Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome

Andrew J. Gasparrini, Bin Wang, Xiaoqing Sun, Elizabeth A. Kennedy, Ariel Hernandez-Leyva, I. Malick Ndao, Phillip I. Tarr, Barbara B. Warner, Gautam Dantas

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)2285-2297
Number of pages13
JournalNature microbiology
Volume4
Issue number12
DOIs
StatePublished - Dec 1 2019

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