The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition

• Published in: Cell host & microbe 2021-06, Vol.29 (6), p.975-987.e4
• Main Authors: Li, Xuanji, Stokholm, Jakob, Brejnrod, Asker, Vestergaard, Gisle Alberg, Russel, Jakob, Trivedi, Urvish, Thorsen, Jonathan, Gupta, Shashank, Hjelmsø, Mathis Hjort, Shah, Shiraz A., Rasmussen, Morten Arendt, Bisgaard, Hans, Sørensen, Søren Johannes
• Format: Article
• Language: English
• Subjects: antibiotic resistance genes; antibiotics; asthma-associated bacterial composition; E. coli; environmental exposure; gut bacterial maturity; gut microbiome; gut resistome; health risk; infant
• ISSN: 1931-3128; 1934-6069
• DOI: 10.1016/j.chom.2021.03.017

Antimicrobial resistance (AMR) is an accelerating global threat, yet the nature of AMR in the gut microbiome and how AMR is acquired during early life remain largely unknown. In a cohort of 662 Danish children, we characterized the antibiotic resistance genes (ARGs) acquired during the first year of life and assessed the impacts of diverse environmental exposures on ARG load. Our study reveals a clear bimodal distribution of ARG richness that is driven by the composition of the gut microbiome, especially E. coli. ARG profiles were significantly affected by various environmental factors. Among these factors, the importance of antibiotics diminished with time since treatment. Finally, ARG load and ARG clusters were also associated with the maturity of the gut microbiome and a bacterial composition associated with increased risk of asthma. These findings broaden our understanding of AMR in early life and have critical implications for efforts to mitigate its spread. [Display omitted] •Distribution of infant gut resistome is bimodal, mainly driven by E. coli•The infant gut resistome is significantly affected by environmental factors•Low maturity of microbiome associates with high ARG load•A similar asthma-associated gut bacterial composition associates with high ARG load In this comprehensive analysis of antibiotic resistance genes (ARGs) distribution in the infant gut, Li et al. show that E. coli is an extremely important reservoir of ARGs. They also reveal associations between infant gut resistome and environmental factors, gut microbiome maturation, and bacteria associated with later development of asthma.