Journal
NATURE MICROBIOLOGY
Volume 4, Issue 12, Pages 2285-2297Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41564-019-0550-2
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Funding
- National Institute of General Medical Sciences of the National Institutes of Health [R01 GM099538]
- National Institute of Allergy and Infectious Diseases of the National Institutes of Health [R01 AI123394]
- US Centers for Disease Control and Prevention [200-2016-91955]
- National Institutes of Health [5P30 DK052574]
- Eunice Kennedy Shriver National Institute Of Child Health and Human Development of the National Institutes of Health [R01 HD092414]
- Children's Discovery Institute at St Louis Children's Hospital
- NIGMS training grant [T32 GM007067]
- NIDDK Pediatric Gastroenterology Research Training Program [T32 DK077653]
- Washington University School of Medicine
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Hospitalized preterm infants receive frequent and often prolonged exposures to antibiotics because they are vulnerable to infection. It is not known whether the 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, culture-based and machine learning techniques to study the gut microbiota and resistome of antibiotic-exposed preterm infants during and after hospitalization, and we compare these readouts to antibiotic-naive healthy infants sampled synchronously. We find a persistently enriched gastrointestinal antibiotic resistome, prolonged carriage of multidrug-resistant Enterobacteriaceae and distinct antibiotic-driven patterns of microbiota and resistome assembly in extremely preterm infants that received early-life antibiotics. The collateral damage of early-life antibiotic treatment and hospitalization in preterm infants is long lasting. We urge the development of strategies to reduce these consequences in highly vulnerable neonatal populations.
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