Using network analysis to identify seasonal patterns and key nodes for risk-based surveillance of pig diseases in Italy

The description of the pattern of livestock movements between herds provides essential information for both improving risk-based surveillance and to understand the likely spread of infectious diseases. This study provides a description of the temporal pattern of pig movements recorded in Italy on a 4-year period (2013–2016). Data, provided by the National Livestock registry, were described by social network analysis and the application of a walk-trap algorithm for community detection. Our results show a highly populated community located in Northern Italy, which is the focal point of the Italian industrial pig production and as a general pattern an overall decline of medium and backyard farms and an increase in the number of large farms, in agreement with the trend observed by other EU pig-producing countries. A seasonal pattern of all the parameters evaluated, including the number of active nodes in both the intensive and smaller production systems, emerged: that is characterized by a higher number of movements in spring and autumn, linked with the breeding and production cycle as pigs moved from the growing to the finishing phase and with periods of increased slaughtering at Christmas and Easter. The same pattern was found when restricting the analysis to imported pig batches. Outbreaks occurring during these periods would have a greater impact on the spread of infectious diseases; therefore, targeted surveillance may be appropriate. Finally, potential super-spreader nodes have been identified and represent 0.47% of the total number of pig holdings (n = 477). Those nodes are present during the whole study period with a similar ranking in their potential of being super-spreaders. Most of them were in Northern Italy, but super-spreaders with high mean out-degree centrality were also located in other Regions. Seasonality, communities and super-spreaders should be considered when planning surveillance activity and when applying disease control strategies

Maximising data to optimise animal disease early warning systems and risk assessment tools within Europe

Timely and reliable data and information availability and sharing is essential for early warning, prevention and control of transboundary diseases. While there are a growing number of global datasets capable of providing information for use in early warning systems and risk assessment (RA) tools, there are currently time-consuming data cleansing and harmonisation activities which need to be carried out before they can be reliably used and combined. Thus, using global datasets as they stand can lead to errors in RA parameterisation and results due to inherent biases in the data, e.g. missing disease prevalence data treated as a zero may inadvertently penalise those countries which do report disease outbreaks as opposed to those countries which are affected by a pathogen but do not report outbreak data. It is therefore of great importance that data are clearly provided and easy to understand and that data providers strive for greater harmonisation of database standards. In this paper the datasets utilised in the SPARE (’Spatial risk assessment framework for assessing exotic disease incursion and spread through Europe’) project are described and discussed in terms of key criteria: accessibility, availability, completeness, consistency and quality. It is evident that most databases exist as information portals and not exclusively for RA purposes. Another striking issue from this assessment is the need for enhanced data sharing specifically with regards to data on illegal seizures, arthropod vector/wildlife abundance, intra-country livestock movement and national animal disease surveillance. It is hoped that the outcomes of this work will promote discussion and exchange between data providers, including the development of standardised data exchange protocols. The transformation of datasets to a common format is a considerable challenge but recommendations could and should be made on the standardisation of datasets and reporting in order to achieve a unified approach across Europe

Using multi-criteria risk ranking methodology to select case studies for a generic risk assessment framework for exotic disease incursion and spread through Europe

We present a novel approach of using the multi-criteria pathogen prioritisation methodology as a basis for selecting the most appropriate case studies for a generic risk assessment framework. The approach uses selective criteria to rank exotic animal health pathogens according to the likelihood of introduction and the impact of an outbreak if it occurred in the European Union (EU). Pathogens were evaluated based on their impact on production at the EU level and international trade. A subsequent analysis included criteria of relevance to quantitative risk assessment case study selection, such as the availability of data for parameterisation, the need for further research and the desire for the case studies to cover different routes of transmission. The framework demonstrated is flexible with the ability to adjust both the criteria and their weightings to the user's requirements. A web based tool has been developed using the RStudio shiny apps software, to facilitate this

Characterization of the Human Risk of Salmonellosis Related to Consumption of Pork Products in Different E.U. Countries Based on a QMRA

In response to the European Food Safety Authority's wish to assess the reduction of human cases of salmonellosis by implementing control measures at different points in the farm-to-consumption chain for pork products, a quantitative microbiological risk assessment (QMRA) was developed. The model simulated the occurrence of Salmonella from the farm to consumption of pork cuts, minced meat, and fermented ready-to-eat sausage, respectively, and a dose-response model was used to estimate the probability of illness at consumption. The QMRA has a generic structure with a defined set of variables, whose values are changed according to the E.U. member state (MS) of interest. In this article we demonstrate the use of the QMRA in four MSs, representing different types of countries. The predicted probability of illness from the QMRA was between 1 in 100,000 and 1 in 10 million per serving across all three product types. Fermented ready-to-eat sausage imposed the highest probability of illness per serving in all countries, whereas the risks per serving of minced meat and pork chops were similar within each MS. For each of the products, the risk varied by a factor of 100 between the four MSs. The influence of lack of information for different variables was assessed by rerunning the model with alternative, more extreme, values. Out of the large number of uncertain variables, only a few of them have a strong influence on the probability of illness, in particular those describing the preparation at home and consumption

A cost-benefit assessment of Salmonella-control strategies in pigs reared in the United Kingdom

Pork and pork products are a major source of human salmonellosis in the United Kingdom (UK). Despite a number of surveillance programmes, the prevalence of Salmonella in the UK slaughter pig population remains over 20%. Here, we present the results of a Cost-Benefit Analysis comparing five on-farm control strategies (where the cost is the cost of implementation and the benefits are the financial savings for both the human health and pig industries). The interventions considered were: wet feed, organic acids in feed, vaccination, enhanced cleaning and disinfection and movement of outdoor breeding units. The data originate from published papers and recent UK studies. The effectiveness was assessed by adapting a previous risk assessment, originally developed for the European Food Safety Authority. Using this method, none of the intervention strategies produced a net cost-benefit. Our results suggest that the cost of implementation outweighed the savings for all interventions, even if the effectiveness could be improved. Therefore, to achieve a net cost-benefit it is essential to reduce the cost of interventions. Analyses concluded that large cost reductions (up to 96%) would be required. Use of organic acids required the smallest reduction in cost (22.7%) to achieve a net cost benefit. Uncertainty analysis suggested that a small net gain might be possible, for some of the intervention measures. But this would imply that the model greatly underestimated some key parameters, which was considered unlikely. Areas of key uncertainty were identified as the under-reporting factor (i.e. the proportion of community cases of Salmonella) and the source attribution factor (i.e. the proportion of human Salmonella cases attributable to pork products)

A cost-benefit assessment of Salmonella-control strategies in pigs reared in the United Kingdom

Pork and pork products are a major source of human salmonellosis in the United Kingdom (UK). Despite a number of surveillance programmes, the prevalence of Salmonella in the UK slaughter pig population remains over 20%. Here, we present the results of a Cost-Benefit Analysis comparing five on-farm control strategies (where the cost is the cost of implementation and the benefits are the financial savings for both the human health and pig industries). The interventions considered were: wet feed, organic acids in feed, vaccination, enhanced cleaning and disinfection and movement of outdoor breeding units. The data originate from published papers and recent UK studies. The effectiveness was assessed by adapting a previous risk assessment, originally developed for the European Food Safety Authority. Using this method, none of the intervention strategies produced a net cost-benefit. Our results suggest that the cost of implementation outweighed the savings for all interventions, even if the effectiveness could be improved. Therefore, to achieve a net cost-benefit it is essential to reduce the cost of interventions. Analyses concluded that large cost reductions (up to 96%) would be required. Use of organic acids required the smallest reduction in cost (22.7%) to achieve a net cost benefit. Uncertainty analysis suggested that a small net gain might be possible, for some of the intervention measures. But this would imply that the model greatly underestimated some key parameters, which was considered unlikely. Areas of key uncertainty were identified as the under-reporting factor (i.e. the proportion of community cases of Salmonella) and the source attribution factor (i.e. the proportion of human Salmonella cases attributable to pork products)

Validation of generic risk assessment tools using a case study of African swine fever

Generic risk assessment (RA) tools can be applied to assess the incursion risk of multiple animal diseases, allowing for a rapid response to a variety of newly emerging or re-emerging diseases. To explore the opportunities for cross-validation of generic RA tools, seven tools were used to assess the incursion risk of African swine fever (ASF) for the Netherlands and Finland for the 2017 situation and for two hypothetical scenarios in which ASF cases were reported in wild boar and/or domestic pigs in Germany. The generic tools ranged from qualitative risk assessment tools to stochastic spatial risk models but were all parameterised using the same global databases. The tools had different outputs and endpoints and therefore the cross-validation focused on the relative risks across countries and scenarios. All tools evaluated the risk to the Netherlands to be higher than Finland for the live animal trade pathway. The risk to Finland was the same or higher as the Netherlands for the wild boar pathway, but the tools were inconclusive on the animal products pathway. All tools agreed that the hypothetical presence of ASF in Germany increased the risk for the Netherlands, but not for Finland. The case study illustrated that conclusions on the ASF risk were similar across the generic RA tools, despite differences observed in calculated risks. Hence, it was concluded that the cross-validation contributed to the credibility of their results