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In Ireland, the interferon-gamma (IFN-γ) assay is routinely used as an ancillary test interpreted in parallel with the single intradermal comparative tuberculin test (SICTT) to maximize the detection of bovine tuberculosis (bTB) infected animals. Up until 2018, a positive test result was recorded in the IFN-γ ELISA assay following whole blood stimulation with purified protein derivative (PPD)-bovine (B), PPD-avian (A) and nil sample (N), using the interpretation criteria, B-N > 50 optical density units (OD), B > 100 and B-A > 0. Following a review of available data, the threshold of the B-A component changed to B-A > 80. As predicting the impact of changing the cut-off thresholds for the IFN-γ test de novo is challenging, the aims of this study were to follow animals that initially tested negative using the new IFN-γ assay interpretation criteria and investigate their future risk of disclosure with bTB, with a focus on animals that otherwise would have been removed when using the older interpretation criteria (0 < B-A ≤ 80). Enrolled animals (n = 28,669 cattle from 527 herds) were followed up for two years (2019-2021), or to point of bTB detection or death. At the end of follow-up, 1151 (4.0%) of enrolled animals were bTB cases. The majority of these cases were diagnosed using SICTT (80.5%). The cumulative number of positive animals that would have been removed if the old cut-off (0 < B-A ≤ 80) was used amounted to 1680 cattle (5.9% of the enrolled cohort). Of these, 127 (7.5%) were diagnosed with bTB during follow-up. In contrast, 1024 of the 1151 cattle which subsequently tested positive during the study period following a negative IFN-γ test would not have been identified with the old or new IFN-γ cut-off criteria. Survival analysis showed that animals that would have been removed under the old interpretation criteria were at increased risk of a positive diagnosis with bTB during follow-up compared to other test negative animals. A newly developed risk prediction model (using a Cox proportional hazard model) showed that age, animal number of SICTT tests, number of inconclusive SICTT tests, B-A (IFN-γ assay), B-N (IFN-γ assay), animals from store herds and the percentage of the rest of the herd that were positive during the breakdown were statistically significantly associated with bTB detection. However, inclusion of the IFN-γ OD variables did not show added value in terms of prediction performance of the model., Competing Interests: Declaration of Competing Interest None declared., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

We used logistic regression to investigate whether the risk of an Irish cattle herd undergoing a bovine tuberculosis (bTB) breakdown increased with the size of the Ingoing Contact Chain (ICC) of previous herd to herd cattle movements, in a sequence up to eight moves back from the most recent, direct, movement into the herd. We further examined whether taking into account the bTB test history of each herd in the chain would improve model fit. We found that measures of cattle movements directly into the herd were risk factors for subsequent bTB restrictions, and the number of herds that animals were coming from was the most important of these. However, in contrast to a previous study in Great Britain, the ICC herd count at steps more remote than direct movements into the herd did not result in better fitting models than restricting the count to direct movements. Restricting the ICC counts to herds which had previously or would in the future test positive for bTB resulted in improved model fits, but this was not the case if only the previous test status was considered. This suggests that in many cases bTB infected animals are moving out of herds before being identified through testing, and that risk-based trading approaches should not rely solely on the previous test history of source herds as a proxy for future risk. Model fit was also improved by the inclusion of variables measuring bTB history of the herd, bTB in neighbouring herds, herd size, herd type, the movement network measures "in strength" and "betweenness", altitude, modelled badger abundance and county. Rainfall was not a good predictor. The most influential measures of bTB in nearby herds (a proxy for neighbourhood infection) were the proportion of herds with a history of bTB whose centroids were within 6 km, or whose boundaries were within 4 km, of the index herd. As well as informing national control and surveillance measures, our models can be used to identify areas where bTB rates are anomalously high, to prompt further investigation in these areas., Competing Interests: Conflicts of interest None., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

In the last decade and a half, emerging vector-borne diseases have become a substantial threat to cattle across Europe. To mitigate the impact of the emergence of new diseases, outbreaks must be detected early. However, the clinical signs associated with many diseases may be nonspecific. Furthermore, there is often a delay in the development of new diagnostic tests for novel pathogens which limits the ability to detect emerging disease in the initial stages. Syndromic Surveillance has been proposed as an additional surveillance method that could augment traditional methods by detecting aberrations in non-specific disease indicators. The aim of this study was to develop a syndromic surveillance system for Irish dairy herds based on routinely collected milk recording and meteorological data. We sought to determine whether the system would have detected the 2012 Schmallenberg virus (SBV) incursion into Ireland earlier than conventional surveillance methods. Using 7,743,138 milk recordings from 730,724 cows in 7037 herds between 2007 and 2012, linear mixed-effects models were developed to predict milk yield and alarms generated with temporally clustered deviations from predicted values. Additionally, hotspot spatial analyses were conducted at corresponding time points. Using a range of thresholds, our model generated alarms throughout September 2012, between 4 and 6 weeks prior to the first laboratory confirmation of SBV in Ireland. This system for monitoring milk yield represents both a potentially useful tool for early detection of disease, and a valuable foundation for developing similar tools using other metrics., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

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. The study population comprised bovine herds that had calves born and tested negative for BVD virus (BVDV) every year from 2013 to 2019 (n = 46,219 herds). We defined cases as herds which had one or more test positive calves for the first time in 2019 (n = 204). Controls (n = 816) were randomly sampled from the herds which remained test negative in 2019. The effects of herd size, management system, inward movements, including those of potential trojan dams (pregnant animals brought into the herd that could potentially be carrying infected calves in utero), and proximity to herds testing positive in the preceding year, were investigated. Network analysis approaches were used to generate variables measuring connections with test positive herds through inward cattle movements. A generalised linear mixed model, including a county-level random effect, was used to explore these risk factors., Results: Our final model retained ln (herd size) (Odds Ratio (95% CI): 1.72 (1.40, 2.12)), distance from test positive herds (0.54 (0.44, 0.66) for each extra land-parcel boundary crossed to reach the closest herd which tested positive the preceding year), and ln (potential trojan dams + 1) (1.29 (1.05, 1.60)). The same variables were retained in the model where herds with confirmed transient infections only (n = 25) were excluded., Conclusions: Our findings suggest that care with biosecurity at farm boundaries and visitors and equipment entering the farm, and avoidance or careful risk assessment of purchasing potentially pregnant animals, may help prevent introduction of BVDV to low-risk herds. At policy level, consideration of herd size, proximity to test positive herds and purchasing patterns of potentially pregnant cattle may help target surveillance measures towards the end of the eradication programme., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Bovine tuberculosis (bTB) is a chronic infectious disease caused by Mycobacterium bovis which results in a significant economic cost to cattle industries and governments where it is endemic. In Ireland, the European badger is the main wildlife reservoir of infection. In this study, we investigated whether (motorway) road construction was associated with an increased risk of bTB in associated cattle herds. For this study, we considered three observation periods: pre-construction (2011-2014), construction (2015-2017) and post-construction (2018-2019). We selected 1543 herds situated, based on proximity, between >50 m and <5 km of the roadworks, and extracted information about their herd-size, herd-type, inward animal movements, bTB history, and distance to the roadworks. Generalized linear mixed models were performed, whose outcome were whether a herd experienced a bTB breakdown with ≥1 or ≥3 standard reactor/s, respectively. Herds located at a distance of >3 km from the roadworks were found to be at reduced risk of a bTB breakdown over the construction period compared with those situated within 1 km of the roadworks for ≥1 reactor/s (>3 km and construction vs. <1 km: OR: 0.595, 95 % Confidence Interval (CI): 0.354-0.999) or ≥3 reactors (>3 km and construction vs. <1 km: OR: 0.431, 95 % CI: 0.174-1.067). Other previously reported risk factors such as inward movements, herd-size and herd-type were also associated with bTB risk in the final models (≥1 reactor/s and ≥3 reactors). These findings appear to be consistent with bTB breakdowns being a consequence as opposed to coincident to road construction, given the temporal and spatial consistency of the evidence. The potential for badger social group disturbance leading to the spatial spread of infection to cattle herds, as previously described in the United Kingdom, could be a hypothetical mechanism to explain these findings. However, our findings are not consistent with previous Irish studies, including recent work from another road construction project, albeit running alongside and cross over an existing road rather than construction of a new road as in this case, or experiences from national targeted badger removal. Further research is warranted to verify this pattern occurs elsewhere, and the underlying biological mechanism. Until further data are available, we recommend that badgers are vaccinated, as a precautionary measure, in advance of the commencement of major roadworks., (Copyright © 2021 Elsevier B.V. All rights reserved.)

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. An innovative feature of our model is the inclusion of herd typing, thereby extending these beyond the categories of dairy, beef and mixed herds that are frequently considered in other regional modelling studies. This detailed representation of herd type-specific management facilitates comparative assessment of BoHV-1 eradication strategies targeting different production types with individual strategy protocols. Finally, we apply our model to support current discussions regarding the structure and implementation of a potential national BoHV-1 eradication programme in Ireland., (Copyright © 2021 Elsevier B.V. All rights reserved.)

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. For each distinct herd to herd contact in a given direction, over 90 % occurred only once, whereas the maximum number of occurrences was 62. Herd-level Spearman rank correlations between inward moves (represented as in degree, in contacts, in transfers) and outward moves (out degree, out contacts, out transfers) were weak or even negative whereas correlations between different measures of outward moves or inward moves (e.g. out degree vs. out contacts, in transfers vs. in degree) were stronger. Correlations between these variables and the network measure betweenness varied between r = 0.513 and r = 0.587. Some herds took part in a relatively large number of movements whilst also retaining their cattle for long periods (> 100 days) between moves. In and out degree, contacts and transfers were mapped across Ireland on a 5 km grid, and additionally normalized per 1000 animals and per herd. We found considerable variation in the number of movements by county. Approximately half of transfers were conducted within a single county, but the number and distance of between county movements varied considerably by county of origin and county of destination, with the proportion of moves completed within a single county correlated with its size. Herds exchanging cattle via a market were generally further apart than when moves were made directly herd to herd. For contacts, the distances moved away from the herd were on average greater for origin herds in the west of ROI whereas distances moved to a herd were generally greater for destination herds in the centre-east and the north-west., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

Mechanistic simulation models are being increasingly used as tools to assist with animal health decision-making in the cattle sector. We reviewed scientific literature for studies reporting age-structured cattle management models in application to infectious diseases. Our emphasis was on papers dedicated to support decision making in the field. In this systematic review we considered 1290 manuscripts and identified 76 eligible studies. These are based on 52 individual models from 10 countries addressing 9 different pathogens. We provide an overview of these models and present in detail their theoretical foundations, design paradigms and incorporated processes. We propose a structure of the characteristics of cattle disease models using three main features: [1] biological processes, [2] farming-related processes and [3] pathogen-related processes. It would be of benefit if future cattle disease models were to follow this structure to facilitate science communication and to allow increased model transparency., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Estimation of the true prevalence of infected individuals involves the application of a diagnostic test to a population and adjusting according to test performance, sensitivity and specificity. Bayesian latent class analysis for the estimation of herd and animal-level true prevalence, has become increasingly used in veterinary epidemiology and is particularly useful in incorporating uncertainty and variability into analyses in a flexible framework. However, the approach has not yet been evaluated using simulated data where the true prevalence is known. Furthermore, using this approach, the within-herd true prevalence is often assumed to follow a beta distribution, the parameters of which may be modelled using hyperpriors to incorporate both uncertainty and variability associated with this parameter. Recently however, the authors of the current study highlighted a potential issue with this approach, in particular, with fitting the distributions and a tendency for the resulting distribution to invert and become clustered at zero. Therefore, the objective of the present study was to evaluate commonly specified models using simulated datasets where the herd-level true prevalence was known. The specific purpose was to compare findings from models using hyperpriors to those using a simple beta distribution to model within-herd prevalence. A second objective was to investigate sources of error by varying characteristics of the simulated dataset. Mycobacterium avium subspecies paratuberculosis infection was used as an example for the baseline dataset. Data were simulated for 1000 herds across a range of herd-level true prevalence scenarios, and models were fitted using priors from recently published studies. The results demonstrated poor performance of these latent class models for diseases characterised by poor diagnostic test sensitivity and low within-herd true prevalence. All variations of the model appeared to be sensitive to the prior and tended to overestimate herd-level true prevalence. Estimates were substantially improved in different infection scenarios by increasing test sensitivity and within-herd true prevalence. The results of this study raise questions about the accuracy of published estimates for the herd-level true prevalence of paratuberculosis based on serological testing, using latent class analysis. This study highlights the importance of conducting more rigorous sensitivity analyses than have been carried out in previous analyses published to date., (Copyright © 2018. Published by Elsevier B.V.)

In the epidemiology of Bovine Viral Diarrhoea (BVD), Trojan dams (animals that are not persistently infected (PI) with BVD (BVDv) virus but carrying PI foetuses) are a vehicle through which infection can be transmitted. We investigated the degree to which restricting movement of cattle from BVDv infected herds would prevent Trojan births in other herds (effectiveness) and the extent to which this would reduce other, non-Trojan, movements (proportionality). We focussed on Irish herds with BVD + animal(s) present during 2014 and/or 2015. The effect of restricting movements of female animals over 12 months of age from these herds was compared with data collected on Trojan dams that calved in 2015. Four different potential restriction lengths were considered, varying from the period when a BVD + animal was present in the herd, to extending this to 12 months after removal of the last BVD + animal. In terms of effectiveness, none of the four restriction measures evaluated was effective at preventing the movement of all Trojan dams. Between 18.3% and 37.3% of Trojan births in 2015 would have been prevented under the proposed measures, and all Trojan births would have been prevented in between 14.4% and 32.5% of herds with BVD + births. In terms of proportionality, between 4.4% and 15.4% of all females > 12 months of age that moved between herds during 2015 would have been prevented from moving, and between 3.5% and 10.1% of Irish herds with at least one such movement would have been affected. These results show how measures to control the movement of Trojan dams should be targeted in a way that fits the Irish context and reduces the spread of BVDv, without unduly impacting other trade., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

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. We examined the costs faced by each breeding herd if testing were conducted using serology on a sample of young stock, in contrast to the current method of tissue-tag testing of all newborn calves. Following best knowledge of the likely costs, the following input values were used: i) €2.50 per test for tissue-tag testing and €7.66 for serology, ii) serology conducted on a sample of 10 young stock per management group from either the 6-12 month or 9-18 month cohorts; iii) 3 scenarios for the number of management groups: one per herd (M∞), one per 100 cows (M100) and one per 50 cows (M50). We found that many herds would often not be able to supply a suitable sample of young stock for serology or would face higher testing costs than when using tissue tag testing. The largest number (25%) of herds would benefit from participating in the change if sampling were done in October. These could annually save between €2.1 million under M∞ and €0.8 million under M50 (€108 - €49 per herd). However, analysing herd-level data we found that 90% of all Irish breeding herds would save less than €1.42 per cow or €99 in total per annum under M∞, and €0.59 per cow or €36 in total under M50. In a sensitivity analysis, we allowed serology costs to vary between €2 and €10 per animal. Herds at the 10 t h percentile of most savings made from switching would save at most €155 (M∞ at €2 per serology test) but would not save anything under M50 at costs ≥ €10. We conclude that, under these assumptions, the expected reduction in testing costs for the majority of beneficiaries would barely outweigh the practical implications of the strategy switch or the risks to the eradication programme associated with sample based surveillance. This study does not assess the cost-effectiveness of alternatives post-eradication., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

There has been little assessment of the methodological quality of studies measuring the performance (sensitivity and/or specificity) of diagnostic tests for animal diseases. In a systematic review, 190 studies of tests for bovine tuberculosis (bTB) in cattle (published 1934-2009) were assessed by at least one of 18 reviewers using the QUADAS (Quality Assessment of Diagnostic Accuracy Studies) checklist adapted for animal disease tests. VETQUADAS (VQ) included items measuring clarity in reporting (n = 3), internal validity (n = 9) and external validity (n = 2). A similar pattern for compliance was observed in studies of different diagnostic test types. Compliance significantly improved with year of publication for all items measuring clarity in reporting and external validity but only improved in four of the nine items measuring internal validity (p < 0.05). 107 references, of which 83 had performance data eligible for inclusion in a meta-analysis were reviewed by two reviewers. In these references, agreement between reviewers' responses was 71% for compliance, 32% for unsure and 29% for non-compliance. Mean compliance with reporting items was 2, 5.2 for internal validity and 1.5 for external validity. The index test result was described in sufficient detail in 80.1% of studies and was interpreted without knowledge of the reference standard test result in only 33.1%. Loss to follow-up was adequately explained in only 31.1% of studies. The prevalence of deficiencies observed may be due to inadequate reporting but may also reflect lack of attention to methodological issues that could bias the results of diagnostic test performance estimates. QUADAS was a useful tool for assessing and comparing the quality of studies measuring the performance of diagnostic tests but might be improved further by including explicit assessment of population sampling strategy., (Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.)

Bovine Tuberculosis (bTB) in cattle is a global health problem and eradication of the disease requires accurate estimates of diagnostic test performance to optimize their efficiency. The objective of this study was, through statistical meta-analyses, to obtain estimates of sensitivity (Se) and specificity (Sp), for 14 different ante-mortem and post-mortem diagnostic tests for bTB in cattle. Using data from a systematic review of the scientific literature (published 1934-2009) diagnostic Se and Sp were estimated using Bayesian logistic regression models adjusting for confounding factors. Random effect terms were used to account for unexplained heterogeneity. Parameters in the models were implemented using Markov Chain Monte Carlo (MCMC), and posterior distributions for the diagnostic parameters with adjustment for covariates (confounding factors) were obtained using the inverse logit function. Estimates for Se and/or Sp of the tuberculin skin tests and the IFN-γ blood test were compared with estimates published 2010-2015. Median Se for the single intradermal comparative cervical tuberculin skin (SICCT) test (standard interpretation) was 0.50 and Bayesian credible intervals (CrI) were wide (95% CrI 0.26, 0.78). Median Sp for the SICCT test was 1.00 (95% CrI 0.99, 1.00). Estimates for the IFN-γ blood test Bovine Purified Protein Derivative (PPD)-Avian PPD and Early Secreted Antigen target 6 and Culture Filtrate Protein 10 (ESAT-6/CFP10) ESAT6/CFP10 were 0.67 (95% CrI 0.49, 0.82) and 0.78 (95% CrI 0.60, 0.90) respectively for Se, and 0.98 (95% CrI 0.96, 0.99) and 0.99 (95% CrI 0.99, 1.00) for Sp. The study provides an overview of the accuracy of a range of contemporary diagnostic tests for bTB in cattle. Better understanding of diagnostic test performance is essential for the design of effective control strategies and their evaluation., (Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.)

A systematic review was conducted to identify studies with data for statistical meta-analyses of sensitivity (Se) and specificity (Sp) of ante-mortem and post-mortem diagnostic tests for bovine tuberculosis (bTB) in cattle. Members of a working group (WG) developed and tested search criteria and developed a standardised two-stage review process, to identify primary studies with numerator and denominator data for test performance and an agreed range of covariate data. No limits were applied to year, language, region or type of test in initial searches of electronic databases. In stage 1, titles and available abstracts were reviewed. References that complied with stage 1 selection criteria were reviewed in entirety and agreed data were extracted from references that complied with stage 2 selection criteria. At stage 1, 9782 references were reviewed and 261 (2.6%) passed through to stage 2 where 215 English language references were each randomly allocated to two of 18 WG reviewers and 46 references in other languages were allocated to native speakers. Agreement regarding eligibility between reviewers of the same reference at stage 2 was moderate (Kappa statistic = 0.51) and a resolution procedure was conducted. Only 119 references (published 1934-2009) were identified with eligible performance estimates for one or more of 14 different diagnostic test types; despite a comprehensive search strategy and the global impact of bTB. Searches of electronic databases for diagnostic test performance data were found to be nonspecific with regard to identifying references with diagnostic test Se or Sp data. Guidelines for the content of abstracts to research papers reporting diagnostic test performance are presented. The results of meta-analyses of the sensitivity and specificity of the tests, and of an evaluation of the methodological quality of the source references, are presented in accompanying papers (Nuñez-Garcia et al., 2017; Downs et al., 2017)., (Copyright © 2017. Published by Elsevier B.V.)

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. BVD+ calves included all calves on the national programme database with an initial positive or inconclusive virus test, without a confirmatory re-test (status BVDPOS) and those with an initial positive or inconclusive test and a positive confirmatory test (status BVDPI). The Trojan status of dams was determined after considering their history of movement and of potential BVDV exposure, relative to a defined window of susceptibility (WOS; days 30-120 of gestation). During 2013-15, there were 29,422 BVD+ birth events to dams that were not themselves BVD+, including 2526 (8.6%) most-likely attributable to Trojan dams. The percentage of these birth events attributable to Trojan dams was significantly different (P < 0.001) between years, being 7.1% in 2013, 9.2% in 2014 and 10.6% in 2015. During 2013, in 9.9% of herds with one or more BVD+ birth to non-BVD+ dams, at least one of these births was attributed to a Trojan dam. In 2014 and 2015, the percentages were 11.8% and 13.3%, respectively. In 2013, in 7.8% of herds with one or more BVD+ birth to non-BVD+ dams, all of these births were attributable to Trojan dams. In 2014 and 2015, the percentages were 9.2% and 10.7%, respectively. A logistic GEE regression identified dam parity, herd size and an interaction between herd type and season as significant predictors for the birth of a BVD+ calf to a Trojan dam. Significant predictors for the sale of a Trojan dam from BVD+ herds included those selling more than one pregnant female and those with more than 2 BVD+ animals in the herd. Introduction of pregnant adult females is a potential source of BVD+ births in BVD-free herds and may add to the burden of infection in non-BVD-free herds. Addressing this route of transmission will be critical for herds that are now free of infection and wish to continue to purchase animals without introducing it., (Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.)

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. To examine the potential practicality of this system, we identified birth profiles and movements of calves born in Ireland during 2014 and 2015. We found that birth profiles for both beef and dairy animals were more evenly distributed throughout the year than often assumed, which should be borne in mind when evaluating the suitability of a single round of serological testing in the autumn for every herd. A large amount of movement was identified, with approximately 43% of calves experiencing a move before they reached 10 months of age, including moves to another Irish herd, to a knackery, to export, or to slaughter. Approximately 19% of calves had moved to other breeding herds in Ireland within this period. There were distinct patterns according to movement type, month of birth and herd type. The majority of herds moved either all or none of their calves in the first 10 months of life. These results indicate that young stock serological testing is unlikely to be an appropriate surveillance mechanism for all BVDv-free herds, as (i) many herds would not be able to supply a large enough sample of suitably aged home-bred young stock at a single point in time and (ii) PIs which would have been picked up by tissue-tag testing soon after birth would have moved from their home herd, to infect other herds, before serological testing could be conducted., (Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.)

Bovine Johne's Disease (JD) is a disease characterised by chronic granulomatous enteritis which manifests clinically as a protein-losing enteropathy causing diarrhoea, hypoproteinaemia, emaciation and, eventually death. Some research exists to suggest that the aetiologic pathogen Mycobacterium avium subspecies paratuberculosis may pose a zoonotic risk. Nationally coordinated control programmes have been introduced in many of the major milk producing countries across the world. However, JD is challenging to control in infected herds owing to limitations of diagnostic tests and the long incubation period of the disease. Internationally, research increasingly recognises that improved understanding of farmers' subjective views and behaviours may inform and enhance disease management strategies and support the identification and implementation of best practice at farm level. The aim of this study was to use qualitative research methods to explore the values and knowledges of farmers relative to the control of JD at farm level. The Biographical Narrative Interpretive Method (BNIM) was used to generate data from both infected and presumed uninfected farms in Ireland. Qualitative analysis revealed that cultural and social capital informed farmers' decisions on whether to introduce control and preventive measures. Cultural capital refers to the pride and esteem farmers associate with particular objects and actions whereas social capital is the value that farmers associate with social relationships with others. On-farm controls were often evaluated by farmers as impractical and were frequently at odds with farmers' knowledge of calf management. Knowledge from farmers of infected herds did not disseminate among peer farmers. Owners of herds believed to be uninfected expressed a view that controls and preventive measures were not worthy of adoption until there was clear evidence of JD in the herd. These findings highlight important barriers and potential aids to prevention and control in both infected and uninfected herds., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Bovine paratuberculosis is a disease characterised by chronic granulomatous enteritis which manifests clinically as a protein-losing enteropathy causing diarrhoea, hypoproteinaemia, emaciation and, eventually death. Some evidence exists to suggest a possible zoonotic link and a national voluntary Johne's Disease Control Programme was initiated by Animal Health Ireland in 2013. The objective of this study was to estimate herd-level true prevalence (HTP) and animal-level true prevalence (ATP) of paratuberculosis in Irish herds enrolled in the national voluntary JD control programme during 2013-14. Two datasets were used in this study. The first dataset had been collected in Ireland during 2005 (5822 animals from 119 herds), and was used to construct model priors. Model priors were updated with a primary (2013-14) dataset which included test records from 99,101 animals in 1039 dairy herds and was generated as part of the national voluntary JD control programme. The posterior estimate of HTP from the final Bayesian model was 0.23-0.34 with a 95% probability. Across all herds, the median ATP was found to be 0.032 (0.009, 0.145). This study represents the first use of Bayesian methodology to estimate the prevalence of paratuberculosis in Irish dairy herds. The HTP estimate was higher than previous Irish estimates but still lower than estimates from other major dairy producing countries., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Schmallenberg virus (SBV) disease emerged in Europe in 2011, with the virus initially identified in Germany, and the first confirmed case of SBV infection in Ireland diagnosed in a dairy calf in October 2012. SBV was subsequently confirmed by RT-PCR in 49 cattle herds and 39 sheep flocks. While these studies provide a good representation of the spatial distribution of SBV in Ireland, they do not quantify the impact of SBV on productivity. The objectives of this study were to assess the impact of SBV on weaning rate in Irish sheep flocks, based on data reported by Irish sheep farmers, and to evaluate weaning rate in sheep flocks as an indicator to be used in emerging disease surveillance systems. A questionnaire on productivity and management practices in sheep flocks was developed to gather data from sheep farmers. Valid responses from 267 sheep farmers were received. Negative binomial regression indicated that flocks with a confirmed SBV diagnosis had a weaning rate 0.9 times that of flocks free of SBV. The 10% reduction in weaning rates as a result of SBV is a justifiable concern for farmers and should be considered in formulating flock breeding policy. This study shows the value of a production database as an indicator of an emerging disease and the economic impact of that disease in Irish sheep flocks., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Paratuberculosis is a challenging disease to control at farm level, in part due to the poor sensitivity of diagnostic tests and a prolonged incubation period. Simulation studies have highlighted on-farm management to be the most important factor in preventing on-farm spread. A risk assessment (RA) and management plan (MP) approach (collectively, RAMP) has been adopted around the world as the most appropriate method of controlling disease in infected farms. However, there are problems with RAMP that remain to be resolved. The RA relies heavily on farmer recollection and estimation resulting in subjectivity and substantial inter-observer variability. MPs consist of a series of qualitative, farm specific recommendations showing how management can be improved. However, MP assessment is generally conducted informally, and progress is monitored through 'end-point' diagnostic testing of adult animals and repeated risk assessments. Hazard analysis and critical control point (HACCP) has been developed as a proactive alternative to end-point testing. We hypothesise that farm-based HACCP systems may be a useful alternative to RAMP on farms where more intensive monitoring and evaluation of controls for paratuberculosis is required. Therefore, the objective of this methodological study was to develop a HACCP-based system for paratuberculosis control. Critical control points (CCPs) relating to peri-parturient area management, calving, new-born calf management and colostrum management were identified as areas where additional control could be exerted above existing methods. Novel monitoring systems were developed for each CCP, along with targets and corrective actions. This system is intended for use in high prevalence herds, or farms where more robust monitoring of key control points may be beneficial. It is currently being trialled on infected commercial dairy herds in Ireland., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Mycobacterium 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., (Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.)

The Pacific oyster, Crassostrea gigas, plays a significant role in the aquaculture industry in Ireland. Episodes of increased mortality in C. gigas have been described in many countries, and in Ireland since 2008. The cause of mortality events in C. gigas spat and larvae is suspected to be multifactorial, with ostreid herpesvirus 1 (OsHV-1, in particular OsHV-1μvar) considered a necessary, but not sufficient, cause. The objectives of the current study were to describe mortality events that occurred in C. gigas in Ireland during the summer of 2011 and to identify any associated environmental, husbandry and oyster endogenous factors. A prospective cohort study was conducted during 2010-2012, involving 80 study batches, located at 24 sites within 17 bays. All 17 bays had previously tested positive for OsHV-1μvar. All study farmers were initially surveyed to gather relevant data on each study batch, which was then tracked from placement in the bay to first grading. The outcome of interest was cumulative batch-level mortality (%). Environmental data at high and low mortality sites were compared, and a risk factor analysis, using a multiple linear regression mixed effects model, was conducted. Cumulative batch mortality ranged from 2% to 100% (median=16%, interquartile range: 10-34%). The final multivariable risk factor model indicated that batches imported from French hatcheries had significantly lower mortalities than non-French hatcheries; sites which tested negative for OsHV-1μvar during the study had significantly lower mortalities than sites which tested positive and mortalities increased with temperature until a peak was reached. There were several differences between the seed stocks from French and non-French hatcheries, including prior OsHV-1μvar exposure and ploidy. A range of risk factors relating to farm management were also considered, but were not found significant. The relative importance of prior OsHV-1μvar infection and ploidy will become clearer with ongoing selection towards OsHV-1μvar resistant oysters. Work is currently underway in Ireland to investigate these factors further, by tracking seed from various hatchery sources which were put to sea in 2012 under similar husbandry and environmental conditions., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Local persistence of infection is a key feature of bovine tuberculosis (bTB) among cattle herds in the Republic of Ireland. The aim of this study was to determine the relative importance of 'neighbourhood', specifically farm-to-farm spread and spread from wildlife, in the persistence of bTB by investigating herds having a bTB episode in 2006. A case-control study was conducted on the association between the occurrence of a bTB episode in 2006 and the occurrence of bTB in previous years among neighbouring herd(s) within 1 km, while controlling for each herd's bTB history and other risk factors. Neighbouring herds were grouped into three zones, based on distance, and bTB incidence measures summarised within each zone and by calendar year (2001-2005). The incidence of bTB was associated with an increased animal incidence in two subsets of neighbouring herds: (i) herds directly contiguous during the previous 2 years (attributable fraction=0.20), and (ii) herds at a distance of >25 m in the previous year (attributable fraction=0.19). Other predictors of bTB in a herd in 2006 included the occurrence of a bTB episode within that herd in any of the previous 5 years, herd size, and the number of animals purchased at age greater than 12 months. An infected wildlife source best explains the existence of a "neighbouring herd risk" for bTB at distances greater than 25 m. Further studies will be necessary to determine to what extent neighbouring herd risk within 25 m may be confounded by the same wildlife (badger) source., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Bovine spongiform encephalopathy (BSE) is a prion disease spread by the inclusion in cattle feed of meat and bone meal made from cattle infected with the BSE agent. In the Republic of Ireland, a reinforced feed ban on mammalian meat and bone meal (MMBM) was introduced on 17th October 1996 to stop further infection of cattle. Between then and July 2010, 44 cases of BSE from 40 herds have been born, termed "born after the reinforced ban" or "BARB" cases. The objectives of this project were: (a) to describe the epidemiology of these BARB cases, (b) to determine area-level risk factors for BSE herds and how they related to the stage of the BSE epidemic, and (c) to evaluate whether the spatial pattern of BSE cases was non-random and had changed over time. The BSE epidemic was divided into three phases: cases born prior to 1991, born 1991-October 1996 and BARB cases. To determine the area level risk factors for BSE herds, a case-control study was conducted for each phase of the epidemic. We selected four control herds for each herd with one or more BSE cases. A grid of hexagons of 10 km diameter was created covering the territory of the Republic of Ireland and BSE herds and control herds were assigned to a hexagon. The numbers of cattle herds, dairy herds, piggeries and poultry holdings within the hexagons containing these case and control herds were enumerated. To evaluate the spatial pattern of BSE cases, standardised mortality ratios were calculated for each hexagon, and Oden's Ipop was used to investigate clustering. The descriptive analysis showed "feeding of concentrates" as the only common factor to all BARB cases for which information existed. The case-control study identified being a dairy herd as a risk factor during the pre-1991 phase of the BSE epidemic. Dairy herd type, a large proportion of local herds which were dairy and large numbers of piggeries and poultry holdings locally were also risk factors during the 1991-1996 phase. For the post-October 1996 phase (BARBs), dairy herd type and large numbers of other herds locally were risk factors. The spatial pattern of BSE cases changed over the three phases of the epidemic and was non-random, with evidence of clustering. The evidence supports the hypothesis that BARB cases do not arise spontaneously but rather are caused by the same food-borne infectious route as other BSE cases., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Agriculture is a very important contributor to the Irish economy. In Ireland, national animal health services have been a government, rather than an industry, responsibility. In 2009, Animal Health Ireland (AHI) was established to provide a partnership approach to national leadership of non-regulatory animal health issues (those not subject to national and/or EU regulation). The objectives of this study were to elicit opinion from experts and farmers about non-regulatory animal health issues facing Irish livestock industries, including prioritisation of animal health issues and identification of opportunities to maximise the effective use of AHI resources. The study was conducted with experts using Policy Delphi methodology over three rounds, and with farmers using a priority identification survey. Non-regulatory bovine diseases/conditions were prioritised by both experts and farmers based on impact and international competitiveness. For each high-priority disease/condition, experts were asked to provide an assessment based on cost, impact, international perception, impediment to international market access and current resource usage effectiveness. Further information was also sought from experts about resource allocation preferences, methods to improve education and coordination, and innovative measures to improve prevention and management. There was close agreement between responses from experts and dairy farmers: each gave highest priority to 3 diseases with a biosecurity risk (subsequently termed 'biosecure diseases') (bovine viral diarrhoea [BVD], infectious bovine rhinotracheitis [IBR], paratuberculosis) and 4 diseases/conditions generally without a biosecurity risk ('non-biosecure diseases/conditions') (fertility, udder health/milk quality, lameness, calf health). Beef farmers also prioritised parasitic conditions and weanling pneumonia. The adverse impact of biosecure diseases is currently considered relatively minor by experts, but would increase substantially in time. There are already substantial costs to farms and agribusiness from non-biosecure diseases/conditions. Experts preferred an equal allocation of resources between these biosecure and non-biosecure diseases/conditions, with emphasis on adopting/adapting international models, education and awareness-raising. The results from this study provide robust insights about non-regulatory animal health priorities in Ireland, as perceived by experts and farmers, using methodologies that are both transparent and inclusive. They have already been extremely influential in shaping national policy, as a foundation for interdisciplinary (and multi-agency) cooperation, as a contribution to efforts to encourage stakeholder responsibility-taking, and to ongoing development of postgraduate and undergraduate veterinary education in Ireland., (Copyright (c) 2010. Published by Elsevier B.V.)

There is a good understanding of factors associated with bovine tuberculosis (BTB) risk in Irish herds. As yet, however, this knowledge has not been incorporated into predictive models with the potential for improved, risk-based surveillance. The goal of the study was to enhance the national herd scoring system for BTB risk, thus leading to improved identification of cattle herds at high risk of recurrent BTB episodes. A retrospective cohort study was conducted to develop a statistical model predictive of recurrent bovine tuberculosis episodes in cattle herds in the Republic of Ireland. Herd-level disease history data for the previous 12 years, the previous 3 years, the previous episode, and the current-episode were used in survival analyses to determine the aspects of disease history that were predictive of a recurrent breakdown within 3 years of a cleared BTB episode. Relative to herds with 0-1 standard reactors in the current BTB episode, hazard ratios increased to 1.3 and 1.6 for herds with 2-5 and >5 standard reactors, respectively. Compared to herds with <30 animals, hazard ratios increased from 1.8 to 2.5 and then to 3.1 for herds with 30-79, 80-173, and >174 animals respectively. Relative to herds with <4 herd-level tests in the previous 3 years, herds with 4-5 and >5 tests had 1.1 and 1.4 times greater hazard of a BTB breakdown. Herds that did not have a BTB episode in the 5 years prior to their 2001 episode were 0.8 times less likely to breakdown in the next 3 years than herds that did. Herds breaking down in the spring or summer were 0.8 times less likely to suffer a recurrent breakdown than herds breaking down in autumn or winter (this was likely due to seasonality in testing regimes). The presence of a confirmed BTB lesion was not predictive of increased risk of recurrent BTB. Despite the availability of detailed disease history, the predictive ability of the model was poor. One explanation for this was that herds suffering a recurrence of BTB on their first test after clearing a BTB episode were different from herds that broke down later in the period at risk. Future research might need to include additional variables to identify which subsets of herd BTB episodes, if any, have identifiable features that are predictive of recurrent breakdowns., (Copyright 2010 Elsevier B.V. All rights reserved.)

Published data on aspects of domestic pet demographics are available in many countries. Several of these studies have linked household demographics, such as the presence of children in the household, to pet ownership. There is very little published information about the demography of domestic pets on the island of Ireland (the Republic of Ireland, Northern Ireland). This study was conducted to describe the demography of the pet dog and cat populations on the island of Ireland and to identify human factors influencing pet ownership. A questionnaire was designed and administered to households to collect data about the demographics of households and their dogs and cats. The questions related to location, building structure, social class, nationality and family structure of the household, and the sex, age and source of each pet dog and/or cat. The survey was administered by a commercial company, using computer-assisted telephone interview techniques to 1250 households selected using random digit dialling and quota controls. In this study, a pet dog was defined as a dog that was been fed by a household and considered a pet by the participant of the study. A pet cat was defined as a cat that was both fed by the household and allowed into the house. The results show that 35.6% of households in Ireland have one or more pet dogs and 10.4% of households have one or more pet cats. In total, 47.3% of pet dogs and 76.1% of pet cats were neutered. Females of both species are more likely to be neutered than males. Factors associated with dog ownership included location, house type, household social class, household composition, the presence of school children in the house, and the presence of a cat in the house. Factors associated with pet cat ownership included the type of house structure, the presence of a dog in the house and the gender and age of the participant. Cats tend to stray into households. This study was the first to provide detailed information about the demographics of the pet dog and cat populations on the island of Ireland, and has identified areas for further research, in particular the effect of stray dogs and cats on the owned pet dog and cat population, and of future demographic trends in these populations.

Within the European Union (EU), detailed legislation has been developed for cattle, but not deer, to minimise disease risks associated with trade in animals and animal products. This legislation is expressed as input-based standards, providing a detailed outline of the activity required (for example, testing of animals and application of defined control measures), on the expectation that an adequate output (for example, confidence in freedom) will be achieved. Input-based standards are at odds with the increasing shift towards output-based standards, particularly in OIE rules governing international trade. In this paper, we define output-based standards to achieve and maintain freedom from tuberculosis (TB) in farmed deer, with reference to EU member states. After considering the probability of freedom achieved for cattle under existing EU legislation, we defined a 'free farmed deer holding' as one with a probability of freedom from infection of at least 99%. We then developed an epidemiological model of TB surveillance systems for deer holdings, incorporating different surveillance strategies, including combinations of diagnostic tests, and a variety of different scenarios relating to the potential for introduction of infection. A range of surveillance strategies were identified to achieve and maintain a free farmed deer holding, and worked examples are presented. The surveillance system sensitivity for varying combinations of screening and confirmatory tests in live animals, animals at slaughter and on-farm deaths is also presented. Using a single test at a single point in time, none of the TB tests routinely used in farmed deer is able to achieve an acceptable probability of TB freedom. If repeat testing were undertaken, an acceptable probability of TB freedom could be achieved, with differing combinations of the surveillance system sensitivity, frequency of testing and risk of introduction. The probability of introduction of infection through the importation of infected deer was influenced by the use of a pre-movement test (assumed 90% test sensitivity and negative test results), the TB prevalence in the source herd and the number of animals imported. A surveillance system sensitivity of at least 81% was achieved with different combinations of annual live animal surveillance and surveillance of animals at slaughter or on-farm deaths. This methodology has broad applicability and could also be extended to other diseases in both deer and other species with relevance to trade in animals and animal products.

We conducted a longitudinal study to obtain baseline information about the health and growth of growing pigs raised by smallholder pig raisers in the Philippines, and to test constraints and opportunities to smallholder growing pig production that had been identified in a cross-sectional study [More, S.J., Lee, J.-A.L.M., Lañada, E.B., Taveros, A.A., Cotiw-an, B.S., 1999. Weight-for-age of growing pigs raised by smallholder farmers in the Philippines. Prev. Vet. Med. 41, 151-169]. Using monthly on-farm visits over 12-18 months at two sites, we collected data about 824 growing pigs raised in 115 separate herds. Weight-for-age (median value of 4.8 kg/month) was clustered strongly at the herd level, and the daily ration to growing pigs was substantially deficient (particularly in protein). Using repeated-measures and time-to-event analyses, we identified a range of animal- and herd-level variables associated with increased growth and health. These results confirm results from our earlier study, and suggest that improved nutrition and targeted extension on a range of management issues could be useful.

We conducted a longitudinal study to obtain baseline information about the health and productivity of sows and boars raised by smallholder-pig raisers in the Philippines, and test constraints and opportunities to smallholder-sow production that had been identified previously in a cross-sectional study [More, S.J., Lee, J.-A.L.M., Lañada, E.B., Taveros, A.A., Cotiw-an, B.S., 1999. Weight-for-age of growing pigs raised by smallholder farmers in the Philippines. Prev. Vet. Med. 41, 151-169]. Over 12-18 months, we collected data during monthly on-farm visits about 213 sows raised in 119 herds at 2 sites and 32 boars in 31 herds at 1 site. Sow reproductive performance was low and boars were used only infrequently (an average of 0.9 services/month). Using repeated-measure analyses, we identified sow nutrition and piglet care (such as provision of creep feed and unrestricted access to the sow) as important husbandry issues associated with increased sow productivity.

We conducted a longitudinal study to obtain detailed baseline information about the health and productivity of unweaned piglets raised by smallholder pig raisers in the Philippines, and to identify constraints and opportunities to smallholder-piglet production. At two sites in the Philippines, we collected data about 242 litters from 173 sows in 102 herds during on-farm visits over 12-18 months. Preweaning mortality at the northern and southern sites was 17 and 9%, respectively. Of the piglet deaths at the northern site, 49% occurred within 24h of birth. Pig raisers used few of the recognised interventions known to reduce neonatal piglet mortality, although >50% of litters were given iron injections at the northern site and kept in a farrowing pen with a barrier at the southern site. Creep feeding was more common at the northern site but the nutritive value of the feeds given to piglets was low. We used repeated-measures and time-to-event analyses. Our results suggest that targeted extension (addressing, in particular, management issues relating to neonatal piglets) can contribute to increased productivity of unweaned piglets.

Pony Club is one of the leading junior equestrian organisations in the world, and was established to teach young people the many aspects of horsemanship. The aim of this study was to gain an understanding of the health and performance of Pony Club horses from the perspective of their owners. In-depth interviews were conducted with Pony Club members at two sites in Australia, and topics relating to participants' background with horses, horse attributes valued by participants, horse health and performance, and Pony Club-related matters. The in-depth interviews were taped, transcribed and analysed, by describing the themes and issues recorded in the dialogue and conducting cross-case analysis (finding similarities and dissimilarities between participants with respect to each of the above-mentioned topics). A total of 32 interviews were conducted. The participants' background with horses varied greatly. The horse attributes valued by > or =59% of participants included temperament, size, ability and suitability for riders. A range of issues relating to health and performance were important to > or =53% of participants, including horse temperament, nutrition, internal parasites, lameness and foot-care, and colic. Soundness and preventive health measures were rarely mentioned (< or =16% of participants). Friends or knowledgeable horse people were identified as the first point of contact for horse-health matters, and veterinarians were only used as a last resort or for serious problems. Members of Pony Club learned about their horses by trial and error. Optimal performance was described as a horse that was willing to do as the rider asked. Poor performance was usually the result of the horse misbehaving, and could include a resistance to rider commands, pigrooting and bucking.