Hypothesis Generating

At this point in the investigation, spinach, berries, nuts, and seeds are food items of interest. However, it is still early in the investigation so all plausible hypotheses should be explored.

Question 2-5: What would you do to develop or strengthen hypotheses?

  • Review the literature for sources of past Salmonella Newport outbreaks
  • Determine if the current cluster is closely related to any other isolates observed elsewhere in the food chain and outside Canada by asking:
    • PulseNet Canada (CLSN)
    • United States Centers for Disease Control (US-CDC) epidemiology colleagues
    • International colleagues through an Epidemic Intelligence Information System (EPIS) posting
  • Interview cases with a standardized questionnaire to identify common food exposures and gather specific details about these exposures (e.g., type, brand, size, purchase location, purchase date).

Day 19: Tuesday May 26, 2020 (n=9)

A review of the literature reveals that Salmonella Newport outbreaks have been associated with a wide variety of food products, as well as animal contact. Some of the associated food exposures include: fresh produce such as onions, watermelon, cantaloupe, cucumber and sprouts; beef, and nuts and seeds.

To identify possible sources of this outbreak, you meet with PulseNet Canada to examine whole genome sequencing (WGS) trees for any genetically related isolates/clusters within 10 alleles, as well as any isolates/clusters within 25 alleles, of the current cluster. PulseNet Canada notes that there are no genetically related isolates/clusters within 10 alleles, but that this cluster is within 25 alleles of a cluster of four Ontario cases from 2019 (1908NEWWGS-1ON). The onset dates for this cluster ranged from August 8, 2019 to September 2, 2019. PulseNet Canada also confirms that the outbreak cluster is not within 25 alleles of any non-clinical (i.e., animal, food, environmental) isolates.

Following this meeting, you decide to email Ontario regarding the historic cluster of four cases in 2019. If an investigation was conducted for this cluster and a source identified, this may help with hypothesis generation for this investigation.

Ontario responds and informs you that a source was never confirmed when this cluster was investigated, although various nuts and seeds were explored as potential hypotheses.

Day 20: Wednesday May 27, 2020 (n=9)

You attend a weekly teleconference call with the US-CDC. The epidemiologists on the call note that they are also seeing an increase in Salmonella Newport cases in two states.

Question 2-6: What is a potential next step for determining if any of the cases in the United States (US) may be related to the cases in Canada?

Whole genome sequencing can help determine if the cases in Canada are genetically related to the cases in the US.

While on the call, you ask the US-CDC if WGS has been conducted on the isolates. The US-CDC notes that WGS has been completed. Based on this information, you decide to send a request to PulseNet Canada for them to check if any of the US cases match the Canadian cluster. You provide PulseNet Canada the US cluster code provided by the US-CDC. PulseNet Canada notes they are working on the request and will let you know the results of the comparison as soon as they are available.


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