# Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children

## TL;DR

This study shows that recent antibiotic use in young Bangladeshi children temporarily changes their gut bacteria and increases antibiotic resistance genes.

## Contribution

The study provides empirical evidence of short-term gut microbiome changes and resistance gene enrichment due to recent oral antibiotic use in infants.

## Key findings

- Recent antibiotic use in infants reduces gut microbiome diversity and increases Enterococcus and Escherichia/Shigella.
- Antibiotic resistance genes decline over time but are enriched in children with recent antibiotic exposure.
- Antimicrobial resistance gene presence correlates with gut microbiome composition.

## Abstract

Antibiotics may alter the gut microbiome, and this is one of the mechanisms by which antimicrobial resistance may be promoted. Suboptimal antimicrobial stewardship in Asia has been linked to antimicrobial resistance. We aim to examine the relationship between oral antibiotic use and composition and antimicrobial resistance in the gut microbiome in 1093 Bangladeshi infants. We leverage a trial of 8-month-old infants in rural Bangladesh: 61% of children were cumulatively exposed to antibiotics (most commonly cephalosporins and macrolides) over the 12-month study period, including 47% in the first 3 months of the study, usually for fever or respiratory infection. 16S rRNA amplicon sequencing in 11-month-old infants reveals that alpha diversity of the intestinal microbiome is reduced in children who received antibiotics within the previous 7 days; these samples also exhibit enrichment for Enterococcus and Escherichia/Shigella genera. No effect is seen in children who received antibiotics earlier. Using shotgun metagenomics, overall abundance of antimicrobial resistance genes declines over time. Enrichment for an Enterococcus-related antimicrobial resistance gene is observed in children receiving antibiotics within the previous 7 days, but not earlier. Presence of antimicrobial resistance genes is correlated to microbiome composition. In Bangladeshi children, community use of antibiotics transiently reprofiles the gut microbiome.

In this study, the authors examined the relationship between oral antibiotic use and composition and antimicrobial resistance in the gut microbiome in Bangladeshi infants with a high exposure to community-administered antibiotics.