Impact of antibiotics and hospitalization on the nasopharyngeal microbiome in very preterm infants

Abstract

AbstractRationalePreterm infants are often exposed to antibiotics early in life. They are at increased risk for inflammation and infection due to immature immune system, weak mucosal barriers of the intestinal and respiratory tract and ineffective defense from non-pathogens of normal flora. Longitudinal research of respiratory microbiota of preterm infants is limited.ObjectivesInvestigate the development of nasopharyngeal microbiota in preterm infants from birth until six months corrected age.MethodsIn our observational cohort study, we obtained 369 nasopharyngeal aspirates from 66 very preterm infants sampled at six time points spanning from birth until six months corrected age. Deep shotgun metagenomic sequencing was used to determine the microbiome composition.Measurements and Main ResultsPreterm infants were grouped according to postnatal antibiotic exposure (naïve; n=21, “Only Early antibiotics”; n=24 and “Other antibiotics”; n=21). Inter-individual variability, followed by postmenstrual age had the largest significant effect on the overall microbiome composition. We identified six microbial community types, determined by various abundances ofCutibacterium,Gemella, Serratia, Streptococcus and Staphylococcus. Antibiotic exposure resulted in significant, apparently transient diversity changes. The abundance ofSerratiaindicates that hospitalization can lead to microbiome scars lasting for at least six months after discharge.ConclusionsGenera associated with respiratory health in non-premature populations were sparse. The respiratory microbiome of preterm infants is transiently affected by antibiotic exposure, while signatures of hospitalization may persist for at least six months after hospital discharge.