oru.sePublikationer
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA
Addenbrookes Hosp, Clin Microbiol & Publ Hlth Lab, Hlth Protect Agcy, Cambridge, England..
Show others and affiliations
2013 (English)In: Nature Protocols, ISSN 1754-2189, E-ISSN 1750-2799, Vol. 8, no 12, 2404-2412 p.Article in journal (Refereed) Published
Abstract [en]

The study of bacterial populations using whole-genome sequencing is of considerable scientific and clinical interest. However, obtaining bacterial genomic information is not always trivial: the target bacteria may be difficult to culture or uncultured, and they may be found within samples containing complex mixtures of other contaminating microbes and/or host cells, from which it is very difficult to derive robust sequencing data. Here we describe our procedure to generate sufficient DNA for whole-genome sequencing from clinical samples and without the need for culture, as successfully used on the difficult-to-culture, obligate intracellular pathogen Chlamydia trachomatis. Our protocol combines immunomagnetic separation (IMS) for targeted bacterial enrichment with multiple displacement amplification (MDA) for whole-genome amplification (WGA), which is followed by high-throughput sequencing. Compared with other techniques that might be used to generate such data, IMS-MDA is an inexpensive, low-technology and highly transferable process that provides amplified genomic DNA for sequencing from target bacteria in under 5 h, with little hands-on time.

Place, publisher, year, edition, pages
Nature Publishing Group, 2013. Vol. 8, no 12, 2404-2412 p.
National Category
Cell and Molecular Biology
Identifiers
URN: urn:nbn:se:oru:diva-56735DOI: 10.1038/nprot.2013.147ISI: 000328125800007PubMedID: 24202554OAI: oai:DiVA.org:oru-56735DiVA: diva2:1083949
Available from: 2017-03-23 Created: 2017-03-23 Last updated: 2017-03-23Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Harris, Simon R.Unemo, MagnusClarke, Ian N.Parkhill, Julian
By organisation
Orebro University Hospital
In the same journal
Nature Protocols
Cell and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar

Altmetric score

Total: 2 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf