Challenges of the Unknown: Clinical Application of Microbial Metagenomics
Joint Authors
Rose, Graham
Wooldridge, David J.
Anscombe, Catherine
Mee, Edward T.
Misra, Raju V.
Gharbia, Saheer
Source
International Journal of Genomics
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-09-14
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
Availability of fast, high throughput and low cost whole genome sequencing holds great promise within public health microbiology, with applications ranging from outbreak detection and tracking transmission events to understanding the role played by microbial communities in health and disease.
Within clinical metagenomics, identifying microorganisms from a complex and host enriched background remains a central computational challenge.
As proof of principle, we sequenced two metagenomic samples, a known viral mixture of 25 human pathogens and an unknown complex biological model using benchtop technology.
The datasets were then analysed using a bioinformatic pipeline developed around recent fast classification methods.
A targeted approach was able to detect 20 of the viruses against a background of host contamination from multiple sources and bacterial contamination.
An alternative untargeted identification method was highly correlated with these classifications, and over 1,600 species were identified when applied to the complex biological model, including several species captured at over 50% genome coverage.
In summary, this study demonstrates the great potential of applying metagenomics within the clinical laboratory setting and that this can be achieved using infrastructure available to nondedicated sequencing centres.
American Psychological Association (APA)
Rose, Graham& Wooldridge, David J.& Anscombe, Catherine& Mee, Edward T.& Misra, Raju V.& Gharbia, Saheer. 2015. Challenges of the Unknown: Clinical Application of Microbial Metagenomics. International Journal of Genomics،Vol. 2015, no. 2015, pp.1-10.
https://search.emarefa.net/detail/BIM-1066008
Modern Language Association (MLA)
Rose, Graham…[et al.]. Challenges of the Unknown: Clinical Application of Microbial Metagenomics. International Journal of Genomics No. 2015 (2015), pp.1-10.
https://search.emarefa.net/detail/BIM-1066008
American Medical Association (AMA)
Rose, Graham& Wooldridge, David J.& Anscombe, Catherine& Mee, Edward T.& Misra, Raju V.& Gharbia, Saheer. Challenges of the Unknown: Clinical Application of Microbial Metagenomics. International Journal of Genomics. 2015. Vol. 2015, no. 2015, pp.1-10.
https://search.emarefa.net/detail/BIM-1066008
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1066008