Differential Responses of the Gut Microbiome and Resistome to Antibiotic Exposures in Infants and Adults

Abstract

Despite their crucial importance for human health, little is known about how the gut resistome changes with age or in response to antibiotic treatment across ages. Here, we used fecal metagenomic data from Danish infants and young adults to fill this gap. The gut resistomes were characterized by a bimodal distribution driven by E. coli composition. The typical profile of the gut resistome differed significantly between adults and infants, with the latter distinguished by higher gene and plasmid abundances. However, the predominant antibiotic resistance genes (ARGs) were the same. Antibiotic treatment reduced bacterial diversity and increased ARG and plasmid abundances in both cohorts, especially core ARGs. The effects of antibiotic treatments on the gut microbiome lasted longer in adults than in infants, and different antibiotics were associated with distinct impacts. Overall, this study broadens our current understanding of gut resistome dynamics and the impact of antibiotic treatment across age groups.

Note:
Funding Information: This research has been funded by Novo Nordisk Foundation Grant no. NNF19OC0057934598, Novo Nordisk Foundation Grant no. NNF17OC0025014 and Research Council of Norway project no. 300489.

Declaration of Interests: The authors declare no competing interests.

Ethics Approval Statement: The study was designed with the guiding principles of the Declaration of Helsinki in mind and was approved by the Local Ethics Committee of the Danish Capital Region (COPSAC2000: KF 01-289/96, COPSAC2010: (H-B-2008-093)) and the Danish Data Protection Authority (both cohorts: 2015-41-3696).

Keywords: Gut microbiome·antibiotics·different ages·duration·antibiotics resistance genes·E. coli·distribution diversity·infants·adults