Metagenomics, Infectious Disease Diagnostics, and Outbreak Investigations Sequence First, Ask Questions Later?

JAMA The Journal of the American Medical Association (Impact Factor: 35.29). 04/2013; 309(14):1531-2. DOI: 10.1001/jama.2013.3678
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    • "Despite the successes described above, the application of metagenomics to laboratory-based diagnostics is still in its infancy (Table 4). A recent study using metagenomics to investigate diarrhea samples that were positive for Shiga-Toxigenic E. coli showed a sensitivity of only 67% compared to culture [12,78], implying that further advances are necessary if metagenomics is to replace traditional culture-based and molecular diagnostics. However, the same study demonstrated metagenomics’ utility in identifying ‘unknown unknowns’, with the authors able to identify co-infections that were not detected by conventional testing. "
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    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.
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  • JAMA The Journal of the American Medical Association 04/2013; 309(14):1522-4. DOI:10.1001/jama.2013.3818 · 35.29 Impact Factor
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    ABSTRACT: In the twenty-first century, the clinical microbiology laboratory plays a central part in optimizing the management of infectious diseases and surveying local and global epidemiology. This pivotal role is made possible by the adoption of rational sampling, point-of-care tests, extended automation and new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and versatile and permissive culture systems. When balanced with cost, these developments can improve the workflow and output of clinical microbiology laboratories and, by identifying and characterizing microbial pathogens, provide significant input to scientific discovery.
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