Human infant gut metagenome, infant shotgun sequencing

Because hospitalized preterm infants are vulnerable to infection, they receive frequent and often prolonged exposures to antibiotic therapy. It is not known if the demonstrated short-term effects of antibiotics on the preterm infant gut microbiota and resistome persist after discharge from neonatal intensive care units. Here, we use complementary metagenomic and culture based techniques to interrogate the gut microbiota and resistome of antibiotic-exposed preterm infants both during, and after, hospitalization, and compare these readouts to antibiotic-naïve healthy infants sampled synchronously. We find an enriched gastrointestinal antibiotic resistome, prolonged carriage of multidrug resistant Enterobacteriaceae, and distinct antibiotic-driven patterns of microbiota and resistome assembly in extremely preterm infants who received early life antibiotics. Our results demonstrate persistent collateral damage of early life antibiotic treatment and hospitalization in preterm infants and highlight the need for alternative strategies for infection management in highly vulnerable neonatal populations.