This package provides function to evaluate the Dose-Response models from the the manuscript “Updated parameters for the dose-response model for Listeria monocytogenes considering pathogen virulence and age and sex of consumer”. from Régis Pouillot, Andreas Kiermeier, Laurent Guillier, Vasco Cadavez, and Moez Sanaa. Foods 2024, 13(5), 751 (https://doi.org/10.3390/foods13050751).
R package for Dose Response models
Package installation
install.packages("devtools")
devtools::install_github("WorldHealthOrganization/doseresponsemodels")Usage
The doseresponsemodels::DRQuick() function provides a “quick” version of the function to derive the marginal (over individuals and servings) probability of invasive listeriosis in a given population for a given dose in CFU (actual dose if the argument Poisson = FALSE or average dose if the argument Poisson = TRUE) using the “JEMRA” 2004, the “Pouillot” et al., 2015, the “Fritsch” et al. 2018, the “EFSA”, 2018 dose-response models or the model developed within this project (“EFSAMV” for more virulent strains, “EFSAV” for virulent strains, or “EFSALV” for the less virulent strains).
library("doseresponsemodels")
help('DRQuick')
DRQuick(1:10, model="JEMRA", population = 1:2)
DRQuick(1:10, model="Pouillot", population = 1:11)
DRQuick(1:10, model="EFSA", population = 1:14)
DRQuick(1:10, model="EFSAMV", population = 1:14)This function uses (for all model but JEMRA) a linear approximation (approxfun) from the exact doseresponsemodels::DR() function.
| Model | Population | Characteristics |
|---|---|---|
| JEMRA | 0 | Marginal over subpopulations |
| JEMRA | 1 | Healthy population |
| JEMRA | 2 | Increased susceptibility |
| Pouillot | 0 | Marginal over subpopulations |
| Pouillot | 1 | Less than 65 years old |
| Pouillot | 2 | More than 65 years old |
| Pouillot | 3 | Pregnancy |
| Pouillot | 4 | Nonhematological Cancer |
| Pouillot | 5 | Hematological cancer |
| Pouillot | 6 | Renal or Liver failure |
| Pouillot | 7 | Solid organ transplant |
| Pouillot | 8 | Inflammatory diseases |
| Pouillot | 9 | HIV/AIDS |
| Pouillot | 10 | Diabetes |
| Pouillot | 11 | Heart diseases |
| Fritsch | 0 | Marginal over virulence |
| Fritsch | 1 | Highly virulent |
| Fritsch | 2 | Medium virulent |
| Fritsch | 3 | Hypovirulent |
| EFSA-EFSALV-EFSAV-EFSAMV | 0 | Marginal over subpopulations |
| EFSA-EFSALV-EFSAV-EFSAMV | 1 | Female 1-4 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 2 | Male 1-4 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 3 | Female 5-14 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 4 | Male 5-14 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 5 | Female 15-24 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 6 | Male 15-24 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 7 | Female 25-44 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 8 | Male 25-44 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 9 | Female 45-64 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 10 | Male 45-64 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 11 | Female 65-74 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 12 | Male 65-74 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 13 | Female >75 yo |
| EFSA-EFSALV-EFSAV-EFSAMV | 14 | Male >75 yo |
References
EFSA (2018). “Scientific opinion on the Listeria monocytogenes contamination of ready-to-eat foods and the risk from human health in the EU.” EFSA Journal, 16(1), 5134 (https://doi.org/10.2903/j.efsa.2018.5134).
FAO-WHO (2004). “Risk assessment of Listeria monocytogenes in ready-to-eat foods: Technical report.” World Health Organization and Food and Agriculture Organization of the United Nations (https://www.fao.org/3/y5394e/y5394e00.pdf).
Fritsch L, Guillier L, Augustin J (2018). “Next generation quantitative microbiological risk assessment: Refinement of the cold smoked salmon-related listeriosis risk model by integrating genomic data.” Microbial Risk Analysis, 10, 20–27. (https://doi.org/10.1016/j.mran.2018.06.003).
Pouillot R, Hoelzer K, Chen Y, Dennis SB (2015). “Listeria monocytogenes dose response revisited–incorporating adjustments for variability in strain virulence and host susceptibility.” Risk Analysis, 35(1), 90–108. (https://doi.org/10.1111/risa.12235).