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

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.

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Outcomes Randomization of participants in the main BRISC study was performed using a computer-generated randomization list with block randomization, stratified according to child sex and union, to link sequential participant identification numbers to trial groups.A hard-copy list was used for randomization in the field.
Note that the antibiotic and AMR-related analysis was undertaken retrospectively according to antibiotic use, irrespective of trial intervention arm.Definitions of antibiotic use in relation to the sampling timepoint were used to conduct the analysis.These are outlined in the Methods section.
The main BRISC study was a three-group, double-blind, double-dummy, individually randomized, placebo-controlled trial.As the microbiome sub study was nested within this trial, these attributes were identical.
Investigators were blinded to group allocation throughout both data collection and analysis.Samples were also sequenced in random order (i.e.PCR plates and sequencing runs included samples from different timepoints) to minimise any batch effects.The antibiotic/AMR analysis was a post-hoc analysis and not defined in the main study protocol.
Microbiome sub study participants were recruited as the last 1093 children on the main BRISC study, over the period September 2018 to February 2019.The last follow-up stool samples were therefore collected in February 2020.
Primary outcome measures were alpha diversity (Shannon and inverse Simpson indices), beta diversity and differential abundance (taxonomy and AMR gene) with respect to reported antibiotic use at the pre-defined time definitions outlined in the Methods section.Secondary outcomes were not pre-defined.However, additional analyses were performed on the data to examine taxonomic-AMR relationships based on the primary outcome findings.

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The microbiome sub study was part of the Benefits and Risks of Iron InterventionS in Children (BRISC) trial (Australian New Zealand Clinical Trials Registry number ACTRN12617000660381). The protocol for the main BRISC study has been published previously: Hasan MI, Hossain SJ, Braat S, et al.Benefits and risks of Iron interventions in children (BRISC): protocol for a three-arm parallel-group randomised controlled field trial in Bangladesh.BMJ Open 2017; 7(11): e018325.(https://doi.org/10.1136/bmjopen-2017-018325)