Outbreak is a story of an outbreak investigation and the science behind it. Nine established epidemiological principles are employed by Outbreak’s investigators as they work to track down the source of a disease infecting an unusually large number of people (a group, a cluster). Using data from real-world outbreaks and new developments in epidemiologic analysis, Outbreak highlights how scientific advances can inform future outbreak response efforts.
The emergence of whole genome sequencing (WGS) technology for the genetic subtyping of clinical, environmental, and food isolates has transformed outbreak investigation. In traditional foodborne illness investigations, a cluster of illnesses is identified based on microbial subtyping and an epidemiologic investigation is initiated to identify a suspect vehicle. Traditionally, this investigation requires a combination of epidemiologic and traceback investigation and product and environmental sampling.
Sample-initiated retrospective outbreak investigations (SIROIs) differ from these traditional methods by identifying a potential vehicle based on the phylogenetic linkage of the WGS-subtyped isolates uploaded to a public database. The identification of a vehicle triggers an investigation by a public health agency and its food safety partners, enabling them to focus on the vehicle’s product or food source (e.g., a restaurant, farm, or food manufacturer).
This approach allows SIROIs to provide a much-needed signal of the likely vehicle at the beginning of an investigation and avoid the delay associated with deducing this information from case patient interviews. In turn, this process helps support a prevention-centric approach to outbreak response and improves the speed of identifying pathogen/commodity pairs that could be implicated in outbreaks.