priority setting for food borne pathogens angela vargas supervisors: dr. arie havelaar prof. dr....
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Priority Setting for Food Borne Pathogens
Angela Vargas
Supervisors:Dr. Arie Havelaar
Prof. Dr. Roger Cooke
12, June 2007TU Delft
Overview
• Introduction• Problem Description• Methodology• Paired Comparisons• Probabilistic Inversion• Elicitation and Analysis• Results• Conclusions and Recommendations
Introduction
Disease Burden
YLD Years Lived with a Disability
YLL Years of Live Lost
DALY Disability-Adjusted Life Years
Cost-of-illness
COI Cost-of-illness
DHC Direct Health care Costs
DNHC Direct Non-health care Costs
INHC Indirect Non-health care Costs
Fraction of cases attributable to Food
Fraction of cases attributable to Food Group
Pathways
Pathways
Food borne Environmental Human-human Direct animal Traveling
Food borneTransmission through food that is contaminated when it enters the kitchen or during preparation (e.g. by food handlers).
EnvironmentalTransmission through contaminated water (drinking water, recreational water), soil, air or other environmental media.
Human-human Transmission from person to person by the fecal-oral route.
Direct animalTransmission by direct contact with live animals including pets, farm animals, petting zoos etc.
AbroadCases when exposure takes place by any of the above pathways during foreign travel.
Pathways Description
Food
Categories
Beef and lamb
Pork
Chicken and other poultry
EggsDairy products
Fish and shellfish
Fruit and vegetables
Beverages
Bread, grains, pastas and bakery products
Other foods incl. composite foods
Infected humans or animals
Food Categories
Problem Description
• Determine the fraction of transmission route for each pathogen and the fraction of transmission due to specific food groups.
•The objective is to find a fast, not resource intensive and accurate method of estimation for these fractions.
• Estimated fractions that will sum to one
• Insufficient data
Methodology
Paired Comparisons
• Compare pair wise of all items in order to determine preference.• The result is a score for each item.• Lighter elicitation for experts.• The resulting scores sum to one.
Probabilistic Inversion
• Experts give quantiles for the query variables. • It is possible to estimate results that sum up to one. • …
Paired Comparisons
10000 0001 1 11110 01 101
Paired Comparisons Results
Item name Score Conf L. Conf U.
Food Ingestion 0.9557 0.8335 0.9978
Environment 0.0123 0.0003 0.0528
Contact with sick person
0.0015 0.0000 0.0054
Direct animal contact
0.0046 0.0001 0.0145
Contamination abroad
0.0259 0.0010 0.1058Pairec Comparisons Results for Pathways Salmonella
0.9557
0.0259
0.0046
0.0123
0.0015
Food Ingestion
Environment
Contact with sick person
Direct animal contact
Contamination abroad
Paired Comparisons Results
Item name Score Conf L. Conf U.
Beef and lamb0.052
40.0189 0.1079
Pork0.160
10.0632 0.2745
Chicken and poultry
0.2909
0.1619 0.4658
Eggs0.449
20.2756 0.6481
Dairy products0.009
80.0016 0.0211
Fish and shellfish0.006
90.0012 0.0163
Fruit and vegetables
0.0061
0.0013 0.0148
Beverages0.001
20.0001 0.0029
Bread, grains, pasta
0.0023
0.0003 0.0049
Composite Foods0.011
80.0026 0.0251
Food Handlers0.009
30.0015 0.0195
Paired Comparisons Results for Food Categories Salmonella
0.1601
0.2909
0.4492
0.0093
0.05240.0069
0.0098
0.0012 0.01180.0023
0.0061Beef and lamb
Pork
Chicken
Eggs
Dairy
Fish
F & V
Beverages
Bread, grains
Composite
Food Handlers
Probabilistic Inversion
BACK
u1 u2
0.11 0.89
0.19 0.81
0.83 0.17
0.12 0.88
0.31 0.69
0.11 0.89
0.73 0.27
0.59 0.41
0.77 0.23
0.94 0.06
0.73 0.27
0.15 0.85
1
1
1
1
1
1
1
1
1
1
1
1
00.160.15
0.130.220.12
0.100.140
0.31
0.46
0.24
0.220.510.26
IPF – One iteration
0 0.25 0.02
0.02 0.38 0.03
0.03 0.27 0
1 2 3
,
,
( ) 0.05 0.9 0.05
jj
iji
ii
ijj
p p p p
Column j
pa
a
Row i
pa
a
0.05 0.9 0.05
0.268
0.430
0.302
0 0.046 0.004
0.05 0.79 0.06
0.004 0.045 0
0.050
0.900
0.050
0.05 0.89 0.06
00.160.15
0.130.220.12
0.100.140
0.31
0.46
0.24
0.220.510.26
Re-Sampling
0 0.047 0.003
0.045 0.808 0.047
0.005 0.045 0
0.05
0.9
0.05
0.05 0.9 0.05
w1
w2
w3
w4
w5
w6
w7
w8
…
W n
Re- sample
Elicitation and Analysis
Specify an interval which contains the probability of occurrence with 90% certainty.
A case of illness due to Bacillus cereus toxin was transmitted by ingestion of Pork:
≤ 100% ≤0% ≤
16 experts participated in the elicitation.
Results
“Seed Variables”
Some probabilities are believed to be zero therefore that value was used as the true value and used as a seed variable.
Additionally 50%
Fit was done based on the 5%, 50% and 95% quantile of the equal weight distribution
5% and 95% Fit was done based on the 5% and 95% quantile of the equal weight distribution
Issues
Data Recollection• Finding the experts. Encouraging them to participate and actually answer.• No opportunity to give them guidance• Number of experts per pathogen
Validation• How to evaluate the quality of the estimates
Results
QUESTIONS
Expert 27
Food Salmonella
0% 20% 40% 60% 80% 100%
E3 E9 E11 E12 E22 E27 E33 E36 E37Equal W.
Food Salmonella w ithout expert 27
0% 20% 40% 60% 80% 100%
E3 E9 E11 E12 E22 E33 E36 E37Equal W.
Environment Salmonella
0% 20% 40% 60% 80% 100%
E3 E9 E11 E12 E22 E27 E33 E36 E37Equal W.
Environment Salmonella w ithout expert 27
0% 20% 40% 60% 80% 100%
E3 E9 E11
E12 E22 E33
E36 E37Equal W.
Expert 27
Sick Salmonella
0% 20% 40% 60% 80% 100%
E3 E9 E11 E12 E22 E27 E33 E36 E37Equal W.
Amimal Salmonella
0% 20% 40% 60% 80% 100%
E3 E9 E11 E12 E22 E27 E33 E36 E37Equal W.
Sick Salmonella w ithout expert 27
0% 20% 40% 60% 80% 100%
E3 E9
E11 E12
E22 E33 E36
E37Equal W.
Amimal Salmonella w ithout expert 27
0% 20% 40% 60% 80% 100%
E3
E9 E11
E12
E22 E33
E36
E37Equal W.
Abroad Salmonella
0% 20% 40% 60% 80% 100%
E3
E9
E11
E12
E22 E27
E33
E36
E37
Equal W.
Abroad Salmonella without expert 27
0% 20% 40% 60% 80% 100%
E3
E9
E11
E12
E22
E33
E36
E37
Equal W.
BACK