Corporate Banner
Satellite Banner
Next Gen Sequencing
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

Foodborne Pathogen Detection Speeds Up Dramatically

Published: Monday, July 21, 2014
Last Updated: Monday, July 21, 2014
Bookmark and Share
Next-generation sequencing techniques allow rapidly identification of strains of salmonella, quickening responses to potential outbreaks.

New York is on the front lines of detecting foodborne pathogen outbreaks, thanks to a partnership between public health scientists and Cornell researchers.

Members of the Cornell Food Safety Lab, led by food science professor Martin Wiedmann and research associate Henk den Bakker, are helping the New York State Department of Health (NYSDOH) harness the capabilities and cost efficiencies of next-generation DNA sequencing techniques to rapidly identify strains of salmonella and read the results in a way that could quicken responses to potential outbreaks.

Traditional methods of assessing bacteria samples submitted to public health laboratories, based on pulsed-field gel electrophoresis (PFGE), often do not deliver the level of precision needed to pinpoint specific strains of pathogens, their relationships to each other and whether they share a common origin – vital information when trying to trace the source of illness outbreaks.

For Salmonella enterica serovar Enteritidis, for instance, 85 percent of isolates can be classified into just five PFGE types, and 40 percent belong to one subtype in particular.

“There’s so little variation in the genome, and when there’s an outbreak, it’s almost impossible to differentiate using that method,” den Bakker said.

By sequencing all 4.5 million base pairs of the bacteria’s DNA using single nucleotide polymorphisms (SNPS) in a technique known as rapid whole-genome sequencing, scientists are able to get much more nuanced information.

“This kind of detailed information improves our ability to tell whether outbreaks are isolated, sporadic or part of a cluster, which allows for more thorough epidemiologic investigations,” said NYSDOH collaborator William J. Wolfgang.

The introduction of small, affordable, bench-top, whole-genome sequencing equipment has made it possible for clinical and public health labs to consider adding the technology to their arsenal. The NYSDOH’s Wadsworth Center in Albany, New York, was one of the first public health labs to make the investment – Cornell was able to provide the bioinformatics expertise to enable the lab to make sense of the data it would be collecting and to analyze it quickly.

Their proof of concept was published July 16 in the Centers of Disease Control journal Emerging Infectious Diseases in a paper that uses a case study of a salmonella outbreak in a long-term care facility to demonstrate how the technique could benefit public health labs.

In a regional collaboration, samples collected by the Connecticut Department of Public Health were sequenced by NYSDOH and analyzed by Cornell, and researchers discovered the outbreak was even larger than suspected. In addition to the seven residents identified in 2010 as being sickened in the outbreak, nine additional samples from patients in surrounding communities matched the main strain.

“This suggests a common contaminated source outside the long-term care facility. Knowledge of these cases at the time of the outbreak might have improved the chances of finding the outbreak source, which was never identified,” the researchers wrote in the paper.

The technique is already gaining traction in several other states through the GenomeTrakr initiative sponsored by the U.S. Food and Drug Administration (FDA), which is providing sequencing equipment, reagents, funds for personnel, and training on the equipment to seven State Public Health Laboratories including New York. In return, the public health labs upload raw sequence data to a centralized site for analysis. Any clusters that appear are reported back to local labs and epidemiologists, allowing for a quick, coordinated response.

The study was partly funded by a grant from the USDA Agriculture and Food Research Initiative, the Center for Food Safety and Applied Nutrition at the FDA and the NYSDOH Wadsworth Center).


Further Information

Join For Free

Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 3,200+ scientific posters on ePosters
  • More than 4,700+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Genome Offers Clues to Amphibian-Killing Fungus
A fungus that has decimated amphibians globally is much older than previously thought.
Thursday, May 30, 2013
New DNA Cattle Test Beefs up Dairy and Meat Quality
A genomics technique developed at Cornell to improve corn can now be used to improve the quality of milk and meat.
Wednesday, May 22, 2013
Studies on Domesticated Maize Identify Genes that Evolved from Wild Ancestors
Studies identify genes that played a role in corn domestication as well as variations and similarities between domesticated maize and its wild relatives.
Wednesday, June 06, 2012
Scientific News
Four Newly-Identified Genes Could Improve Rice
A Japanese research team have applied a method used in human genetic analysis to rice and rapidly discovered four new genes that are potentially significant for agriculture. These findings could influence crop breeding and help combat food shortages caused by a growing population.
What Makes a Good Scientist?
It’s the journey, not just the destination that counts as a scientist when conducting research.
Biomarkers That Could Help Give Cancer Patients Better Survival Estimates Discovered
UCLA research may also help scientists suppress dangerous genetic sequences.
Mobile Laboratories Help Track Zika Spread Across Brazil
Researchers from the University of Birmingham are working with health partners in Brazil to combat the spread of Zika virus by deploying a pair of mobile DNA sequencing laboratories on a medical ‘road trip’ through the worst-hit areas of the country.
How “Silent” Genetic Changes Drive Cancer
The researchers found that EXOSC2 expression is enhanced in metastatic tumors because their cells have increased levels of a tRNA called GluUUC.
‘Jumping Gene’ Took Peppered Moths To The Dark Side
Researchers from the University of Liverpool have identified and dated the genetic mutation that gave rise to the black form of the peppered moth, which spread rapidly during Britain’s Industrial Revolution.
Benchtop Automation Trends
Gain a better understanding of current interest in and future deployment of benchtop automated systems.
How Did The Giraffe Get Its Long Neck?
Clues about the evolution of the giraffe’s long neck have now been revealed by new genome sequencing.
Big Data Can Save Lives
The sharing of genetic information from millions of cancer patients around the world could be key to revolutionising cancer prevention and care, according to a leading cancer expert from Queen's University Belfast.
Making Genetic Data Easier to Search
Scripps team streamlines biomedical research by making genetic data easier to search.
Skyscraper Banner

SELECTBIO Market Reports
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
3,200+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,700+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!