Enteric surveillance and outbreak detection

Day 1: Friday May 8, 2020

You are a federal epidemiologist working for the Public Health Agency of Canada (PHAC). On Friday May 8, you attend your weekly meeting to review the National Enteric Surveillance Program (NESP) numbers from the previous week (April 26 to May 2, NESP Week 2020-18).

The NESP provides timely analysis and reporting for laboratory-confirmed isolations of enteric pathogens in Canada, including bacteria, viruses, and parasites. Provincial public health laboratories submit aggregate counts of enteric pathogens, including genus, species, and serotype information, on a weekly basis. These counts can act as an “early warning” to give public health advanced notice of potential outbreaks. Organisms are reported at the serotype level on a weekly basis by the provincial public health laboratories. The NESP is administered by PHAC and surveillance data are disseminated to federal, provincial/territorial, and local stakeholders through the weekly NESP report, other summary reports, and web-based applications.

The NESP numbers of confirmed Salmonella Newport cases are summarized in Table 1 below. Salmonella Newport numbers are significantly above expected in Ontario (6 cases reported, 1 expected). Numbers are not significantly above expected nationally and for all other provinces and territories.

Table 1: NESP numbers of confirmed Salmonella Newport cases, by province, Week 2020-18* (April 26 – May 2, 2020)

Jurisdiction	Reported	Expected	Significantly higher than expected?
National	10	6	No
British Columbia	1	1	No
Alberta	0	1	No
Saskatchewan	1	0	No
Manitoba	0	1	No
Ontario	6	1	Yes
Quebec	1	1	No
New Brunswick	0	0	No
Nova Scotia	0	0	No
Newfoundland and Labrador	0	0	No
Prince Edward Island	1	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 1-1: A significantly higher than expected number of Salmonella Newport cases were reported in Ontario. What additional laboratory information may be needed to determine if any of these cases may be related?

As the NESP captures serotype information only; additional subtyping information is likely needed to determine if the cases are related. In Canada, Salmonella isolates are further subtyped using whole genome sequencing (WGS). Information on the genetic relatedness of the cases by WGS can help assess if the Ontario cases are related to each other or if cases from another province/territory may be related as well.