Associations of diet, race, and other environmental factors with antimicrobial resistance genes in the gut bacterial communities of pregnant women and 3-month-old infants

The emergence of pathogens resistant to antimicrobials has become a forefront concern for clinicians and patients alike. Antimicrobial resistance (AMR) is exacerbated by the misuse and overuse of antibiotics. Pregnant women and their infants are an important area of focus, as antibiotic use during this vulnerable period of development may generate reservoirs of AMR genes, which would contribute to future risk. Identifying the extent of antibiotic use and its association with ARG composition and persistence within this window is crucial. We sought to characterize the gut resistomes of 3-month-old infants (<i>n</i> = 212) and pregnant women in their third trimester (<i>n</i> = 99) to assess ARG burden in these populations. For a subset of women and their infants (<i>n</i> = 33 pairs), we explored overlap of ARG. Preliminary analyses demonstrated that pregnant women and infants had markedly different resistome communities and identified other environmental and demographic characteristics to be associated with univariate differences in infant ARG composition. When controlling for the race of the mother, infant diet, and infant antibiotic exposure since birth, delivery by cesarean section was associated with increased diversity of ARG relative to the diversity of ARG in the samples from vaginally born infants. Cesarean-born infants had increased richness of aminoglycoside ARG and increased diversity of beta-lactamase and tetracycline ARG relative to vaginally born infants. Furthermore, infants consuming any formula had increased overall richness and diversity of ARG in multivariate analyses. This study provides further insight into how diet and method of delivery are associated with resistome composition within the first 3 months of infant microbiome development.<b>IMPORTANCE</b>Pregnancy and the first 3 months of life are vulnerable periods for antibiotic exposure and subsequent development of antimicrobial resistance (AMR). AMR is an increasingly worrisome problem for global public health. The full repertoire of AMR genes present in the gut collectively is referred to as the resistome. Herein, the associations between a variety of demographic and environmental factors, including race of the pregnant women, sex of the infant, mode of delivery, amount of breast milk consumed in infant diet, and antibiotic exposure during the first 3 months of life, with resistome composition are reported. Infants consuming any formula had a greater richness and diversity of ARG overall, and cesarean-born infants had greater diversity of ARG within their resistomes. These findings give insight into the early seeding of the infant resistome, which is crucial to understanding how the resistome develops throughout life.