Mra HW1

Quantitative risk assessment of
Campylobacter in döner kebab consumed in

the west of Algeria
Microbial Risk Assessment

Homework 1
2022-2023
2nd Year Master of Statistics and Data Sciences

Hasselt University
Presented by:
Edmond Sacla Aide (2159278)
Melvin Estolano (2159122)
Fan Huang (2263527)
Submission Date: 15 November 2022
Lecturer:
Prof. Dr. Christel Faes
Prof. Dr. Marc Aerts
Microbial Risk Assessment (MRA) - Project1 (2022–2023)
Project Summary
Benamar et al (2021) published a quantitative risk assessment of Campylobacter in döner kebab

consumed in the west of Algeria. In this homework, we will redo part of the quantitative risk
assessment.
In this paper, we will perform a quantitative microbial risk assessment (QMRA) to evaluate the
risk posed by Campylobacteriosis infection considering the food pathway for the whole döner kebab
processing.
Firstly, we will describe and simulate the number of Campylobacter in positive samples of chicken
meat. Secondly, we will describe and simulate the number of Campylobacter in döner kebab before
and after cooking. From this, we will estimate the contamination level. Third, we will simulate
the probability of infection and illness and predict the number of cases per 106 servings. Fourth,
we will investigate the impact of ingested dose on infection level by using Spearman’s rank corre-
lation coefficients. Lastly, three scenarios for sensitivity analyses will be performed to estimate the
number of Campylobacter in döner kebab.
All analyses were done using R software version 4.2.1. All simulations are seeded at 1 to reproduce
a particular sequence of random numbers.
1
Contents
1 Simulation of the number of Campylobacter in positive samples of chicken meat 3
1.1 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 Result . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2 Simulation of the number of Campylobacter in döner kebab (before and after

cooking) 4
2.1 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.2 Result . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
3 Simulated mean probability of infection and of illness 7

3.1 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
3.2 Result . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
4 Spearman’s rank correlation coefficients on the impact of ingested dose and on

infection level 10
4.1 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
4.2 Result . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
5 First sensitivity analysis: Uncertainty on the prevalence estimate of the number

of Campylobacter in döner kebab 11
5.1 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
5.2 Result . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
6 Second sensitivity analysis: Impact of the portion consumed by a triangular

distribution with minimal value 75, maximal value of 350 and mode 150 12
6.1 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
6.2 Result . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
7 Third sensitivity analysis: Impact of the negative association between the amount
an individual would consume and the concentration in the meal 13
7.1 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
7.2 Result . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2
1 Simulation of the number of Campylobacter in positive samples

of chicken meat
1.1 Methodology
The Campylobacter concentrations (log cfu/g) in a positive sample can be described as follows:
CRawmeat ∼ N ormal(mCRawmeat , sdCRawmeat )

where, mCRawmeat refers to the mean concentration an sdCRawmeat refers to the standard deviation.
Based on the data from this study, we have mCRawmeat = 3.816 log cfu/g and a sdCRawmeat = 1.474
log cfu/g. To estimate the number of Campylobacter concentrations in positive samples, we made
use of Monte Carlo simulations. The simulation algorithm are as follows:
• Draw 1000,000 samples of CRawmeat from a normal distribution given by N(mean=3.618,

sd=1.474)
• Re-scale back the original value to log etc.
1.2 Result
Figure 1: Histogram plot of the mean Campylobacter concentration in positive samples of chicken
meat: (a) Log scale (b) Re-scaled
Table 1: Summary statistics for the mean Campylobacter concentration in positive samples of
chicken meat
Min. 1st Qu. Median Mean 3rd Qu. Max.

Log scale -2.879 2.812 3.817 3.813 4.806 10.174
Re-scaled 0.091 16.839 45.616 134.590 122.809 23669.488
3
Figure 2: Proportion of mean Campylobacter concentration (cfu/g) from raw chicken meat
Figure 1 shows the histogram plot of the mean Campylobacter concentration for both the log and
re-scaled version of the simulated data. Rescaling back to the original unit of concentration (cfu/g)
it can be seen that the distribution is skewed. Moreover, from the rescaled unit of concentration
in table 1, it can be seen that the median Campylobacter concentration is 45.616 cfu/g.
In addition, the pie chart of mean Campylobacter concentration from raw chicken meat was re-
constructed, revealing that the proportion of categorized concentration in the simulated data is
different as compared to the original result in the article.
2 Simulation of the number of Campylobacter in döner kebab

(before and after cooking)
2.1 Methodology
To simulate the number of Campylobacter before and after cooking, we refer to the concentration
in the kebab at the moment of consumption or the final load equation. This can be calculated as:
Ckebabbef orecooking = Ckebab × 10Hs eas × 10Mm ar × 10Sf reezing
Ckebabprepaf tercooking = Ckebab × 10Hs eas × 10Mm ar × 10Sf reezing × 10HS urvCooking
To estimate the number of Campylobacter in döner kebab before and after cooking, we made use
of Monte Carlo simulations. The simulation algorithm is as follows:
4
• Creating a vector of the weight of kebab skewers to which a vector of the weight of each
chicken was simulated from a normal distribution with mChickenunit = 1.928 and standard
deviation sdChickenunit = 0.178 until 1 kebab skewer is at least 10kg.
• Calculating the number of Campylobacter per chicken by adding the simulated log chicken’s
weight (logUchicken,i ) and the simulated raw meat Campylobacter concentration (Crawmeat ).
• Simulating the contamination status from a Bernoulli distribution considering a prevalence

of Campylobacter in raw chicken meat coming from the data (PRawm eat = 86.27%)
• Calculating the number of bacteria per contaminated kebab by summing the number of
Campylobacter to the power of 10 if its contaminated.
• Considering the fixed effect of Marination given by Mmar = −2
• Considering the fixed effect of Seasoning given by HSeas = 0.5
• Calculating the decrease of Campylobacter in the freezing step (if the time is smaller than 1,
then SF reezing = −0.56 × ST ime , otherwise SF reezing = −0.465 − 0.095 × ST ime )
• Calculating the concentration in the kebab at the moment of consumption before and after
cooking
2.2 Result
Figure 3: Histogram of the weight of kebab skewers
From the histogram plot, we can see that the distribution of the weight of kebab skewers is skewed.
It can also be seen that it has two peaks, around 10,000 grams and 11,500 grams. Referring from
table ??, the average Kebab skewer weight is 11,216 grams.
5
Table 2: Summary statistics for the Kebab skewer weight in grams

Kebab skewer weight 10000 10920 11360 11216 11645 12526
From the plot of the histogram, the distribution of the estimated Campylobacter in the kebab
skewer is highly skewed for both before and after cooking.
Figure 4: Histogram plot of the number of Campylobacter : (a) Before cooking (b) After cooking
From table ??, it can be seen that the average number estimated number of Campylobacter con-
centration in the kebab skewer before cooking gives a huge value as compared with after cooking.
So the concentration of Campylobacter in a kebab before cooking is around 22830 cfu/g while after
cooking this concentration is reduced to around 50 cfu/g.
Table 3: Summary statistics for the estimated number of Campylobacter concentration in the kebab
skewer

Before cooking 0 58150 577800 228300000 5686000 2065000000000
After cooking 0 0 0 503700 0 9828000000
Figure 5 shows the impact of cooking on the estimated number of Campylobacter concentration
in the kebab skewer (10 kg). Similar interpretations can be gained that the estimated number of
Campylobacter concentration in the kebab gradually decreases after cooking. Thus, the cooking
step is very important in the kebab production chain in reducing the concentration of Campylobac-
ter.
6
Figure 5: Impact of cooking
3 Simulated mean probability of infection and of illness

3.1 Methodology
To calculate for the probability of infection we refer to the Beta-Poisson dose-response model given
by:
−α
Ding
Pinf (Ding ; α, β) = 1+
β
where α=0.145 and β=7.59 from the data given in the article. From the article, it was also assumed
that the portion of size eaten is given by UEaten equals 150 grams. The ingested dose, given by Ding ,
of Campylobacter in döner kebab can be sampled from a binomial distribution with n=Ckebabf inal
and p=Ueaten /Ukebab , and is given as follows:
Ding ∼ Binomial(Ckebabf inal , Ueaten /Ukebab )

The mean probability of infection is calculated by taking the average of the output from the dose-
response model, denoted by M.Pinf = M ean(Pinf ).
7
It was also noted by previous studies (Black et al. [1988], Havelaar et al. [2000], Nauta et al. [2007])
that the probability of illness given the infection is given by 1/3. Thus, we can calculate the prob-
ability of illness by Pill = M.PInf × Pill|inf .
Therefore, the cases per year, assuming that the estimated Kebab’s serving persons per year
(NServed ) is 1,000,000, can be calculated by multiplying the Probability of illness with the Ke-
bab’s serving persons per year.
3.2 Result
The mean probability of infection is given by M.Pinf which is equal to 0.043212. In addition,
the probability of illness Pill is equal to 0.014404. By looking at the histogram of probability of
infection, it can be seen that the distribution is left skewed. Moreover, the plot can also tell us that
if we relate this to a person eating kebab, he/she can have a probability of infection approximately
about 1.4%. Although this figure seems low, if we take the variability into account, then eating a
kebab that does not have good hygiene can still have risk of being contaminated.
The number of cases per year was derived by multiplying the Probability of illness with the Kebab’s
serving persons per year. This is equivalent to 14,404 cases per year.
Figure 6: Histogram of the probability of infection
8
Figure 7: Histogram of the probability of illness
Table 4: Summary statistics for the probability of infection and illness

Probability of Infection 0.000 0.000 0.000 0.043 0.000 0.910
9
4 Spearman’s rank correlation coefficients on the impact of in-

gested dose and on infection level
4.1 Methodology
If we look at plot of correlation, then it can be seen that log reduction is highly correlated with
the probability of infection, meaning that if we have higher decimal reduction time it will lead to
lower temperature thus less Campylobacter will be killed from cooking. With freezing time, it can
be seen that it has not gained any effect in the probability of infection. Lastly, cooking time shows
a negative correlation with the probability of infection, which means that cooking the kebab longer
can lead to lower probability of infection.
4.2 Result
Figure 8: Barplot of the correlation on the impact of process
10
5 First sensitivity analysis: Uncertainty on the prevalence esti-

mate of the number of Campylobacter in döner kebab
5.1 Methodology
To take into account the uncertainty on the prevalence of contaminated raw chicken, we use a
triangular distribution with minimal value 0.758, maximal value of 0.877 and mode 0.862 to describe
the prevalence. The minimal and maximal values are based on two other studies Authority [2011]
and Messad et al. [2014] that show different contamination rate. the number of Campylobacter in
döner kebab is calculated using the same formula described in the paper.
5.2 Result
Since it is easier to obtain a value that is smaller than 0.862 from the triangular distribution that
we specify, we can see from table 2 that when the contamination rate is not fixed, the number of
Campylobacter in döner kebab tends to be smaller.
Table 5: Mean of number of Campylobacter in döner kebab with fixed prevalence and sampled
prevalence
Fixed Prevalence Sampled Prevalence
Mean of number of Campylobacter 18,748,599,212 18,259,281,453
11
6 Second sensitivity analysis: Impact of the portion consumed by

a triangular distribution with minimal value 75, maximal value
of 350 and mode 150
6.1 Methodology
Instead of using a fixed value for the amount of consumption, it is sampled from a triangle distri-
bution with minimal value 75, maximal value of 350 and mode 150. Ingested dose and cases per
year are obtained using the same formulas as described in the paper.
6.2 Result
When the amount of consumption is sampled from a triangular distribution, we can see from the
histograms that the probability to obtain a döner kebab with high ingested does is higher, leading to
higher cases per year. When the portion consumed is fixed, the predicted number of cases is about
14,404 per year, whereas when the portion consumed is sampled from a triangular distribution, the
predicted number of cases becomes around 15,025 per year.
Figure 9: Histogram of ingested dose with fixed consumption (left) and sampled consumption
(right)
12
7 Third sensitivity analysis: Impact of the negative association

between the amount an individual would consume and the con-
centration in the meal
7.1 Methodology
We use a simple linear regression to describe the negative association between the amount an
individual would consume and the the concentration in the meal:
(10 − 150)
amount consumed = ∗ concentration in meal + 150 (1)
max(concentration in meal)
When the concentration equals the maximal value, a person will only consume 10g of kebab but
when the concentration is close to or equals 0, the consumption amount becomes 150g. Ingested
dose and cases per year are calculated using the same formulas as described in the paper.
7.2 Result
From the histograms, we can see that when there’s a negative association, the frequency to obtain
a döner kebab with high ingested does is lower (shorter tail), leading to lower cases per year. When
the portion consumed is fixed, the predicted number of cases per year is about 14,404 per year,
whereas when there’s negative association between consumption amount and the concentration in
the meal, the predicted number of cases decreases to 14,396 per year.
Figure 10: Histogram of ingested dose with fixed consumption (left) and negative association (right)
13
References
Robert E. Black, Myron M. Levine, Mary Lou Clements, Timothy P. Hughes, and Martin J.
Blaser. Experimental Campylobacter jejuni Infection in Humans. The Journal of Infectious
Diseases, 157(3):472–479, 03 1988. ISSN 0022-1899. doi: 10.1093/infdis/157.3.472. URL
https://doi.org/10.1093/infdis/157.3.472.
A. H. Havelaar, M. A. S. de Wit, R. van Koningsveld, and E. van Kempen. Health

burden in the netherlands due to infection with thermophilic campylobacter spp. Epi-
demiology and Infection, 125(3):505–522, 2000. ISSN 09502688, 14694409. URL
http://www.jstor.org/stable/3864846.
Maarten J. Nauta, Wilma F. Jacobs-Reitsma, and Arie H. Havelaar. A risk

assessment model for campylobacter in broiler meat. Risk Analysis, 27(4):
845–861, 2007. doi: https://doi.org/10.1111/j.1539-6924.2006.00834.x. URL
https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1539-6924.2006.00834.x.
European Food Safety Authority. Analysis of the baseline survey on the prevalence of campylobacter
in broiler batches and of campylobacter and salmonella on broiler carcasses, in the eu, 2008-part
b: Analysis of factors associated with salmonella contamination of broiler carcasses. EFSA
Journal, 9(2):2017, 2011.
Sara Messad, Taha-Mossadak Hamdi, Radia Bouhamed, Nadjia Ramdani-Bouguessa, and Mo-
hamed Tazir. Frequency of contamination and antimicrobial resistance of thermotolerant campy-
lobacter isolated from some broiler farms and slaughterhouses in the region of algiers. Food
control, 40:324–328, 2014.
14
Appendices
R Codes
# - - - - - ----- Libraries
library ( triangle )
library ( tidyverse )
library ( Rlab )
library ( ggplot2 )
# - - - - - ----- Setting the number of simulation and seed

sims <- 100000
set . seed (1)
# - - - - - ----- Campylobacter concentration

mu _ con _ raw <- 3.816
sd _ con _ raw <- 1.474
C _ raw _ meat _ log <- rnorm ( sims , mu _ con _ raw , sd _ con _ raw )
C _ raw _ meat <- exp ( rnorm ( sims , mu _ con _ raw , sd _ con _ raw ) )
# - - - - - ----- Histogram plot of Campylobacter concentration

hist ( C _ raw _ meat _ log , main = " " , xlab = " mean Campylobacter concentration ( log cfu / g ) " )
abline ( v = mean ( C _ raw _ meat _ log ) , col = ' red ' , lwd =3)
hist ( C _ raw _ meat , main = " " , xlab = " mean Campylobacter concentration ( cfu / g ) " )
abline ( v = mean ( C _ raw _ meat ) , col = ' red ' , lwd =3)
# - - - - - ----- Summary of Campylobacter concentration

summary ( C _ raw _ meat _ log )
summary ( C _ raw _ meat )
# - - - - - ----- weight of a kebab skewer

mu _ weight _ chicken <- 1.928
sd _ weight _ chicken <- 0.178
w _ chickens <- vector ( ' list ' , sims )

U _ kebab <- vector ( ' numeric ' , sims )
for ( i in 1: sims ) {
row _ w _ chickens <- c ()
while ( U _ kebab [ i ] < 10000) {
w _ chicken <- 1000 * rnorm (1 , mu _ weight _ chicken , sd _ weight _ chicken )
U _ kebab [ i ] <- U _ kebab [ i ] + w _ chicken
row _ w _ chickens <- c ( row _ w _ chickens , w _ chicken )
}
w _ chickens [[ i ]] <- row _ w _ chickens
}
# - - - - - ----- Number of Campylobacter per chicken

num _ Camp _ per _ chicken <- vector ( ' list ' , sims )
15
num _ Camp _ per _ chicken [ i ] <- list ( log ( w _ chickens [[ i ]] , base =10) + C _ raw _ meat [ i ])
}
# -- - - - ----- Contamination status of each boneless chicken

P _ chicken <- vector ( ' list ' , sims )
P _ chicken [ i ] <- list ( rbern ( length ( w _ chickens [[ i ]]) ,176 / 204) )
}
# - -- - - ----- Total number of bacteria per contaminated kebab

C _ kebab <- vector ( ' numeric ' , sims )
C _ kebab [ i ] <- sum ( P _ chicken [[ i ]] * 10^ num _ Camp _ per _ chicken [[ i ]])
}
# - - - - - ----- Decrease of Campylobacter concentration in freezing step

S _ freezing <- vector ( ' numeric ' , sims )
S _ time <- rtriangle (1 , a =0 , b =3 , c =1)
if ( S _ time < 1) {
S _ freezing [ i ] = -0.56 * S _ time
} else {
S _ freezing [ i ] = -0.456 - 0.095 * S _ time
}
}
# -- - - - ----- Inactivation on Campylobacter during heating

log _ D50 <- ( -0.16 * 50) + 9.29
log _ D70 <- ( -0.16 * 70) + 9.29
log _ Dtr <- runif ( sims , log _ D70 , log _ D50 )
t _ heating <- rtriangle ( sims ,15 ,35 ,25)
H _ surv _ cooking <- -t _ heating / 10^ log _ Dtr
# - - - - - ----- Concentration in the kebab at the moment of consumption

C _ kebab _ prep <- C _ kebab * 10^0.5 * 10^( -2) * 10^ S _ freezing *
10^ H _ surv _ cooking
C _ kebab _ prep _ before <- C _ kebab * 10^0.5 * 10^( -2) * 10^ S _ freezing *
10^ H _ surv _ cooking
C _ kebab _ prep _ after <- C _ kebab * 10^0.5 * 10^( -2) * 10^ S _ freezing
# - - - - - ----- Histogram Plot of Concentration in the kebab at the moment of

consumption
hist ( C _ kebab _ prep _ before , main = " " , xlab = " Estimated number of Campylobacter before
cooking ( cfu / kebab ) " )
hist ( C _ kebab _ prep _ after , main = " " , xlab = " Estimated number of Campylobacter after
cooking ( cfu / kebab ) " )
# - - - - - ----- Ingested dose on a kebab portion eaten per serving

D _ ing <- vector ( ' numeric ' , sims )
16
D _ ing [ i ] <- rbinom (1 , round ( C _ kebab _ prep [ i ]) ,150 / U _ kebab [ i ])
}
# - - - - - ----- Dose - response model

alpha <- 0.145
beta <- 7.59
P _ inf <- 1 - (1 + D _ ing / beta ) ^( - alpha )
P _ ill . inf <-P _ inf / 3
P _ ill <- mean ( P _ inf , na . rm = TRUE ) / 3
cases _ per _ year <- P _ ill * 1000000 # 15100 cases / year in the paper
# - - - - - ----- Summary of the probabilities

summary ( P _ inf )
summary ( P _ ill . inf )
# - - - - - ----- Histogram plot of the probabilities

hist ( P _ inf , main = " " , xlab = " Probability of Infection " )
hist ( P _ ill . inf , main = " " , xlab = " Probability of Illness " )
# - - - - - ----- Correlation
r1 <-c ( cor ( P _ inf , t _ heating , method = " spearman " , use = " complete . obs " ) ,
cor ( P _ inf , S _ freezing , method = " spearman " , use = " complete . obs " ) ,
cor ( P _ inf , log _ Dtr , method = " spearman " , use = " complete . obs " ) )
barplot ( r1 , horiz = TRUE ,
names . arg = c ( " cooking time " ,
" freezing time " ,
" log reduction time " ) ,
xlim = c ( -0.2 ,1) ,
xlab = " Correlation " )
# - - - - - ----- Sensitivity analysis for contamination status

P _ chicken _ SA <- vector ( ' list ' , sims )
P _ raw _ meat <- rtriangle (1 ,0.758 ,0.877 ,0.863)
P _ chicken _ SA [ i ] <- list ( rbern ( length ( w _ chickens [[ i ]]) ,P _ raw _ meat ) )
}
C _ kebab _ SA <- vector ( ' numeric ' , sims )

C _ kebab _ SA [ i ] <- sum ( P _ chicken _ SA [[ i ]] * 10^ num _ Camp _ per _ chicken [[ i ]])
}
mean ( C _ kebab )
mean ( C _ kebab _ SA )
# - - - - - ----- Sensitivity analysis for assumption of consumption

D _ ing _ SA <- vector ( ' numeric ' , sims )
17
portion _ consumed <- rtriangle (1 ,75 ,350 ,150)

D _ ing _ SA [ i ] <- rbinom (1 , round ( C _ kebab _ prep [ i ]) , portion _ consumed / U _ kebab [ i ])
}
P _ inf _ SA <- 1 - (1 + D _ ing _ SA / beta ) ^( - alpha )

cases _ per _ year _ SA <- 1000000 * mean ( P _ inf _ SA ) / 3
par ( mfrow = c (1 ,2) )

hist ( log ( D _ ing , base =10) , xlab = " Ingested dose " , main = " " )
hist ( log ( D _ ing _ SA , base =10) , xlab = " Ingested dose " , main = " " )
cases _ per _ year

cases _ per _ year _ SA
# - - - - - ----- Sensitivity analysis for negative association

D _ ing _ SA2 <- vector ( ' numeric ' , sims )
portion _ consumed <- (10 -150) / max ( C _ kebab _ prep ) * C _ kebab _ prep [ i ] + 150
D _ ing _ SA2 [ i ] <- rbinom (1 , round ( C _ kebab _ prep [ i ]) , portion _ consumed / U _ kebab [ i ])
}
P _ inf _ SA2 <- 1 - (1 + D _ ing _ SA2 / beta ) ^( - alpha )

cases _ per _ year _ SA2 <- 1000000 * mean ( P _ inf _ SA2 ) / 3
par ( mfrow = c (1 ,2) )

hist ( log ( D _ ing , base =10) , xlab = " Ingested dose " , main = " " )
hist ( log ( D _ ing _ SA2 , base =10) , xlab = " Ingested dose " , main = " " )
cases _ per _ year

cases _ per _ year _ SA2
18

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Quantitative risk assessment of

Campylobacter in döner kebab consumed in

Microbial Risk Assessment

2nd Year Master of Statistics and Data Sciences

Submission Date: 15 November 2022

Benamar et al (2021) published a quantitative risk assessment of Campylobacter in döner kebab

2 Simulation of the number of Campylobacter in döner kebab (before and after

3 Simulated mean probability of infection and of illness 7

4 Spearman’s rank correlation coefficients on the impact of ingested dose and on

5 First sensitivity analysis: Uncertainty on the prevalence estimate of the number

6 Second sensitivity analysis: Impact of the portion consumed by a triangular

1 Simulation of the number of Campylobacter in positive samples

CRawmeat ∼ N ormal(mCRawmeat , sdCRawmeat )

• Draw 1000,000 samples of CRawmeat from a normal distribution given by N(mean=3.618,

• Re-scale back the original value to log etc.

Min. 1st Qu. Median Mean 3rd Qu. Max.

2 Simulation of the number of Campylobacter in döner kebab

Ckebabbef orecooking = Ckebab × 10Hs eas × 10Mm ar × 10Sf reezing

• Simulating the contamination status from a Bernoulli distribution considering a prevalence

• Considering the fixed effect of Marination given by Mmar = −2

• Considering the fixed effect of Seasoning given by HSeas = 0.5

Figure 3: Histogram of the weight of kebab skewers

Table 2: Summary statistics for the Kebab skewer weight in grams

Min. 1st Qu. Median Mean 3rd Qu. Max.

Min. 1st Qu. Median Mean 3rd Qu. Max.

Figure 5: Impact of cooking

3 Simulated mean probability of infection and of illness

Ding ∼ Binomial(Ckebabf inal , Ueaten /Ukebab )

Figure 6: Histogram of the probability of infection

Figure 7: Histogram of the probability of illness

Table 4: Summary statistics for the probability of infection and illness

Min. 1st Qu. Median Mean 3rd Qu. Max.

4 Spearman’s rank correlation coefficients on the impact of in-

Figure 8: Barplot of the correlation on the impact of process

5 First sensitivity analysis: Uncertainty on the prevalence esti-

6 Second sensitivity analysis: Impact of the portion consumed by

7 Third sensitivity analysis: Impact of the negative association

A. H. Havelaar, M. A. S. de Wit, R. van Koningsveld, and E. van Kempen. Health

Maarten J. Nauta, Wilma F. Jacobs-Reitsma, and Arie H. Havelaar. A risk

# - - - - - ----- Setting the number of simulation and seed

# - - - - - ----- Campylobacter concentration

# - - - - - ----- Histogram plot of Campylobacter concentration

# - - - - - ----- Summary of Campylobacter concentration

# - - - - - ----- weight of a kebab skewer

w _ chickens <- vector ( ' list ' , sims )

# - - - - - ----- Number of Campylobacter per chicken

# -- - - - ----- Contamination status of each boneless chicken

# - -- - - ----- Total number of bacteria per contaminated kebab

# - - - - - ----- Decrease of Campylobacter concentration in freezing step

# -- - - - ----- Inactivation on Campylobacter during heating

# - - - - - ----- Concentration in the kebab at the moment of consumption

# - - - - - ----- Histogram Plot of Concentration in the kebab at the moment of

# - - - - - ----- Ingested dose on a kebab portion eaten per serving

# - - - - - ----- Dose - response model

# - - - - - ----- Summary of the probabilities

# - - - - - ----- Histogram plot of the probabilities

# - - - - - ----- Sensitivity analysis for contamination status

C _ kebab _ SA <- vector ( ' numeric ' , sims )

# - - - - - ----- Sensitivity analysis for assumption of consumption

portion _ consumed <- rtriangle (1 ,75 ,350 ,150)

P _ inf _ SA <- 1 - (1 + D _ ing _ SA / beta ) ^( - alpha )

par ( mfrow = c (1 ,2) )