Module 2 epi summary

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Preliminary information and subject to change throughout the day

Case study: [2020-060] Multi-provincial outbreak of Salmonella Newport

Cluster Code: 2005NEWWGS-1ON-MP

Epidemiologic Update, June 1, 2020 as of 11:00 EDT

 

Confirmed cases (n=14)

P/T Case Count

QC=1
ON=7
AB=3
BC=3

Estimated Burden of Illness[1]

365

Age (years)
Mean
Median
Range

32.0
26.5
17-57

Sex:  % Female

79% (11/14)

Hospitalizations

0

Deaths

0

Onset date range

April 22, 2020 – May 11, 2020

Reporting Delay (days)

Median
Range

 

22
17-26

Epidemic curve

S.  Newport cases by symptom onset and province (n=14)

 

 

UPDATES

Epidemiological:

  • Exposure information is available for 7/14 cases
    • 7/14 cases have been re-interviewed by PHAC-OMD using the hypothesis-generating questionnaire ( ON=5, BC=2)
    • 3/14 cases are lost to follow up
    • 4/14 cases are pending re-interview
  • The following foods were reported in higher than expected frequencies during re-interviews (See Appendix B):
    • Spinach
      • 4/5 (80%) report exposure to spinach
        • 4 report baby spinach
        • 3 report purchasing brand X in a plastic container from Grocery Store Chain 1
        • 1 reports purchasing brand Y in a plastic bag from Grocery Store Chain 2
      • Blueberries
        • 5/7 (71%) report exposure to blueberries
          • 1 reports purchasing from Grocery Store Chain 1
          • 1 reports purchasing from local independent grocery store
          • 1 reports purchasing from a Farmer’s Market
        • Nuts & Seeds
          • 4/6 (67%) report exposure to walnuts
            • 1 reports purchasing from Grocery Store Chain 1
          • 5/6 (83%) report exposure to almonds
            • 1 reports purchasing from Grocery Store Chain 2
            • 1 reports “Plain and Simple” brand
          • 4/6 (67%) report exposure to sesame seeds
            • 1 reports purchasing from Grocery Store Chain 2
          • 5/7 (71%) report exposure to chia seeds
            • 1 reports purchasing from local independent grocery store
          • 4/6 (67%) report exposure to flax seeds

 

Laboratory:

  • All confirmed cases are related by 0-6 wgMLST allele differences (See Appendix C).
  • This cluster of cases is within 0-25 alleles of a historic cluster of four Ontario cases from 2019 (1908NEWWGS-1ON). The onset dates for this cluster ranged from August 8, 2019 to September 2, 2019. The source of this outbreak was never confirmed, although some type of nut or seed product was suspected. PulseNet Canada confirms that this cluster is not within 25 alleles of any non-clinical isolates.

 

Food Safety:

  • CFIA has begun traceback activities for the spinach reported by four cases that all purchased their spinach from the same grocery chain to determine where the baby spinach was sourced from.

Communications:

  • A Public Health Alert (PHA) was posted to CNPHI on May 25, 2020.

Appendix A: Case Definitions

Confirmed case:

A resident of or visitor to Canada with:

  • Laboratory confirmation of Salmonella Newport AND
  • Isolate matching PulseNet Canada cluster 2005NEWWGS-1ON-MP by whole genome sequencing* AND
  • Symptom onset or laboratory confirmation on or after April 1, 2020

*Guidelines for whole genome sequencing interpretation are determined by the Public Health Agency of Canada’s National Microbiology Laboratory.

Appendix B – Food exposure frequencies of confirmed cases compared to Foodbook Canada reference values (n=7).

 

Food Item

Confirmed Cases

 

Reference

Binomial Probability

Yes

Prob

No

DK

%Y+P

Foodbook Canada*

p-value

MEATS

Any chicken (not including deli meat)

3

0

3

1

50.0

85.6

0.0375

Any pork (not including deli meat)

1

2

3

1

50.0

55.1

0.3028

Any beef (not including deli meat)

1

1

4

1

33.3

78.4

0.0201

EGGS

Any eggs

2

3

2

0

71.4

80.7

0.2677

DAIRY PRODUCTS

Any dairy (excluding cheese)

3

1

3

0

57.1

84.6

0.0655

Non-dairy milk

3

0

3

1

50.0

No data

No data

Any cheese

4

0

3

0

57.1

88.8

0.00306

VEGETABLES

Tomatoes

3

1

3

0

57.1

72.9

0.1967

Any lettuce or leafy greens

4

1

1

1

83.3

82.4

0.4011

Iceberg

0

2

3

2

40.0

41.1

0.3452

Romaine

2

1

3

1

50.0

48.8

0.312

Spinach

4

0

1

2

80.0

28.4

0.0233

Sprouts

2

1

4

0

42.9

12.9

0.0432

Cucumbers

3

2

2

0

71.4

62.9

0.2846

Bell peppers

4

0

2

1

66.7

63.6

0.3252

Broccoli

3

0

3

1

50.0

55.5

0.3013

Cauliflower

4

0

3

0

57.1

33.0

0.1248

Mushrooms

4

0

3

0

57.1

50.0

0.2734

Zucchini

3

1

3

0

57.1

21.1

0.0341

FRUITS

Melons

3

0

3

1

50.0

39.7

0.2744

Apples

4

1

2

0

71.4

72.3

0.3183

Bananas

4

2

1

0

85.7

76.7

0.3321

Citrus fruits

4

0

3

0

57.1

65.0

0.2679

Any berries

5

0

2

0

71.4

65.2

0.2997

Strawberries

2

2

2

1

66.7

49.6

0.2306

Raspberries

2

0

3

2

40.0

27.5

0.2882

Blueberries

3

2

2

0

71.4

31.3

0.0298

Blackberries

3

1

3

0

57.1

10.5

0.003

Mangoes

4

0

3

0

57.1

15.7

0.0127

Pineapple

1

1

5

0

28.6

30.0

0.3177

NUTS & SEEDS

Peanuts

4

0

3

0

57.1

33.6

0.1306

Almonds

2

3

1

1

83.3

41.0

0.041

Walnuts

3

1

2

1

66.7

18.5

0.0117

Hazelnuts (filberts)

0

0

6

1

0.0

10.1

0.5279

Cashews

2

0

1

4

66.7

26.8

0.1577

Pecans

2

1

3

1

50.0

12.9

0.0284

Pistachios

0

0

4

3

0.0

No data

No data

Other nuts

1

0

3

3

25.0

No data

No data

Peanut butter

4

0

3

0

57.1

55.0

0.2918

Other nut butters/pastes/spreads

2

1

3

1

50.0

18.3

0.0668

Sunflower seeds

2

1

3

1

50.0

18.3

0.0668

Sesame seeds

2

2

2

1

66.7

17.1

0.0088

Chia seeds

3

2

2

0

71.4

No data

No data

Flax seeds

2

2

2

1

66.7

No data

No data

Other seeds

1

0

3

3

25.0

No data

No data

OTHER

Cold cereals

2

0

4

1

33.3

54.3

0.1929

Hot cereals

2

0

2

3

50.0

28.5

0.2491

Vegetarian/Vegan

2

0

3

2

40.0

No data

No data

Supplements

3

0

4

0

42.9

28.2

0.2086

*Canada. Infectious Disease Prevention and Control Branch. Foodbook Report. Guelph: Public Health Agency of Canada; 2015.

 

Text description: WGS analysis illustrating genetic relatedness of 14 cases. Cases are all genetically related by 0-5.7 wgMLST allele differences.

Appendix C: wgMLST Analysis for event 2020-060 (cluster code 2005NEWWGS-1ON-MP )

Text description: WGS analysis illustrating genetic relatedness of 14 cases. Cases are all genetically related by 0-5.7 wgMLST allele differences.

 

[1] Based on multiplier for Salmonella (26.1) obtained from Thomas MK, Murray R, Flockhart L, et al. Estimates of the burden of foodborne illness in Canada for 30 specified pathogens and unspecified agents, Circa 2006. Foodborne Pathog Dis 2013;10(7):639-648.