Using metagenomics to investigate human and environmental resistomes - PubMed (original) (raw)

Review

. 2017 Oct 1;72(10):2690-2703.

doi: 10.1093/jac/dkx199.

Affiliations

• PMID: 28673041
• DOI: 10.1093/jac/dkx199

Review

Using metagenomics to investigate human and environmental resistomes

Johan Bengtsson-Palme et al. J Antimicrob Chemother. 2017.

Abstract

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.

© The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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