Distinct infant resistome trajectories shaped by country income and geography revealed through global metagenomics reanalysis

A large meta-analysis of 1,944 infant gut metagenomes shows that antimicrobial resistance gene (ARG) patterns diverge early in life and are strongly shaped by socioeconomic and clinical factors. While ARG levels are similar across income settings in the first three months, by six months infants in low-income countries exhibit significantly higher ARG abundance, closely associated with increased Escherichia coli carriage. Factors such as Caesarean section rates, antibiotic use, and income inequality correlate positively with ARG levels in early infancy, whereas higher physician density is linked to lower ARG abundance later on. These findings highlight how early-life exposures and health system context influence the developing resistome, pointing to targeted, age-specific interventions to limit AMR emergence in vulnerable pediatric populations.