Using metagenomics to investigate human and environmental resistomes
Journal article, 2017

Antibiotic resistance is a global health concern declared by the WHO as one of the largest threats to modern healthcare. In recent years, metagenomic DNA sequencing has started to be applied as a tool to study antibiotic resistance in different environments, including the human microbiota. However, a multitude of methods exist for metagenomic data analysis, and not all methods are suitable for the investigation of resistance genes, particularly if the desired outcome is an assessment of risks to human health. In this review, we outline the current state of methods for sequence handling, mapping to databases of resistance genes, statistical analysis and metagenomic assembly. In addition, we provide an overview of important considerations related to the analysis of resistance genes, and recommend some of the currently used tools and methods that are best equipped to inform research and clinical practice related to antibiotic resistance.

Author

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[Person 6a268f42-44e8-4c30-a8a1-3586cee413d4 not found]

University of Gothenburg

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

Journal of Antimicrobial Chemotherapy

0305-7453 (ISSN) 1460-2091 (eISSN)

Vol. 72 10 2690-2703

Subject Categories

Microbiology

Areas of Advance

Life Science Engineering (2010-2018)

DOI

10.1093/jac/dkx199

PubMed

28673041

More information

Latest update

7/3/2018 7