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Graham, David A.
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Graham, David A.
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Graham, David A.
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- PublicationA modelling framework for the prediction of the herd-level probability of infection from longitudinal data(Peer Community In, 2022-01-07)
; ; ; ; ; he 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.44 - PublicationThe Irish cattle population structured by enterprise type: overview, trade & trends(Springer Nature, 2022-04-04)
; ; ; ; ; ; ; Background: The cattle sector is the most important economic production unit of the Irish farming and agri-food sector. Despite its relevance, there has been limited quantitative information about the structure of differing cattle production types and of the connections between them. This paper addresses this gap by providing, for the first time, an overview of the Irish cattle population structured by enterprise type. Methods & Results: We collected data from the cattle register for the period 2015 to 2019 and assigned registered herds to one of 18 different herd types using a recently published herd type classification approach. This allows, for the first time, to exploring changes in enterprise types and subtypes over time, and describing the movements between these subtypes and from these subtypes to slaughter. Conclusions: The overview and associated classification presented in this study will form the basis for a number of future comparative studies, including cross-sectoral assessments of profitability, estimation of the extent of animal health losses on Irish cattle farms or structural analysis of Greenhouse Gas (GHG) emissions across production systems.78Scopus© Citations 1 - PublicationA review of bovine Johne's disease control activities in 6 endemically infected countriesMycobacterium avium subspecies paratuberculosis (MAP) is endemic in the bovine populations of many countries and can cause a significant reduction in animal welfare and production efficiency making control desirable. Effective control has proved very difficult to achieve despite multiple regionally coordinated programmes being in existence since the 1920s. The international community increasingly recognises the value in learning from the collective experiences of existing programmes to improve the effectiveness of control. The aim of this review is to outline key aspects of bovine Johne's disease control activities across 6 endemically infected countries to facilitate comparison of current international practice. The background, control activities and monitoring components of programmes in Australia, Canada, Denmark, the Netherlands, the United Kingdom and the United States of America were individually reviewed. Factual accuracy of each review was checked by individuals involved in the respective programmes before the reviews were condensed and combined into a single document presented here, with the complete reviews of each programme available as supplementary material. There was considerable heterogeneity in key aspects of control activity design including goals, responses to declining participation, herd classification, recommended control measures and associated test requirements. The data presented will be of interest to organisations that are involved in developing new or existing regionally coordinated BJD control activities.
233Scopus© Citations 91 - PublicationStakeholder perceptions of non-regulatory bovine health issues in Ireland: past and future perspectives(Springer, 2020-11-26)
; ; ; In recent years, there have been multiple (political, environmental, cultural) drivers of change in Irish agriculture, including the establishment of Animal Health Ireland (AHI) in 2009, to provide leadership of non-regulatory livestock health issues (diseases and conditions of livestock that are endemic in Ireland but which are not currently subject to international legislation). In this study, we describe the opinion of stakeholders (farmers, veterinary practitioners and agricultural industry professional service providers), elicited by means of a survey, on their perceptions of changes in selected non-regulatory bovine health issues over the last 10 years and priority issues relevant to non-regulatory bovine health to be tackled over the next 10 years. Results: A total of 673 individuals participated in the online questionnaire. For the majority of the non-regulatory bovine health issues, most participants felt there had been improvements over the last 10 years. However, professional service providers were generally more conservative in their response to improvements on-farm compared to farmers. Several issues, particularly BVD and udder health/milk quality, were viewed more positively by all relevant respondents. There was reasonable agreement between responses from different respondent types and sectors regarding the top three priorities relevant to non-regulatory bovine animal health for the next 10 years in Ireland, which included antimicrobial resistance (highlighting measures to reduce both on-farm usage and resistance), anthelmintic resistance, greenhouse emissions and calf welfare. Conclusions: The results are encouraging, demonstrating a perception of improvement in a number of non-regulatory bovine health issues in Ireland over the last ten years. With respect to the next 10 years, stakeholders prioritised antimicrobial and anthelmintic resistance, greenhouse gas emissions and calf welfare, which aligns closely with broader societal concerns. This information is useful to AHI, particularly with respect to future priorities. However, these concerns are broad in scope and will require further considerations, including collaborations, between AHI and partnering organisations. Given that there were differences between farmers and professional service providers in responses, it is useful to consider how the aims and the benefits of future AHI programmes are framed and communicated to all stakeholders.137Scopus© Citations 3 - PublicationThe Irish Programme to Eradicate Bovine Viral Diarrhoea Virus—Organization, Challenges, and Progress(Frontiers Media, 2021-06-01)
; ; ; ; A mandatory national Irish bovine viral diarrhoea (BVD) eradication programme, coordinated by Animal Health Ireland, commenced in 2013. Key decisions and programme review are undertaken by a cross-industry Implementation Group (BVDIG) supported by a Technical Working Group. Ear notch tissue is collected from all new-born calves using modified official identity tags, supplemented by additional blood sampling, including for confirmatory testing of calves with initial positive results and testing of their dams. Testing is delivered by private laboratories in conjunction with the National Reference Laboratory, with all results reported to a central database. This database manages key elements of the programme, issuing results to herdowners by short message service messaging supplemented by letters; assigning and exchanging animal-level statuses with government databases of the Department of Agriculture, Food and the Marine to enable legislated restrictions on animal movements; assigning negative herd status based on test results; generating regular reports for programme management and evaluation and providing herd-specific dashboards for a range of users. Legislation supporting the programme has been in place throughout but has not thus far mandated the slaughter of persistently infected (PI) calves. A key challenge in the early years, highlighted by modeling, was the retention of PI animals by some herd owners. This has largely been resolved by measures including graduated financial supports to encourage their early removal, herd-level movement restrictions, ongoing programme communications and the input of private veterinary practitioners (PVPs). A framework for funded investigations by PVPs in positive herds was developed to identify plausible sources of infection, to resolve the status of all animals in the herd and to agree up to three measures to prevent re-introduction of the virus. The prevalence of PI calves in 2013 was 0.66%, within 11.3% of herds, reducing in each subsequent year, to 0.03 and 0.55%, respectively, at the end of 2020. Recent regulatory changes within the European Union for the first time make provision for official approval of national eradication programmes, or recognition of BVD freedom, and planning is underway to seek approval and, in due course, recognition of freedom within this framework by 2023.115Scopus© Citations 7 - PublicationConsiderations on BVD eradication for the Irish livestock industry(Springer (Biomed Central Ltd.), 2011)
; ; ; Animal Health Ireland has produced clear guidelines for the control of Bovine Viral Diarrhoea (BVD) infection in Irish cattle herds. In the course of developing these guidelines it was clear that a framework for regional and/or national BVD control would be required to increase the uptake of BVD control at farm level and reduce the overall prevalence of the disease. This paper assessed the economic impact of BVD, epidemiological aspects of the disease to its control, models of BVD control, international experiences of BVD control programmes. The technical knowledge and test technology exists to eradicate BVD. Indeed, many countries have successfully and others are embarking on control of the disease. The identification and prompt elimination of PI cattle will form the basis of any control programme. The trade of such animals must be curtailed. Pregnant and potentially pregnant carrying PI foetuses pose a significant threat. International experience indicates systematic, well coordinated programmes have the most success, while voluntary programmes can make good initial progress but ultimately fail. The farming community must buy into any proposed programme, and without their support, failure is likely. To buy into the programme and create such a demand for BVD control, farmers must first be well informed. It is likely that stemming economic loss and improving productivity will be the primary motivator at individual farm level.459Scopus© Citations 43 - PublicationAspects of bovine herpesvirus 1 and bovine viral diarrhoea virus herd-level seroprevalence and vaccination in dairy and beef herds in Northern Ireland(BioMed Central, 2014-08-15)
; ; ; ; Background: Infections with bovine herpesvirus 1 (BoHV-1) and bovine viral diarrhoea (BVD) virus cause diseases of cattle with a worldwide distribution. The primary objective of the present study was to describe aspects of herd-level BoHV-1 and BVDV seroprevalence (based on testing of pooled sera) and control on farms in Northern Ireland, including vaccine usage. An indirect antibody ELISA test (SVANOVA, Biotech AB, Uppsala, Sweden) was applied to serum pools which were constructed from serum samples taken for a cross-sectional study of a convenience sample of 500 Northern Irish dairy and beef cow herds in 2010, for which vaccination status was determined by telephone survey. The herd-level seroprevalence of BoHV-1 and BVDV in Northern Ireland was estimated in non-vaccinating herds and associations between possible risk factors (herd type and herd size (quartiles)) and herd-level prevalence were determined using chi-squared analysis. Results:The herd-level seroprevalence (of BoHV-1 and BVDV) in non-vaccinating herds was 77.3% (95% CI: 73.6-80.9%) and 98.4% (95% CI: 97.3-99.5%) respectively in the cross-sectional study. A significant difference existed in BoHV-1 herd-level seroprevalence between dairy and beef herds (74.7% vs 86.5% respectively; p < 0.02) though not for BVDV seroprevalence (98.5% vs 98.3% respectively; p > 0.91). A significant association was found between herd size (quartiles) and herd-level classification for BoHV-1 herd-level seroprevalence based on cut-off percentage positivity (COPP) (p < 0.01) while no such association was found for BVDV (p = 0.22). 15.5% and 23.8% of farmers used BoHV-1 and BVDV vaccines, respectively. BoHV-1 vaccine was used in 30% of dairy herds and in 11% of beef herds, while BVDV vaccine was used in 46% and 16% of dairy and beef herds, respectively. Conclusions: The results from this study indicate that the true herd-level seroprevalences to bovine herpesvirus 1 and bovine virus diarrhoea virus in non-vaccinating herds in Northern Northern Ireland are 77.3% (95% CI: 73.6-80.9%) and 98.4% (95% CI: 97.3-99.5%), respectively. The present study will assist in guiding regional policy development and establish a baseline against which the progress of current and future control and eradication programmes can be measured.227Scopus© Citations 14 - PublicationSTOC Free: An Innovative Framework to Compare Probability of Freedom From Infection in Heterogeneous Control Programmes(Frontiers, 2019-04-26)
; ; ; ; The existence, stage of eradication and design of control programmes (CPs) for diseases that are not regulated by the EU differ between Member States. When freedom from infection is reached (or being pursued), safe trade is essential to protect (or reach) that status. The aim of STOC free, a collaborative project between six countries, is to develop and validate a framework that enables a transparent and standardized comparison of confidence of freedom for CPs across herds, regions or countries. The framework consists of a model combined with a tool to facilitate the collection of the necessary parameters. All relevant actions taken in a CP are included in a Bayesian network model, which allows prior distributions for most parameters. In addition, frequency of occurrence and risk estimates for factors that influence either the probability of introduction or temporary misclassification leading to delayed detection of the infection are included in the model. Bovine viral diarrhoea virus (BVDV) is used as an example disease. Many countries have CPs in place for BVDV and although elements of the CPs are similar, biosecurity measures and testing protocols, including types of tests and testing frequency, as well as target groups, differ widely. Although the initially developed framework is based on BVDV, the aim is to make it sufficiently generic to be adaptable to CPs for other diseases and possibly other species. Thus, STOC free will result in a single general framework, adaptable to multiple disease CPs, which aims to enhance the safety of trade.178Scopus© Citations 7 - PublicationCombining expert knowledge and machine-learning to classify herd types in livestock systems(Springer, 2021-02-04)
; ; ; ; ; ; A detailed understanding of herd types is needed for animal disease control and surveillance activities, to inform epidemiological study design and interpretation, and to guide effective policy decision-making. In this paper, we present a new approach to classify herd types in livestock systems by combining expert knowledge and a machine-learning algorithm called self-organising-maps (SOMs). This approach is applied to the cattle sector in Ireland, where a detailed understanding of herd types can assist with on-going discussions on control and surveillance for endemic cattle diseases. To our knowledge, this is the first time that the SOM algorithm has been used to differentiate livestock systems. In compliance with European Union (EU) requirements, relevant data in the Irish livestock register includes the birth, movements and disposal of each individual bovine, and also the sex and breed of each bovine and its dam. In total, 17 herd types were identified in Ireland using 9 variables. We provide a data-driven classification tree using decisions derived from the Irish livestock registration data. Because of the visual capabilities of the SOM algorithm, the interpretation of results is relatively straightforward and we believe our approach, with adaptation, can be used to classify herd type in any other livestock system.91Scopus© Citations 8 - PublicationThe Irish Johne’s Control Programme(Frontiers Media, 2021-08-27)
; ; ; The Irish Johne’s Control Programme (IJCP) provides a long-term approach to the voluntary control of Johne’s disease (JD) in Ireland, strongly supported by Irish cattle industry leadership. It leverages the establishment of Animal Health Ireland for control of animal diseases not regulated by the European Union. The IJCP has four objectives: facilitate protection against spread of JD to uninfected farms; reduce the level of infection when present; assure markets of JD control in Ireland; and improve calf health and farm biosecurity. Key IJCP elements are an annual veterinary risk assessment and management plan (VRAMP), annual whole herd test (WHT) by ELISA on blood or milk samples with ancillary faecal PCR testing of ELISA reactors, and Targeted Advisory Service on Animal Health (TASAH) investigations of infected herds. There are pathways for assurance of herds with continuing negative tests and for management of test-positive herds. Herdowners are responsible for on-farm activities, and specifically-trained (approved) veterinary practitioners have a pivotal role as technical advisors and service providers. The programme is supported by training of veterinarians, performance of testing in designated laboratories, documentation of policies and procedures, innovative data management for herd and test activities and for programme administration, training, and broad communication and awareness activities. Tools and systems are refined to address emerging issues and enhance the value of the programme. An Implementation: Group comprising industry, government and technical leaders sets strategic direction and policy, advised by a Technical Working Group. Shared funding responsibilities are agreed by key stakeholders until 2022 to support herds in the programme to complete requirements. Herd registrations have increased steadily to exceed 1,800. National bulk tank milk surveillance is also being deployed to identify and recruit test-positive herds with the expectation that they have a relatively high proportion of seropositive animals. The programme will continue to innovate and improve to meet farmer and industry needs.13Scopus© Citations 3