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Using metagenomics to investigate human and environmental resistomes.

Journal article
Authors Johan Bengtsson-Palme
D. G. Joakim Larsson
Erik Kristiansson
Published in The Journal of antimicrobial chemotherapy
Volume 72
Issue 10
Pages 2690-2703
ISSN 1460-2091
Publication year 2017
Published at Department of Mathematical Sciences, Applied Mathematics and Statistics
Centre for antibiotic resistance research, CARe
Institute of Biomedicine, Department of Infectious Medicine
Pages 2690-2703
Language en
Keywords antibiotic resistance, risk assessment, sequence analysis, metagenomics, resistance genes
Subject categories Bacteriology, Medical microbiology, Bioinformatics (Computational Biology)


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.

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