A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4

Nicholas J Loman; Chrystala Constantinidou; Martin Christner; Holger Rohde; Jacqueline Z-M Chan; Joshua Quick; Jacqueline C Weir; Christopher Quince; Geoffrey P Smith; Jason R Betley; Martin Aepfelbacher; Mark J Pallen

doi:10.1001/jama.2013.3231

A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4

Nicholas J Loman, Chrystala Constantinidou, Martin Christner, Holger Rohde, Jacqueline Z-M Chan, Joshua Quick, Jacqueline C Weir, Christopher Quince, Geoffrey P Smith, Jason R Betley, Martin Aepfelbacher, Mark J Pallen

Biosciences

Research output: Contribution to journal › Article › peer-review

194 Citations (Scopus)

Abstract

Identification of the bacterium responsible for an outbreak can aid in disease management. However, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain.

Original language	English
Pages (from-to)	1502-10
Number of pages	9
Journal	JAMA The Journal of the American Medical Association
Volume	309
Issue number	14
DOIs	https://doi.org/10.1001/jama.2013.3231
Publication status	Published - 10 Apr 2013

Keywords

Computational Biology
DNA, Bacterial
Diarrhea
Disease Outbreaks
Escherichia coli Infections
Feces
Humans
Metagenomics
Retrospective Studies
Sensitivity and Specificity
Sequence Analysis, DNA
Shiga Toxin
Shiga-Toxigenic Escherichia coli
Time Factors

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1001/jama.2013.3231

Development of robust analytical pipelines for the analysis of microbial community data from clinical samples
Loman, N. (Principal Investigator)
Medical Research Council
1/09/12 → 31/08/15
Project: Research Councils
Acinetobacter baumannii: genomic profiling of an emerging hospital pathogen
Pallen, M. (Principal Investigator) & Constantinidou, M. (Co-Investigator)
Medical Research Council
1/09/10 → 31/08/13
Project: Research Councils
xBASE: A bioinformatics resource for the AgriFood Bacteriology Community
Pallen, M. (Principal Investigator) & Stekel, D. (Co-Investigator)
Biotechnology & Biological Sciences Research Council
1/02/07 → 31/01/12
Project: Research Councils

Cite this

Loman, N. J., Constantinidou, C., Christner, M., Rohde, H., Chan, J. Z.-M., Quick, J., Weir, J. C., Quince, C., Smith, G. P., Betley, J. R., Aepfelbacher, M., & Pallen, M. J. (2013). A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA The Journal of the American Medical Association, 309(14), 1502-10. https://doi.org/10.1001/jama.2013.3231

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title = "A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4",

abstract = "Identification of the bacterium responsible for an outbreak can aid in disease management. However, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain.",

keywords = "Computational Biology, DNA, Bacterial, Diarrhea, Disease Outbreaks, Escherichia coli Infections, Feces, Humans, Metagenomics, Retrospective Studies, Sensitivity and Specificity, Sequence Analysis, DNA, Shiga Toxin, Shiga-Toxigenic Escherichia coli, Time Factors",

author = "Loman, {Nicholas J} and Chrystala Constantinidou and Martin Christner and Holger Rohde and Chan, {Jacqueline Z-M} and Joshua Quick and Weir, {Jacqueline C} and Christopher Quince and Smith, {Geoffrey P} and Betley, {Jason R} and Martin Aepfelbacher and Pallen, {Mark J}",

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day = "10",

doi = "10.1001/jama.2013.3231",

language = "English",

volume = "309",

pages = "1502--10",

journal = "JAMA The Journal of the American Medical Association",

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Loman, NJ, Constantinidou, C, Christner, M, Rohde, H, Chan, JZ-M, Quick, J, Weir, JC, Quince, C, Smith, GP, Betley, JR, Aepfelbacher, M & Pallen, MJ 2013, 'A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4', JAMA The Journal of the American Medical Association, vol. 309, no. 14, pp. 1502-10. https://doi.org/10.1001/jama.2013.3231

A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. / Loman, Nicholas J; Constantinidou, Chrystala; Christner, Martin et al.
In: JAMA The Journal of the American Medical Association, Vol. 309, No. 14, 10.04.2013, p. 1502-10.

Research output: Contribution to journal › Article › peer-review

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T1 - A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4

AU - Loman, Nicholas J

AU - Constantinidou, Chrystala

AU - Christner, Martin

AU - Rohde, Holger

AU - Chan, Jacqueline Z-M

AU - Quick, Joshua

AU - Weir, Jacqueline C

AU - Quince, Christopher

AU - Smith, Geoffrey P

AU - Betley, Jason R

AU - Aepfelbacher, Martin

AU - Pallen, Mark J

PY - 2013/4/10

Y1 - 2013/4/10

N2 - Identification of the bacterium responsible for an outbreak can aid in disease management. However, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain.

AB - Identification of the bacterium responsible for an outbreak can aid in disease management. However, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain.

KW - Computational Biology

KW - DNA, Bacterial

KW - Diarrhea

KW - Disease Outbreaks

KW - Escherichia coli Infections

KW - Feces

KW - Humans

KW - Metagenomics

KW - Retrospective Studies

KW - Sensitivity and Specificity

KW - Sequence Analysis, DNA

KW - Shiga Toxin

KW - Shiga-Toxigenic Escherichia coli

KW - Time Factors

U2 - 10.1001/jama.2013.3231

DO - 10.1001/jama.2013.3231

M3 - Article

C2 - 23571589

SN - 0098-7484

VL - 309

SP - 1502

EP - 1510

JO - JAMA The Journal of the American Medical Association

JF - JAMA The Journal of the American Medical Association

IS - 14

ER -

A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4

Abstract

Keywords

UN SDGs

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Projects

Development of robust analytical pipelines for the analysis of microbial community data from clinical samples

Acinetobacter baumannii: genomic profiling of an emerging hospital pathogen

xBASE: A bioinformatics resource for the AgriFood Bacteriology Community

Cite this