Streptococcus pneumoniae (SPN) remains a leading cause of respiratory disease in young children despite widespread vaccination. Understanding the duration of pneumococcal carriage, patterns of co-colonization, and the influence of viral infections and the respiratory microbiome is essential to evaluate next-generation pneumococcal vaccines and inform public health strategies. Current data on Streptococcus pneumoniae carriage dynamics are limited in U.S. pediatric populations. This study aims to generate updated estimates of Streptococcus pneumoniae colonization and explore microbial interactions using high-resolution longitudinal sampling and genomic methods.