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The collective control programmes (CPs) that exist for many infectious diseases of farm animals rely on the application of diagnostic testing at regular time intervals for the identification of infected animals or herds. The diversity of these CPs complicates the trade of animals between regions or countries because the definition of freedom from infection differs from one CP to another. In this paper, we describe a statistical model for the prediction of herd-level probabilities of infection from longitudinal data collected as part of CPs against infectious diseases of cattle. The model was applied to data collected as part of a CP against bovine viral diarrhoea virus (BVDV) infection in Loire-Atlantique, France. The model represents infection as a herd latent status with a monthly dynamics. This latent status determines test results through test sensitivity and test specificity. The probability of becoming status positive between consecutive months is modelled as a function of risk factors (when available) using logistic regression. Modelling is performed in a Bayesian framework, using either Stan or JAGS. Prior distributions need to be provided for the sensitivities and specificities of the different tests used, for the probability of remaining status positive between months as well as for the probability of becoming positive between months. When risk factors are available, prior distributions need to be provided for the coefficients of the logistic regression, replacing the prior for the probability of becoming positive. From these prior distributions and from the longitudinal data, the model returns posterior probability distributions for being status positive for all herds on the current month. Data from the previous months are used for parameter estimation. The impact of using different prior distributions and model implementations on parameter estimation was evaluated. The main advantage of this model is its ability to predict a probability of being status positive in a month from inputs that can vary in terms of nature of test, frequency of testing and risk factor availability/presence. The main challenge in applying the model to the BVDV CP data was in identifying prior distributions, especially for test characteristics, that corresponded to the latent status of interest, i.e. herds with at least one persistently infected (PI) animal. The model is available on Github as an R package (https://github.com/AurMad/STOCfree) and can be used to carry out output-based evaluation of disease CPs. European Food Safety Authority (EFSA)

A correction has been made to Abstract. The corrected section is shown below. 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 selected 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 selected 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 the selected cattle diseases is very heterogenous in Europe. Therefore, the standardising of the outputs of these programmes to enable comparison represents a challenge.

Amoebic gill disease (AGD) and complex gill disease (CGD) are the most significant marine gill diseases in salmon aquaculture in Scotland. Little is published about diagnostic performance of tests to detect these diseases, making it difficult to interpret test results. We estimated diagnostic sensitivity (DSe) and specificity (DSp) of common tests for AGD (gross AGD score, qPCR for Neoparamoeba perurans, histopathology) and CGD (gross proliferative gill disease (PGD) score, gross total gill score, histopathology). Because specifications in our sampling protocol implemented to encourage consistency across the farms might affect diagnostic performance of histopathology (historically the reference standard for gill diseases), we used Bayesian latent class models without reference standard. Cases and non-cases were based on less, medium, and severe stringent case definitions, representing different cut-off levels for the different tests. Gross gill scores for both diseases were excellent in designating non-diseased fish, DSps were generally around 1. To detect CGD, DSe of gross total gill score and gross PGD score were between respectively 0.81 (0.73 - 0.91 lower to upper 95% credible interval) and 0.53 (0.46 - 0.64) for medium stringent case definitions, and to detect AGD the DSe for the gross AGD score was between 0.53 (0.48-0.57) and 0.14 (0.07 - 0.22) for respectively the less and severe stringent case definition. Thus, gross gill scores were medium to good in designating truly diseased fish, implying some false negatives are expected. For CGD the DSe for gross total gill scores were the highest, for AGD it was the qPCR test at a DSe of 0.92 (0.86 - 0.99). For both diseases, DSe was lowest for histopathology, e.g. 0.23 (0.16 - 0.30) for AGD and 0.1 (0.07 - 0.14) for CGD under medium stringent case definitions, perhaps due to collecting the second gill arch on the right rather than the worst affected arch, whilst PCR sampling and gross gill scoring included multiple (PCR) or all (gross scoring) gill arches. The diagnostic goals of these tests differ; gross gill scoring provides a low-cost presumptive diagnosis, PCR a non-lethal confirmation of the presence of a specific pathogen and histopathology provides information on the underlying aetiology of gill damage as well as the extent, severity, and chronology of gill disease. An effective gill health surveillance strategy is likely to incorporate multiple diagnostic tools used in a complementary manner.

Cattle are reservoirs for Shiga toxin Escherichia coli (STEC), bacteria shed in animal feces. Humans are infected through consumption of contaminated food or water and by direct contact, causing serious disease and kidney failure in the most vulnerable., Cattle are a reservoir for Shiga toxin-producing Escherichia coli (STEC), zoonotic pathogens that cause serious clinical disease. Scotland has a higher incidence of STEC infection in the human population than the European average. The aim of this study was to investigate the prevalence and epidemiology of non-O157 serogroups O26, O103, O111, and O145 and Shiga toxin gene carriage in Scottish cattle. Fecal samples (n = 2783) were collected from 110 herds in 2014 and 2015 and screened by real-time PCR. Herd-level prevalence (95% confidence interval [CI]) for O103, O26, and O145 was estimated as 0.71 (0.62, 0.79), 0.43 (0.34, 0.52), and 0.23 (0.16, 0.32), respectively. Only two herds were positive for O111. Shiga toxin prevalence was high in both herds and pats, particularly for stx2 (herd level: 0.99; 95% CI: 0.94, 1.0). O26 bacterial strains were isolated from 36 herds on culture. Fifteen herds yielded O26 stx-positive isolates that additionally harbored the intimin gene; six of these herds shed highly pathogenic stx2-positive strains. Multiple serogroups were detected in herds and pats, with only 25 herds negative for all serogroups. Despite overlap in detection, regional and seasonal effects were observed. Higher herd prevalence for O26, O103, and stx1 occurred in the South West, and this region was significant for stx2 at the pat level (P = 0.015). Significant seasonal variation was observed for O145 prevalence, with the highest prevalence in autumn (P = 0.032). Negative herds were associated with Central Scotland and winter. Herds positive for all serogroups were associated with autumn and larger herd size and were not housed at sampling. IMPORTANCE Cattle are reservoirs for Shiga toxin-producing Escherichia coli (STEC), bacteria shed in animal feces. Humans are infected through consumption of contaminated food or water and by direct contact, resulting in serious disease and kidney failure in the most vulnerable. The contribution of non-O157 serogroups to STEC illness was underestimated for many years due to the lack of specific tests. Recently, non-O157 human cases have increased, with O26 STEC of particular note. It is therefore vital to investigate the level and composition of non-O157 in the cattle reservoir and to compare them historically and by the clinical situation. In this study, we found cattle prevalence high for toxin, as well as for O103 and O26 serogroups. Pathogenic O26 STEC were isolated from 14% of study herds, with toxin subtypes similar to those seen in Scottish clinical cases. This study highlights the current risk to public health from non-O157 STEC in Scottish cattle.

The modelling of disease spread is crucial to the farming industry and policy makers. In some of these industries, excellent data exist on animal movements, along with the networks that these movements create, and allow researchers to model spread of disease (both epidemic and endemic). The Cattle Tracing System is an online recording system for cattle births, deaths and between-herd movements in the United Kingdom and is an excellent resource for any researchers interested in networks or modelling infectious disease spread through the UK cattle system. Data exist that cover many years, and it can be useful to know how much change is occurring in a network, to help judge the merit of using historical data within a modelling context. This article uses the data to construct weighted directed monthly movement networks for two distinct periods of time, 2004–2006 and 2015–2017, to quantify by how much the underlying structure of the network has changed. Substantial changes in network structure may influence policy-makers directly or may influence models built upon the network data, and these in turn could impact policy-makers and their assessment of risk. We examined 13 network metrics, ranging from general descriptive metrics such as total number of nodes with movements and total movements, through to metrics to describe the network (e.g., Giant weakly and strongly connected components) and metrics calculated per node (betweenness, degree and strength). Mixed effect models show that there is a statistically significant effect of the period (2004–2006 vs 2015–2017) in the values of nine of the 13 network metrics. For example median total degree decreased by 19%. In addition to examining networks for two time periods, two updates of the data were examined to determine by how much the movement data stored for 2004–2006 had been cleansed between updates. Examination of these updates shows that there are small decreases in problem movements (such as animals leaving slaughterhouses) and therefore evidence of historical data being improved between updates. In combination with the significant effect of period on many of the network metrics, the modification of data between updates provides further evidence that the most recent available data should be used for network modelling. This will ensure that the most representative descriptions of the network are available to provide accurate modelling results to best inform policy makers.

This paper proposes Ir-Man (Information Retrieval for Marine Animal Necropsies), a framework for retrieving discrete information from marine mammal post-mortem reports for statistical analysis. When a marine mammal is reported dead after stranding in Scotland, the carcass is examined by the Scottish Marine Animal Strandings Scheme (SMASS) to establish the circumstances of the animal's death. This involves the creation of a "post-mortem" (or necropsy) report, which systematically describes the body. These semi-structured reports record lesions (damage or abnormalities to anatomical regions) as well as other observations. Observations embedded within these texts are used to determine cause of death. While a cause of death is recorded separately, many other descriptions may be of pathological and epidemiological significance when aggregated and analysed collectively. As manual extraction of these descriptions is costly, time consuming and at times erroneous, there is a need for an automated information retrieval mechanism which is a non-trivial task given the wide variety of possible descriptions, pathologies and species. The Ir-Man framework consists of a new ontology, a lexicon of observations and anatomical terms and an entity relation engine for information retrieval and statistics generation from a pool of necropsy reports. We demonstrate the effectiveness of our framework by creating a rule-based binary classifier for identifying bottlenose dolphin attacks (BDA) in harbour porpoise gross pathology reports and achieved an accuracy of 83.4%.

BACKGROUND Accurate estimation of antimicrobial use (AMU) is important in assessing reduction of agricultural AMU. This cross-sectional study aimed to evaluate several approaches for estimating AMU at the herd level and to report on AMU for beef and dairy farms in Scotland. METHODS Pharmaceutical sales data for 75 cattle herds (2011-2015) were screened for antimicrobial products and aggregated by herd and year. Several denominators for usage estimates were calculated and compared for their suitability at the herd level. RESULTS The median total mass of active ingredient sold per kg of bovine livestock was 9.5 mg/kg for beef herds and 14.3 mg/kg for dairy herds. The 'highest priority critically important' antimicrobials (HPCIA) were by total mass of active ingredient, 10.6% of all sales; by total defined daily dose veterinary (DDDVet), 29.8% and by DCDvet, 20.0%. These are the first estimates of AMU for beef cattle in the UK, and for cattle of any kind in Scotland. Estimates of herd-level usage based on population correction unit (PCU) were sensitive to low values for PCU for specific herd-years due to their demographic composition. CONCLUSION Pharmaceutical sales data can provide useful estimates of AMU, but estimating usage per PCU is not appropriate for comparing groups of cattle with different demographic compositions or for setting herd-level targets. Total mass of active ingredient per kilogram of livestock is more stable and hence suitable than PCU-based methods for assessing AMU at the herd level.

The design of surveillance strategies is often a compromise between science, feasibility, and available resources, especially when sampling is based at fixed locations, such as slaughter-houses. Advances in animal identification, movement recording and traceability should provide data that can facilitate the development, design and interpretation of surveillance activities. Here, for the first time since the introduction of electronic identification of sheep, the utility of a statutory sheep movement database to inform the design and interpretation of slaughter-house based surveillance activities has been investigated. Scottish sheep movement records for 2015–2018 were analyzed in combination with several other data sources. Patterns of off-farm movements of Scottish sheep to slaughter were described and the spatial distribution of several distinct slaughter populations, throughputs and catchment areas for Scottish slaughterhouses were determined. These were used to evaluate the coverage of a convenience-sample slaughter-house based survey for antimicrobial resistance (AMR). In addition, non-slaughter sheep movements within and between Scottish regions were described and inter-and intra-regional movement matrices were produced. There is potential at a number of levels for bias in spatially-associated factors for ovine surveillance activities based at Scottish slaughterhouses. The first is intrinsic because the slaughtered in Scotland population differs from the overall Scottish sheep slaughter population. Other levels will be survey-dependent and occur when the catchment area differs from the slaughtered in Scotland population and when the sampled sheep differ from the catchment area. These are both observed in the AMR survey. Furthermore, the Scottish non-slaughter sheep population is dynamic. Inter-regional movements vary seasonally, driven by the sheep calendar year, structure of the Scottish sheep industry and management practices. These sheep movement data provide a valuable resource for surveillance purposes, despite a number of challenges and limitations that were encountered. They can be used to identify and characterize the spatial origin of relevant populations and so inform the interpretation of existing slaughterhouse-based surveillance activities. They can be used to improve future design by exploring the feasibility and cost:benefit of alternative sampling strategies. Further development could also contribute to other surveillance activities, such as situational awareness and resource allocation, for the benefit of stakeholders.

The BVDFree Scheme, the national voluntary programme for the elimination of BVD from cattle herds in England, was launched on July 1, 2016. Cattle keepers can join BVDFree online (bvdfree.org.uk) or by completing a BVDFree registration form. Over 1000 farmers registered with BVDFree in the first year of operation. Laboratories designated by BVDFree upload the results of testing for BVD virus and for BVD antibodies to the BVDFree database. 40 220 unique records pertaining to tests for BVD were uploaded to the database in the first year of operation. Of the 32 909 samples from individual animals tested for presence of BVD virus, 180 (0.55%) were positive and 20 (0.06%) were inconclusive. Of 2853 samples from individual animals tested for presence of antibodies to BVD virus, 286 (10%) were positive. In 2018 the BVDFree Scheme will introduce a process for assigning a BVDFree herd status. The backing of veterinary surgeons and veterinary practices and all organisations which have signed the BVD Statement of Intent for BVDFree is key to improving engagement with the BVDFree Scheme and achieving the aim of the Scheme which is to deliver the next generation of cattle free of BVD to the next generation of farmers.

Small-scale keepers are less likely to engage with production organisations and may therefore be less aware of legislation, rules and biosecurity practices which are implemented in the livestock sector. Their role in the transmission of endemic and exotic diseases is not well studied, but is believed to be important. The authors use small-scale pig keepers in Scotland as an example of how important small-scale livestock keepers might be for national biosecurity. In Scotland more than two thirds of pig producers report that they keep less than 10 pigs, meaning that biosecurity practices and pig health status on a substantial number of holdings are largely unknown; it is considered important to fill this knowledge gap. A questionnaire was designed and implemented in order to gather some of this information. The questionnaire comprised a total of 37 questions divided into seven sections (location of the enterprise, interest in pigs, details about the pig enterprise, marketing of pigs, transport of pigs, pig husbandry, and pig health/biosecurity). Over 610 questionnaires were sent through the post and the questionnaire was also available online. The questionnaire was implemented from June to October 2013 and 135 questionnaires were returned by target respondents. The responses for each question are discussed in detail in this paper. Overall, our results suggest that the level of disease identified by small-scale pig keepers is low but the majority of the small-scale pig keepers are mixed farms, with associated increased risk for disease transmission between species. Almost all respondents implemented at least one biosecurity measure, although the measures taken were not comprehensive in the majority of cases. Overall as interaction between small-scale keepers and commercial producers exists in Scotland the former can pose a risk for commercial production. This investigation fills gaps in knowledge which will allow industry stakeholders and policy makers to adapt their current disease programmes and contingency plans to the reality of small-scale pig-keeping enterprises' health and biosecurity status. We predict that some conclusions from this work will be relevant to countries with similar pig production systems and importantly some of these findings will relate to small-scale producers in other livestock sectors.

Aquaculture is an increasingly important source of animal protein for a growing global population. Disease is a major constraint to production, with resultant socio-economic impacts for individuals, communities and economies which rely on aquaculture. Aquatic animal health is also strongly influenced by human factors, ranging from international trade regulations to the behaviours of individuals working in aquaculture. This article summarises the human factors associated with aquaculture production using international examples for illustration.

Generic frameworks for the economic analysis of farm animal disease are now well established. The paper, therefore, uses bovine viral diarrhoea (BVD) as an example to explore how these frameworks need to be adapted to fit the characteristics of a particular disease and the specific objectives of the analysis. In the case of BVD, given the relative strength of tests available to correctly identify virus-positive animals, thus enabling them to be culled, the emphasis has been on cost-benefit analysis of regional and national certification/eradication schemes. Such analyses in turn raise interesting questions about farmer uptake and maintenance of certification schemes and the equity and cost-effective implementation of these schemes. The complex epidemiology of BVD virus infections and the long-term, widespread and often occult nature of BVD effects make economic analysis of the disease and its control particularly challenging. However, this has resulted in a wider whole-farm perspective that captures the influence of multiple decisions, not just those directly associated with disease prevention and control. There is a need to include management of reproduction, risk and enterprise mix in the research on farmer decision-making, as all these factors impinge on, and are affected by, the spread of BVD.

Background Escherichia coli O157 is a bacterial pathogen associated with severe disease in humans for which cattle are an important reservoir of infection. The identification of possible risk factors for infection in cattle could facilitate the development of control strategies and interventions to mitigate the risk to human health. The purpose of this study was to utilize data collected in 2014–2015 during the two contemporaneous cross-sectional surveys of the British E. coli O157 in Cattle Study (BECS) to investigate potential risk factors for E. coli O157 status in cattle destined for the food chain. Results In the England & Wales survey only one variable, herd size, was associated with the outcome farm-level E. coli O157 positive status. The odds increased for each additional animal in the herd. In the Scotland survey, as well as a measure of herd size (the number of cattle aged 12–30 months), having brought breeding females on to the farm in the last year also increased the odds, whereas farms sampled in spring were less likely to be positive compared to those sampled in autumn. On the positive farms, in both surveys, an increase in the proportion of pats positive for E. coli O157 was associated with animals being housed at the time of sampling. However, the effect of housing on pat-level prevalence within positive groups was lower on farms from England & Wales than from Scotland (OR 0.45 (95% C.I. 0.24–0.86)). Conclusion For the first time, factors associated with farm-level E. coli O157 status have been investigated in two contemporaneous surveys with comparable study design. Although factors associated with farm-level E. coli O157 status differed between the two surveys, one consistent factor was an association with a measure of herd size. Factors associated with the proportion of E. coli O157 positive pats within a positive farm were similar in both surveys but differed from those associated with farm-level status. These findings raise the hypothesis that measures to protect public health by reducing the risk from cattle may need to be tailored, rather than by assuming that a GB-wide protocol is the best approach.

During the 2001 UK FMD outbreak, local authorities restricted rural access to try to prevent further disease spread by people and animals, which had major socio-economic consequences for rural communities. This study describes the results of qualitative veterinary risk assessments to assess the likelihood of different recreational activities causing new outbreaks of foot and mouth disease, as part of contingency planning for future outbreaks. For most activities, the likelihood of causing new outbreaks of foot and mouth disease is considered to vary from very low to medium depending on the control zone (which is based on distance to the nearest infected premises), assuming compliance with specified mitigation strategies. The likelihood of new outbreaks associated with hunting, shooting, stalking, and equestrian activities is considered to be greater. There are areas of significant uncertainty associated with data paucity, particularly regarding the likelihood of transmission via fomites. This study provides scientific evidence to underpin refinement of rural access management plans and inform decision-making in future disease outbreaks.

Determining the Bovine Viral Diarrhoea (BVD) infection status of cattle herds is a challenge for control and eradication schemes. Given the changing dynamics of BVD virus (BVDV) antibody responses in cattle, classifying herds based on longitudinal changes in the results of BVDV antibody tests could offer a novel, complementary approach to categorising herds that is less likely than the present system to result in a herd’s status changing from year to year, as it is more likely to capture the true exposure dynamics of the farms. This paper describes the dynamics of BVDV antibody test values (measured as percentage positivity (PP)) obtained from 15,500 bovines between 2007 and 2010 from thirty nine cattle herds located in Scotland and Northern England. It explores approaches of classifying herds based on trend, magnitude and shape of their antibody PP trajectories and investigates the epidemiological similarities between farms within the same cluster. Gaussian mixture models were used for the magnitude and shape clustering. Epidemiologically meaningful clusters were obtained. Farm cluster membership depends on clustering approach used. Moderate concordance was found between the shape and magnitude clusters. These methods hold potential for application to enhance control efforts for BVD and other infectious livestock diseases.

There are calls from policy-makers and industry to use existing data sources to contribute to livestock surveillance systems, especially for syndromic surveillance. However, the practical implications of attempting to use such data sources are challenging; development often requires incremental steps in an iterative cycle. In this study the utility of business operational data from a voluntary fallen stock collection service was investigated, to determine if they could be used as a proxy for the mortality experienced by the British sheep population. Retrospectively, Scottish ovine fallen stock collection data (2011–2014) were transformed into meaningful units for analysis, temporal and spatial patterns were described, time-series methods and a temporal aberration detection algorithm applied. Distinct annual and spatial trends plus seasonal patterns were observed in the three age groups investigated. The algorithm produced an alarm at the point of an historic known departure from normal (April 2013) for two age groups, across Scotland as a whole and in specific postcode areas. The analysis was then extended. Initially, to determine if similar methods could be applied to ovine fallen stock collections from England and Wales for the same time period. Additionally, Scottish contemporaneous laboratory diagnostic submission data were analyzed to see if they could provide further insight for interpretation of statistical alarms. Collaboration was required between the primary data holders, those with industry sector knowledge, plus veterinary, epidemiological and statistical expertise, in order to turn data and analytical outcomes into potentially useful information. A number of limitations were identified and recommendations were made as to how some could be addressed in order to facilitate use of these data as surveillance “intelligence.” e.g., improvements to data collection and provision. A recent update of the fallen stock collections data has enabled a longer temporal period to be analyzed, with evidence of changes made in line with the recommendations. Further development will be required before a functional system can be implemented. However, there is potential for use of these data as: a proxy measure for mortality in the sheep population; complementary components in a future surveillance system, and to inform the design of additional surveillance system components.

A vet at Scotland’s Rural College, his practical knowledge and experience enabled him to support rural veterinary practices, as well as to foster his own interest in wildlife.

Traditional indicator-based livestock surveillance has been focused on case definitions, definitive diagnoses and laboratory confirmation. The use of syndromic disease surveillance would increase the population base from which animal health data are captured and facilitate earlier detection of new and re-emerging threats to animal health. Veterinary practitioners could potentially play a vital role in such activities. In a pilot study, specialist private veterinary practitioners (PVP) working in the English pig industry were asked to collect and transfer background data and disease incident reports for pig farms visited during the study period. Baseline data from 110 pig farms were received, along with 68 disease incident reports. Reports took an average of approximately 25 minutes to complete. Feedback from the PVPs indicated that they saw value in syndromic surveillance. Maintenance of anonymity in the outputs would be essential, as would timely access for the PVPs to relevant information on syndromic trends. Further guidance and standardisation would also be required. Syndromic surveillance by PVPs is possible for the pig industry. It has potential to fill current gaps in the collection of animal health data, as long as the engagement and participation of data providers can be obtained and maintained.

SUMMARYThe incursion of Bluetongue disease into the UK and elsewhere in Northern Europe in 2008 raised concerns about maintaining an appropriate level of preparedness for the encroachment of exotic diseases as circumstances and risks change. Consequently the Scottish government commissioned the present study to inform policy on the specific threat of Bluetongue virus 8 (BTV8) incursion into Scotland. An interdisciplinary expert panel, including BTV and midge experts, agreed a range of feasible BTV incursion scenarios, patterns of disease spread and specific control strategies. The study was primarily desk-based, applying quantitative methodologies with existing models, where possible, and utilizing data already held by different members of the project team. The most likely distribution of the disease was explored given Scotland's agricultural systems, unique landscape and climate. Epidemiological and economic models are integrated in an ex-ante cost-benefit appraisal of successful prevention of hypothetical BTV8 incursion into Scotland under various feasible incursion scenarios identified by the interdisciplinary panel. The costs of current public and private surveillance efforts are compared to the benefits of the avoided losses of potential disease outbreaks. These avoided losses included the direct costs of alternative vaccination, protection zone (PZ) strategies and their influence on other costs arising from an outbreak as predicted by the epidemiological model. Benefit-cost ratios were ranked within each incursion scenario to evaluate alternative strategies. In all incursion scenarios, the ranking indicated that a strategy, including 100% vaccination within a PZ set at Scottish counties along the England–Scotland border yielded the least benefit in terms of the extent of avoided outbreak losses (per unit cost). The economically optimal vaccination strategy was the scenario that employed 50% vaccination and all Scotland as a PZ. The results provide an indicator of how resources can best be targeted for an efficient ex-ante control strategy.

Animal diseases are global issues affecting the productivity and financial profitability of affected farms. Johne’s disease is distributed on farms worldwide and is an endemic contagious bacterial infection in ruminants caused by Mycobacterium avium subspecies paratuberculosis. In cattle, the clinical disease manifests itself as chronic enteritis resulting in reduced production, weight loss, and eventually death. Johne’s disease is prevalent in the UK, including Scotland. Direct costs and losses associated with Johne’s disease have been estimated in previous research, confirming an important economic impact of the disease in UK herds. Despite this, the distributional impact of Johne’s disease among milk consumers and producers in Scotland has not been estimated. In this paper, we evaluate the change in society’s economic welfare, namely to dairy producers (i.e. infected and uninfected herds) and milk consumers in Scotland induced by the introduction of Johne’s disease in the national Scottish dairy herd. At the national-level, we conclude that the economic burden falls mainly on producers of infected herds and, to a lesser extent, milk consumers, while producers of uninfected herds benefit from the presence of Johne’s. An infected producer’s loss per cow is approximately two times larger in magnitude than that of an uninfected producer’s gain. Such economic welfare estimates are an important comparison of the relative costs of national herd prevalence and the wider economic welfare implications for both producers and consumers. This is particularly important from a policy, public good, cost sharing, and human health perspective. The economic welfare framework presented in this paper can be applied to other diseases to examine the relative burden of society’s economic welfare of alternative livestock disease scenarios. In addition, the sensitivity analysis evaluates uncertainty in economic welfare given limited data and uncertainty in the national herd prevalence, and other input parameters, associated with Johne’s disease in Scotland. Therefore, until the prevalence of Johne’s is better understood, the full economic cost to Scottish dairy herds remains uncertain but in the meantime the sensitivity analysis evaluates the robustness of economic welfare to such uncertainties.

Data from 255 Scottish beef suckler herds and 189 Scottish dairy herds surveyed as part of national bovine viral diarrhoea virus (BVDV) prevalence studies from October 2006 to May 2008 were examined retrospectively to determine the relationship between serological status and key performance indicators derived from national cattle movement records. On average, calf mortality rates were 1.35 percentage points higher in seropositive beef herds and 3.05 percentage points higher in seropositive dairy herds than in negative control herds. Seropositive beef herds were also more likely to show increases in calf mortality rates and culling rates between successive years. There were no discernible effects of BVDV on the average age at first calving or calving interval for either herd type. Accompanying questionnaire data revealed that only 27% of beef farmers and 25% of dairy farmers with seropositive herds thought their cattle were affected by BVDV, which suggests that the clinical effects of exposure may be inapparent under field conditions or masked by other causes of reproductive failure and culling. Beef farmers were significantly more likely to perceive a problem when their herd experienced acute changes in calf mortality rates, culling rates, and calving intervals between successive years. However, only 35% of these perceived positive herds were actually seropositive for BVDV. These findings emphasize both the importance of routinely screening herds to determine their true infection status and the potential for using national cattle movement records to identify herds that may be experiencing outbreaks from BVDV or other infectious diseases that impact herd performance.

The paper analyses the impact of a priori determinants of biosecurity behaviour of farmers in Great Britain. We use a dataset collected through a stratified telephone survey of 900 cattle and sheep farmers in Great Britain (400 in England and a further 250 in Wales and Scotland respectively) which took place between 25 March 2010 and 18 June 2010. The survey was stratified by farm type, farm size and region. To test the influence of a priori determinants on biosecurity behaviour we used a behavioural economics method, structural equation modelling (SEM) with observed and latent variables. SEM is a statistical technique for testing and estimating causal relationships amongst variables, some of which may be latent using a combination of statistical data and qualitative causal assumptions. Thirteen latent variables were identified and extracted, expressing the behaviour and the underlying determining factors. The variables were: experience, economic factors, organic certification of farm, membership in a cattle/sheep health scheme, perceived usefulness of biosecurity information sources, knowledge about biosecurity measures, perceived importance of specific biosecurity strategies, perceived effect (on farm business in the past five years) of welfare/health regulation, perceived effect of severe outbreaks of animal diseases, attitudes towards livestock biosecurity, attitudes towards animal welfare, influence on decision to apply biosecurity measures and biosecurity behaviour. The SEM model applied on the Great Britain sample has an adequate fit according to the measures of absolute, incremental and parsimonious fit. The results suggest that farmers’ perceived importance of specific biosecurity strategies, organic certification of farm, knowledge about biosecurity measures, attitudes towards animal welfare, perceived usefulness of biosecurity information sources, perceived effect on business during the past five years of severe outbreaks of animal diseases, membership in a cattle/sheep health scheme, attitudes towards livestock biosecurity, influence on decision to apply biosecurity measures, experience and economic factors are significantly influencing behaviour (overall explaining 64% of the variance in behaviour). Three other models were run for the individual regions (England, Scotland and Wales). A smaller number of variables were included in each model to account for the smaller sample sizes. Results show lower but still high levels of variance explained for the individual models (about 40% for each country). The individual models’ results are consistent with those of the total sample model. The results might suggest that ways to achieve behavioural change could include ensuring increased access of farmers to biosecurity information and advice sources.

Collection of abattoir data related to public health is common worldwide. Standardised on-going programmes that collect information from abattoirs that inform producers about the presence and frequency of disease that are important to them rather than public health hazards are less common. The three voluntary pig health schemes, implemented in the United Kingdom, are integrated systems which capture information on different macroscopic disease conditions detected in slaughtered pigs. Many of these conditions have been associated with a reduction in performance traits and consequent increases in production costs. The schemes are the Wholesome Pigs Scotland in Scotland, the British Pig Health Scheme in England and Wales and the Pig Regen Ltd. health and welfare checks in Northern Ireland. In this study, four post mortem conditions (pericarditis, milk spots, papular dermatitis and tail damage) were surveyed and analysed over a ten and half year period, with the aim to compare the prevalence, monthly variations, and yearly trends between schemes. Liver milk spot was the most frequently recorded condition while tail damage was the least frequently observed condition. The prevalence of papular dermatitis was relatively low compared to liver milk spot and pericarditis in the three schemes. A general decreasing trend was observed for milk spots and papular dermatitis for all three schemes. The prevalence of pericarditis increased in Northern Ireland and England and Wales; while Scotland in recent years showed a decreasing trend. An increasing trend of tail damage was depicted in Scotland and Northern Ireland until 2013/2014 followed by a decline in recent years compared to that of England and Wales with a decreasing trend over the full study period. Monthly effects were more evident for milk spots and papular dermatitis. Similarity of the modus operandi of the schemes made the comparison of temporal variations and patterns in gross pathology between countries possible over time, especially between countries with similar pig production profile. This study of temporal patterns enables early detection of prevalence increases and alerts industry and researchers to investigate the reasons behind such changes. These schemes are, therefore, valuable assets for endemic disease surveillance, early warning for emerging disease and also for monitoring of welfare outcomes.

Modelling is an important component of contingency planning and control of disease outbreaks. Dynamic network models are considered more useful than static models because they capture important dynamic patterns of farm behaviour as evidenced through animal movements. This study evaluates the usefulness of a dynamic network model of swine fever to predict pre-detection spread via movements of pigs, when there may be considerable uncertainty surrounding the time of incursion of infection. It explores the utility and limitations of animal movement data to inform such models and as such, provides some insight into the impact of improving traceability through real-time animal movement reporting and the use of electronic animal movement databases. The study concludes that the type of premises and uncertainty of the time of disease incursion will affect model accuracy and highlights the need for improvements in these areas.

Sheep have been proposed as a source of human verocytotoxigenic Escherichia coli infection on a number of occasions but few prevalence studies have focused on identifying rates of carriage of these pathogens in this species. The purpose of this work was to establish the frequency of excretion of E. coli of serogroups O157, O26, O103, O111 and O145 in sheep presented for slaughter in Scotland and to examine their carriage of known virulence determinants. The study involved microbiological isolation of E. coli from 1082 sheep presented for slaughter in four Scottish abattoirs between July 2005 and June 2006. Using faecal enrichment and immunomagnetic separation, the isolation rate from these samples was 3.4 % for E. coli serogroup O157, 5.2 % for E. coli serogroup O26, 2.3 % for E. coli serogroup O103 and 0.1 % for E. coli serogroup O145. E. coli O111 was not isolated. In the last month of testing, which coincided with sorbitol-fermenting E. coli O157 (SFO157) cases in children in Scotland, all 83 recta received were screened and tested negative for SFO157 strains. The study found no verocytotoxin-positive strains amongst the E. coli serogroup O103 or O145 isolates. Verocytotoxin-positive strains were identified amongst isolates of E. coli serotypes O157 : H7 and O26 : H11. E. coli O157 : H7 was not isolated from samples collected between January and March, a statistically significant drop (P

Bovine viral diarrhoea (BVD) is an endemic disease of cattle that causes substantial losses to both beef and dairy production worldwide. The goal of this study was to estimate the prevalence of active BVD virus (BVDV) infection in beef suckler herds in Scotland. Information was collected from 301 herds using a stratified random sampling design based on agricultural census data. Herds were classified as with and without active infection based on the within-herd BVDV seroprevalence in young stock using Bayesian finite mixture modelling. This method accounted for within- and between-herd variability and allowed for classification error by the diagnostic tests. The observed sample data enabled the discrimination of three distinct seroprevalence cohorts. The results provided evidence of active BVDV infection in 16% of herds and no evidence of recent exposure in approximately two thirds of herds. The epidemiological significance of the further 16% of herds containing young stock with a median BVDV seroprevalence of 26.3–38.5% remains unclear. The fact that a large percentage of herds did not show evidence of recent infection is encouraging from an animal health and welfare perspective and the study provides a model for the further exploration of strategies aimed at BVD control at national level.

The prevalence of Pasteurella multocida, a cause of bovine respiratory disease, was studied in a random sample of beef suckler and dairy farms throughout Scotland, by means of a cross-sectional survey. A total of 637 calves from 68 farms from six geographical regions of Scotland were sampled between February and June 2008. Deep nasal swabs were taken, and samples that were culture-positive for P multocida were confirmed by PCR. Prevalence of P multocida was 17 per cent (105 of 616 calves); 47 per cent of farms had at least one positive animal. A higher prevalence was detected in dairy calves than beef calves (P=0.04). It was found that P multocida was associated with Mycoplasma-like organisms (P=0.06) and bovine parainfluenza type 3 virus (BPI-3) (P=0.04), detected by culture and quantitative PCR of nasal swabs, respectively. Detection of P multocida was not associated with bovine respiratory syncytial virus (BRSV), bovine herpesvirus type 1 (BoHV-1) or bovine viral diarrhoea virus (BVDV). Mycoplasma-like organisms, BPI-3, BRSV, BoHV-1 and BVDV were detected in 58, 17, four, 0 and eight calves, on 25, five, two, 0 and five of the 68 farms, respectively.

Ascariosis is the most important internal parasitism present worldwide in farmed pigs. Milk spots are healing lesions occurring when Ascaris suum larvae migrate through the liver. This study aimed to identify current husbandry practices (e.g. wet/compound feeding, outdoors/indoors production, bedded/slatted floors) that influence the prevalence of milk spots in batches of slaughtered pigs, accounting for geographical locations and seasonality. Farm information was accessed through the British farm quality assurance programmes (QAPs) and information on milk spots was obtained from the pig abattoir based health schemes. Two working datasets were created. The first consisted of 505 farms recruited from the whole of Great Britain (GB). The second combined 338 farms from England and Wales (EW) with housing and feed category-specific information (e.g. for growers and finishers separately), which was not fully available for inclusion in the previous dataset. The variables were studied in multivariable beta-binomial models with the presence of milk spots being the response variable. Solid floor with bedding appeared as a risk factor, OR 1.52 (95% confidence intervals (CI) 1.26–1.85) for the GB sample, and OR 1.47 (CI 1.19–1.81) for the EW subset. Those GB herds that had all the stages of production indoors appeared to be at lower risk of milk spots (OR 0.4, CI 0.32–0.49). Changes were detected within year, with higher risk of milk spots in the second 6 months of the year OR 1.17 (CI 1.02–1.35) in the GB sample and 1.21 (95% CI 1.04–1.41) in EW farms. Overall this study suggests that those husbandry practices facilitating optimal levels of hygiene posed lower risk of milk spots in slaughtered pigs, potentially reflecting lower levels of ascariosis in the later stages of production.

Following the arrival of bluetongue virus serotype 8 (BTV-8) in southeast England in September 2007, the Scottish Government commissioned research to assess the economic consequences of a BTV-8 incursion to Scotland. Here we present the first component of the assessment, which entailed identifying feasible incursion scenarios for the virus. Our analyses focused on three routes of introduction: wind-borne dispersal of infected vectors, import of infected animals and northwards spread of BTV from affected areas in GB. These analyses were further refined by considering the spatial and temporal variation in the probability of onward transmission from an initial incursion. Keywords: Epidemiology, Culicoides, Wind-borne dispersal, Animal movements

Bluetongue is a viral disease of ruminants transmitted by Culicoides biting midges, which has spread across Europe over the past decade. The disease arrived in south-east England in 2007, raising the possibility that it could pose a risk to the valuable Scottish livestock industry. As part of an assessment of the economic consequences of a bluetongue virus incursion into Scotland commissioned by Scottish Government, we investigated a defined set of feasible incursion scenarios under different vaccination strategies. Our epidemiological simulations, based on expert knowledge, highlighted that infection will rarely spread in Scotland after the initial incursion and will be efficiently controlled by vaccination. Keywords: Epidemiology, modelling, disease control

A previously published model was re-employed to examine the potential impact of different epidemiological circumstances on output losses due to bovine viral diarrhoea virus (BVDV) infection in typical British hill cow-calf enterprises. The average annuity equivalent of unchecked losses from 100 simulated 10-year disease scenarios ranged from almost pound0/cow to approximately pound40/cow. Significant differences were found under certain circumstances, depending on the initial disease status of the herd, the initial source of virus, the probability and source of further infection, the probability of virus transmission within the herd and herd size. For naive herds, losses depended only on the risk of incursion. In most other circumstances, the losses could be mitigated if the annual risk of incursion was

The viability of eradicating bovine viral diarrhoea (BVD) in Scottish suckler herds is dependent on the continued compliance with eradication schemes. At the farm level, the costs of BVD have been identified in previous studies and show a substantial financial imperative to avoid infection. At a regional level the incentives of BVD eradication to individuals are unclear, for example the requirement for vaccination strategies despite achieving disease-free status. Ensuring farmer compliance with an eradication scheme is therefore difficult. Experience of eradicating BVD from beef-dominated areas is limited and theoretical models have tended to focus on the dairy sector. Here we present a stochastic epidemiological model of a typical beef suckler herd to explore the interaction of a farm with a regional pool of replacements, utilising information from a BVD virus seroprevalence survey of Scottish beef suckler herds. Our epidemiological model is then used to assess the relative costs to individuals assuming different regional endemic prevalences, which are used to represent the likelihood of BVD re-introduction. We explore the relative cost of BVD, taken as likelihood and consequence, at an endemic steady state in contrast to previous models that have assumed the introduction or control of BVD in an epidemic state (e.g. a closed and mostly susceptible population). Where endemic, BVD is unlikely to affect all farms evenly and will cost most farmers very little due to herd immunity or self-clearance of the virus. Compliance is likely to be boosted by pump-priming to initiate and complete eradication schemes with cost-sharing.

The article describes the influence of a disease control scheme (the Norfolk-Suffolk Bovine Viral Diarrhoea Disease (BVD) Eradication scheme) on farmers' bio-security attitudes and behaviours. In 2010, a survey of 100 cattle farmers (53 scheme members vs. 47 out of scheme farmers) was undertaken among cattle farmers residing in Norfolk and Suffolk counties in the UK. A cross-sectional independent measures design was employed. The main analytical tool was content analysis. The following variables at the farmer-level were explored: the specific BVD control measures adopted, livestock disease priorities, motivation for scheme membership, wider knowledge acquisition, biosecurity behaviours employed and training course attendance. The findings suggest that participation in the BVD scheme improved farmers' perception of the scheme benefits and participation in training courses. However, no association was found between the taking part in the BVD scheme and livestock disease priorities or motivation for scheme participation, or knowledge about BVD bio-security measures employed. Equally importantly, scheme membership did appear to influence the importance accorded specific bio-security measures. Yet such ranking did not appear to reflect the actual behaviours undertaken. As such, disease control efforts alone while necessary, are insufficient. Rather, to enhance farmer bio-security behaviours significant effort must be made to address underlying attitudes to the specific disease threat involved.

When a few individuals generate disproportionately many secondary cases, targeted interventions can theoretically lead to highly efficient control of the spread of infection. Practical exploitation of heterogeneous transmission requires the sources of variability to be quantified, yet it is unusual to have empirical data of sufficient resolution to distinguish their effects. Here, we exploit extensive data on pathogen shedding densities and the distribution of cases, collected from the same population within the same spatio-temporal window, to expose the comparative epidemiology of independent Escherichia coli O157 strains. For this zoonotic pathogen, which exhibits high-density shedding (supershedding) and heterogeneous transmission in its cattle reservoir, whether targeting supershedding could be an effective control depends critically on the proposed link between shedding density and transmissibility. We substantiate this link by showing that our supershedder strain has nearly triple the R0 of our non-supershedder strain. We show that observed transmission heterogeneities are strongly driven by superspreading in addition to supershedding, but that for the supershedder strain, the dominant strain in our study population, there remains sufficient heterogeneity in contribution to R0 from different shedding densities to allow exploitation for control. However, in the presence of substantial within-host variability, our results indicate that rather than seek out supershedders themselves, the most effective controls would directly target the phenomenon of pathogen supershedding with the aim of interrupting or preventing high shedding densities. In this system, multiple sources of heterogeneity have masked the role of shedding densities—our potential targets for control. This analysis demonstrates the critical importance of disentangling the effects of multiple sources of heterogeneity when designing targeted interventions.

Chlamydophila (C.) abortus, responsible for chlamydial abortion (commonly known as Enzootic Abortion of Ewes [EAE]), causes major financial losses to the sheep industry worldwide. There remain many uncertainties surrounding the epidemiology of EAE. The aim of this study was to construct an epidemiological model to simulate EAE based on current knowledge of the disease, and in doing so, identify knowledge gaps that need to be addressed through further research. Key parameters that impact upon the development of the disease, such as the rate of contact between naïve ewes and infected material, are defined. Sensitivity analysis was undertaken for parameter values that are unknown to explore their impact upon the pattern of disease. The simulated results show the importance of the transmission rate (i.e. contact) and the number of infected replacements introduced at the start of an outbreak. Depending upon the rate of transmission, the year in which the peak number of affected ewes occurs and the number of years over which a high number of animals are affected varies. This suggests that a better understanding of the underlying processes that drive transmission of C. abortus is needed. Furthermore, if infected ewes could be identified prior to parturition, when they shed the organism in large numbers, the impact of EAE on sheep flocks could be greatly reduced.

In this paper we evaluated the distributional effects on actors in the milk market of a hypothetical programme to eradicate bovine viral diarrhoea (BVD) from the Scottish dairy herd. With this in mind, we applied an economic welfare methodology which utilizes data on price, on output quantity, on elasticities of supply and demand and on simulated cost and yield effects of an eradication programme. Our analysis is based on Markov-chain Monte Carlo simulation of BVD spread in the dairy herd. We found that consequent upon the eradication of the disease milk yield per cow increased for all herd sizes in Scotland whereas milk price received by farmers fell. Consequently, milk consumers gained around pound11 million in discounted economic surplus and producers with infected herds gained around pound39 million whereas producers with un-infected herds lost around pound2 million in discounted surplus. On balance, however, the eradication programme generated around pound 47 million in discounted economic gain for Scotland. We found that the results are sensitive to changes in yield gains made by owners of the infected herd.

SUMMARYIn beef suckler herds, reproductive failure is a major cause of financial loss during a bovine viral diarrhoea (BVD) outbreak due to reduction in the numbers of calves, increased calving spread and the financial implications of dealing with infertile cows. These losses may be hidden and/or not fully attributed to BVD. A model of herd dynamics was built and combined with an epidemiological model to encapsulate the disruptions to reproduction that BVD may cause in beef suckler herds and to estimate the associated financial consequences of such disruptions.Results from the model suggest that the average losses associated with BVD in Scottish beef suckler herds via impaired reproduction alone may vary between £43 and £22/cow/year during the course of a BVD epidemic. These results indicate that an outbreak can be costly and these losses may be hidden by the use of low risk management practices such as a long breeding season, not only in herds with no evidence of antibodies but also in herds where there are some antibody positive (immune) animals.

The putative source of hide contamination for 236 cattle in Scotland followed from the farm through to slaughter was determined using phage and verocytotoxin type data. The majority of cattle (84%) were found to have subtypes of Escherichia coli O157 on their hide that had not been found previously in any animal from the farm of origin, strongly suggesting that contamination occurred once animals had left the farm of origin. Using logistic regression analysis, several variables and factors were found to be strongly associated ( P < 0.01) with cross-contamination of cattle hides at the univariate level; commercial transport to slaughter, transport with other animals, use of a crush, line automation, and increasing slaughterhouse throughput were all risk factors, while feeding hay in lairage, processing an animal earlier in a slaughter cohort, and cleaning the landing area poststunning were protective. In the multivariable model, with the slaughterhouse and the farm group included as random effects, factors associated with the cross-contamination of cattle hides were identified. Transport to the slaughterhouse by a commercial hauler had a borderline-significant association with increased odds of an animal having a cross-contaminated hide (odds ratio [OR] [95% confidence interval {CI}] = 5.7 [0.99, 33.0]; P = 0.05). At the slaughterhouse, providing hay to cattle waiting in lairage (OR [95% CI] = 0.04 [P = 0.05) and cleaning the landing area (OR [95% CI] = 0.03 [P = 0.06) also had a borderline-significant association with decreased odds of an animal having a cross-contaminated hide. Although the prevalence of carcass contamination remains very low, targeted intervention at the preslaughter stage may have the potential to reduce further the risk to public health.

Aims: To compare rhamnose MacConkey agar supplemented with cefixime and tellurite (CT-RMac) and tryptone bile X-glucuronide (TBX) agars as isolation media for Vero cytotoxin-producing Escherichia coli (VTEC) serogroup O26 from animal faeces. Methods and Results: Nine VTEC O26 were isolated from sheep faeces; out of which six were isolated only on CT-RMac and one was isolated only on TBX. One hundred and twelve VTEC O26 were isolated from calf faeces; out of which 97% were from CT-RMac and 52% were from TBX. In a study of E. coli O26 strains, 84% of VT-positive O26 did not ferment rhamnose when compared with 16% of VT-negative O26. VT-positive (19%) and VT-negative (39%) E. coli O26 strains did not grow on CT-RMac agar. Conclusions: It is important to consider that VTEC O26 strains either may ferment rhamnose or may be sensitive to the CT supplement of CT-RMac agar. Significance and Impact of the Study: This work compares CT-RMac and TBX agars as isolation medium for VTEC O26 from Scottish animal faeces and highlights that VTEC O26 may be missed if only CT-RMac agar is used.

Using the example of bovine viral diarrhoea (BVD) in Scottish suckler (cow-calf) beef herds, this paper demonstrated a method to establish the maximum average net benefit of disease control under specific epidemiological and farm business circumstances. Data were generated for the method using a stochastic epidemiological model set to estimate the mean and variance of control costs and output losses from BVD for 50-cow or 120-cow herds, either free of BVD at the outset or of unknown BVD status. Control of disease was by increased investment in a variety of ('biosecurity') measures aimed at reducing the probability of virus entering the closed herd in any 1 year of a 10-year period of simulated exposure to risk from BVD virus introduction either with or without vaccination. Herds free of BVD at the outset enjoyed much greater maximum average net benefits than herds of unknown BVD status. Best allocations of hypothetical incentives to encourage farmers to establish their freedom from BVD were therefore outlined. Vaccination and biosecurity were generally found to be complementary rather than substitutes for one another. The advantages of the maximum net benefit measure over the more usual average total cost of endemic disease were demonstrated and discussed. The maximum net benefit method focuses on the relationship between costs and benefits, which often exhibits diminishing marginal returns meaning that profit maximisation and disease minimisation are incompatible. The method can also allow for constraints on and competition for limited farm resources. It was argued that these attributes are important to persuade farmers to invest in animal health.

The prevalence of verocytotoxin-producing Escherichia coli (VTEC) O157 in 12–30-month-old beef finishing cattle in Scotland was determined using 1 g faeces samples enriched in buffered peptone water, followed by immunomagnetic separation (IMS) and isolation on sorbitol MacConkey agar with cefixime and tellurite supplement (CT-SMAC). A validated questionnaire was used to collect information that could be associated with the samples. Generalised Linear Models and Generalised Linear Mixed Models were used to identify factors associated with shedding both between and within groups. A total of 14,856 samples were collected from 952 farms, of which 1231 were positive for VTEC O157. Prevalence levels were calculated with 95% confidence intervals as follows: 7.9% (6.5%, 9.6%) of animals sampled were estimated to be shedding VTEC O157, while 22.8% (19.6%, 26.3%) of farms were estimated as having at least one animal shedding in the group sampled. The median percentage of animals shedding in positive groups was 25% (20%, 32%). An increased probability of a group containing a shedding animal was associated with larger numbers of finishing cattle, the presence of pigs on the farm, or the farm being classed as a dairy unit stocking beef animals. Farms that spread slurry on grazing land were more likely to have shedding animals, while those that spread manure were at lower risk. Groups with older animals were less likely to be identified as positive. There was no significant regional difference in group shedding probabilities, but the proportion of positive groups dropped over two successive years of the study. Higher mean levels of shedding in positive groups were associated with animals being housed rather than at pasture, and this effect was stronger in groups which had recently had a change in housing or diet. Farms with animals at pasture had lower mean prevalence where water was supplied from a natural source, as had farms with higher numbers of finishing cattle. There remained unexplained variability in mean prevalence levels on positive farms in different areas of Scotland.

The objective of this study was to investigate epidemiological risk factors for porcine non-specific colitis (NSC). Forty-seven Scottish pig farms, with and without a clinical history of diarrhoea during the growing period (15-40 kg), were selected. The study included farm visits, clinical inspection of pigs, completion of farm management questionnaires, pathological tests into the cause of the diarrhoea and analysis of the non-starch polysaccharide (NSP) content of feeds. The results from 17 farms designated as NSC and 10 control farms suggest dietary associations with NSC. Farms with NSC fed diets with significantly higher levels of NSPs, especially containing the sugars glucose, arabinose and xylose. Few management factors were identified, although the high prevalence of infectious colitis reduced the power of the study.

Shiga-toxin-producing Escherichia coli (STEC) O157:H7 is a recently emerged zoonotic pathogen with considerable morbidity. Since the emergence of this serotype in the 1980s, research has focussed on unravelling the evolutionary events from the E. coli O55:H7 ancestor to the contemporaneous globally dispersed strains observed today. In this study, the genomes of over 1000 isolates from both human clinical cases and cattle, spanning the history of STEC O157:H7 in the UK, were sequenced. Phylogenetic analysis revealed the ancestry, key acquisition events and global context of the strains. Dated phylogenies estimated the time to evolution of the most recent common ancestor of the current circulating global clone to be 175 years ago. This event was followed by rapid diversification. We show the acquisition of specific virulence determinates has occurred relatively recently and coincides with its recent detection in the human population. We used clinical outcome data from 493 cases of STEC O157:H7 to assess the relative risk of severe disease including haemolytic uraemic syndrome from each of the defined clades in the population and show the dramatic effect Shiga toxin repertoire has on virulence. We describe two strain replacement events that have occurred in the cattle population in the UK over the last 30 years, one resulting in a highly virulent strain that has accounted for the majority of clinical cases in the UK over the last decade. There is a need to understand the selection pressures maintaining Shiga-toxin-encoding bacteriophages in the ruminant reservoir and the study affirms the requirement for close surveillance of this pathogen in both ruminant and human populations.