- Traditional outbreak investigations capture only a small fraction of foodborne illnesses, as many cases are linked to strains that cause illness intermittently or persist over time rather than causing single, well-defined outbreaks.
- Advances in whole-genome sequencing (WGS) allow investigators to identify genetically related strains responsible for illnesses occurring across months to years, revealing patterns previously undetectable using older typing methods.
- Reoccurring, Emerging, and Persisting (REP) strains are defined by epidemiologic patterns:
- Reoccurring strains: cause periodic outbreaks separated by quiet intervals.
- Emerging strains: show increasing frequency or geographic expansion.
- Persisting strains: cause ongoing illnesses over long periods.
- Understanding REP strains shifts surveillance from reactive outbreak response to proactive prevention, allowing earlier identification of contamination pathways across food, animal, and environmental reservoirs.
Key Findings: This paper proposes adoption of the REP strain concept as a structured framework for long-term pathogen surveillance and investigation.1
- Introduction of the REP framework: The authors propose categorizing certain pathogens as Reoccurring, Emerging, and Persisting (REP) based on long-term illness trends rather than single outbreak events, addressing a gap in traditional outbreak-focused surveillance models.
- Evolution of subtyping technologies: The shift from serotyping and PFGE to WGS has dramatically improved the ability to link cases across time and geography, enabling identification of persistent strain clusters.
- Long-term strain tracking across reservoirs: Case examples demonstrate that REP strains of pathogens such as Salmonella, Shiga toxin–producing E. coli, and Listeria move between humans, foods, animals, and environmental sources, maintaining transmission over extended periods.
- Multiple epidemiologic patterns observed: The paper presents six case studies illustrating how REP strains exhibit distinct behaviors, including repeated seasonal outbreaks, steady endemic transmission, and gradual increases in incidence.
- Need for cross-sector collaboration: Effective REP strain surveillance requires coordinated efforts across public health agencies, regulatory authorities, academia, and industry.
- Expanded surveillance beyond outbreak response: responding to acute illness REP investigations emphasize identifying root causes and environmental reservoirs, not just responding to acute illness clusters.
Bigger Picture: The REP framework represents a significant conceptual shift in food safety and public health microbiology. Historically, surveillance systems were designed to detect discrete outbreaks, yet many pathogens do not follow this pattern. Instead, they persist in environmental niches or repeatedly re-enter the food system, causing illnesses that appear sporadic but are genetically linked. The integration of genomics-driven surveillance enables investigators to identify these hidden transmission networks and understand how pathogens adapt to survive in food processing environments, agricultural systems, and natural reservoirs.
From a regulatory and industry perspective, the REP model highlights the importance of long-term environmental control and hazard monitoring, particularly for pathogens capable of forming biofilms or surviving under stress conditions. Rather than viewing contamination events as isolated failures, REP analysis encourages recognition of persistent ecological risks that require sustained mitigation strategies. Overall, the REP framework supports a transition from episodic outbreak management to continuous risk-based surveillance, strengthening the ability to prevent illnesses before they escalate into recognized outbreaks.
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