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Review

Metagenomics for pathogen detection in public health

Ruth R Miller1, Vincent Montoya2, Jennifer L Gardy1, David M Patrick1 and Patrick Tang23*

Author Affiliations

1 UBC School of Population and Public Health, Faculty of Medicine, University of British Columbia, 2206 East Mall, Vancouver, BC V6T 1Z3, Canada

2 Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada

3 Public Health Microbiology and Reference Laboratory, British Columbia Centre for Disease Control, 655 West 12th Avenue, Vancouver, BC V5Z 2B4, Canada

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Genome Medicine 2013, 5:81  doi:10.1186/gm485

Published: 20 September 2013

Abstract

Traditional pathogen detection methods in public health infectious disease surveillance rely upon the identification of agents that are already known to be associated with a particular clinical syndrome. The emerging field of metagenomics has the potential to revolutionize pathogen detection in public health laboratories by allowing the simultaneous detection of all microorganisms in a clinical sample, without a priori knowledge of their identities, through the use of next-generation DNA sequencing. A single metagenomics analysis has the potential to detect rare and novel pathogens, and to uncover the role of dysbiotic microbiomes in infectious and chronic human disease. Making use of advances in sequencing platforms and bioinformatics tools, recent studies have shown that metagenomics can even determine the whole-genome sequences of pathogens, allowing inferences about antibiotic resistance, virulence, evolution and transmission to be made. We are entering an era in which more novel infectious diseases will be identified through metagenomics-based methods than through traditional laboratory methods. The impetus is now on public health laboratories to integrate metagenomics techniques into their diagnostic arsenals.