High-resolution characterization of nasal microbial dynamics in young children

Nasal carriage of bacteria and viruses is common in young children. However, these carriage dynamics remain poorly understood due to the lack of high-resolution studies. Therefore, we conducted a 29-day prospective study in which 45 children, 1-5 years of age, provided daily nasosorption samples from which we analyzed 16 viruses, 6 bacteria, and 21 Streptococcus pneumoniae serotypes/groups. Bacterial densities fluctuated rapidly, with autocorrelations lasting only eight days. Inter-species but also intra-species interactions were observed; co-carriage of multiple Streptococcus pneumoniae serotypes increased clearance of non-dominant strains. Staphylococcus aureus carriage was associated with reduced viral acquisition and accelerated viral clearance. Rhinovirus triggered rhinitis on the day of acquisition, with bacterial densities rising three days later. This high-resolution sampling approach elucidated complex microbial and host-pathogen interactions in children.