A product of the New York Integrated Food Safety Center of Excellence October 2019 Training Objective To provide public health staff or students of public health with an understanding of how whole genome sequencing WGS and particularly whole genome multi locus sequence typing ID: 935727
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Slide1
Whole Genome Sequencing Training Activity
A product of the New York Integrated Food Safety Center of Excellence October 2019
Slide2Training Objective
To provide public health staff or students of public health with an understanding of how whole genome sequencing (WGS), and particularly whole genome multi locus sequence typing (
wgMLST
), works as a subtyping method
Slide3Mock Case Study
Three new cases of listeriosis were identified in County X in the last 2 weeks (historical average = 1 case
/
year)
The three clinical
L.
monocytogenes
isolates were sent to the State Public Health Laboratory for WGS analyisis
Once analysis was complete, WGS results were reported back to the State Health Department
Slide4Question 1: Are the 3 cases WGS-related?
Refer to Student Handout
Complete Chart 1
For each gene, identify which allele is present in each isolate
Leave “Cheese” column blank
Complete Chart 2
Count the number of differences between each pair of isolates
Leave “Cheese” row/column blank
Activity should take approx. 15 min
Slide5Question 1: Results
Chart 1.
Allelic table
Clinical 1
Clinical 2
Clinical 3
Cheese
Gene 1
Allele 3
Allele 8Allele 3Gene 2Allele 1Allele 1Allele 1Gene 3Allele 8Allele 3Allele 4Gene 4Allele 2New AlleleAllele 2Gene 5Allele 2Allele 7Allele 2Gene 6Allele 5Allele 4Allele 5
Clinical 1Clinical 2Clinical 3CheeseClinical 1051Clinical 2505Clinical 3150Cheese
Chart 2.
Allelic differences matrix
Slide6Question 1: Answer
Two of the clinical isolates are WGS-related
Clinical 1
Clinical 3
Clinical 2 is unrelated to the other isolates
Slide7Mock Case Study, Part 2
Upon interview, the two WGS-related cases claim having consumed soft cheese a month ago but do not remember the manufacturer
They both bought the cheese from the same store
Leftovers not available for testing
An environmental assessment at the store determines that two brands of soft cheese are available for purchase
One cheese sample from each brand was collected and sent to the State Public Health Laboratory for
L. monocytogenes
testing
Brand A was positive for
L. monocytogenesWGS was requestedOnce analysis was complete, WGS results were reported back to the State Health Department
Slide8Question 2:
Is the cheese related to any of the three clinical isolates?
Refer to Student Handout
Complete “Cheese” column of Chart 1
Complete “Cheese” row/column of Chart 2
Activity should take approx. 10 min
Slide9Question 2: Results
Chart 1.
Allelic table
Clinical 1
Clinical 2
Clinical 3
Cheese
Gene 1
Allele 3
Allele 8Allele 3New AlleleGene 2Allele 1Allele 1Allele 1Allele 1Gene 3Allele 8Allele 3Allele 4Allele 3Gene 4Allele 2New AlleleAllele 2Allele 4Gene 5Allele 2Allele 7Allele 2Allele 7Gene 6Allele 5Allele 4
Allele 5Allele 4 Clinical 1Clinical 2Clinical 3CheeseClinical 10515Clinical 25052Clinical 31505Cheese
5
2
5
0
Chart 2.
Allelic differences matrix
Slide10Question 2: Answer
Cheese isolate is WGS-related to Clinical 2
Cheese isolate is unrelated to the other isolates
Slide11Question 3: Draw a WGS tree showing the clustering of the isolates
Refer to Student Handout
Draw a WGS Tree (Tree 1.)
Starting from the pair with fewer differences, cluster the isolates in a stepwise manner until a tree is drawn
Activity should take approx. 10 min
Slide12Question 3: Answer
Tree 1.