A new peer-reviewed article published in the Journal of Food Protection introduces a framework for describing Reoccurring, Emerging, and Persisting (REP) strains of foodborne pathogens. The paper, written by scientists from CDC, FDA, USDA-FSIS, Association of Public Health Laboratories, ASRT, Inc., and Gret Hill Solutions, outlines a framework for understanding strains that cause human illness over extended periods of time rather than appearing only as sporadic outbreaks. 

The paper also reflects how advances in whole genome sequencing (WGS) have improved pathogen surveillance, and how WGS now provides much higher resolution for determining genetic relationships between bacterial isolates. These tools allow investigators to identify groups of closely related strains and link illnesses that occur across multiple years, geographic regions, or exposure pathways. To illustrate the application of the proposed framework, the paper presents six case studies representing REP strains identified through historical foodborne disease outbreaks. 

Key Takeaways from the Article 

1. Most illnesses are not part of recognized outbreaks: The authors note that acute outbreaks represent only a small fraction of foodborne illnesses reported through surveillance systems. As a result, many infections appear sporadic and are difficult to link to specific sources using traditional outbreak investigation methods. 

• Some pathogen strains persist in the food system or environment: With the use of genomic surveillance, investigators have identified groups of genetically related strains that cause illnesses over months or years. These strains may appear repeatedly or continuously in surveillance data, even when they are not associated with a single outbreak event. 

• The REP framework classifies strains based on illness patterns. The framework groups strain into three categories: 
  • Reoccurring strains: trains that periodically cause a substantial number of illnesses, typically in outbreaks, separated by periods when the strain is not isolated from humans or causes very few illnesses. 
  • Emerging strains: trains that cause illnesses that are increasing in frequency or are thought to have the potential to increase in frequency. 
  • Persisting strains: cause illnesses consistently over time, although the number of illnesses may fluctuate from month to month or year to year. 

The authors emphasize that these designations are dynamic, meaning a strain may move between categories as new information becomes available. They also note that the term “persisting” refers to continued detection in human clinical isolates, not necessarily persistence in animals or environmental reservoirs.  

• High-resolution genomic methods are essential for identifying REP strains: REP strains are defined as groups of genetically related isolates that cause illness over long periods, typically a year or more. The paper explains that these strains are most effectively identified and tracked using WGS-based methods that allow for differentiation between isolates. 

• 6 case studies demonstrate how the framework can be applied: The article presents six case studies representing the three REP categories. These include: 
  • A reoccurring E. coli O157:H7 strain linked to outbreaks associated with leafy greens 
  • A reoccurring Salmonella Typhimurium strain associated with contact with pet hedgehogs 
  • An emerging multidrug-resistant Salmonella Newport strain linked to multiple exposure pathways 
  • An emerging Salmonella Reading strain associated with turkey products 
  • A persisting Listeria monocytogenes strain with a possible link to potatoes 
  • A persisting multidrug-resistant Salmonella Infantis strain linked to chicken products 

These examples demonstrate how strains can cause illnesses over extended timeframes and across different reservoirs, including food, animals, and environmental sources. For the leafy greens case study, the paper describes a reoccurring STEC O157:H7 strain (REPEXH02) that caused several outbreaks between 2016 and 2020 in the United States and Canada. Whole genome sequencing allowed investigators to determine that the illnesses across multiple years were caused by closely related isolates, connecting events that would otherwise appear as separate outbreaks. During investigations, the strain was detected in environmental samples, including sediment from an agricultural water reservoir used for irrigation and post-harvest activities. 

Why this matters: 

The REP framework represents a new way in how REP strains are characterized. Rather than focusing only on isolated outbreaks, this approach emphasizes long-term surveillance and understanding of pathogens. By identifying strains that repeatedly cause illness, investigators can begin to better understand potential transmission pathways and factors that may contribute to illness. The authors note that effective monitoring and control of REP strains will require continued collaboration among public health agencies, regulatory partners, academia, and industry, along with further development of genomic and epidemiologic tools to support these investigations.