Journal Article

Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome

Reiss-Mandel, Aylana, Franzosa, Eric A., Joice Cordy, Regina, Hsu, Tiffany, Huttenhower, Curtis, Accorsi, Emma K., Maayan-Metzger, Ayala, Kline, Madeleine, Lipsitch, Marc, Jaber, Hanaa, DuLong, Casey, Regev-Yochay, Gili

2020

Overview

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.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Acinetobacter / Animal Genetics and Genomics / antibiotic resistance / Antibiotics / Antimicrobial resistance / Babies / Binding sites / Bioinformatics / Biomedical and Life Sciences / Carnobacteriaceae / Carriage / Colonization / Daycare / Development / Dolosigranulum pigrum / Drug resistance / Evolutionary Biology / Female / genes / Human Genetics / Humans / Infant / Infants / Life Sciences / Metagenomics / Microbial Genetics and Genomics / Microbiome / Microbiomes / Microbiota / Mothers / Nasal / nose / Nose - microbiology / Penicillin / Plant Genetics and Genomics / Risk factors / RNA, Ribosomal, 16S / S. aureus / Species / Staphylococcal Infections - microbiology / Staphylococcus aureus / Staphylococcus aureus - genetics / Staphylococcus infections / Streptococcus / Streptococcus infections / Streptococcus parasanguinis / Streptococcus salivarius / Veillonella