Abstract
The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk, as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element (MGE) profiles of infants are more similar to those of their own mothers than to those of unrelated mothers. MGEs in mothers’ breast milk are also shared with their own infants. Termination of breastfeeding and intrapartum antibiotic prophylaxis of mothers, which have the potential to affect microbial community composition, are associated with higher abundances of specific ARGs, the composition of which is largely shaped by bacterial phylogeny in the infant gut. Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes, but microbiota composition still strongly impacts the overall resistance load.
Highlights
The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure
The diversity of the mobile genetic element (MGE) and ARGs did not significantly differ between the two groups despite that the taxonomic diversity was significantly lower in infants (p < 0.05, analysis of variance (ANOVA) and Tukey’s post hoc test, Fig. 1a, b and Supplementary Fig. 1, Supplementary Tables 3–6)
The high abundance of MGEs may cause health risks as it is likely that resistance genes associated with MGEs are more likely to be transferred from commensal bacteria to pathogens[37]
Summary
The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. We assessed whether mothers’ gut and breast milk microbiota influence the infant gut resistome and MGEs during the first 6 months of life by quantifying sharing of genes and bacteria between mothers and infants. This was done using deep metagenomic sequencing of 16 mother-infant pairs over a period of 8 months, totaling in 96 breast milk or fecal samples of which half overlapped by sampling time (Supplementary Data 1–3). The results suggest that mothers contribute to the infant gut microbiota’s resistome and mobilome development by sharing genes from their gut and breast milk bacteria
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