Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Georgia Tech develops software for the rapid analysis of foodborne pathogens

14.02.2012
Tool can help save lives by quickly tracing origins

2011 brought two of the deadliest bacterial outbreaks the world has seen during the last 25 years. The two epidemics accounted for more than 4,200 cases of infectious disease and 80 deaths. Software developed at Georgia Tech was used to help characterize the bacteria that caused each outbreak. This helps scientists to better understand the underlying microbiologic features of the disease-causing organisms and shows promise for supporting faster and more efficient outbreak investigations in the future.

From 2008 to 2010, a team of bioinformatics graduate students, led by School of Biology Associate Professor King Jordan, worked in close collaboration with the Centers for Disease Control and Prevention (CDC) to create an integrated suite of computational tools for the analysis of microbial genome sequences. At that time, CDC scientists were in need of a fast and accurate system that could automate the analysis of sequenced genomes from disease-causing bacteria. They turned to the Jordan lab at Georgia Tech to help develop such a tool. The Georgia Tech scientists created an open source software package, the Computational Genomics Pipeline (CG-pipeline), to help meet CDC’s need. The software platform is now used worldwide in public health research and response efforts.

“Determining the order of DNA bases for an entire genome has become relatively cheap and easy in recent years because of technological advancements,” said Jordan. “The hard part is figuring out what the genome sequence information means. Our software takes that next step. It analyzes the sequences, finds the genes and provides clues as to which genes are involved in making people sick. Manually, this process used to take weeks, months or a year. Now it takes us about 24 hours.”

The CG-pipeline software has been used to analyze last summer’s outbreak of severe Escherichia coli (E. coli) infections that started in Germany and eventually led to illnesses in 16 European countries, Canada and the United States. It was one of the largest E. coli outbreaks in history, causing 50 deaths and 4,075 confirmed worldwide cases. The bacterium was traced to sprouts. Andrey Kislyuk, a graduate of the Bioinformatics Ph.D. program who helped Jordan create the software, used the CG-pipeline while working at Pacific Biosciences to understand why the strain of the bacteria that caused the outbreak was so virulent.

“The software was used to determine that genetic material from two previously distinct strains of E. coli was combined in a new, hyper-virulent strain,” said Kislyuk. “The resulting hybrid strain seems to be more lethal than either of the parent strains.”

Another Bioinformatics Ph.D. graduate who helped design and implement the pipeline, Lee Katz, analyzed the bacteria that caused last year’s outbreak of listeriosis in the United States while working at the CDC. That outbreak was traced back to cantaloupes from a single farm in Colorado that were tainted with Listeria. Over the span of several months, there were 146 confirmed cases of listeriosis and 30 deaths, making it the deadliest outbreak of foodborne illness in the U.S. in 25 years. Using the CG-pipeline, Katz was able to identify an important epidemiological genomic marker, which will help track invasive strains of Listeria.

The CG-pipeline software platform can be used to analyze any microbial genome sequence. It has already been applied to bacteria that cause a variety of infectious diseases, including cholera, salmonella and bacterial meningitis.

Katz continues to work closely with the Jordan lab to improve the software. This collaboration is important in CDC’s efforts to mine genome sequence information in the service of public health using software developed at Georgia Tech.

Jason Maderer | EurekAlert!
Further information:
http://www.gatech.edu

More articles from Life Sciences:

nachricht Repairing damaged hearts with self-healing heart cells
22.08.2017 | National University Health System

nachricht Biochemical 'fingerprints' reveal diabetes progression
22.08.2017 | Umea University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

Cholesterol-lowering drugs may fight infectious disease

22.08.2017 | Health and Medicine

Meter-sized single-crystal graphene growth becomes possible

22.08.2017 | Materials Sciences

Repairing damaged hearts with self-healing heart cells

22.08.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>