To determine the likelihood that isolates are related and may have originated from a common source, molecular or genetic tests are performed. The molecular/genetic characterization is an important component of outbreak investigations: isolates with more closely related genetic fingerprints or profiles are more likely to have originated from a common source, or have an epidemiological relationship, than those with different profiles. If pathogens are identified in a food sample, their genetic profiles are compared to those isolated from the human cases in an outbreak investigation. Determining if the isolates are genetically related provides critical evidence for an outbreak investigation. Laboratory methods used for genetic profiling, and the criteria for interpreting the results, are based on procedures of the PulseNet Canada network. Whole genome sequencing (WGS) is the current method used by PulseNet Canada and provides the most accurate bacterial genetic fingerprint possible.
The following table provides details on the guidelines used to interpret WGS data for outbreak detection. These criteria are used to assess matches among human cases, and to assess matches between food or animal isolates and human cases.
Guidelines to interpret WGS data for outbreak detection:
|What is the genetic diversity among the isolates of interest?||
Number of genetic differences, typically measured as the number of wgMLST allele differences between isolates, expressed as a range.
PulseNet Canada uses 0-10 allele differences as the starting point for cluster detection. Rigid threshold definitions are not appropriate for WGS data.
|Within the group of isolates of interest, what are the genetic relationships (i.e., are there isolates that are more closely related)?||
Factors to consider include: are isolates dispersed within the cluster, or are they tightly grouped? What is the nature of the relationships within the cluster?
|What is the broader surveillance context and genomic diversity for this organism?||
Factors to consider include: genetic distance to other clusters or isolates; population diversity; genetic relationships within the broader surveillance picture (including international data).
For other foodborne pathogens, including foodborne viruses and parasites, standardized genetic profiling tests either may not be routinely used via the PulseNet Canada network, or methods may not exist. Laboratory tests and their interpretation are determined for each situation in consultation with stakeholders.
When new tests are applied during outbreak investigations for this purpose, they are applied in parallel to the primary tests and are carefully interpreted on a case-by-case basis.