Impact of azithromycin mass drug administration on the antibiotic-resistant gut microbiome in children: a randomized, controlled trial

Abstract

Background: Mass drug administration (MDA) with azithromycin is the primary strategy for global trachoma control efforts. Numerous studies have reported secondary effects of MDA with azithromycin, including reductions in childhood mortality, diarrhoeal disease and malaria. Most recently, the MORDOR clinical trial demonstrated that MDA led to an overall reduction in all-cause childhood mortality in targeted communities. There is however concern about the potential of increased antimicrobial resistance in treated communities. This study evaluated the impact of azithromycin MDA on the prevalence of gastrointestinal carriage of macrolide-resistant bacteria in communities within the MORDOR Malawi study, additionally profiling changes in the gut microbiome after treatment. For faecal metagenomics, 60 children were sampled prior to treatment and 122 children after four rounds of MDA, half receiving azithromycin and half placebo.

Results: The proportion of bacteria carrying macrolide resistance increased after azithromycin treatment. Diversity and global community structure of the gut was minimally impacted by treatment, however abundance of several species was altered by treatment. Notably, the putative human enteropathogen Escherichia albertii was more abundant after treatment.

Conclusions: MDA with azithromycin increased carriage of macrolide-resistant bacteria, but had limited impact on clinically relevant bacteria. However, increased abundance of enteropathogenic Escherichia species after treatment requires further, higher resolution investigation. Future studies should focus on the number of treatments and administration schedule to ensure clinical benefits continue to outweigh costs in antimicrobial resistance carriage. Trial registration ClinicalTrial.gov, NCT02047981. Registered January 29th 2014, https://clinicaltrials.gov/ct2/show/NCT02047981.

Keywords: Antimicrobial resistance; Azithromycin; Childhood mortality; Gut metagenomics; Gut microbiome; Macrolide resistance; Mass drug administration; Metagenomics; Microbial.

Fig. 1

Study design. Flowchart illustrating the study protocol

Fig. 2

Antimicrobial resistance profile in children receiving either placebo or azithromycin treatment. a The proportion of macrolide-resistant bacteria at 24-month follow-up in children receiving either placebo (blue) or azithromycin (red). b Univariate analysis of antibiotic classes with increased evidence of resistance (linear regression coefficient > 0) or decreased evidence of resistance (linear regression coefficient < 0) after azithromycin treatment. Flat-headed lines indicate the standard error around the coefficient. c The proportion of macrolide-resistant bacteria during 24-month follow-up in children receiving azithromycin 6 months or 12–24 months previously. P-values were considered significant at < 0.05 and are denominated as follows: ***p < 0.001

Fig. 3

Gut microbial diversity, composition and specific bacteria in children receiving either placebo or azithromycin treatment. a Alpha diversity, determined by Shannon’s H, at 24-month follow-up in children receiving either placebo (blue) or azithromycin (red). b Principal coordinates analysis (PCoA) of Bray-Curtis dissimilarity between children by treatment arm. Axes labels indicate the plotted component and percentage variance explained. c Univariate analysis of bacterial species with increased abundance (linear regression coefficient > 0) or decreased abundance (linear regression coefficient < 0) after azithromycin treatment

Fig. 4

Gut microbial composition and antibiotic-resistance profile in children who received azithromycin 6-months or 12–24-months previously. a Principal coordinates analysis (PCoA) of Bray-Curtis dissimilarity between children by time since last azithromycin treatment (12–24 months = green, 6 months = orange). Axes labels indicate the plotted component and percentage variance explained. b Univariate analysis of antibiotic classes with increased evidence of resistance (linear regression coefficient > 0) or decreased evidence of resistance (linear regression coefficient < 0) in children who received azithromycin 6 months previously compared to 1–24 months previously