Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Scientists develop strategy to rapidly describe outbreak strains with next-generation DNA sequencing

11.04.2008
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.

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.

Scientists from the University of the Mediterranean (Marseilles, France) contributed to this study.

This work was supported by Sanofi-Aventis France, Bayer Pharma, and the European Commission.

Media contacts:

Bernard La Scola, M.D., Ph.D. (bernard.lascola@medecine.univ-mrs.fr; +33-4-91385517) and Didier Raoult, M.D., Ph.D. (didier.raoult@medecine.univ-mrs.fr, +33-4-91385517) have agreed to be contacted for more information.

Interested reporters may obtain copies of the manuscript from Peggy Calicchia, Editorial Secretary, Genome Research (calicchi@cshl.org; +1-516-422-4012).

About the article:

The manuscript will be published online ahead of print on April 11, 2008. Its full citation is as follows: La Scola, B., Elkarkouri, K., Li, W., Wahab, T., Fournous, G., Rolain, J., Biswas, S., Drancourt, M., Robert, C., Audic, S., Löfdahl, S., and Raoult, D. Rapid comparative genomic analysis for clinical microbiology: The Francisella tularensis paradigm. Genome Res. doi:10.1101/gr.7126608.

About Genome Research:

Genome Research (www.genome.org) is an international, continuously published, peer-reviewed journal published by Cold Spring Harbor Laboratory Press. Launched in 1995, it is one of the five most highly cited primary research journals in genetics and genomics.

About Cold Spring Harbor Laboratory Press:

Cold Spring Harbor Laboratory Press is an internationally renowned publisher of books, journals, and electronic media, located on Long Island, New York. It is a division of Cold Spring Harbor Laboratory, an innovator in life science research and the education of scientists, students, and the public. For more information, visit www.cshlpress.com.

Genome Research issues press releases to highlight significant research studies that are published in the journal.

Peggy Calicchia | EurekAlert!
Further information:
http://www.cshl.org
http://www.genome.org

Further reports about: Comparative DNA Genetic Genom Genome Scola Strategy genomic outbreak required strain tularensis

More articles from Life Sciences:

nachricht Multi-institutional collaboration uncovers how molecular machines assemble
02.12.2016 | Salk Institute

nachricht Fertilized egg cells trigger and monitor loss of sperm’s epigenetic memory
02.12.2016 | IMBA - Institut für Molekulare Biotechnologie der Österreichischen Akademie der Wissenschaften GmbH

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

Im Focus: MADMAX: Max Planck Institute for Physics takes up axion research

The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.

The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...

Im Focus: Molecules change shape when wet

Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water

In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...

Im Focus: Fraunhofer ISE Develops Highly Compact, High Frequency DC/DC Converter for Aviation

The efficiency of power electronic systems is not solely dependent on electrical efficiency but also on weight, for example, in mobile systems. When the weight of relevant components and devices in airplanes, for instance, is reduced, fuel savings can be achieved and correspondingly greenhouse gas emissions decreased. New materials and components based on gallium nitride (GaN) can help to reduce weight and increase the efficiency. With these new materials, power electronic switches can be operated at higher switching frequency, resulting in higher power density and lower material costs.

Researchers at the Fraunhofer Institute for Solar Energy Systems ISE together with partners have investigated how these materials can be used to make power...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

UTSA study describes new minimally invasive device to treat cancer and other illnesses

02.12.2016 | Medical Engineering

Plasma-zapping process could yield trans fat-free soybean oil product

02.12.2016 | Agricultural and Forestry Science

What do Netflix, Google and planetary systems have in common?

02.12.2016 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>