Attributing Salmonellosis to food sources and water in Latin America and the Caribbean using data from outbreak investigations (Salmonella)

Source attribution using outbreak data utilizes readily available data from outbreak surveillance to estimate the contribution of different sources to human disease. A probabilistic model was developed based on outbreak data that attributes Salmonellosis to sources in Latin America and the Caribbean (LA&C). Foods implicated in outbreaks were classified by their ingredients as simple foods (i.e. belonging to one single food category), or complex foods (i.e. belonging to multiple food categories). For each agent, the data from simple-food outbreaks were summarized, and the proportion of outbreaks caused by each category was used to define the probability that an outbreak was caused by a source. For the calculation of the number of outbreaks attributed to each source, simple-food outbreaks were attributed to the single food category in question, and complex-food outbreaks were partitioned to each category proportionally to the estimated probability. We analysed Salmonella and performed analyses by decade.The objectives of the model is to estimate (i) the proportion of Salmonellosis attributed to different sources by decade, and (ii) the probability that an outbreak was caused be each source.

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Model scope
Field Value
Hazard Salmonella
Hazard Salmonella
Hazard Salmonella
Hazard Salmonella
Hazard Salmonella
Hazard Salmonella
Hazard Salmonella
Hazard Salmonella
Hazard Salmonella
Hazard Salmonella
Hazard Salmonella
Hazard Salmonella
Product Meat preparations of meat offals blood animal fats fresh chilled or frozen salted in brine
Product Meat preparations of meat offals blood animal fats fresh chilled or frozen salted in brine
Product Swine
Product Bovine
Product Poultry chicken geese duck turkey and Guinea fowl ostrich pigeon Others
Product Poultry chicken geese duck turkey and Guinea fowl ostrich pigeon Others
Product Poultry chicken geese duck turkey and Guinea fowl ostrich pigeon Others
Product Poultry chicken geese duck turkey and Guinea fowl ostrich pigeon Others
Product Meat preparations of meat offals blood animal fats fresh chilled or frozen salted in brine
Product Dairy products Goat
Product Dairy products Others
Product Eggs Chicken
Model parameters
Field Value
Input Parameter Initial values of the PriorS: []( Vector[number]), Default: c(0.1, 0.01, 0.2, 0.05, 0.3)
Input Parameter Number of product sources: []( Integer), Default: 19
Input Parameter Outbreaks data: []( File), Default: read.csv(Salmonella-all.csv, header=TRUE, as.is=TRUE, dec=,, sep=;)
Input Parameter Number of burn-in iterations: []( Integer), Default: 0
Input Parameter Number of Gibbs chains: []( Integer), Default: 5
Input Parameter Number of Gibbs iterations per chain: []( Integer), Default: 20
Output Parameter Proportions of outbreaks with unknown source (mean): %( Vector[number])
Output Parameter Proportion of disease attributed to each source per time period (mean, sd, 2.5th percentile, median and 97.5th percentile of all simulated values): %( Matrix[number,number])
Output Parameter Probability that an outbreak was caused by a specific source (mean, sd, 2.5th percentile, median and 97.5th percentile of all simulated values): [Probability]( Vector[number])
Output Parameter Number of time periods (decades/years/etc): []( Integer)
Additional Info
Field Value
Model Author Nauta, Maarten, [email protected]
Model Creator Stylianos, [email protected]
Model ID PiresOutbLA2011-Salmonella
Model Language R 3
ReadMe This model is made available in the FSK-ML format, i.e. as .fskx file. To execute the model or to perform model-based predictions it is recommended to use the software FSK-Lab. FSK-Lab is an open-source extension of the open-source data analytics platform KNIME. To install FSK-Lab follow the installation instructions available at: https://foodrisklabs.bfr.bund.de/fsk-lab_de/. Once FSK-Lab is installed a new KNIME workflow should be created and the FSKX Reader node should be dragged into it. This FSKX Reader node can be configured to read in the given .fskx file. To perform a model-based prediction connect the out-port of the FSKX Reader node with the FSK Simulation Configurator JS node to adjust if necessary input parameters and store this into a user defined simulation setting, After that connect the output port with the input of a FSK Runner node that perform the simulation and look at the results at the node's outport.
Reference Description Attributing human foodborne illness to food sources and water in Latin America and the Caribbean using data from outbreak investigations DOI: https://doi.org/10.1016/j.ijfoodmicro.2011.04.018
system:type FSKXModel
Management Info
Field Value
Author thomas_schueler
Last Updated 3 February 2021, 17:09 (CET)
Created 17 September 2019, 14:32 (CEST)