Dynamics of gut resistome and mobilome in early life: a meta-analysis
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- dc.contributor.author Bargheet, Ahmed
- dc.contributor.author Noordzij, Hanna Theodora
- dc.contributor.author Ponsero, Alise
- dc.contributor.author Jian, Ching
- dc.contributor.author Korpela, Katri
- dc.contributor.author Vallès Colomer, Mireia
- dc.contributor.author Debelius, Justine
- dc.contributor.author Kurilshikov, Alexander
- dc.contributor.author Pettersen, Veronika Kuchařová
- dc.date.accessioned 2025-05-06T06:15:46Z
- dc.date.available 2025-05-06T06:15:46Z
- dc.date.issued 2025
- dc.description.abstract Background: The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut. Methods: We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers. Findings: We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E. coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults. Interpretation: Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow. Funding: Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Tromsø Research Foundation, Norway.
- dc.format.mimetype application/pdf
- dc.identifier.citation Bargheet A, Noordzij HT, Ponsero AJ, Jian C, Korpela K, Valles-Colomer M, et al. Dynamics of gut resistome and mobilome in early life: a meta-analysis. EBioMedicine. 2025 Mar 5;114:105630. DOI: 10.1016/j.ebiom.2025.105630
- dc.identifier.doi http://dx.doi.org/10.1016/j.ebiom.2025.105630
- dc.identifier.issn 2352-3964
- dc.identifier.uri http://hdl.handle.net/10230/70304
- dc.language.iso eng
- dc.publisher Elsevier
- dc.relation.ispartof EBioMedicine. 2025 Mar 5;114:105630
- dc.rights © 2025 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/
- dc.subject.keyword Bacterial drug resistance
- dc.subject.keyword Cohort studies
- dc.subject.keyword Escherichia coli
- dc.subject.keyword Gut microbiota
- dc.subject.keyword Infant
- dc.subject.keyword Meta-analysis
- dc.subject.keyword Metagenomics
- dc.subject.keyword Mobile genetic elements
- dc.subject.keyword Plasmids
- dc.title Dynamics of gut resistome and mobilome in early life: a meta-analysis
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion