Next generation microbiological risk assessment—Potential of omics data for hazard characterisation
Haddad, Nabila ; Johnson, Nick ; Kathariou, Sophia ; Métris, Aline ; Phister, Trevor ; Pielaat, Annemarie ; Tassou, Chrysoula ; Wells-Bennik, Marjon H.J. ; Zwietering, Marcel H. - \ 2018
International Journal of Food Microbiology 287 (2018). - ISSN 0168-1605 - p. 28 - 39.
Dose-response - Food safety - Functional genomics - Pathogenicity - Public health - Quantitative transcriptomics and proteomics - Risk analysis - Virulence
According to the World Health Organization estimates in 2015, 600 million people fall ill every year from contaminated food and 420,000 die. Microbial risk assessment (MRA) was developed as a tool to reduce and prevent risks presented by pathogens and/or their toxins. MRA is organized in four steps to analyse information and assist in both designing appropriate control options and implementation of regulatory decisions and programs. Among the four steps, hazard characterisation is performed to establish the probability and severity of a disease outcome, which is determined as function of the dose of toxin and/or pathogen ingested. This dose-response relationship is subject to both variability and uncertainty. The purpose of this review/opinion article is to discuss how Next Generation Omics can impact hazard characterisation and, more precisely, how it can improve our understanding of variability and limit the uncertainty in the dose-response relation. The expansion of omics tools (e.g. genomics, transcriptomics, proteomics and metabolomics) allows for a better understanding of pathogenicity mechanisms and virulence levels of bacterial strains. Detection and identification of virulence genes, comparative genomics, analyses of mRNA and protein levels and the development of biomarkers can help in building a mechanistic dose-response model to predict disease severity. In this respect, systems biology can help to identify critical system characteristics that confer virulence and explain variability between strains. Despite challenges in the integration of omics into risk assessment, some omics methods have already been used by regulatory agencies for hazard identification. Standardized methods, reproducibility and datasets obtained from realistic conditions remain a challenge, and are needed to improve accuracy of hazard characterisation. When these improvements are realized, they will allow the health authorities and government policy makers to prioritize hazards more accurately and thus refine surveillance programs with the collaboration of all stakeholders of the food chain.
First step in using molecular data for microbial food safety risk assessment; hazard identification of Escherichia coli O157 : H7 by coupling genomic data with in vitro adherence to human epithelial cells
Pielaat, Annemarie ; Boer, M.P. ; Wijnands, Lucas M. ; Hoek, A.H.A.M. van; Bouw, El ; Barker, G.C. ; Teunis, P.F.M. ; Aarts, Henk J.M. ; Franz, Eelco - \ 2015
International Journal of Food Microbiology 213 (2015). - ISSN 0168-1605 - p. 130 - 138.
GWAS - Microbiology - Risk assessment - SNP - STEC
The potential for using whole genome sequencing (WGS) data in microbiological risk assessment (MRA) has been discussed on several occasions since the beginning of this century. Still, the proposed heuristic approaches have never been applied in a practical framework. This is due to the non-trivial problem of mapping microbial information consisting of thousands of loci onto a probabilistic scale for risks. The paradigm change for MRA involves translation of multidimensional microbial genotypic information to much reduced (integrated) phenotypic information and onwards to a single measure of human risk (i.e. probability of illness).In this paper a first approach in methodology development is described for the application of WGS data in MRA; this is supported by a practical example. That is, combining genetic data (single nucleotide polymorphisms; SNPs) for Shiga toxin-producing Escherichia coli (STEC) O157 with phenotypic data (in vitro adherence to epithelial cells as a proxy for virulence) leads to hazard identification in a Genome Wide Association Study (GWAS).This application revealed practical implications when using SNP data for MRA. These can be summarized by considering the following main issues: optimum sample size for valid inference on population level, correction for population structure, quantification and calibration of results, reproducibility of the analysis, links with epidemiological data, anchoring and integration of results into a systems biology approach for the translation of molecular studies to human health risk.Future developments in genetic data analysis for MRA should aim at resolving the mapping problem of processing genetic sequences to come to a quantitative description of risk. The development of a clustering scheme focusing on biologically relevant information of the microbe involved would be a useful approach in molecular data reduction for risk assessment.
|A foresight study on emerging technologies: State of the art of omics technologies and potential applications. REPORT 1: Review on the state of art of omics technologies in risk assessment related to food and feed safety
Pielaat, A. ; Barker, A. ; Hendriksen, P.J.M. ; Hollman, P.C.H. ; Peijnenburg, A.A.C.M. ; Kuijle, B.H. ter - \ 2013
Parma (I) : EFSA (supporting publications EN-495) - 126 p.
A quantitative approach towards a better understanding of the dynamics of Salmonella spp. in a pork slaughter-line
Hoek, A.H.A.M. van; Jonge, R. de; Overbeek, W.M. van; Bouw, E.M. ; Pielaat, A. ; Smid, J.H. ; Malorny, B. ; Junker, E. ; Lofstrom, C. ; Pedersen, K. ; Aarts, H.J.M. ; Heres, L. - \ 2012
International Journal of Food Microbiology 153 (2012)1-2. - ISSN 0168-1605 - p. 45 - 52.
enterica serovar typhimurium - cross-contamination - carcasses - prevalence - excision - pigs - electrophoresis - identification - abattoirs - gauze
Pork contributes significantly to the public health disease burden caused by Salmonella infections. During the slaughter process pig carcasses can become contaminated with Salmonella. Contamination at the slaughter-line is initiated by pigs carrying Salmonella on their skin or in their faeces. Another contamination route could be resident flora present on the slaughter equipment. To unravel the contribution of these two potential sources of Salmonella a quantitative study was conducted. Process equipment (belly openers and carcass splitters), faeces and carcasses (skin and cutting surfaces) along the slaughter-line were sampled at 11 sampling days spanning a period of 4 months. Most samples taken directly after killing were positive for Salmonella. On 96.6% of the skin samples Salmonella was identified, whereas a lower number of animals tested positive in their rectum (62.5%). The prevalence of Salmonella clearly declined on the carcasses at the re-work station, either on the cut section or on the skin of the carcass or both (35.9%). Throughout the sampling period of the slaughter-line the total number of Salmonella per animal was almost 2log lower at the re-work station in comparison to directly after slaughter. Seven different serovars were identified during the study with S. Derby (41%) and S. Typhimurium (29%) as the most prominent types. A recurring S. Rissen contamination of one of the carcass splitters indicated the presence of an endemic 'house flora' in the slaughterhouse studied. On many instances several serotypes per individual sample were found. The enumeration of Salmonella and the genotyping data gave unique insight in the dynamics of transmission of this pathogen in a slaughter-line. The data of the presented study support the hypothesis that resident flora on slaughter equipment was a relevant source for contamination of pork.
Circulation of Group 2 Coronaviruses in a Bat Species Common to Urban Areas in Western Europe
Reusken, C.B.E.M. ; Lina, P.H.C. ; Pielaat, A. ; Vries, A. de; Dam-Deisz, C. ; Adema, J. ; Drexler, J.F. ; Drosten, C. ; Kooi, E.A. - \ 2010
Vector-Borne and Zoonotic Diseases 10 (2010)8. - ISSN 1530-3667 - p. 785 - 791.
acute respiratory syndrome - chinese horseshoe bats - sequence - prevalence - diversity - humans - virus - swine
Fecal samples of 211 bats representing 13 different bat species from 31 locations in the Netherlands were analyzed for the presence of coronaviruses (CoV) using a genus-wide reverse transcription (RT)-polymerase chain reaction. CoVs are known for their high potential for interspecies transmission, including zoonotic transmission with bats as reservoir hosts. For the first time, a group 2 CoV was found in a bat, Pipistrellus pipistrellus, in Europe. This is of particular interest for public health as the reservoir host is a species that is common to urban areas in most of Europe and notorious for its close interactions with humans. Four verspertilionid bat species were found to excrete group 1 CoVs, viz. Myotis daubentonii, M. dasycneme, P. pipistrellus, and Nyctalus noctula. The last species is a newly identified reservoir. The overall prevalence was 16.9% and positive bats were found at multiple widespread locations. The circulating group 1 CoV lineages were rather species associated than location associated.
Modelling the number of viable vegetative cells of Bacillus cereus passing through the stomach
Wijnands, L.M. ; Pielaat, A. ; Dufrenne, J.B. ; Zwietering, M.H. ; Leusden, F.M. van - \ 2009
Journal of Applied Microbiology 106 (2009)1. - ISSN 1364-5072 - p. 258 - 267.
acid tolerance response - gastrointestinal transit - hemolysin bl - low-ph - healthy - prevalence - strains - growth - spores - foods
Aims: Model the number of viable vegetative cells of B. cereus surviving the gastric passage after experiments in simulated gastric conditions. Materials and Methods: The inactivation of stationary and exponential phase vegetative cells of twelve different strains of Bacillus cereus, both mesophilic and psychrotrophic strains isolated from food and faeces from healthy and ill individuals, in simulated gastric conditions was determined using decimal reduction times at low pH (DpH). Subsequently inactivation rates were calculated. Inclusion of the inactivation rates into models describing the course of the gastric pH after the consumption of meal of solid food and the transfer of food from the stomach to the small intestine resulted in numbers of viable Bacillus cereus vegetative cells able to pass the stomach. Conclusions: According to the model, 3¿26% of the ingested vegetative cells from Bacillus cereus may survive the gastric passage, dependent on the growth phase of the vegetative cells, the type of strains, and the age of the consumer. Significance and Impact of the Study: Vegetative cells of Bacillus cereus may be involved in the onset of diarrhoeal disease to a greater extent than expected since up to 26% of the ingested cells survive simulated gastric conditions.
Towards an integrated approach in supporting microbiological food safety decisions
Havelaar, A.H. ; Bräunig, J. ; Christiansen, K. ; Cornu, M. ; Hald, T. ; Mangen, M.J.J. ; Molbak, K. ; Pielaat, A. ; Snary, E. ; Pelt, W. van; Velthuis, A.G.J. ; Wahlström, H. - \ 2007
Zoonoses and Public Health 54 (2007)3. - ISSN 1863-1959 - p. 103 - 117.
quantitative risk-assessment - salmonella-enteritidis - united-states - campylobacter - netherlands - population - infections - disease - chickens - england
Decisions on food safety involve consideration of a wide range of concerns including the public health impact of foodborne illness, the economic importance of the agricultural sector and the food industry, and the effectiveness and efficiency of interventions. To support such decisions, we propose an integrated scientific approach combining veterinary and medical epidemiology, risk assessment for the farm-to-fork food chain as well as agricultural and health economy. Scientific advice is relevant in all stages of the policy cycle: to assess the magnitude of the food safety problem, to define the priorities for action, to establish the causes for the problem, to choose between different control options, to define targets along the food chain and to measure success.
|Integrating risk assessment, epidemiology and economics to support decision making in food safety
Havelaar, A.H. ; Bräunig, J. ; Christiansen, K. ; Cornu, M. ; Hald, T. ; Mangen, M.J.J. ; Molbak, K. ; Pielaat, A. ; Snary, E. ; Boven, R.M. van; Pelt, W. van; Velthuis, A.G.J. ; Wahlstrom, H. - \ 2006
Surry United Kingdom : EU (Med-Vet-Net 06-001) - 78 p.
|Quantification of the number of surviving B. cereus vegetative cells during passage of the stomach
Wijnands, L.M. ; Pielaat, A. ; Zwietering, M.H. ; Leusden, F.M. van - \ 2006
In: Food safety and food biotechnology: diversity and global impact. - Bologna : Food Micro 2006 - p. 239 - 239.
Splash : the dispersal of fungal plant pathogens in rain events
Pielaat, A. - \ 2000
Agricultural University. Promotor(en): M.J. Jeger; F. van den Bosch. - S.l. : S.n. - ISBN 9789058082121 - 116
plantenziekteverwekkende schimmels - sporen - pyrenopeziza brassicae - colletotrichum acutatum - verspreiding - regen - plant pathogenic fungi - spores - pyrenopeziza brassicae - colletotrichum acutatum - dispersal - rain
Models were developed to study splash dispersal of fungal plant pathogens in space and time. The models incorporate the main mechanisms involved in splash dispersal, that is 1. A raindrop hits the thin water film on the crop surface containing spores and spores are dispersed in the splashing rain droplets, and 2. Splashed spores are redistributed in the crop and on the soil surface. A mechanistic random 'jump' model describes the stochastic processes of splash dispersal over a homogeneous surface from a point source. Numerical analysis showed the importance of ground cover and rain intensity as factors determining model output. More spores were splashed in high intensity rains and, simultaneously, more spores were removed from the system. A diffusion approximation was developed for this mechanistic model which could only be considered a reasonable approximation under certain limiting conditions.
Based on the two-dimensional version of the mechanistic model an equation was developed for the total number of spores in the area surrounding an inoculum source over time, N(t). In addition, equations for the expected mean, E(r), and mean squared distance, E(r 2), spores travel during a rain event at a given time were developed. Observed data and model predictions showed that both N(t) and E(r 2) increased to a maximum over time and then declined due to spore removal from the system and depletion of spores at the source. Factors influencing the process could be assessed by changing parameter values.
Upward displacement of lesions by stem extension and dispersal of fungal conidia by rain-splash are mechanisms contributing to within-crop disease spread. These mechanisms were incorporated into a model based on the interaction between winter oilseed rape and the light leaf spot pathogen ( Pyrenopeziza brassicae ) as an example. Experimental results showed that most conidia were dispersed during a 15 min duration of rainfall. The trajectory of a droplet depended on the impacted plant part, with a mean horizontal travel distance decreasing with increasing incident drop diameter and a maximum splash height which ranged from 0.3 cm when splashed from a flower up to 57 cm for a pod.
These results were incorporated into the model. Stem extension was shown to be an important factor influencing vertical disease spread. Rain events contributed to the splash dispersal of conidia to the plant apex and resulting lesions were directed vertically by internode growth. Periods with frequent rain events in a dense crop canopy were most favorable for disease progress. The upward spread of light leaf spot on winter oilseed rape in experiments at the Institute of Arable Crops Research, Harpenden, UK, was similar to that predicted by the model. Finally, an analytical model was proposed to study the influence of crop characteristics and rain properties on the vertical spread of splashed spores. Splash dispersal was concentrated in the upper layers in a crop having a constant or increasing leaf surface area with height. The greatest splash probabilities occurred and most spores were intercepted in the layers just below the apex of a crop having a decreasing leaf surface area with height.
|Vertical spread of plant diseases in a crop canopy by stem extension and splash dispersal simulations
Pielaat, A. ; Bosch, F. van den; Fitt, B.D.L. - \ 1999
Wageningen : Wageningen University. Department of Agricultural, Environmental and Systems Technology, Subdepartment Mathematic (Technical Note 99-07) - 25 p.
Spores splashing under different environmental conditions: a modeling approach.
Pielaat, A. ; Madden, L.V. ; Gort, G. - \ 1998
Phytopathology 88 (1998). - ISSN 0031-949X - p. 1131 - 1140.
|A model for dispersal of plant pathogens by rainsplash.
Pielaat, A. ; Bosch, F. van den - \ 1998
IMA Journal of Mathematics Applied in Medicine and Biology 15 (1998). - ISSN 0265-0746 - p. 117 - 134.