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You may read about "WGS" vs. "PFGE" in the context of outbreaks. Do you need to care?

Whole Genomes Sequencing represents a huge leap for identifying diseases in an outbreak.

 

WGS, or Whole Genome Sequencing, has become the gold standard for quickly identifying genetically matched diseases that define an outbreak. It’s a technological advance with huge implications and impact and its replacement of other methods as the go-to test for identifying matching bacterial DNA in an outbreak is groundbreaking.W

The CDC used to use PGFE to identify outbreaks.

In the past, the CDC and the 82 state and local agencies who used their lab data to track outbreaks, used a methodology called PFGE or Pulsed Field Gel Electrophoreses to identify outbreaks. 

 

WGS is a newer tool.

Recently, the newer methodology, WGS or Whole Genome Sequencing became another go-to tool in their toolkit. It allows epidemiologists to more quickly identify genetically matched lab results from patients and the CDC detect an outbreaks quicker and with greater certainty. Pulsenet is the molecular surveillance network for foodborne diseases in the US that gathers the information from the 82 agencies. Each of them processes their own lab specimens and then uploads their results to Pulsenet which is then analyzed by the CDC.

Source: CDC

 

What’s the difference between WGS and PFGE?

The best way to describe the difference in information gathered between WGS and PFGE is that with PFGE, they’re looking at 15-30 bars in a pattern. With WGS, they’re using literally millions of bars and comparing them to other outbreaks and their DNA patterns. It ‘s like looking at a few chapters of a book with PFGE vs. looking at every word in the book with WGS.

 

Why does it matter?

WGS is revolutionizing how quickly and accurately outbreaks are identified in the US; enabling contaminated products to be removed more quickly. It’s also been an effective tool for excluding restaurants and products from an investigation. If it doesn’t match, it doesn’t match. However, even a single match is statistically significant.

 

WGS is affordable, provides a high level of information and requires just one test and one scientist to run it. PFGE typically required four separate tests and two or more scientists. The ease of conducting WGS is part of what makes it cheaper and faster. It was first used to identify a Listeria outbreak in 2013 before the more recent wider usage.

 

For more info, good resources include: 

https://www.cdc.gov/pulsenet/pathogens/wgs.html

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5572858/

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