Salmonella: genomics investment leads to faster, more accurate identification

Most Canadians have probably heard of Salmonella, and many have met the bacteria in person—Salmonella is one of the most common causes of food-borne illness in Canada and around the world.

The majority of Salmonella infections are the result of eating foods contaminated with the bacteria, and it can be found on almost any food—from meat and poultry to raw fruit and vegetables. That's why it's so important to follow safe food-handling practices at home. Salmonella can also be spread through contact with someone who has the infection, or infected animals, which may carry the bacteria even when healthy.

For most people, the symptoms of salmonellosis—diarrhea, fever, cramps—disappear after a few days, but in young children, seniors and others with weaker immune systems, Salmonella can cause serious, even fatal illness. The bacteria also carry an economic cost. On a global basis, medical expenses and lost productivity related to Salmonella are measured in the billions of dollars a year.

Containing outbreaks

Because of the risks to public and economic health, Salmonella infections are the subject of careful tracking by public health authorities, who work to identify the source of infection so food recalls or other steps can be taken to prevent it from spreading. Along with asking people who've been infected about where and what they ate, who and what they've been in contact with, confirming the source of an outbreak involves identifying the type of Salmonella that has infected people, and matching that to the suspected source.

As Dr. John Nash, Senior Research Scientist at the Public Health Agency of Canada (PHAC) explains, all this takes time. "Serotyping—the technology used to identify a type of Salmonella or other bacteria—has been around since the 1930s," says Dr. Nash. "It's slow, it's expensive, and it's very specialized—there are only two reference labs in Canada that have the resources to identify all of the different types of the Salmonella bacteria."

Faster, cheaper, easier and more acceptable

Seizing the opportunity genomics offers to improve on the "old ways," Dr. Nash and a colleague at the PHAC, Biologist Catherine Yoshida, have developed a new DNA-based test that reduces the time, cost and skills involved in identifying a particular type of Salmonella.

Mrs. Yoshida, who works at the PHAC National Microbiology Laboratory at Guelph, says the new method—genoserotyping—identifies the type of Salmonella in a sample in a single day, compared to four days using the traditional method. "Our method also cuts the cost of the test by 70 percent," says Mrs. Yoshida. "And it's also much simpler—almost any lab could do the test, so there's no need to be sending samples across the country for identification, making the process even faster."

"It also eliminates the need for animal testing," says Mrs. Yoshida, "That makes genoserotyping an even more attractive option."

Increasing accuracy

Dr. Nash, with the PHAC National Microbiology Laboratory at Toronto, says genoserotyping also makes for a more accurate test. "With serotyping, you identify bacteria from the outside, and the outside of a bacteria can change," says Dr. Nash. "We look at the inside—the DNA—and since DNA doesn't change, you can have a lot more confidence in your identification."

Along with the help of collaborators in the United Kingdom and Austria, funding from the Genomics Research and Development Initiative (GRDI) was key to the success of the project. "GRDI funding enabled us to build a database of DNA sequences from whole genome sequencing of a wide range of strains of Salmonella bacteria," says Mrs. Yoshida."A specialized reader identifies the DNA pattern of the sample we're testing and matches it to the known Salmonella patterns in the database."

Screening and surveillance

Dr. Nash says the lower cost and simplicity of the genoserotyping approach means the test can also be used by public health authorities for routine surveillance for Salmonella. "In fact, it's potential as a tool for surveillance or quality control is probably the most valuable part of this," says Dr. Nash. "If you run a poultry processing plant, for example, you could use this to do regular testing to check for Salmonella contamination, and identify and address a small problem before it becomes a big problem."

The new test method—its official name is the Salmonella Genoserotyping Array (SGSA)—has been accredited by the International Organization for Standardization (ISO 17025 for testing and calibration laboratories), and the SGSA is now being implemented in PHAC national reference labs.

The genoserotyping method for identification of Salmonella types involves four steps, using widely available technologies in a high throughput manner.