Targeted Capture of AMR in children in Botswana

There is limited knowledge of the collection of antibiotic resistance genes in the gut microbiome of children in Sub-Saharan Africa and the selection that results from antibiotic exposures. Using a sensitive and specific targeted capture sequencing strategy, we surveyed antibiotic resistance genes in the gut microbiome of children under 5 years of age in Botswana with non-bloody diarrhoea. There was a diverse set of azithromycin-resistance genes in the gut microbiome of these children at baseline that increased in prevalence 60 days after treatment with either azithromycin or the standard of care.