PROBABILISTIC MODELLING IN FOOD SAFETY: A SCIENCE-BASED APPROACH FOR POLICY DECISIONS

This thesis deals with use of qualitative and quantitative probabilistic models for the animal-derived food safety management. Four unrelated models are presented: three quantitative and one qualitative. Two of the quantitative models concern the risk posed by pathogens in raw milk, in the first study, a probabilistic approach for the inclusion of the variability and the uncertainty in the consumers\u2019 habits and the bacterial pathogenic potential is proposed while the second study, demonstrate how the overlook of the relationship between the storage time and temperature has led to overestimated results in raw milk-related models published so far and an equation to address the issue is provided. In the third study, quantitative modelling techniques are used to simulate the dynamics underlying the spread of Campylobacter in broiler flocks and quantify the potential effects that different on-farm mitigation strategies or management measures have on the microbial load in the intestine of infected birds at the end of the rearing period. In the qualitative study, a general approach for the estimation of the likelihoods of introduction of live parasites in aquaculture implants and the commercialization of infested product is outlined by using the example of Anisakids in farmed Atlantic salmon

Quantitative risk assessment of hepatitis E virus: modelling the occurrence of viraemic pigs and the presence of the virus in organs of food safety interest

Hepatitis E virus (HEV) is a zoonotic pathogen with consumption of pork and derived products identified in different countries as a risk factor for human exposure to HEV. Great efforts have been made to understand the dynamics of virus transmission within domestic swine populations through modelling. However, from a food safety prospective, it is critical to integrate the parameters involved in the transmission dynamics with those governing the actual presence of HEV in the bloodstream, the liver, gallbladder or faeces. To date, several aspects related to the pathogenesis of the disease are still unknown or characterized by significant levels of uncertainty, making this conjunction challenging. We used published serological data obtained from pigs in a farrow-to-finish farm to implement an Immune-Susceptible-Infected-Recovered (MSIR) model reproducing the on-farm dynamics that lead to the occurrence of viraemic pigs at slaughter. Expert opinion on the length of time infectious HEV can be detected in liver, gallbladder/bile and faeces after recovery from viraemic status were used to inform a stochastic model aimed at estimating the expected proportion of viraemic pigs, pigs with infectious HEV in liver, gallbladder/bile and faeces entering the slaughterhouse. To simulate the potential effect of on-farm mitigation strategies, we estimated the changes in outcomes of interest as a function of variations in the baseline transmission parameters. The model predicted a proportion of viraemic pigs entering the slaughterhouse of 13.8% while the proportions of, and ranged from 13.8% to 94.4%, 13.8% to 94.7% and from 25.3% to 30.8% respectively, due to the uncertainty surrounding the experts’ opinions. Variations in MSIR model’s parameters alert of the need to carefully consider the application of mitigation strategies aimed at delaying the decay of maternal immunity or the peak of the within herd transmission. When the rate of decay of maternal immunity and the transmission rate were decreased between 80% and 5% and 40% and 5% from the baseline values respectively, adverse effects on were observed. The model highlights the relevance of specific aspects in the pathogenesis of the disease from a food safety prospective and it was developed to be easily reproducible and updatable as soon as accurate data becomes available. As presented, the model can be directly connected to existing or future pig-related models to estimate the significance of the identified parameters on the risk of human exposure to HEV through consumption of pork products

Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining genomic and epidemiological metadata

Foodborne infection is a result of exposure to complex, dynamic food systems. The efficiency of foodborne infection is driven by ongoing shifts in genetic machinery. Next-generation sequencing technologies can provide high-fidelity data about the genetics of a pathogen. However, food safety surveillance systems do not currently provide similar high-fidelity epidemiological metadata to associate with genetic data. As a consequence, it is rarely possible to transform genetic data into actionable knowledge that can be used to genuinely inform risk assessment or prevent outbreaks. Big data approaches are touted as a revolution in decision support, and pose a potentially attractive method for closing the gap between the fidelity of genetic and epidemiological metadata for food safety surveillance. We therefore developed a simple food chain model to investigate the potential benefits of combining ‘big’ data sources, including both genetic and high-fidelity epidemiological metadata. Our results suggest that, as for any surveillance system, the collected data must be relevant and characterize the important dynamics of a system if we are to properly understand risk: this suggests the need to carefully consider data curation, rather than the more ambitious claims of big data proponents that unstructured and unrelated data sources can be combined to generate consistent insight. Of interest is that the biggest influencers of foodborne infection risk were contamination load and processing temperature, not genotype. This suggests that understanding food chain dynamics would probably more effectively generate insight into foodborne risk than prescribing the hazard in ever more detail in terms of genotype

The transmission dynamics of Campylobacter jejuni among broilers in semi-commercial farms in Jordan

Campylobacter is the leading cause of foodborne bacterial gastroenteritis in humans worldwide, often associated with the consumption of undercooked poultry. In Jordan, the majority of broiler chicken production occurs in semi-commercial farms, where poor housing conditions and low bio-security are likely to promote campylobacter colonisation. While several studies provided estimates of the key parameters describing the within-flock transmission dynamics of campylobacter in typical high-income countries settings, these data are not available for Jordan and Middle-East in general. A Bayesian model framework was applied to a longitudinal dataset on Campylobacter jejuni infection in a Jordan flock to quantify the transmission rate of C. jejuni in broilers within the farm, the day when the flock first became infected, and the within-flock prevalence (WFP) at clearance. Infection with C. jejuni is most likely to have occurred during the first 8 days of the production cycle, followed by a transmission rate value of 0.13 new infections caused by one infected bird/day (95% CI 0.11–0.17), and a WFP at clearance of 34% (95% CI 0.24–0.47). Our results differ from published studies conducted in intensive poultry production systems in high-income countries but are well aligned with the expectations obtained by means of structured questionnaires submitted to academics with expertise on campylobacter in Jordan. This study provides for the first time the most likely estimates and credible intervals of key epidemiological parameters driving the dynamics of C. jejuni infection in broiler production systems commonly found in Jordan and the Middle-East and could be used to inform Quantitative Microbial Risk Assessment models aimed to assess the risk of human exposure/infection to campylobacter through consumption of poultry meat

Viraemic pigs entering the food chain are the most likely source of hepatitis E virus (HEV) in pork meat: Modelling the fate of HEV during slaughtering of pigs

Hepatitis E Virus (HEV) is an emerging foodborne pathogen and consumption of raw or undercooked pork products has been associated with increased risk of human infection. This work represents the first attempt to evaluate the risk of HEV being present on pig carcasses and in meat at the end of the slaughtering process considering the steps of bleeding, scalding, dehairing, singeing, polishing, evisceration and trimming. Based on available knowledge on the epidemiology and biology of HEV, the risk pathways leading to the presence of HEV on carcasses as a consequence of (i) faecal contamination of the skin from environment and contacts with contaminated faeces during transport and lairage, (ii) contact with viraemic blood at bleeding and (iii) faecal/bile cross-contamination during evisceration were assessed qualitatively. The pathway through which HEV could be present in meat of viraemic pigs, as conveyed by residual blood in muscular tissue after bleeding was instead modelled quantitatively. Of the three risk pathways evaluated qualitatively, only the occurrence of HEV on carcasses as a consequence of accidental rupture of the gut or gallbladder at evisceration was found to be non-negligible, but with a very low likelihood of occurrence. The quantitative output for the expected amount of HEV in meat of viraemic pigs shows minimum and maximum values of 0.10 and 1.1 × 104 genome copies (gc)/g respectively with 4.8 × 102 and 5.3 × 103 gc/g at 95th and 99th percentile of the cumulative distribution. These results are consistent with the existing evidence that levels of HEV RNA in meat samples are usually low even in the presence of high viral loads in livers of the same animals. Results of the sensitivity analysis confirm highly viraemic pigs entering the slaughter line as those posing the greater risk for consumers. Our study suggests that prevention of HEV infection through consumption of pork meat at pre-harvest/harvest stages should focus on reducing the flow of highly viraemic pigs into the food chain

A Serpin shapes the extracellular environment to prevent influenza A virus maturation

Interferon-stimulated genes (ISGs) act in concert to provide a tight barrier against viruses. Recent studies have shed light on the contribution of individual ISG effectors to the antiviral state, but most have examined those acting on early, intracellular stages of the viral life cycle. Here, we applied an image-based screen to identify ISGs inhibiting late stages of influenza A virus (IAV) infection. We unraveled a directly antiviral function for the gene SERPINE1, encoding plasminogen activator inhibitor 1 (PAI-1). By targeting extracellular airway proteases, PAI-1 inhibits IAV glycoprotein cleavage, thereby reducing infectivity of progeny viruses. This was biologically relevant for IAV restriction in vivo. Further, partial PAI-1 deficiency, attributable to a polymorphism in human SERPINE1, conferred increased susceptibility to IAV in vitro. Together, our findings reveal that manipulating the extracellular environment to inhibit the last step in a virus life cycle is an important mechanism of the antiviral response