Pathogen Genomics Centers of Excellence
Sources of Foodborne Illness Outbreaks
Foodborne illnesses afflict thousands of Minnesotans every year. The Minnesota Department of Health’s Infectious Disease Laboratory is developing new methods for quickly and efficiently identifying the sources of foodborne disease outbreaks. When the source of an outbreak is identified earlier, it can be quickly remedied so that fewer people get sick.
With funding from the Centers for Disease Control and Prevention (CDC)’s Pathogen Genomics Centers of Excellence (PGCoE) program, the lab is using cutting-edge genomic sequencing and bioinformatics for two main goals. The first is to predict whether individual outbreaks came from chicken, beef, human-to-human contact, or another source. The second is to reveal a possible cluster of related cases. This would allow epidemiologists, using interview data, to identify a common source between cases. Once a source is identified, the Infectious Disease Epidemiology, Prevention and Control (IDEPC) Division can begin searching for a particular food product or other source responsible for the spread of the microorganism.
The PGCoE-sponsored program focuses on the following:
E. coli
Only a few types of E. coli are dangerous to humans, such as shiga toxin-producing E. coli, enterotoxigenic E. coli (ETEC), enteroaggregative E. coli (EAEC), and enteropathogenic E. coli (EPEC). These types previously were not considered a major cause of illness in the United States except in people who traveled to other countries. However, recent research has shown that many illnesses caused by these pathogens were acquired in the U.S.
The Infectious Disease Laboratory is developing better methods to identify outbreaks caused by these pathogens. The lab is also identifying risk factors that lead to infection. These strains typically cause infection by traveling from fecal matter to people’s mouths. As with all the bacteria under study in this program, infection results in gastrointestinal distress and diarrhea.
Salmonella
Like E. coli, Salmonella refers to a genus of bacteria, some strains of which cause gastrointestinal distress and diarrhea. A project led by Dr. Tim Johnson of the University of Minnesota introduced a new concept for identifying high-risk Salmonella strains using a combination of high-resolution genomic analyses, rapid laboratory screens, and predictive modeling.
The project will develop a simple-to-use, web-based tool which can be used by both public health agencies and food producers for real-time surveillance and the early identification of high-risk Salmonella. The goal of this work is to enable food producers to identify these strains quickly and take actions to eliminate them before they cause human foodborne outbreaks.
Campylobacter
Of the microorganisms covered by this program, Campylobacter causes the most documented infections in Minnesota, with 1,192 reported cases in 2021. The Infectious Disease Laboratory takes clinical samples and compares them with the genomes of thousands of Campylobacter isolates from animals, food, and the environment. It can then construct a model to predict the source of any individual Campylobacter isolate, even if it was not part of an identified outbreak.
Cyclospora spp.
Cyclospora spp. are parasites that infect people primarily in the summer. In the past, the Infectious Disease Laboratory would send samples to the CDC for the genotyping necessary for an outbreak investigation. This is a time-consuming process, and the lab would often get results too late to prevent infections.
Now, because of PGCoE funding, the Infectious Disease Laboratory can conduct the genotyping of Cyclospora spp. in-house and complete the outbreak investigation in a timelier manner. This gives epidemiologists a chance to figure out what is making people sick while people are still being exposed to food that is contaminated with the parasite.