Antibiotic Treatment Drives the Diversification of the Human Gut Resistome.
10.1016/j.gpb.2018.12.003
- Author:
Jun LI
1
,
2
;
Elizabeth A RETTEDAL
3
;
Eric VAN DER HELM
3
;
Mostafa ELLABAAN
3
;
Gianni PANAGIOTOU
4
,
5
,
6
;
Morten O A SOMMER
7
Author Information
1. Department of Infectious Diseases and Public Health, Colleague of Veterinary Medicine and Life Sciences, City Univerity of Hong Kong, Hong Kong Special Administrative Region, China
2. School of Data Science, City Univerity of Hong Kong, Hong Kong Special Administrative Region, China.
3. Novo Nordisk Foundation Center for Biosustainability, DK-2900 Hørsholm, Denmark.
4. Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena, Germany
5. Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China
6. Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. Electronic address: gianni.panagiotou@leibniz-hki.de.
7. Novo Nordisk Foundation Center for Biosustainability, DK-2900 Hørsholm, Denmark. Electronic address: msom@bio.dtu.dk.
- Publication Type:Journal Article
- Keywords:
Antibiotics;
Evolution;
Gut microbiome;
Horizontal gene transfer;
Resistome;
Strain
- MeSH:
Adult;
Anti-Bacterial Agents;
pharmacology;
Bacteria;
genetics;
isolation & purification;
Drug Resistance, Bacterial;
genetics;
Female;
Gastrointestinal Microbiome;
drug effects;
Humans;
Metagenomics;
Prospective Studies
- From:
Genomics, Proteomics & Bioinformatics
2019;17(1):39-51
- CountryChina
- Language:English
-
Abstract:
Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.
