NESP Report – Outbreak Toolkit

Day 8: Friday May 15, 2020

You attend your weekly meeting to review the National Enteric Surveillance Program (NESP) numbers from the previous week (May 3 to May 9, NESP Week 2020-19).

The NESP numbers of confirmed Salmonella Newport cases are summarized in Table 2 below. Salmonella Newport numbers are significantly above expected nationally (14 cases reported, 5 expected) as well as provincially in British Columbia (5 cases reported, 1 expected), Alberta (3 cases reported, 1 expected) and Ontario (4 cases reported, 1 expected). Numbers are within expected levels for all other provinces and territories.

Table 2: NESP numbers of confirmed Salmonella Newport cases, by province, Week 2020-19* (May 3-9, 2020)

Jurisdiction	Reported	Expected	Significantly higher than expected?
National	14	5	Yes
British Columbia	5	1	Yes
Alberta	3	1	Yes
Saskatchewan	0	0	No
Manitoba	0	1	No
Ontario	4	1	Yes
Quebec	1	0	No
New Brunswick	0	0	No
Nova Scotia	1	0	No
Newfoundland and Labrador	0	0	No
Prince Edward Island	0	1	No
Yukon	0	0	No
Northwest Territories	0	0	No
Nunavut	0	0	No

Note: The reported and expected case counts in the table above are fictitious and have been created for the sole purpose of this case study. They do not represent actual case counts at the national or provincial/territorial level, and no interpretation or conclusion can be inferred. These data should not be further published or distributed beyond the educational limits of this case study.

Question 1-2: What additional information may you need to assess if a multi-jurisdictional outbreak is occurring? How will you get this information?

In order to determine whether this is a multi-jurisdictional outbreak, you need to determine what would normally be expected in the time frame that these cases were reported. At this point it is interesting that fourteen cases were reported in one week when we would normally only expect five. It is also interesting that this serotype appears to be flagging across multiple provinces. However, this serotype is a common serotype in Canada and you would likely want further laboratory and epidemiological evidence to confirm the relatedness of these cases.
Information on the genetic relatedness of the cases across Canada by WGS can be obtained from PulseNet Canada. PulseNet Canada can also provide an initial line list for these isolates (more on line lists in the next section).
Information on how many Newport cases are pending WGS at P/T labs and at NML can be obtained from PulseNet Canada and P/T labs.

Whole genome sequencing is the current “gold standard” method for comparing the genetic profiles of most foodborne bacterial pathogens in Canada, including Salmonella. Prior to the transition to WGS in 2017, pulsed-field gel electrophoresis (PFGE) and phage typing (PT) were used to determine the relatedness of Salmonella isolates.

Question 1-3: What are the benefits of using WGS for outbreak detection compared to previous laboratory subtyping methods?

Benefits of using WGS for outbreak detection include:

Greater reliability than other laboratory methods when determining if cases are genetically related; and thus, assists with the overall decision to pursue an outbreak investigation.
Further specificity than other laboratory methods that allows for the detection of clusters that were previously difficult to link.
The ability to rule out unrelated clusters and cases, increasing timeliness and epi data accuracy.
More targeted interventions which conserves resources that would be spent investigating common but unrelated cases.
The ability to more definitively link cases to contaminated food samples, increasing the weight of evidence