Early development and dynamics of nasopharyngeal microbiota in infants during the COVID-19 pandemic: a 2-year prospective birth cohort study.

Background: The nasopharyngeal microbiota, which plays a crucial role in respiratory health and disease during infancy, was significantly affected by the COVID-19 pandemic lockdown in children and adults. This study aimed to prospectively explore the dynamics of the nasopharyngeal microbiota in infants during the COVID-19 pandemic.

Methods: We conducted a prospective birth cohort study at Hospital Sant Joan de Déu (Barcelona, Spain) involving 32 neonates born between December 2019 and December 2020. Epidemiological, clinical and microbiological variables as well as nasopharyngeal aspirates were collected during the firsts two years of life. Nasopharyngeal aspirates were used to characterize the nasopharyngeal microbiota through 16 S rRNA gene sequencing.

Results: Our findings highlight the stabilization of the nasopharyngeal microbiota composition by 12 months of age. Key factors influencing nasopharyngeal microbiota patterns in the first two years of life included a history of upper respiratory tract infection episodes, a pattern of rapid post-natal weight gain, pneumococcal carriage detection, recent receipt of systematic vaccination, and the use of antibiotics and corticosteroids. Notably, rapid post-natal weight gain was associated with differences in the microbiota composition, with overrepresentation of potential beneficial bacteria such as Dolosigranulum pigrum and Corynebacterium spp., underrepresentation of Haemophilus influenzae and Moraxella catarrhalis, and functional pathways with enhanced metabolic activity.

Conclusions: These findings demonstrate early stabilization of the nasopharyngeal microbiota composition by 12 months of age during the COVID-19 period and highlight the interplay between nasopharyngeal microbiota dynamics and early post-natal weight gain, with potential long-term impacts on metabolic outcomes.