial species that antagonize S. aureus directly or by selecting for beneficial co-colonizers. These differences may inform novel S. aureus infection prevention strategies in high-risk infants.