Navigation Links
Scientists develop strategy to rapidly describe outbreak strains with next-generation DNA sequencing
Date:4/10/2008

Friday, April 11, 2008 In the event of an outbreak or a bioterrorist attack, rapid identification of the genetic changes responsible for virulence or drug resistance is essential to mounting an effective response. Standard DNA sequencing and analysis of a pathogen genome is time-intensive and likely impractical during an emergency. Researchers have now developed a comparative genomics strategy to drastically reduce the time needed to accurately identify unique genetic properties of a potential outbreak strain. This report, which demonstrates the approach using next-generation sequencing technology, is published online today in Genome Research (www.genome.org).

Sanger DNA sequencing, the established technology used to sequence the genomes of many species, including the genomes of humans and hundreds of bacteria, could potentially be used to sequence and analyze a new human pathogen. However, the time required for sequencing and subsequent analysis, or finishing, is such that this approach is not feasible when a rapid response to an outbreak or bioterrorist attack is required. New sequencing technologies are now available, allowing an entire bacterial genome to be sequenced in several hours, but time-intensive finishing steps are still required to determine the complete genome sequence.

In this study, researchers led by Drs. Bernard La Scola and Didier Raoult of the University of the Mediterranean set out to determine whether a rapidly sequenced incomplete genome could be used to quickly characterize an outbreak strain by comparative analysis. In the context of an outbreak, a quick approach may help to identify immediately the genetic determinants responsible for modified virulence or transmission, explains La Scola. The aim of this work was to evaluate the recently available automated pyrosequencing technology without finishing for this purpose.

F. tularensis, the causative pathogen of tularemia, is one of the most infectious bacteria known, and there is particular concern that this organism could be manipulated for use as a biological weapon. La Scola and colleagues sequenced a strain isolated from a tularemia patient using the Roche/454 Life Sciences GS20 sequencing system, and compared these sequences with several other strains of F. tularensis, including a strain with reduced pathogencity and an antiobiotic-resistant strain.

The researchers demonstrated that next-generation sequencing of a bacterial genome without finishing could be used to effectively identify several unique features of the F. tularensis clinical strain in a matter of weeks. By using this strategy, if there are a sufficient number of bioinformaticians working on the project, DNA extraction to complete analysis of the genome can take approximately 6 weeks, describes La Scola. We demonstrated that this strategy was efficient to detect gene polymorphisms such as a gene modification responsible for antibiotic resistance, and loss of genetic material. Furthermore, La Scola and colleagues were able to distinguish the clinical strain from 80 other strains of F. tularensis.

While high-throughput sequencing technology and the comparative genomic analysis strategy outlined in this work have significantly decreased the time required for characterization of an outbreak strain, La Scola notes that future advances in software for sequence data analysis and genome comparison could speed up the process even further.


'/>"/>

Contact: Peggy Calicchia
calicchi@cshl.org
516-422-4012
Cold Spring Harbor Laboratory
Source:Eurekalert

Related biology technology :

1. Gladstone scientists uncover potential mechanism of memory loss in Alzheimers disease
2. Three Studies by Independent Scientists Highlighting Pressure Cycling Technology (PCT) to be Presented this Week at the British Mass Spectrometry Societys 29th Annual Meeting
3. Social Network for Scientists Marks Ten Years Online
4. Scientists synthesize memory in yeast cells
5. Scientists synthesize memory in yeast cells
6. University of Leicester scientists discover technique to help friendly bacteria
7. Scientists discover how cancer may take hold
8. Yale scientists make 2 giant steps in advancement of quantum computing
9. New Scientists Boost Disease-based Research at Boston Biomedical Research Institute
10. Scientists say sabercat bit like a pussycat
11. New Corporate Website Launched - Focus on Life Scientists, Flow Cytometrists, & Clinicians
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:1/23/2017)... Calif. , Jan. 23, 2017  Alkahest ... innovative treatments for neurodegenerative diseases and other age-related ... joined the company as Chief Medical Officer. In ... and clinical development activities at Alkahest and serve ... Jackson most recently served as Executive Director at ...
(Date:1/21/2017)... ... ... Nipro Corporation (Osaka, Japan) and Transonic Systems Inc. (New York, USA) announced ... and sales rights for all non-OEM Transonic products in Japan. As partners for more ... Nipro - Transonic JV is a natural next step to advance best practices and ...
(Date:1/21/2017)... , Jan. 20, 2017 Aratana Therapeutics, Inc. ... focused on the licensing, development and commercialization of innovative ... Best Company in North America ... the award based on the FDA approval of ... tablets), ENTYCE ® (capromorelin oral solution) and NOCITA ...
(Date:1/20/2017)... Ginkgo Bioworks, the organism company, announced ... the synthesis and assembly of DNA. The acquisition ... synthetic DNA into Ginkgo,s automated organism engineering foundries, ... of new organism designs for application across a ... founded to significantly increase the world,s capacity to ...
Breaking Biology Technology:
(Date:1/11/2017)... NEW BRUNSWICK, N.J. , Jan. 11, 2017  Michael Johnson, ... from Foundation Venture Capital Group, Inc., has been named to the ... Johnson, 27,  was one of 600 people in 20 fields ... only four percent of the 15,000 applicants were selected. ... He is currently a PhD ...
(Date:1/4/2017)... 2017  CES 2017 – Valencell , the ... announced the launch of two new versions of ... biometric sensor modules that incorporate the best of ... expertise. The two new designs include Benchmark BE2.0, ... and Benchmark BW2.0, a 2-LED version of its ...
(Date:12/20/2016)... 2016   Valencell , the leading innovator ... STMicroelectronics (NYSE: STM), a global semiconductor leader serving ... today the launch of a new, highly accurate ... includes ST,s compact SensorTile turnkey multi-sensor ... sensor system. Together, SensorTile and Benchmark deliver the ...
Breaking Biology News(10 mins):