Protecting families from contaminated food and water
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Protecting families from contaminated food and water
Posted in Food Safety,Our Blog,Salmonella on May 28, 2025
Whole genome sequencing can detect Salmonella faster than traditional culture methods. Especially at lower concentrations. Could the “gold standard” of culture identification finally take a back seat to a genetic approach to detect Salmonella in environmental samples?
Scientists with the U.S. Department of Agriculture (USDA) Agricultural Research Service believe so. Their study was published in Microoganisms earlier this year. Their findings could change the way egg manufacturers detect Salmonella on contact surfaces.
Each year, around 153 million cases of gastrointestinal illness are caused by Salmonella acquired from food. This accounts for approximately 57,000 deaths worldwide. Economic losses in the U.S. add up to $17 billion.
In the United States, Salmonella is the second most common germs associated with foodborne outbreaks, and the primary concern in the poultry and egg industry.
Egg processing equipment is particularly vulnerable to Salmonella contamination. Conveyor belts, floor drains, and wash tanks are not only susceptible to Salmonella contamination and growth.
But they are also prone to forming a protecting biofilm – a structure made up of proteins, sugars, fats, and other germs. This biofilm protects the germ from sanitation efforts and helps it grow to infectious numbers. It happens quickly too!
According to the study, “irreversible Salmonella attachment to surfaces can take from 20 min to 4 h, after which biofilm formation may occur.”
Several different types of removal methods have been invented to combat these germs and their biofilms.
Sanitizers, cold plasma, UV, and ultrasound to name a few.
One of the main reasons for attempting to detect Salmonella on equipment is that early and accurate detection of Salmonella on surfaces before biofilms are formed” allow for effective intervention before contamination spreads to other areas or food products.
A previous study aimed to detect Salmonella bacteria on commercial poultry plant equipment at various steps in the sanitation process. They found that 36% of the equipment samples contained Salmonella after poultry processing. This percentage dropped to 12% after cleaning. But 9% of the samples were still positive for Salmonella bacteria after sanitation. This can lead to serious cross-contamination and food safety risk.
So how do poultry manufacturers ensure that their sanitation efforts are successful? They cannot just shut down the processing line for the days it would take for a culture test to show growth.
Faster confirmation that all production surfaces are free from contamination is certainly better.
Enter Whole Genome Sequencing or WGS.
WGS is a technology that analyzes the DNA of an organism. All organisms (including plants, animals, and bacteria) contain DNA. Within that DNA is a genetic code comprised of nucleotide bases.
The sequence that these bases line up in are specific to each organism.
We call this a “genetic fingerprint.”
Slight changes (or mutations) can even characterize related germs. For example, there could be very minor differences in a Salmonella bacteria identified in an outbreak that set it apart from other Salmonella bacteria. Making this technology excellent for tracking down sources of foodborne illness outbreak.
We have been using WGS for quite some time for diagnostic purposes.
So, how does this technology apply to the poultry industry’s ability to detect Salmonella for sanitation purposes?
Using WGS to detect Salmonella is a much faster and more sensitive method to detect Salmonella than other methods.
Historically, plating samples on a culture medium to see if it grows has been fairly standard in the industry. This can take at least 24 hours (sometimes even 48 hours) before results are available. Sensitivity is also limited in this method.
Immunological assays have been a proven method to detect Salmonella in a variety of foods. But this method is quite time consuming. It can take up to three days for results.
Certain biosensor and Raman spectroscopy techniques are very temperamental and generally require a laboratory setting to perform. Very specific antibodies and aptamers must be used to detect a specific germ. Consequently, sensitivity isn’t all that great.
Nucleic acid-based assays often have the highest sensitivity. But they are very specific to the germ you are looking for. Often requiring multiple tests to screen for different organisms.
USDA scientists analyzed the usefulness of long-read WGS technology, an analytical method that has advanced significantly in the past decade, to detect Salmonella in poultry manufacturing samples.
These “nanopore-based sequencers are small and portable, which allows for testing outside of traditional laboratory settings.” WIN!
This type of sequencing is super sensitive, meaning that it doesn’t take much DNA to achieve a detectable amount. WIN-WIN!
Nanopore-based WGS is fast! Results can be available in a little as a few hours. WIN-WIN-WIN!
I think we have a winner!
But does it work on the materials used in poultry and egg processing?
In the paper, Rapid Detection of Salmonella Typhimurium During Cell Attachment on Three Food-Contact Surfaces Using Long-Read Sequencing, USDA scientists put that theory to the test.
Scientists formed the study to identify Salmonella contamination within five hours of cell attachment to three common food-contact surfaces. In this case, they selected stainless steel, silicone, and nylon. They compared the long-read WGS to the traditional culture method.
Silicone was the worst offender, with the greatest number of Salmonella bacteria attached, followed by stainless steel. (In case you were thinking about making changes to your home kitchen appliances and utensils.)
Salmonella was detectable in as little as one hour from sample incubation.
When it comes to diagnostic tests, that is fast!
With this knowledge, it seems like a no-brainer for poultry manufacturers to begin incorporating these tests in-house to better manage contamination risk at their facilities. But how long will it actually take for these companies to take that leap?
It depends.
Larger manufacturers may have the capital to acquire the equipment to perform this type of test. Smaller operations will likely continue to rely on slower culture methods.
But who knows. Peace of mind, after all, is quite valuable.
If you’d like to know more about food safety topics in the news, like “New Use for Existing Technology to Detect Salmonella May Make Eggs Safer,” check out the Make Food Safe Blog. We regularly update trending topics, foodborne infections in the news, recalls, and more! Stay tuned for quality information to help keep your family safe, while The Lange Law Firm, PLLC strives to Make Food Safe!
By: Heather Van Tassell (contributing writer, non-lawyer)