Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome
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RESEARCH
Open Access
Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome Emma K. Accorsi1, Eric A. Franzosa1,2, Tiffany Hsu1,2, Regina Joice Cordy1,3, Ayala Maayan-Metzger4,5, Hanaa Jaber5, Aylana Reiss-Mandel5, Madeleine Kline6, Casey DuLong1, Marc Lipsitch1, Gili Regev-Yochay4,5 and Curtis Huttenhower1,2* * Correspondence: chuttenh@hsph. harvard.edu 1 Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA 2 Broad Institute, 415 Main St., Cambridge, MA 02142, USA Full list of author information is available at the end of the article
Abstract Background: Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically in their nares, a risk factor for later infection, and interactions with other species in the nasal microbiome likely modulate its carriage. It is thus important to identify ecological or functional genetic elements within the maternal or infant nasal microbiomes that influence S. aureus acquisition and retention in early life. Results: We recruited 36 mother-infant pairs and profiled a subset of monthly longitudinal nasal samples from the first year after birth using shotgun metagenomic sequencing. The infant nasal microbiome is highly variable, particularly within the first 2 months. It is weakly influenced by maternal nasal microbiome composition, but primarily shaped by developmental and external factors, such as daycare. Infants display distinctive patterns of S. aureus carriage, positively associated with Acinetobacter species, Streptococcus parasanguinis, Streptococcus salivarius, and Veillonella species and inversely associated with maternal Dolosigranulum pigrum. Furthermore, we identify a gene family, likely acting as a taxonomic marker for an unclassified species, that is significantly anti-correlated with S. aureus in infants and mothers. In gene content-based strain profiling, infant S. aureus strains are more similar to maternal strains. Conclusions: This improved understanding of S. aureus colonization is an important first step toward the development of novel, ecological therapies for controlling S. aureus carriage. Keywords: Nasal, Microbiome, S. aureus, Infant, Development, Carriage, Shotgun metagenomics, Longitudinal
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