From: The eUpdate, 12.6.2011
Genome Testing Pinpoints Pathogens
New method is more accurate than standard PFGE testing
A new genomic test from Cornell University scientists can accurately detect the pathogenic culprit in outbreaks of foodborne illness and rapidly differentiate between outbreak-related and non-outbreak-related cases.
— Martin Wiedmann, DVM, PhD, Cornell University
We’ll get more complicated answers than we did with PFGE, but if we can use this technology right, we’ll make better decisions and improve food safety.
A team led by Cornell food science professor Martin Wiedmann, DVM, PhD, sequenced the genome of 47 samples of Salmonella—20 that had been collected from human sources during the Salmonella Montevideo outbreak linked to salami made with contaminated pepper in 2009 and 2010, and 27 control samples collected before the outbreak. The genome-sequencing approach quickly isolated four samples thought to be connected to the contaminated pepper.
Genome “fingerprinting” can better discriminate between serotypes of pathogens like Salmonella than standard pulsed-field gel electrophoresis (PFGE) testing, said Dr. Wiedmann. “Salmonella has more than 2,400 serotypes, and some have very few differentiating characteristics. If you have the same PFGE patterns in different outbreaks—in isolates from different farms, different foods, different fields—a match becomes relatively meaningless.”
But full genome sequencing can pinpoint more subtle differences than can be seen using PFGE. And, as with human genome sequencing, the cost is coming down. “We will probably soon be able to sequence a bacterial genome for less than $100,” Dr. Wiedmann said. “The challenge remains data analysis and interpretation.”
Genomic analysis of a pathogen doesn’t work the same way as DNA analysis on TV crime shows, Dr. Wiedmann explained. “With that, it’s individual. It tells us that the hair found on the body is Martin’s hair, so he touched the body. Genomic fingerprinting is more like ancestry testing. We’re not looking for something that’s identical, but did that Salmonella have a common grandmother within 20 generations vs. 500 generations ago? This will allow epidemiologists to find the strongest links to outbreak sources.”
Tools like this will require a paradigm shift, Dr. Wiedmann said. “We’ll get more complicated answers than we did with PFGE, but if we can use this technology right, we’ll make better decisions and improve food safety.”
(The research appears in the October 2011 edition of Applied and Environmental Microbiology.)