Outbreak and Postnatal Antibiotic Exposures Drive the Development Trajectory of the Nasopharyngeal Microbiota in the First Year of Life

Early exposure to antibiotics and prolonged hospitalization in preterm infants may perturb microbiome development and contribute to adverse health outcomes. Although nasopharyngeal microbiomes are linked to respiratory infections, their early development is underexplored and often assessed with 16S rRNA sequencing, which lacks species resolution. Here, we investigated nasopharyngeal microbiota dynamics in 66 preterm infants by performing deep shotgun metagenomics on 369 nasopharyngeal aspirates collected from birth until 6 months corrected age (∼7-10 months chronological age). The nasopharyngeal microbiota evolved dynamically, exhibiting age-structured and individualized patterns shaped by postnatal antibiotic exposure and hospitalization. Early-life antibiotic exposure (ampicillin + gentamicin) had transient but significant effects on microbial diversity, composition, stability, and community dynamics. Conversely, an unexpected NICU outbreak left a lasting signature, with persistent S. marcescens carriage observed at 6 months corrected age, which our machine learning algorithm accurately predicted based on microbiome composition in the first days of life. A S. marcescens-dominated community type was present in 45% of total samples and exhibited remarkable stability over time, with minimal transitions to other types regardless of antibiotic exposure. These findings underscore the need for deeper insight into how antibiotics and potential outbreaks can lead to alterations in microbiome trajectories, with possible long-term health implications.