Breastfeeding and the milk resistome shape the establishment and transmission of antibiotic resistance genes in the infant gut microbiome

The infant resistome, the collection of antimicrobial resistance genes (ARGs) of newborns, is critical for gut microbiota establishment. Using metagenomic sequencing data, we analyzed various 1-week and 1-month postpartum samples to study infant resistome establishment, ARG transmission, and its impact on functional redundancy of the microbiota. A total of 431 samples were analyzed; infant stools (1-week, n = 119; 1-month, n = 119), maternal stools (1-month postpartum, n = 120), and breastmilk (1-month postpartum, n = 73). Breastfeeding correlated with increased functional redundancy and altered bacterial-ARG co-occurrence networks in the infant resistome. Escherichia coli dominated early resistome dynamics with a higher abundance correlating with reduced functional redundancy. Bifidobacterium longum exhibited a consistent negative association with 21 ARGs at one-month in breastfed infants, while four negative relationships between ARGs and Bifidobacterium bifidum were observed in formula-fed infants. ARG transmission via breastmilk appears to be gene-specific, with the quinolone resistance gene sdrM likely transmitted under maternal antibiotic use. Delivery mode modulated the microbial environment in ways that interact with resistome structure and changing functional redundancy, particularly through genera like Staphylococcus and Streptococcus. These findings highlight the role of early feeding practices in resistome development and propose functional redundancy as a key ecological framework for understanding infant gut resistome dynamics.