Microbiologists may soon have a new tool to identify sources of infections in humans and track infections across patient populations

Researchers at the University of Georgia Center for Food Safety have developed an algorithm that can identify genetic variations in Salmonella found in the feces of four of the most common hosts of the bacteria—pigs, cows, poultry, and birds.

Led by Xiangyu Deng, PhD, Assistant Professor, Center for Food Safety, University of Georgia (UGA), the research team tested their algorithm on Salmonella genomes from eight separate outbreaks that occurred during the last 20 years. The algorithm accurately identified the animal sources for seven of the eight outbreaks.

Though still in the research phase, the new algorithm, which is based on deep-learning, could give clinical laboratories and medical scientists a new way to track bacterial outbreaks in patient populations. It could also be used by give public health officials and others to identify the source of bacterial outbreaks among animals. 

The researchers published their findings in the federal Centers for Disease Control and Prevention (CDC) journal Emerging Infectious Diseases.


UGA researchers Xiangyu Deng, PhD (above right), led a team of scientists who have trained an algorithm to predict certain animal sources of Salmonella Typhimurium genomes. Once perfected, clinical laboratories could have a new tool for identifying the source of bacterial outbreaks among humans. (Photo copyright: University of Georgia.)

Salmonella in Animals

Salmonella usually resides in the intestines of animals and is spread through animal dung. People contract Salmonella infections by touching their mouths after coming in contact with infected animals or by eating food contaminated by infected animal feces. The deadly bacteria are responsible for more than one million illnesses in the US each year. And according to the CDC, the bacteria also causes 23,000 hospitalizations and 450 deaths.

Worldwide, those numbers are starkly higher.

The researchers studied outbreaks that had previously been linked to a certain animal source by public health investigators. They tested their algorithm against the known results to see how well their machine could predict the animal source of the Salmonella bacteria. The algorithm accurately identified seven of the eight animal sources. And the researchers discovered it was particularly adept at identifying poultry and swine sources.  

The scientists also noticed an interesting pattern regarding the evolution of Salmonella strains attributed to livestock in the US. They found those strains didn’t appear until around 1990 and then spread quickly across the country.

“We suspect that industrialized livestock production may play a role in [the bacteria’s] spread and distribution,” Deng told The Verge.

Salmonella in Humans

The researchers also tested the algorithm on Salmonella samples that came from humans. It identified cow, pig, poultry, and bird sources of the bacteria in about a third of the biological samples. The remaining samples were ambiguous, which could mean that the Salmonella infecting those individuals was a generalist strain of the bacteria that circulates between multiple host species. 

“They just jump around to different hosts and there’s no way for us to predict which source they came from,” Deng told The Verge.

The ambiguous results also could indicate that particular strain of Salmonella originated from an animal other than the four animals the algorithm was “trained” to detect. This means the algorithm needs to study more genomes.

 “As we sequence more genomes, I’m sure the number will go up,” Deng said. “As it stands, the algorithm is a proof of concept. A little bit of information is better than no information at all. There’s still a long way to go.”

How Such a Tool Might Impact Food Safety

An algorithm that can track down the source of a Salmonella outbreak could affect food related public policy.

“Now you have this really amazing evidence through whole genome sequencing that this stuff came from this place,” Bill Marler, a Seattle-based attorney who specializes in food poisoning, told The Verge. “Then really the question is, what can you do both from a food safety perspective, or a regulatory perspective, to solve the problem?”

According to the CDC, persons infected with Salmonella typically develop diarrhea, fever, and abdominal cramps within 12 to 72 hours after being infected. The illness usually lasts four to seven days and most individuals recover without treatment. However, children under the age of five, adults over the age of 65, and persons with a weakened immune system can become severely ill due to a Salmonella infection. 

When two or more people get the same illness from contaminated food or drink, it is called a foodborne disease outbreak. And when two or more individuals get the same illness from contact with the same animal or animal environment, it is known as a zoonotic outbreak. The CDC website lists several Salmonella outbreaks linked to food in 2018. Foods contaminated with the bacteria included chicken products, ground beef, turkey products, eggs, dried and shredded coconut, raw sprouts, pasta salad, kratom, and cereal.

Two zoonotic Salmonella outbreaks also occurred last year due to contact with pet guinea pigs and live poultry in backyards. And in January of 2019, the CDC reported a zoonotic outbreak in individuals who were in contact with pet hedgehogs. 

The algorithm needs more testing, but it is a critical step in learning about Salmonella infections and how to prevent them or minimize their effects on human populations. Many types of animals can spread the bacteria. Determining the origins of outbreaks could help microbiologists and medical laboratories hinder and even prevent Salmonella infections in their patients.

—JP Schlingman

Related Information:

Machine Learning Could Help Figure Out What Pooped on Your Produce

Zoonotic Source Attribution of Salmonella Enterica Serotype Typhimurium Using Genomic Surveillance Data, United States

Scientists Use Machine Learning to ID Source of Salmonella

Salmonella‘Don’t Kiss or Snuggle Hedgehogs’ Because of Salmonella Risk, CDC Warns