Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples

Research output: Contribution to journalJournal article – Annual report year: 2018Researchpeer-review

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Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples. / Andersen, Sandra Christine; Hoorfar, Jeffrey.

In: Genes, Vol. 9, No. 1, 14, 2018.

Research output: Contribution to journalJournal article – Annual report year: 2018Researchpeer-review

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@article{12a628fab08c4316a6d0d49361c4e32e,
title = "Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples",
abstract = "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.",
keywords = "culture independent, fecal sample, shotgun metagenomics, next generation sequencing, Genetics, QH426-470",
author = "Andersen, {Sandra Christine} and Jeffrey Hoorfar",
year = "2018",
doi = "10.3390/genes9010014",
language = "English",
volume = "9",
journal = "Genes",
issn = "2073-4425",
publisher = "M D P I AG",
number = "1",

}

RIS

TY - JOUR

T1 - Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples

AU - Andersen, Sandra Christine

AU - Hoorfar, Jeffrey

PY - 2018

Y1 - 2018

N2 - 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.

AB - 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.

KW - culture independent

KW - fecal sample

KW - shotgun metagenomics

KW - next generation sequencing

KW - Genetics

KW - QH426-470

U2 - 10.3390/genes9010014

DO - 10.3390/genes9010014

M3 - Journal article

VL - 9

JO - Genes

JF - Genes

SN - 2073-4425

IS - 1

M1 - 14

ER -