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

Abstract

Antimicrobial resistance (AMR) costs lives, diminishes antimicrobial effectiveness and increases health care costs. We conducted a re-analysis of pooled fecal metagenomes from individual participants to characterise AMR gene (ARG) distributions in 0-2 year-old healthy infants across income and geography. From 2275 screened studies, we included nine datasets and 1944 fecal metagenomes. Resistome gene identifier (RGI) was used to identify ARGs, and gut microbiomes were profiled using Sylph. We assessed associations between ARGs, Escherichia coli abundance, and national-level indicators. In the first 3 months of life, ARG abundance patterns were not significantly different across income groups; however, by 6 months of age, infants in LICs had higher ARG abundance, associated with increased E. coli carriage. Caesarean section rates, antibiotic use, and income inequality positively correlated with ARG abundance in younger infants; physician density negatively correlated with ARG abundance in older children. These descriptive age- and context-specific associations may inform interventions to mitigate the carriage and spread of ARGs and the rise of AMR in vulnerable pediatric populations.