Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements

• Published in: Nature communications Vol. 9; no. 1; pp. 3891 - 11
• Main Authors: Pärnänen, Katariina, Karkman, Antti, Hultman, Jenni, Lyra, Christina, Bengtsson-Palme, Johan, Larsson, D. G. Joakim, Rautava, Samuli, Isolauri, Erika, Salminen, Seppo, Kumar, Himanshu, Satokari, Reetta, Virta, Marko
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 24-09-2018; Nature Publishing Group; Nature Portfolio
• Subjects: 1st year; 45/23; 631/114; 631/326; Abundance; Adults; alignment; Anti-Bacterial Agents - adverse effects; Antibiotic Prophylaxis - adverse effects; Antibiotic resistance; Antibiotics; association; Babies; Baby foods; Breast; Breast Feeding; Breast milk; Breastfeeding & lactation; Community composition; Composition; diversity; Drug Resistance, Bacterial - genetics; Feces - microbiology; Female; Gastrointestinal Microbiome - drug effects; Gastrointestinal Microbiome - genetics; Genes; Humanities and Social Sciences; Humans; identification; Infant; Infants; Infectious Medicine; Infektionsmedicin; Interspersed Repetitive Sequences - genetics; Intestinal microflora; Load resistance; Maternal Inheritance; Metagenomics; Microbiomes; Microbiota; Microorganisms; Milk; Milk, Human - microbiology; multidisciplinary; necrotizing enterocolitis; Phylogeny; preterm infants; Prophylaxis; read; resistance genes; ribosomal-rna; Science; Science (multidisciplinary); Time Factors
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-06393-w

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.
The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) even in the absence of antibiotic exposure. Here, Pärnänen et al. analyse breast milk as well as infant and maternal gut microbiomes, and show that some of the infant gut ARGs are transferred from the mothers.