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.