Reoccurring, Emerging, and Persisting (REP) Strains: A Framework for Surveillance and Investigation of Pathogens of Public Health Importance.

Acute outbreaks represent only a small fraction of all reported foodborne illness in the United States. Increasing identification of genetically related bacterial strains that cause human illness over periods much longer than traditional outbreaks necessitates a novel framework for understanding and investigating these reoccurring, emerging, and persisting (REP) strains. We describe the evolution of bacterial subtyping methods, from traditional serotyping to whole genome sequencing, which has substantially enhanced the ability to group together illnesses that are likely linked to a common food, animal, or environmental source. The proposed REP strain framework categorizes strains based on the epidemiological pattern of human illnesses: reoccurring strains cause periodic outbreaks, emerging strains demonstrate increasing incidence, and persisting strains consistently cause illnesses over time. We present case studies of six REP strains being tracked by health and regulatory agencies in the United States, including by PulseNet, the national molecular subtyping network for surveillance of bacterial enteric infections. These examples illustrate the diverse epidemiologic and genomic characteristics of REP strains and the opportunity they present to better understand how pathogens move between humans, foods, animals, and the environment. Effective monitoring and control of REP strains requires interdisciplinary collaboration among public health and regulatory agencies, academia, and industry to develop innovative investigational approaches that extend beyond traditional outbreak response. Investigation of REP strains can provide a better understanding of the drivers of illnesses that are not part of recognized outbreaks. Further, it has the potential to provide insights into pathogen transmission pathways that can inform broader prevention strategies aimed at reducing the overall burden of foodborne and other infections.