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

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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.

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Fig. 1: Clinical variables predict microbiota diversity and composition.
Fig. 2: Partial architectural recovery of preterm IGM following discharge from NICU.
Fig. 3: Preterm infants harbour an enriched gut resistome.
Fig. 4: Multidrug-resistant Enterobacteriaceae lineages persist in IGM.
Fig. 5: Enduring damage to the preterm IGM.

Data availability

Assembled functional metagenomic contigs, shotgun metagenomic reads, shotgun genomic reads and assemblies have been deposited to NCBI GenBank and SRA under BioProject ID PRJNA489090.

Code availability

The software packages used in this study are free and open source. Analysis scripts used here (and associated usage notes) are available from the authors on reasonable request.

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Acknowledgements

This work is supported in part by awards to G.D. through the National Institute of General Medical Sciences of the National Institutes of Health (R01 GM099538), the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (R01 AI123394) and the US Centers for Disease Control and Prevention (200-2016-91955); to P.I.T. through the National Institutes of Health (5P30 DK052574 (Biobank, DDRCC)); to G.D., P.I.T. and B.B.W. through the Eunice Kennedy Shriver National Institute Of Child Health and Human Development of the National Institutes of Health (R01 HD092414); to P.I.T. and B.B.W. through the Children’s Discovery Institute at St Louis Children’s Hospital and Washington University School of Medicine; and to A.J.G. through a NIGMS training grant award number T32 GM007067 (J. Skeath, principal investigator) and from the NIDDK Pediatric Gastroenterology Research Training Program award number T32 DK077653 (P.I.T., principal investigator). The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies. We thank members of the Dantas laboratory for helpful discussion of the manuscript, and staff from the Edison Family Center for Genome Sciences & Systems Biology, E. Martin, B. Koebbe and J. Hoisington-López for technical support and sequencing expertise.

Author information

A.J.G. and G.D. conceived and designed the study. P.I.T., B.B.W. and I.M.N. assembled the cohorts, collected the specimens and biological data and maintained the database, oversaw the transfer of specimens and clinical metadata and provided clinical insights. A.J.G. and B.W. extracted metagenomic DNA from stools and prepared shotgun metagenomic sequencing libraries. A.J.G., B.W. and A.H.-L. performed stool culturing experiments and isolate genomic DNA extraction. A.J.G. and B.W. prepared isolate genome sequencing libraries. E.A.K. performed Enterococcus phenotyping experiments. X.S. created functional metagenomic libraries, performed functional selections and prepared functional metagenomic sequencing libraries. A.J.G. analysed clinical metadata, shotgun metagenomic sequencing data, isolate genome sequencing data and functional metagenomic data. A.J.G. wrote the manuscript with input from G.D., B.B.W. and P.I.T.

Correspondence to Gautam Dantas.

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Competing interests

P.I.T. is a member of the Scientific Advisory Board of, holds equity in and is a consultant to MediBeacon. P.I.T. is a coinventor on a filed patent application (US Patent application no. 16/200353) to test intestinal permeability in humans that might generate royalty payments. This involvement is not directly relevant to this manuscript. P.I.T. is also a consultant to Takeda Pharmaceuticals on pediatric gastrointestinal disorders and to the Bill & Melinda Gates Foundation on neonatal infections.

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Supplementary Information

Supplementary Figs. 1–7, and Supplementary Tables 2 and 3.

Reporting Summary

Supplementary Table 1

Clinical and experimental metadata for infants and samples included in this study.

Supplementary Table 4

Statistics for infant gut isolates sequenced in this study.

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