CDC, FDA, USDA Collaboration Defines Framework for Classifying REP Strains, Identifies Strains of Concern
Researchers from the U.S. Centers for Disease Control and Prevention (CDC), the U.S. Food and Drug Administration (FDA), and the U.S. Department of Agriculture’s Food Safety and Inspection Service (USDA-FSIS) have presented a framework for identifying and investigating bacterial strains that cause foodborne illnesses over extended periods of time, rather than through isolated outbreaks, with the goal of improving prevention strategies and reducing the overall burden of foodborne disease.
Officially Defining Reoccurring, Emerging, and Persisting Strains
Published in Food Microbiology, the study describes the framework for classifying reoccurring, emerging, and persisting (REP) strains to help public health agencies better monitor bacterial pathogens that continue to cause illnesses outside of recognized outbreaks.
The REP framework was jointly developed by CDC, FDA, and USDA-FSIS through the Interagency Foodborne Outbreak Response Collaboration. It has been refined over the last several years, as it was increasingly used to track pathogens of public health importance, but the current study is the first peer-reviewed paper formally outlining the concept of REP strains.
Under the framework, REP strains are categorized based on the pattern of illnesses they cause. Reoccurring strains are associated with periodic outbreaks over time, emerging strains show increasing incidence, and persisting strains consistently cause illnesses over extended periods.
The Role of WGS in Identifying and Tracking REP Strains
According to the paper, acute outbreaks account for less than 10 percent of illnesses reported to CDC’s PulseNet network. As a result, most foodborne illnesses are not linked to a known source, limiting opportunities for intervention.
However, advances in whole genome sequencing (WGS) have made it possible to identify genetically related bacterial strains that cause illnesses over much longer periods than traditional outbreaks. These technologies have improved the ability to link illnesses to common food, animal, environmental, or waterborne sources and to track pathogen movement across different reservoirs.
Learning from Important REP Strains and Interventions in the U.S.
The researchers presented six case studies of REP strains currently monitored by U.S. public health and regulatory agencies through PulseNet. The examples demonstrated how specific bacterial strains can spread through foods, animals, agricultural environments, and water sources before causing human illness:
- Shiga toxin-producing Escherichia coli (STEC) O157:H7 REPEXH02: A reoccurring strain linked to multiple outbreaks associated with California-grown romaine lettuce and contaminated agricultural water sources, causing 358 illnesses since 2016
- Salmonella Typhimurium REPJPX02: A reoccurring strain responsible for repeated outbreaks linked to pet hedgehog contact, resulting in 180 illnesses across 42 states since 2012
- Salmonella Newport REPJJP01: An emerging multidrug-resistant strain associated with beef and dairy products, particularly among travelers to Mexico or consumers of Mexican beef and dairy, with more than 3,200 illnesses identified across all 50 states since 2015
- Salmonella Reading REPJLG01: An emerging multidrug-resistant strain linked to turkey products and turkey production environments that has caused 855 reported illnesses since 2012
- Listeria monocytogenes REPGX601: A persisting strain potentially associated with potatoes that has caused 88 illnesses since 2011; extensive investigations that have not yet identified a definitive source
- Salmonella Infantis REPJFX01: A persisting multidrug-resistant strain, likely originating from South America and linked primarily to raw chicken products, that has caused nearly 4,000 illnesses since 2012; although a chicken-associated outbreak has not been identified since 2019, it causes approximately 500–600 human illnesses per year and it remains prevalent in poultry production.
The study highlighted several examples in which interventions targeting animal or environmental reservoirs were followed by substantial declines in human illnesses, suggesting that identifying and monitoring REP strains may help prevent illnesses before they occur. For example, S. Reading REPJLG01 declined after interventions were applied in turkey production, and agricultural water and land use changes resulted in fewer STEC REPEXH02 illnesses.
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The Need for Advanced Genomic Analysis, Cross-Sector Collaboration
The researchers also emphasized the need for new surveillance and investigation approaches. Existing outbreak detection methods may miss REP strains that occur below standard cluster detection thresholds or exhibit greater genetic diversity than traditional outbreaks. The authors suggested that new detection algorithms capable of analyzing large genomic datasets could improve identification of previously unrecognized REP strains.
In addition to genomic analysis, the study called for expanded collaboration among public health agencies, regulators, academia, and industry to better understand how pathogens persist in animals and the environment, move through agricultural systems, and ultimately infect people.
The authors concluded that investigating REP strains could provide insights into the drivers of sporadic foodborne illnesses and support broader prevention strategies aimed at reducing foodborne, zoonotic, and waterborne disease.
