Nasopharyngeal microbiota in infants during COVID-19 pandemic

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 16S rRNA gene sequencing. Our findings highlight the stabilization of the nasopharyngeal microbiota composition by 12 monthsof 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 pigrumand Corynebacterium spp., underrepresentation of Haemophilus influenzaeand Moraxella catarrhalis, and functional pathways with enhanced metabolic activity.