The use of data for health and welfare management of farmed salmons in Norway, Scotland, and Ireland.

Data-driven solutions can support stakeholders' decision-making when managing health and welfare in Atlantic salmon production. While many different types of data are being collected, knowledge about stakeholders' use and needs regarding this data and data tools in their day-to-day work is limited. The current study explores the status quo of using data and data tools in salmon health management and needs of the stakeholders.

A multi-methods, multi-actor exploration of the benefits and barriers to milk recording on Irish farms using the COM-B model.

Milk recording is a critical tool in dairy farming, providing individual cow information. When used effectively, this data contributes to on-farm productivity, herd health management decisions and supports prudent veterinary prescribing of antimicrobials. Although an industry and government priority, uptake has been relatively slow in Ireland.

Risk factors for detection of bovine viral diarrhoea virus in low-risk herds during the latter stages of Ireland's eradication programme.

Background: A national programme to eradicate bovine viral diarrhoea (BVD) has been in place in Ireland since 2013. To inform decision making in the end stages of eradication, and support the development of post-eradication surveillance strategies, an understanding of risks of infection in a low prevalence system is required.

Methods: A case-control study design was implemented.

A Herd Investigation Tool in Support of the Irish Bovine Viral Diarrhoea Eradication Programme.

Bovine viral diarrhoea (BVD) is an important endemic disease of cattle. In Ireland, an industry-led compulsory eradication programme began in January 2013. The main elements of this programme are the identification and elimination of persistently infected (PI) calves by testing all new-borns, the implementation of biosecurity to prevent re-introduction of disease and continuous surveillance.

A large-scale epidemiological model of BoHV-1 spread in the Irish cattle population to support decision-making in conformity with the European Animal Health Law.

We present a new modelling framework to address the evaluation of national control/surveillance programs planned in line with the European Animal Health Law (AHL) for livestock diseases. Our modelling framework is applied to the cattle sector in Ireland where there is need for policy support to design an optimal programme to achieve bovine herpesvirus type 1 (BoHV-1) free status under the AHL. In this contribution, we show how our framework establishes a regional model that is able to mechanistically reproduce the demography, management practices and transport patterns of an entire cattle population without being dependent on continuous livestock registry data.

Combining expert knowledge and machine-learning to classify herd types in livestock systems.

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.

Stakeholder perceptions of non-regulatory bovine health issues in Ireland: past and future perspectives.

Background: 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.

Spatial and network characteristics of Irish cattle movements.

Our aim was to examine, for the first time, the spatial and network characteristics of cattle movements between herds in the Republic of Ireland (ROI), to inform policy and research of relevance to the surveillance and management of disease in Irish cattle. We analysed movements in 2016 as discrete herd to herd pairings (degree), herd to herd pairings by date of move (contacts) and herd to herd pairings by date and individual animal (transfers), and looked at each of these as movements out of a herd (out degree, out contacts, out transfers) and into a herd (in degree, in contacts, in transfers). We found that the frequency distributions, by herd, of these six move types were all heavily right skewed but in the case of the 'out' data types more closely followed a log-normal than the scale free distribution often reported for livestock movement data.

The impact of liver fluke infection on steers in Ireland: A meta-analytic approach.

Post-mortem liver inspection results together with production parameters are often used to estimate the impact of liver fluke infection on farm animal populations. However, post mortem liver inspection is an imperfect method of determining the liver fluke infection status of cattle. This work estimates the difference in mean lifetime weight gain at 819 days (ΔLWG) between steers assigned liver fluke negative (LFN) and liver fluke positive (LFP) status at post-mortem meat inspection, quantifies the potential impact of imperfect sensitivity and specificity on these results and estimates the economic impact of these differences.

Genome-wide association study of endo-parasite phenotypes using imputed whole-genome sequence data in dairy and beef cattle.

Background: Quantitative genetic studies suggest the existence of variation at the genome level that affects the ability of cattle to resist to parasitic diseases. The objective of the current study was to identify regions of the bovine genome that are associated with resistance to endo-parasites.

Methods: Individual cattle records were available for Fasciola hepatica-damaged liver from 18 abattoirs.

Investigation of the potential for sera from cattle persistently infected with bovine viral diarrhea virus to generate false-negative antibody ELISA results in pooled serum from seropositive and seronegative cattle.

We investigated the potential for viremic sera from cattle persistently infected with bovine viral diarrhea virus to create false-negative antibody results when testing pools of 10 sera by indirect or blocking ELISAs. Seronegative viremic sera ( n = 23) were each added to a series of artificially constructed pools containing various percentages (0-90%) of antibody-positive sera, and the resulting pools were assayed for antibody. In all 23 cases, a negative antibody result was obtained in the pool containing no seropositive sera.

Genetic parameters for variability in the birth of persistently infected cattle following likely in utero exposure to bovine viral diarrhea virus.

Genetic selection is an inexpensive and complementary strategy to traditional methods of improving animal health and welfare. Nonetheless, endeavors to incorporate animal health and welfare traits in international breeding programs have been hampered by the availability of informative phenotypes. The recent eradication program for bovine viral diarrhea (BVD) in the Republic of Ireland has provided an opportunity to quantify the potential benefits that genetic selection could offer BVD eradication programs elsewhere, as well as inform possible eradication programs for other diseases in the Republic of Ireland.

Decision support beyond total savings-Eligibility and potential savings for individual participants from changes in the national surveillance strategy for bovine viral diarrhoea (BVD) in Ireland.

Surveillance and management of livestock diseases is often evaluated with reference to expected sector-wide costs. In contrast, we calculate losses or savings for individual herd owners of a change in monitoring strategy during a national cattle disease eradication programme: bovine viral diarrhoea (BVD) in Ireland. The alternative strategy differs in how the disease is identified; by its sample- rather than census-based approach; and by its greater cost per test.

Little genetic variability in resilience among cattle exists for a range of performance traits across herds in Ireland differing in Fasciola hepatica prevalence.

It is anticipated that in the future, livestock will be exposed to a greater risk of infection from parasitic diseases. Therefore, future breeding strategies for livestock, which are generally long-term strategies for change, should target animals adaptable to environments with a high parasitic load. Covariance components were estimated in the present study for a selection of dairy and beef performance traits over herd-years differing in Fasciola hepatica load using random regression sire models.

Quantifying the role of Trojan dams in the between-herd spread of bovine viral diarrhoea virus (BVDv) in Ireland.

A compulsory national programme to eradicate bovine viral diarrhoea virus (BVDv) began in Ireland on 1 January, 2013. The objective of the current study was to quantify the role of Trojan dams (animal(s) not persistently infected (PI) with BVDv but carrying PI foetus(es) and introduced to the herd while pregnant with the PI foetus(es)) in the farm-to-farm spread of BVDv in Ireland, and to identify herd-level risk factors for producing or introducing a Trojan dam. The study population included all BVD+ calves born in Ireland between 1 January, 2013 and 31 December, 2015, along with their dams.

Genetic correlations between endo-parasite phenotypes and economically important traits in dairy and beef cattle.

Parasitic diseases have economic consequences in cattle production systems. Although breeding for parasite resistance can complement current control practices to reduce the prevalence globally, there is little knowledge of the implications of such a strategy on other performance traits. Records on individual animal antibody responses to Fasciola hepatica, Ostertagia ostertagi, and Neospora caninum were available from cows in 68 dairy herds (study herds); national abattoir data on F.

A protocol to identify and minimise selection and information bias in abattoir surveys estimating prevalence, using Fasciola hepatica as an example.

Abattoir surveys and findings from post-mortem meat inspection are commonly used to estimate infection or disease prevalence in farm animal populations. However, the function of an abattoir is to slaughter animals for human consumption, and the collection of information on animal health for research purposes is a secondary objective. This can result in methodological shortcomings leading to biased prevalence estimates.

Associations between paratuberculosis ELISA results and test-day records of cows enrolled in the Irish Johne's Disease Control Program.

The effect of the Mycobacterium avium ssp. paratuberculosis (MAP) ELISA status on test-day milk performance of cows from Irish herds enrolled in the pilot national voluntary Johne's disease control program during 2013 to 2015 was estimated. A data set comprising 92,854 cows and 592,623 complete test-day records distributed across 1,700 herds was used in this study.

Patterns of calving and young stock movement in Ireland and their implications for BVD serosurveillance.

The Republic of Ireland has a national eradication programme for bovine viral diarrhoea virus (BVDv) based on tissue-tag testing of calves to identify persistently infected animals (PIs). It has been proposed that serological testing of a sample of home-bred young stock would be a more cost effective surveillance mechanism than continued tissue-tag testing in herds which have previously been found to be BVD-free. These animals would have to be at least 6 months of age to avoid interference from maternal antibodies in test results.

A survey of free-ranging deer in Ireland for serological evidence of exposure to bovine viral diarrhoea virus, bovine herpes virus-1, bluetongue virus and Schmallenberg virus.

Background: Deer are an important wildlife species in both the Republic of Ireland and Northern Ireland having colonised most regions across the island of Ireland. In comparison to cattle and sheep which represent the main farmed ruminant species on the island, there is a lack of data concerning their exposure, as measured by the presence of antibodies, to important viral pathogens of ruminants. A study was therefore undertaken to investigate the seroprevalence of wild deer to four viruses, namely bovine viral diarrhoea virus (BVDV), bovine herpesvirus-1 (BoHV-1), Schmallenberg virus (SBV) and bluetongue virus (BTV).

Impact of three inactivated bovine viral diarrhoea virus vaccines on bulk milk p80 (NS3) ELISA test results in dairy herds.

Bovine viral diarrhoea virus (BVDV) is endemic in many countries and vaccines are used as a component of control and eradication strategies. Surveillance programmes to detect exposure to BVDV often incorporate the use of bulk milk (BM) testing for antibodies against BVDV p80 (NS3), but vaccination can interfere with these results. The aim of this study was to evaluate whether BVDV vaccines would confound BM testing for specific antibodies in a nationally representative group of commercial dairy farms in the Republic of Ireland.

Genetic diversity of ruminant Pestivirus strains collected in Northern Ireland between 1999 and 2011 and the role of live ruminant imports.

Background: The genus pestivirus within the family Flaviviridae includes bovine viral diarrhoea virus (BVDV) types 1 and 2, border disease virus (BDV) and classical swine fever virus. The two recognised genotypes of BVDV are divided into subtypes based on phylogenetic analysis, namely a-p for BVDV-1 and a-c for BVDV-2.

Methods: Three studies were conducted to investigate the phylogenetic diversity of pestiviruses present in Northern Ireland.