Using scenario tree modelling to evaluate the probability of freedom from Enzootic bovine leukosis (EBL) in Italy and Slovenia.

Documented freedom from disease is paramount for international free trade of animals and animal products. This study describes a scenario tree analysis to estimate the probability of freedom from Enzootic bovine leukosis (EBL) in Italy and Slovenia using information gathered via the data collection tool developed in the COST action project SOUND-control. Data on EBL control programmes (CPs) from 2018 to 2021 were used to build the models. Since animals are only sampled on the farm, one surveillance system component (SSC) was considered. The posterior probability of freedom (PostPfree) was estimated in time steps of one year, from 2018 to 2021.  After each year, the calculated from the previous year, combined with the probability of introduction, was used as a prior probability for the next year.  The herd level design prevalence was set to 0.2% in accordance with the Council Directive 64/432/EEC and the within herd design prevalence was set to 15%.  As Slovenia implemented a risk-based surveillance, targeting the herds importing cattle, in its model the design herd prevalence was combined with an average adjusted risk to calculate the effective probability of a herd importing cattle being infected.  The models were run for 10,000 iterations.  Over the study period the mean estimates were: i) for Italy both the surveillance system sensitivity ( SSe) and PostPFree 100%, with no differences between simulations and years, ii) for Slovenia the SSe was 50.5% while the PostPFree was 81.6%.

Needs and capabilities for improving poultry production and health management in Indonesia.

In Indonesia, the development of the poultry industry is facing numerous challenges. Major constraints include high disease burdens, large fluctuations in farm input and output prices, and inadequate biosecurity. Timely and reliable information about animal production and health can help stakeholders at all levels of the value chain make appropriate management decisions to optimize their profitability and productivity while reducing risks to public health. This study aimed to describe the challenges in the Indonesian poultry industry, assess stakeholders' needs and capabilities in terms of generating and using poultry information for making production and health management decisions, and identify levers for improvement. Interviews were conducted with a diversity of key informants and value chain actors in five Indonesian provinces. Thematic analysis was applied with an interpretivist approach to gain an in-depth understanding of the lived experiences of various stakeholders and their opinions as to what might constitute appropriate solutions. Our findings indicate that market and political instability, ineffective management of poultry data, and limited inter-sectoral collaboration are limiting the development of the sector. Increased intersectoral cooperation is needed to implement standards for data collection and sharing across the industry, provide education and practical training on the use of information technologies for farm management, and accelerate research and innovation. Our study can contribute to the development of data-driven tools to support evidence-based decision-making at all levels of the poultry system.

Review state-of-the-art of output-based methodological approaches for substantiating freedom from infection.

A wide variety of control and surveillance programmes that are designed and implemented based on country-specific conditions exists for infectious cattle diseases that are not regulated. This heterogeneity renders difficult the comparison of probabilities of freedom from infection estimated from collected surveillance data. The objectives of this review were to outline the methodological and epidemiological considerations for the estimation of probabilities of freedom from infection from surveillance information and review state-of-the-art methods estimating the probabilities of freedom from infection from heterogeneous surveillance data. Substantiating freedom from infection consists in quantifying the evidence of absence from the absence of evidence. The quantification usually consists in estimating the probability of observing no positive test result, in a given sample, assuming that the infection is present at a chosen (low) prevalence, called the design prevalence. The usual surveillance outputs are the sensitivity of surveillance and the probability of freedom from infection. A variety of factors influencing the choice of a method are presented; disease prevalence context, performance of the tests used, risk factors of infection, structure of the surveillance programme and frequency of testing. The existing methods for estimating the probability of freedom from infection are scenario trees, Bayesian belief networks, simulation methods, Bayesian prevalence estimation methods and the STOC free model. Scenario trees analysis is the current reference method for proving freedom from infection and is widely used in countries that claim freedom. Bayesian belief networks and simulation methods are considered extensions of scenario trees. They can be applied to more complex surveillance schemes and represent complex infection dynamics. Bayesian prevalence estimation methods and the STOC free model allow freedom from infection estimation at the herd-level from longitudinal surveillance data, considering risk factor information and the structure of the population. Comparison of surveillance outputs from heterogeneous surveillance programmes for estimating the probability of freedom from infection is a difficult task. This paper is a 'guide towards substantiating freedom from infection' that describes both all assumptions-limitations and available methods that can be applied in different settings.

"It's a habit. They've been doing it for decades and they feel good and safe.": A qualitative study of barriers and opportunities to changing antimicrobial use in the Indonesian poultry sector.

Interventions to change antimicrobial use (AMU) practices can help mitigate the risk of antimicrobial resistance (AMR) development. However, changing AMU practices can be challenging due to the complex nature of the factors influencing AMU-related behaviours. This study used a qualitative approach to explore the factors that influenced decision-making on AMU by farmers and other actors in the Indonesian poultry sector. Thirty-five semi-structured interviews were conducted with farmers, technical services staff from the private sector, and representatives of associations, universities, and international organisations in Central Java, West Java, and East Java. Thematic analysis identified three patterns of influence on AMU: how farmers used information to make AMU-related decisions, the importance of farmers' social and advisory networks, and the motivations driving changes in AMU behaviours. Key barriers identified included a lack of shared understanding around when to use antibiotics, financial pressures in the poultry sector, and a lack of engagement with government veterinary services. Potential opportunities identified included high farmer awareness of AMU, identification of private sector actors and peer networks as the stakeholders with established relationships of trust with farmers, and the importance of farmers' conceptions of good farming practices, which could be engaged with to improve AMU practices.

The DECIDE project: from surveillance data to decision-support for farmers and veterinarians.

Farmers, veterinarians and other animal health managers in the livestock sector are currently missing sufficient information on prevalence and burden of contagious endemic animal diseases. They need adequate tools for risk assessment and prioritization of control measures for these diseases. The DECIDE project develops data-driven decision-support tools, which present (i) robust and early signals of disease emergence and options for diagnostic confirmation; and (ii) options for controlling the disease along with their implications in terms of disease spread, economic burden and animal welfare. DECIDE focuses on respiratory and gastro-intestinal syndromes in the three most important terrestrial livestock species (pigs, poultry, cattle) and on reduced growth and mortality in two of the most important aquaculture species (salmon and trout). For each of these, we (i) identify the stakeholder needs; (ii) determine the burden of disease and costs of control measures; (iii) develop data sharing frameworks based on federated data access and meta-information sharing; (iv) build multivariate and multi-level models for creating early warning systems; and (v) rank interventions based on multiple criteria. Together, all of this forms decision-support tools to be integrated in existing farm management systems wherever possible and to be evaluated in several pilot implementations in farms across Europe. The results of DECIDE lead to improved use of surveillance data and evidence-based decisions on disease control. Improved disease control is essential for a sustainable food chain in Europe with increased animal health and welfare and that protects human health.

Corrigendum: Overview of Cattle Diseases Listed Under Category C, D or E in the Animal Health Law for Which Control Programmes Are in Place Within Europe.

[This corrects the article DOI: 10.3389/fvets.2021.688078.].

Electronic information systems for One Health surveillance of antimicrobial resistance: a systematic scoping review.

INTRODUCTION: Electronic information systems (EIS) that implement a 'One Health' approach by integrating antimicrobial resistance (AMR) data across the human, animal and environmental health sectors, have been identified as a global priority. However, evidence on the availability, technical capacities and effectiveness of such EIS is scarce. METHODS: Through a qualitative synthesis of evidence, this systematic scoping review aims to: identify EIS for AMR surveillance that operate across human, animal and environmental health sectors; describe their technical characteristics and capabilities; and assess whether there is evidence for the effectiveness of the various EIS for AMR surveillance. Studies and reports between 1 January 2000 and 21 July 2021 from peer-reviewed and grey literature in the English language were included. RESULTS: 26 studies and reports were included in the final review, of which 27 EIS were described. None of the EIS integrated AMR data in a One Health approach across all three sectors. While there was a lack of evidence of thorough evaluations of the effectiveness of the identified EIS, several surveillance system effectiveness indicators were reported for most EIS. Standardised reporting of the effectiveness of EIS is recommended for future publications. The capabilities of the EIS varied in their technical design features, in terms of usability, data display tools and desired outputs. EIS that included interactive features, and geospatial maps are increasingly relevant for future trends in AMR data analytics. CONCLUSION: No EIS for AMR surveillance was identified that was designed to integrate a broad range of AMR data from humans, animals and the environment, representing a major gap in global efforts to implement One Health approaches to address AMR.

Existence and Quality of Data on Control Programs for EU Non-regulated Cattle Diseases: Consequences for Estimation and Comparison of the Probability of Freedom From Infection.

Some European countries have successfully implemented country-specific control programs (CPs) for infectious cattle diseases that are not regulated or are regulated only to a limited extent at the European Union (EU) level. Examples of such diseases include bovine viral diarrhea (BVD), infectious bovine rhinotracheitis (IBR), and Johne's disease (JD). The CPs vary between countries in the design and quality of collected data as well as methods used to detect infection and estimate prevalence or probability of freedom from infection. Differences in disease status between countries and non-standardized approaches to assess freedom from infection pose a risk for countries with CPs for non-regulated diseases as infected animals may influence the progress of the disease control or eradication program. The implementation of output-based standards allows estimation and comparison of the probability of freedom for non-regulated cattle diseases in European countries. The aim of the current study was to assess the existence and quality of data that could be used for estimating freedom from infection in European countries. The online data collection tool was sent to 32 countries participating in the SOUND control COST Action and was completed by 24 countries. Data on cattle demographics and data from CPs of IBR and BVD exist in more than 50% of the response countries. However, data describing risk factors and CP of JD was reported as existing in <25% of the countries. The overall quality of data in the sections on demographics and CPs of IBR and BVD were evaluated as "good", but risk factors and JD data were mostly evaluated as "fair." Data quality was considered less good mainly due to two quality criteria: accessibility and accuracy. The results of this study show that the quantity and quality of data about cattle populations and CPs are relatively similar in many surveyed countries. The outcome of this work provides an overview of the current situation in the European countries regarding data on EU non-regulated cattle diseases and will further assist in the development and implementation of output-based standards.

Overview of Cattle Diseases Listed Under Category C, D or E in the Animal Health Law for Which Control Programmes Are in Place Within Europe.

The COST action "Standardising output-based surveillance to control non-regulated diseases of cattle in the European Union (SOUND control)," aims to harmonise the results of surveillance and control programmes (CPs) for non-EU regulated cattle diseases to facilitate safe trade and improve overall control of cattle infectious diseases. In this paper we aimed to provide an overview on the diversity of control for these diseases in Europe. A non-EU regulated cattle disease was defined as an infectious disease of cattle with no or limited control at EU level, which is not included in the European Union Animal health law Categories A or B under Commission Implementing Regulation (EU) 2020/2002. A CP was defined as surveillance and/or intervention strategies designed to lower the incidence, prevalence, mortality or prove freedom from a specific disease in a region or country. Passive surveillance, and active surveillance of breeding bulls under Council Directive 88/407/EEC were not considered as CPs. A questionnaire was designed to obtain country-specific information about CPs for each disease. Animal health experts from 33 European countries completed the questionnaire. Overall, there are 23 diseases for which a CP exists in one or more of the countries studied. The diseases for which CPs exist in the highest number of countries are enzootic bovine leukosis, bluetongue, infectious bovine rhinotracheitis, bovine viral diarrhoea and anthrax (CPs reported by between 16 and 31 countries). Every participating country has on average, 6 CPs (min-max: 1-13) in place. Most programmes are implemented at a national level (86%) and are applied to both dairy and non-dairy cattle (75%). Approximately one-third of the CPs are voluntary, and the funding structure is divided between government and private resources. Countries that have eradicated diseases like enzootic bovine leukosis, bluetongue, infectious bovine rhinotracheitis and bovine viral diarrhoea have implemented CPs for other diseases to further improve the health status of cattle in their country. The control of non-EU regulated cattle diseases is very heterogenous in Europe. Therefore, the standardising of the outputs of these programmes to enable comparison represents a challenge.

Systematic review of the status of veterinary epidemiological research in two species regarding the FAIR guiding principles.

BACKGROUND: The FAIR (Findable, Accessible, Interoperable, Reusable) principles were proposed in 2016 to set a path towards reusability of research datasets. In this systematic review, we assessed the FAIRness of datasets associated with peer-reviewed articles in veterinary epidemiology research published since 2017, specifically looking at salmonids and dairy cattle. We considered the differences in practices between molecular epidemiology, the branch of epidemiology using genetic sequences of pathogens and hosts to describe disease patterns, and non-molecular epidemiology. RESULTS: A total of 152 articles were included in the assessment. Consistent with previous assessments conducted in other disciplines, our results showed that most datasets used in non-molecular epidemiological studies were not available (i.e., neither findable nor accessible). Data availability was much higher for molecular epidemiology papers, in line with a strong repository base available to scientists in this discipline. The available data objects generally scored favourably for Findable, Accessible and Reusable indicators, but Interoperability was more problematic. CONCLUSIONS: None of the datasets assessed in this study met all the requirements set by the FAIR principles. Interoperability, in particular, requires specific skills in data management which may not yet be broadly available in the epidemiology community. In the discussion, we present recommendations on how veterinary research could move towards greater reusability according to FAIR principles. Overall, although many initiatives to improve data access have been started in the research community, their impact on the availability of datasets underlying published articles remains unclear to date.

Key Learnings During the Development of a Generic Data Collection Tool to Support Assessment of Freedom of Infection in Cattle Herds.

Various European Member States have implemented control or eradication programmes for endemic infectious diseases in cattle. The design of these programmes varies between countries and therefore comparison of the outputs of different control programmes is complex. Although output-based methods to estimate the confidence of freedom resulting from these programmes are under development, as yet there is no practical modeling framework applicable to a variety of infectious diseases. Therefore, a data collection tool was developed to evaluate data availability and quality and to collect actual input data required for such a modeling framework. The aim of the current paper is to present the key learnings from the process of the development of this data collection tool. The data collection tool was developed by experts from two international projects: STOC free (Surveillance Tool for Outcome-based Comparison of FREEdom from infection, www.stocfree.eu) and SOUND control (Standardizing OUtput-based surveillance to control Non-regulated Diseases of cattle in the EU, www.sound-control.eu). Initially a data collection tool was developed for assessment of freedom of bovine viral diarrhea virus in six Western European countries. This tool was then further generalized to enable inclusion of data for other cattle diseases i.e., infectious bovine rhinotracheitis and Johne's disease. Subsequently, the tool was pilot-tested by a Western and Eastern European country, discussed with animal health experts from 32 different European countries and further developed for use throughout Europe. The developed online data collection tool includes a wide range of variables that could reasonably influence confidence of freedom, including those relating to cattle demographics, risk factors for introduction and characteristics of disease control programmes. Our results highlight the fact that data requirements for different cattle diseases can be generalized and easily included in a data collection tool. However, there are large differences in data availability and comparability across European countries, presenting challenges to the development of a standardized data collection tool and modeling framework. These key learnings are important for development of any generic data collection tool for animal disease control purposes. Further, the results can facilitate development of output-based modeling frameworks that aim to calculate confidence of freedom from disease.

Factors associated with cattle necropsy submissions in Switzerland, and their importance for surveillance.

Pathology data have been reported to be important for surveillance, as they are crucial for correctly recognizing and identifying new or re-emerging diseases in animal populations. However, there are no reports in the literature of necropsy data being compared or complemented with other data. In our study, we compared cattle necropsy reports extracted from 3 laboratories with the Swiss fallen stock data and clinical data collected by the association of Swiss Cattle Breeders. The objective was to assess the completeness, validity and representativeness of the necropsy data, as well as evaluate potential factors for necropsy submission and how they can benefit animal health surveillance. Our results showed that, on average, 1% of Swiss cattle that die are submitted for post-mortem examinations. However, different factors influence cattle necropsy submissions, such as the age of the animal, the geographical location and the number of sick and/or dead animals on the farm. There was a median of five animals reported sick and two animals reported dead within 30 days prior to a necropsy submission, providing quantitative evidence of a correlation between on farm morbidity/mortality and post-mortem examination. Our results also showed that necropsy data can help improve the accuracy and completeness of health data for surveillance systems. In this study, we were able to demonstrate the importance of veterinary pathology data for AHS by providing quantitative evidence that necropsied animals are indicative of farms with important disease problems and are therefore critically important for surveillance. Furthermore, thanks to the amount of information provided by combined data sources, the epidemiology (e.g. season, geographic region, risk factors) of potential diseases can be analysed more precisely and help supporting animal health surveillance systems.

Risk-based early detection system of African Swine Fever using mortality thresholds.

African swine fever (ASF) is an infectious disease of swine causing major losses in the swine industry worldwide. Early detection of ASF is challenging because of the wide range of non-specific clinical signs produced and its relatively low contagiousness. Monitoring pig mortality is a promising approach for early detection of ASF, but such approach has been associated with delay in disease detection in large pig farms. The purpose of this study was to compare the effectiveness and suitability of early detection strategies for ASF in large commercial pig farms using mortality monitoring at the pen, room or barn level. The within-barn spread of the disease was modelled including the non-homogeneous probabilities of transmission within pens, between pens and between rooms. The performances of early detection surveillance based on mortality thresholds established for different epidemiological units were compared in terms of sensitivity, time to detection and number of false alarms per year. A barn with a capacity of 3,200 pigs divided into 8 rooms with 10 pens each containing 40 pigs per pen was used as an example. Our results show that using room- or pen-based mortality thresholds provided a time to detection of 8 days post-disease introduction. Similar detection performances could be achieved with barn-level mortality threshold but at the cost of an increased number of pigs to be tested each year. The different scenarios tested also show that barn characteristics such as baseline mortality rate and pen size had a limited impact on the pen-level mortality thresholds required for disease early detection. These results offer strong support for using mortality data for early detection of ASF not only in small pig herds but also in large commercial barns. Furthermore, the mortality thresholds defined in this study might be relevant to a wide range of pig production sites.

Evidence That Higher Temperatures Are Associated With a Marginally Lower Incidence of COVID-19 Cases.

Seasonal variations in COVID-19 incidence have been suggested as a potentially important factor in the future trajectory of the pandemic. Using global line-list data on COVID-19 cases reported until 17th of March 2020 and global gridded weather data, we assessed the effects of air temperature and relative humidity on the daily incidence of confirmed COVID-19 local cases at the subnational level (first-level administrative divisions). After adjusting for surveillance capacity and time since first imported case, average temperature had a statistically significant, negative association with COVID-19 incidence for temperatures of -15°C and above. However, temperature only explained a relatively modest amount of the total variation in COVID-19 cases. The effect of relative humidity was not statistically significant. These results suggest that warmer weather may modestly reduce the rate of spread of COVID-19, but anticipation of a substantial decline in transmission due to temperature alone with onset of summer in the northern hemisphere, or in tropical regions, is not warranted by these findings.

Evaluating 5.5 Years of Equinella: A Veterinary-Based Voluntary Infectious Disease Surveillance System of Equines in Switzerland.

Equine health is important in regard to trade, economy, society, and the veterinary, as well as public health. To reduce the burden of equine infectious diseases internationally, it is important to collect, review, and distribute equine health surveillance data as accurate and timely as possible. Within this study, we aimed at providing a comprehensive descriptive analysis of data submitted to Equinella, a voluntary veterinary-based surveillance system of non-notifiable equine infectious diseases and clinical signs, in Switzerland. This was achieved by reviewing the reports submitted since its relaunch in November 2013 and until April 2019, as well as assessing the data validity, activeness of participating veterinarians, coverage of the equine population, geographical representativeness, and timeliness of the system. In total, 630 reports have been submitted. Data validity ranged between 88.2 and 100%. The coverage of Equinella was assessed to be 50.8% of the Swiss equine population. Over the 5.5 years, of all 102 registered veterinarians, 67 (65.7%) submitted at least one report. On average, these veterinarians submitted 1.7 reports per year (median = 4 reports). More recently, in 2018, approximately only one-third [29 (28.4%)] of all registered veterinarians submitted at least one report. However, 59 (57.8%) have responded to the monthly reminder emails to confirm that they have not observed any relevant clinical case to be reported at least once (median number of confirmation per veterinarian = 9 of 12 reminder emails). The incidence of reports varied between cantons (member states of the Swiss confederation). The median timeliness of report submission was found to be 7 days. Overall, Equinella has been receiving reports since its initiation and contributed continuously to the surveillance of infectious diseases in the Swiss equine population and provided an output for the international equine community. Challenges encountered in achieving a higher number of submitted reports and increasing the coverage of the equine population, as well as the overall activeness of veterinarians, require further work. With our study, we provide a comprehensive overview of a veterinary-based voluntary surveillance system for equine health, assessed challenges of such, and suggest concrete improvements with transdisciplinary approaches for similar veterinary-based surveillance systems.

Simulation Based Evaluation of Time Series for Syndromic Surveillance of Cattle in Switzerland.

Choosing the syndrome time series to monitor in a syndromic surveillance system is not a straight forward process. Defining which syndromes to monitor in order to maximize detection performance has been recently identified as one of the research priorities in Syndromic surveillance. Estimating the minimum size of an epidemic that could potentially be detected in a specific syndrome could be used as a criteria for comparing the performance of different syndrome time series, and could provide some guidance for syndrome selection. The aim of our study was to estimate the potential value of different time series for building a national syndromic surveillance system for cattle in Switzerland. Simulations were used to produce outbreaks of different size and shape and to estimate the ability of each time series and aberration detection algorithm to detect them with high sensitivity, specificity and timeliness. Two temporal aberration detection algorithms were also compared: Holt-Winters generalized exponential smoothing (HW) and Exponential Weighted Moving Average (EWMA). Our results indicated that a specific aberration detection algorithm should be used for each time series. In addition, time series with high counts per unit of time had good overall detection performance, but poor detection performance for small epidemics making them of limited use for an early detection system. Estimating the minimum size of simulated epidemics that could potentially be detected in syndrome TS-event detection pairs can help surveillance system designers choosing the most appropriate syndrome TS to include in their early epidemic surveillance system.

Multivariate syndromic surveillance for cattle diseases: Epidemic simulation and algorithm performance evaluation.

Multivariate Syndromic Surveillance (SyS) systems that simultaneously assess and combine information from different data sources are especially useful for strengthening surveillance systems for early detection of infectious disease epidemics. Despite the strong motivation for implementing multivariate SyS and there being numerous methods reported, the number of operational multivariate SyS systems in veterinary medicine is still very small. One possible reason is that assessing the performance of such surveillance systems remains challenging because field epidemic data are often unavailable. The objective of this study is to demonstrate a practical multivariate event detection method (directionally sensitive multivariate control charts) that can be easily applied in livestock disease SyS, using syndrome time series data from the Swiss cattle population as an example. We present a standardized method for simulating multivariate epidemics of different diseases using four diseases as examples: Bovine Virus Diarrhea (BVD), Infectious Bovine Rhinotracheitis (IBR), Bluetongue virus (BTV) and Schmallenberg virus (SV). Two directional multivariate control chart algorithms, Multivariate Exponentially Weighted Moving Average (MEWMA) and Multivariate Cumulative Sum (MCUSUM) were compared. The two algorithms were evaluated using 12 syndrome time series extracted from two Swiss national databases. The two algorithms were able to detect all simulated epidemics around 4.5 months after the start of the epidemic, with a specificity of 95%. However, the results varied depending on the algorithm and the disease. The MEWMA algorithm always detected epidemics earlier than the MCUSUM, and epidemics of IBR and SV were detected earlier than epidemics of BVD and BTV. Our results show that the two directional multivariate control charts are promising methods for combining information from multiple time series for early detection of subtle changes in time series from a population without producing an unreasonable amount of false alarms. The approach that we used for simulating multivariate epidemics is relatively easy to implement and could be used in other situations where real epidemic data are unavailable. We believe that our study results can support the implementation and assessment of multivariate SyS systems in animal health.

A Transdisciplinary Approach Supporting the Implementation of a Big Data Project in Livestock Production: An Example From the Swiss Pig Production Industry.

Big Data approaches offer potential benefits for improving animal health, but they have not been broadly implemented in livestock production systems. Privacy issues, the large number of stakeholders, and the competitive environment all make data sharing, and integration a challenge in livestock production systems. The Swiss pig production industry illustrates these and other Big Data issues. It is a highly decentralized and fragmented complex network made up of a large number of small independent actors collecting a large amount of heterogeneous data. Transdisciplinary approaches hold promise for overcoming some of the barriers to implementing Big Data approaches in livestock production systems. The purpose of our paper is to describe the use of a transdisciplinary approach in a Big Data research project in the Swiss pig industry. We provide a brief overview of the research project named "Pig Data," describing the structure of the project, the tools developed for collaboration and knowledge transfer, the data received, and some of the challenges. Our experience provides insight and direction for researchers looking to use similar approaches in livestock production system research.

Complex System Approaches for Animal Health Surveillance.

Many new and highly variable data are currently being produced by the many participants in farmed animal productions systems. These data hold the promise of new information with potential value for animal health surveillance. The current analytical paradigm for dealing with these new data is to implement syndromic surveillance systems, which focus mainly on univariate event detection methods applied to individual time series, with the goal of identifying epidemics in the population. This approach is relatively limited in the scope and not well-suited for extracting much of the additional information that is contained within these data. These approaches have value and should not be abandoned. However, an additional, new analytical paradigm will be needed if surveillance and disease control agencies wish to extract additional information from these data. We propose a more holistic analytical approach borrowed from complex system science that considers animal disease to be a product of the complex interactions between the many individuals, organizations and other factors that are involved in, or influence food production systems. We will discuss the characteristics of farmed animal food production systems that make them complex adaptive systems and propose practical applications of methods borrowed from complex system science to help animal health surveillance practitioners extract additional information from these new data.

The pig transport network in Switzerland: Structure, patterns, and implications for the transmission of infectious diseases between animal holdings.

The topology of animal transport networks contributes substantially to how fast and to what extent a disease can transmit between animal holdings. Therefore, public authorities in many countries mandate livestock holdings to report all movements of animals. However, the reported data often does not contain information about the exact sequence of transports, making it impossible to assess the effect of truck sharing and truck contamination on disease transmission. The aim of this study was to analyze the topology of the Swiss pig transport network by means of social network analysis and to assess the implications for disease transmission between animal holdings. In particular, we studied how additional information about transport sequences changes the topology of the contact network. The study is based on the official animal movement database in Switzerland and a sample of transport data from one transport company. The results show that the Swiss pig transport network is highly fragmented, which mitigates the risk of a large-scale disease outbreak. By considering the time sequence of transports, we found that even in the worst case, only 0.34% of all farm-pairs were connected within one month. However, both network connectivity and individual connectedness of farms increased if truck sharing and especially truck contamination were considered. Therefore, the extent to which a disease may be transmitted between animal holdings may be underestimated if we only consider data from the official animal movement database. Our results highlight the need for a comprehensive analysis of contacts between farms that includes indirect contacts due to truck sharing and contamination. As the nature of animal transport networks is inherently temporal, we strongly suggest the use of temporal network measures in order to evaluate individual and overall risk of disease transmission through animal transportation.