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Genes 2018, 9(1), 14;

Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples

National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark
Author to whom correspondence should be addressed.
Received: 6 November 2017 / Revised: 5 December 2017 / Accepted: 19 December 2017 / Published: 4 January 2018
(This article belongs to the Special Issue Genetics and Genomics of Foodborne Pathogens)
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Diagnostic metagenomics is a rapidly evolving laboratory tool for culture-independent tracing of foodborne pathogens. The method has the potential to become a generic platform for detection of most pathogens and many sample types. Today, however, it is still at an early and experimental stage. Studies show that metagenomic methods, from sample storage and DNA extraction to library preparation and shotgun sequencing, have a great influence on data output. To construct protocols that extract the complete metagenome but with minimal bias is an ongoing challenge. Many different software strategies for data analysis are being developed, and several studies applying diagnostic metagenomics to human clinical samples have been published, detecting, and sometimes, typing bacterial infections. It is possible to obtain a draft genome of the pathogen and to develop methods that can theoretically be applied in real-time. Finally, diagnostic metagenomics can theoretically be better geared than conventional methods to detect co-infections. The present review focuses on the current state of test development, as well as practical implementation of diagnostic metagenomics to trace foodborne bacterial infections in fecal samples from animals and humans. View Full-Text
Keywords: culture independent; fecal sample; shotgun metagenomics; next generation sequencing culture independent; fecal sample; shotgun metagenomics; next generation sequencing
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Andersen, S.C.; Hoorfar, J. Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples. Genes 2018, 9, 14.

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