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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.

There are two different contexts in the Irish bTB eradication programme in which the interferon-gamma assay (IFN-γ) is applied. Firstly, the IFN-γ assay is applied routinely to high risk cohorts in herds with four or more reactors to the SICTT. The IFN-γ test is then carried out on blood samples submitted to the laboratory within 8 h of collection (diagnostic testing). Secondly, the use of the IFN-γ assay has recently been extended to test SICTT reactors as part of a general quality assurance (QA) scheme to monitor the performance of the SICTT. Blood samples from reactors are tested one day after blood collection (QA testing). In this study, we analysed the relative performance of the SICTT and IFN-γ when used in parallel as an 8 h diagnostic test and as a 24 h QA test on SICTT reactors. A total of 17,725 IFN-γ tests were included in the analysis (11,658 diagnostic tests and 6067 QA tests). Of the samples submitted for diagnostic testing, the proportion positive to IFN-γ decreased with the severity of interpretation of the SICTT result. Of the standard reactors that were tested with IFN-γ in the QA programme, 92.2% were positive to the IFN-γ test. Among animals that were SICTT −ve/IFN-γ +ve, 18.9% were positive at post-mortem compared to 11.8% of those that were SICTT +ve (standard reactor)/IFN-γ −ve. These results highlight the risk associated with retaining SICTT −ve/IFN-γ +ve animals, and suggest that prompt removal of these animals is necessary to reduce the potential for future transmission.

We examined the pathogens, morphologic patterns, and risk factors associated with bovine respiratory disease (BRD) in 136 recently weaned cattle (“weanlings”), 6–12 mo of age, that were submitted for postmortem examination to regional veterinary laboratories in Ireland. A standardized sampling protocol included routine microbiologic investigations as well as polymerase chain reaction and immunohistochemistry. Lungs with histologic lesions were categorized into 1 of 5 morphologic patterns of pneumonia. Fibrinosuppurative bronchopneumonia (49%) and interstitial pneumonia (48%) were the morphologic patterns recorded most frequently. The various morphologic patterns of pulmonary lesions suggest the involvement of variable combinations of initiating and compounding infectious agents that hindered any simple classification of the etiopathogenesis of the pneumonias. Dual infections were detected in 58% of lungs, with Mannheimia haemolytica and Histophilus somni most frequently recorded in concert. M. haemolytica (43%) was the most frequently detected respiratory pathogen; H. somni was also shown to be frequently implicated in pneumonia in this age group of cattle. Bovine parainfluenza virus 3 (BPIV-3) and Bovine respiratory syncytial virus (16% each) were the viral agents detected most frequently. Potential respiratory pathogens (particularly Pasteurella multocida, BPIV-3, and H. somni) were frequently detected (64%) in lungs that had neither gross nor histologic pulmonary lesions, raising questions regarding their role in the pathogenesis of BRD. The breadth of respiratory pathogens detected in bovine lungs by various detection methods highlights the diagnostic value of parallel analyses in respiratory disease postmortem investigation.

Bovine respiratory disease (BRD) is a multifactorial disease and the primary cause of both bovine morbidity and mortality in Ireland. The risk factors associated with a primary necropsy diagnosis of BRD among cattle in the traditional (non-feedlot) husbandry systems prevalent in Ireland have not been investigated previously. The aim of this case-control study was to investigate those risk factors among cattle of all ages over an 8 year period. A total of 3,090 BRD cases and 5,236 controls were matched by submitting veterinary practitioner. Univariable and multivariable analyses were performed to examine the association of selected animallevel, herd-level and environmental risk factors with case or control status using a conditional logistical regression model. Male cattle aged more than 31 days were significantly more likely to record a primary necropsy diagnosis of BRD than female cattle. Older cattle of both sexes were at increased odds of a BRD necropsy diagnosis than younger calves with the exception of female cattle aged greater than 165 days. The risk of a primary necropsy diagnosis of BRD increased with increasing herd size and decreased with increasing time in days since the last animal movement into the submitting herd. There were significantly reduced odds of a primary necropsy diagnosis of BRD in the summer (June to August) when compared with the autumn (September to November). These findings identify significant risk factors for a necropsy diagnosis of BRD under non-feedlot-type husbandry conditions.

The control of bovine viral diarrhoea virus (BVDV) mainly focuses on the identification and restriction of persistently infected (PI) animals. However, other transmission pathways can also result in new breakdowns, including the movement of animals pregnant with PI calves (Trojan animals) and the spread of infection between contiguous farms. Contiguous spread is likely an important problem in the BVD eradication programme in Ireland, given the spatial distribution of residual infection, and the highly fragmented nature of land holdings on many Irish farms. In this study, we seek to quantify the risk of BVD spread between contiguous herds in Ireland. Multivariable logistic models were used to estimate the risk of a herd having BVD positive calves in January to June 2014 (the study period) when contiguous to a herd that had at least one BVD positive calf born in 2013. The models included risk factors relating to the study herd and to neighbouring herds. Separate multivariable models were built for each of four “PI-neighbour” factors relating to the presence of BVD+ animals and/or the presence of offspring of PI breeding animals. In total, 58,483 study herds were enrolled. The final model contained the province, the log of the number of calf births born during the study period, the number of cattle purchased between January 2013 and January 2014, and with a two-way interaction between the number of animals of unknown BVD status in the study herd and the PI-neighbour risk factor. When the number of PI-neighbour herds was used as the PI-neighbour risk factor, the odds ratio (OR) associated with the number of PI-neighbour herds ranged from 1.07 to 3.02, depending on the number of unknown animals present. To further explore the risk associated with PI-neighbour factors, the models were repeated using a subset of the study herds ( n = 7440) that contained no animals of unknown status. The best fitting model including “any PI-neighbour” as the PI-neighbour factor and also contained the log of the number of calf births born during the study period and the number of cattle purchased. The OR associated with “any PI-neighbour” was 1.92 (95% C.I. 1.37–2.70). This study provides the first quantitative information on the risks posed by the presence of BVD+ animals in neighbouring herds and also highlights the importance of clarifying the BVD status of animals that have not yet been tested in the context of the Irish eradication programme.

A compulsory national BVD eradication programme commenced in Ireland in 2013. Since then considerable progress has been made, with the animal-level prevalence of calves born persistently infected (PI) falling from 0.67 % in 2013 to 0.06 % in 2018. The herd-level prevalence fell from 11.3 % in 2013 to 1.1 % in 2018. In the Irish programme, herds in which all animals have a known negative status and which have not contained any PI animals for 12 months or more are assigned a negative herd status (NHS). While considerable progress towards eradication has been made, PI calves have been identified in a small proportion of herds that had previously been assigned NHS. Given this context, a case-control study was conducted to investigate potential risk factors associated with loss of NHS in 2017. 546 herds which had NHS on 1 January 2017 and lost that status during 2017 (case herds) were matched with 2191 herds (control herds) that retained their NHS status throughout 2017. Previous history of BVD infection, herd size, herd expansion, the purchase of cattle including potential Trojan cattle and the density of BVD infection within 10 km of the herd emerged as significant factors in a multivariable logistic regression model. This work adds to the evidence base in support of the BVD eradication programme, particularly establishing why BVD re-emerged in herds which had been free of BVD for at least the previous 12 months prior to the identification of a BVD positive calf. This information will be especially important in the context of identifying herds which may be more likely to contain BVD positive animals once the programme moves to herd-based serology status for trading purposes in the post-eradication phase. Department of Agriculture, Food and the Marine

The IFN-γ (interferon gamma) assay is used in Ireland as an ancillary diagnostic test to the single intradermal comparative tuberculin test (SICTT) to maximise the detection of Mycobacterium bovis infected animals (bTB) in cattle herds. Understanding the relationships between herd and animal risk factors and IFN-γ test results is critical to enable the development and evaluation of policy measures on how best to use the test. In this study, we set out to characterise Irish herds with IFN-γ test positive animals in terms of herd size, number of SICTT reactors and number of IFN-γ positive tests, and to evaluate the IFN-γ test in terms of the test cut-off values. The results showed that larger herds with more SICTT reactors were likely to have more IFN-γ positives in the herd, and herds with an IFN-γ test positive animal that was also positive for bTB lesions at post-mortem had higher numbers of IFN-γ positive animals in the herd. Raising the cut-off values for the IFN-γ test only marginally decreased the combined sensitivity of the IFN-γ and the SICTT for diagnosis of bTB lesioned animals. The analysis has provided valuable information on the performance of the IFN-γ test as it is used under current bTB infection levels in Ireland. Department of Agriculture, Food and the Marine

In recent years, there has been increasing recognition of the value of multiple data sources available to fulfill surveillance objectives, and the use of these has been applied to address many questions relating to animal health surveillance. In Ireland, we face a slightly different problem, namely, best use of an existing surveillance resource (serological samples collected over many years from cull cows at slaughter), which has been used to substantiate freedom from Brucella abortus following its successful eradication in 2009. In this study, we evaluate a sampling methodology to use this resource to substantiate freedom from bluetongue virus (BTV) infection. An examination of the degree to which cull cows were resident in the same herd throughout the midge biting season showed that, of 50,640 samples collected between 17 October and 23 December 2016, 80.2% were from animals resident in the same herd between 01 April 2016 and 2 months prior to their slaughter date, 74.1% for 1 month prior, 70.1% for 2 weeks prior, 66.4% for 1 week prior, and 56.4% up to 1 day prior to slaughter. An examination was made of the degree to which individual samples within the same 88-well frozen storage block came from geographically clustered herds, whether from a concentration of animals from the same herd in a single block, or from clustering around the slaughterhouse where the samples were taken. On the basis of these analyses, a sampling strategy was derived aimed at minimizing the number of storage blocks which needed to be thawed, whilst ensuring a large enough and representative sample, geographically stratified according to the bovine population of 51 squares, each 45 × 45 km, covering the entirety of Ireland. None of the 503 samples tested were positive for BTV, providing reassurance of national BTV freedom. More broadly, the study demonstrates the use of abattoir-based serological samples collected for one large scale surveillance programme in surveillance for other bovine infections.

Ongoing objective assessment of national bovine tuberculosis (bTB) policy in Ireland is important to monitor efforts towards improved bTB control. The study objective was to investigate temporal trends in the risk of herd recurrence. The study included all herds derestricted following a bTB episode ending in 1998, 2008 or 2012. The respective 'study periods' were up to the end of 2001 for 1998-derestricted herds, to the end of 2011 for 2008-derestricted herds, and to the end of 2015 for 2012-derestricted herds. A multivariable Cox proportional-hazard model was developed to examine time to next restriction. The results from the model showed a continuing significant decreasing trend in herd recurrence of bTB in Ireland from 1998 until 2015: herds derestricted in 2008 were 0.75 (95 per cent CI 0.68 to 0.82) times as likely to develop a further restriction compared with 1998 herds, and herds derestricted in 2012 were 0.85 (95per cent CI 0.76 to 0.95) times as likely as 2008 herds. However, despite significant improvements, recurrence of bTB remains a concern, with 30.2 per cent (95 per cent CI 28.0 to 32.4 per cent) of herds derestricted in 2012 being re-restricted over the subsequent three years. Further work is needed to address the two key drivers of herd recurrence, namely residual infection and local reinfection.

Persistence of bovine tuberculosis (bTB) in cattle is an important feature of Mycobacterium bovis infection, presenting either as herd recurrence or local persistence. One risk factor associated with the risk of recurrent episodes is the severity of a previous bTB episode (severity reflecting the number of bTB reactors identified during the episode). In this study, we have sought to identify predictors that can distinguish between small (less severe) and large (more severe) bTB episodes, and to describe nationally the severity of bTB episodes over time. The study included descriptive statistics of the proportion of episodes by severity from 2004 to 2015 and a case-control study. The case-control study population included all herds with at least one episode beginning in 2014 or 2015, with at least two full herd tests during the episode and a minimum herd-size of 60 animals. Case herds included study herds with at least 13 reactors whereas control herds had between 2 to 4 (inclusive) reactors during the first 2 tests of the episode. A logistic regression model was developed to identify risk factors associated with a large episode. Although there has been a general trend towards less severe herd bTB episodes in Ireland over time (2004–2015), the proportion of large episodes has remained relatively consistent. From the case-control study, the main predictors of a large episode were the year the episode started, increasing herd-size, previous exposure to bTB, increasing bTB incidence in the local area, an animal with a bTB lesion and a bTB episode in an associated herd. Herds that introduced more animals were more likely to have a smaller bTB episode, reflecting the reduced risk of within-herd transmission when an episode was due to an introduced infected bTB animal. Some of the risk factors identified in this study such as reactors in previous bTB episodes, herds with an associated herd undergoing a bTB episode, herds in high incidence areas etc. may help to target future policy measures to specific herds or animals for additional surveillance measures. This information has important policy implications.

The European Food Safety Authority (EFSA) has published a series of opinions to assess the impact of changing from the current meat inspection procedures (CMI) to visual-only inspection (VOI) procedures. Concern has been raised that changes from CMI to VOI would adversely affect the effectiveness of surveillance for bovine tuberculosis (bTB) in EU member states, both for countries with and without official status of bTB freedom (OTF and non-OTF countries, respectively). This study was conducted to estimate the impact of a change from CMI to VOI in abattoirs on herd-level detection sensitivity in Ireland, a non-OTF country. Using national Irish data, we identified all herds that sold at least one animal to slaughter during 2010-12 whilst unrestricted for bTB. For each of these herds, we calculated the number of cattle sent to slaughter whilst unrestricted, the number of factory lesion tests (FLT) that had been performed, and estimated the apparent within-herd prevalence (APwh). A FLT is a whole-herd test conducted in a herd following the confirmation of bTB in an animal at slaughter. We considered five different inspection scenarios, each based on meat inspection and bacteriology in series, including current meat inspection (CMI) and four visual-only inspection scenarios (VOI2, VOI3, VOI4, VOI5) with reducing inspection sensitivities. Separately for each inspection scenario, a simulation model was used to estimate the herd-level detection sensitivity and the number of bTB-herds (that is, herds that sent at least one animal detected with M. bovis to slaughter when unrestricted during 2010-12) that would and would not be detected. The simulated mean herd-level detection sensitivity estimates were 0.24 for CMI, and 0.16, 0.12, 0.10 and 0.08 for VOI2-5, assuming a 2-, 3-, 4-and 5-fold decrease, respectively, in the animal-level detection sensitivity of VOI relative to that of CMI. The estimated number of non-detected bTB-herds is substantial with CMI, and increases in the series of VOI scenarios with decreasing herd-level detection sensitivity. If VOI were introduced without alternative surveillance means to compensate for the decrease in animal-level inspection sensitivity, such changes might jeopardise bTB surveillance, control and eradication programmes in cattle herds of non-OTF countries, including Ireland. Department of Agriculture, Food and the Marine

While resistance to anticoagulant rodenticides is known to occur in many European populations of Norway rat and house mouse, to-date no data is available on the occurrence in Ireland of such resistance. No genetic evidence for the occurrence of resistance was found in 65 Norway rat samples analysed, indicative of an absence, or low prevalence, of resistance in rats in at least the Eastern region of the island of Ireland. The presence of two of the most commonly found amino acid substitutions Leu128Ser and Tyr139Cys associated with house mouse resistance to anticoagulant rodenticides was confirmed. The occurrence of two such mutations is indicative of the occurrence of resistance to anticoagulant rodenticides in house mice in the Eastern region of the island of Ireland.

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.

A retrospective case–control study was undertaken to investigate the temporal pattern of, and factors associated with, the survival of BVD virus-positive calves, identified between January and July 2012 during the voluntary phase of the Irish national eradication programme. Potential statuses for case and control calves consisted of: alive in birth herd; slaughtered; sold; dead (due to culling or death from natural causes and termed ‘involuntary removal’). An initial comparison of cases and controls found significant differences between the outcomes for cases and controls and also between cases in relation to herd type (beef, dairy, dual purpose), sex, age and test status (BVDPOS – no confirmatory test; BVDPI – positive on confirmatory test). Key differences included a higher level of case animals still alive in, or slaughtered from, beef herds, a greater proportion of BVDPI animals being retained relative to those with a BVDPOS status and a significantly lower slaughter weight (89 kg) for case animals relative to controls. Separate multivariable models were constructed for dairy and beef cases. In the final dairy model breed (Jersey or non-Jersey), county and BVD status were retained, with the last two found to be time-varying covariates with significant changes in hazard ratios (HR) over time. In the beef model, herd size, county and BVD status were retained, with the HR for the last two factors again varying significantly over time. With the exception of the addition of the number of BVD positive calves in the herd to the dairy model, the same factors were identified when models were restricted to the first 90 days following the birth of case animals. A greater knowledge and understanding of all of these factors will allow refinement of programme communications and incentives to encourage prompt removal of PI calves from all sectors of the Irish breeding herd during the compulsory phase of the national eradication programme.

In Ireland, new bovine tuberculosis (bTB) cases are detected using both field and abattoir surveillance. Field surveillance is conducted on all cattle annually using the single intradermal comparative tuberculin test (SICTT). Testing is reliant on the skills and experience of the tester and a broad range of factors may adversely affect test accuracy. There is considerable emphasis on quality control (QC) within the national programme and field inspection of testers has been conducted in Ireland for many years. Since 2008, inspection has been supplemented with quantitative performance reports, enabling testers to be evaluated and ranked using a range of performance indicators. The objectives of this study were first, to quantify the relative effectiveness of testers during field surveillance and, second, to assess whether there has been any change in the performance of testers between 2008 and 2011. Mixed logistic regression was used to assess the relative effectiveness of testers. The study population included all testers who carried out at least ten eligible tests in Ireland during 2008 or 2011. The outcome measure was a herd restriction at the eligible test. Results from the mixed model indicated that the variation by tester had significantly (p = 0.039) decreased from 0.589 in 2008 to 0.426 in 2011, indicating an increase in consistency of testing, after accounting for other known risk factors. This study provides objective data on the variation in tester performance over time and the relative performance of testers during field surveillance in Ireland.

Bovine Viral Diarrhoea is an infectious production disease of major importance in many cattle sectors of the world. The infection is predominantly transmitted by animal contact. Postnatal infections are transient, leading to immunologically protected cattle. However, for a certain window of pregnancy, in utero infection of the foetus results in persistently infected (PI) calves being the major risk of BVD spread, but also an efficient target for controlling the infection. There are two acknowledged strategies to identify PI animals for removal: tissue tag testing (direct; also known as the Swiss model) and serological screening (indirect by interpreting the serological status of the herd; the Scandinavian model). Both strategies are effective in reducing PI prevalence and herd incidence. During the first four years of the Irish national BVD eradication programme (2013–16), it has been mandatory for all newborn calves to be tested using tissue tag testing. During this period, PI incidence has substantially declined. In recent times, there has been interest among stakeholders in a change to an indirect testing strategy, with potential benefit to the overall programme, particularly with respect to cost to farmers. Advice was sought on the usefulness of implementing the necessary changes. Here we review available data from the national eradication programme and strategy performance predictions from an expert system model to quantify expected benefits of the strategy change from strategic, budgetary and implementation points of view. Key findings from our work include (i) drawbacks associated with changes to programme implementation, in particular the loss of epidemiological information to allow real-time monitoring of eradication progress or to reliably predict time to eradication, (ii) the fact that only 25% of the herds in the Irish cattle sector (14% beef, 78% dairy herds) would benefit financially from a change to serosurveillance, with half of these participants benefiting by less than EUR 75 per annum at herd level or an average of EUR 1.22 per cow, and (iii) opportunities to enhance the effectiveness of the current programme, particularly in terms of time to eradication, through enforced compliance with PI removal as currently outlined in programme recommendations. The assembled information provides scientific arguments, contributing to an informed debate of the pros and cons of a change in eradication strategy in Ireland.

Within the Irish national bovine tuberculosis (bTB) eradication programme, controls are tighter on higher risk herds, known as H-herds. These H-herds are defined as herds that have previously had a bTB restriction (also known as a bTB episode), with at least 2 animals positive to the single intradermal comparative tuberculin test (SICTT) or with a bTB lesion detected at slaughter. Such herds are considered at higher risk of recurrence following the end of the bTB episode. In this study, we examined if, and when, the future bTB risk of H-herds returned to a similar level comparable to herds with no history of bTB. In addition, the proportion of bTB episodes in 2012 that could be attributed to the recent introduction of an infected animal was also estimated, providing an update of earlier work. The study population consisted of all Irish herds that were not bTB restricted at the start of 2012 and with at least one whole-herd SICTT in 2012, with the herd being the unit of interest. The outcome measure was a bTB restriction, defined as any herd where at least 1 standard SICTT reactor or an animal with a bTB lesion at slaughter in 2012 was identified. A logistic regression model was used to model the probability of a herd being restricted in 2012. Herds that were previously restricted had significantly higher odds of being restricted in 2012 compared to herds that had not. Similarly, the odds of being restricted in 2012 decreased as the time since the previous restriction increased, but increased as the severity of the previous restriction increased. Odds of being restricted also increased with an increase (although not linear) in herd size, the number of animals greater than 1 year of age purchased in 2011, the county incidence rate and the proportion of cows in the herd. The recent introduction of an infected animal accounted for 7.4% (6.7–8.2) of herd restrictions. This study confirms the key role of past bTB history in determining the future risk of Irish herds, with the odds related to both the severity of and time since the previous restriction. It also illustrates the difficulty in clearly defining H-herds, noting that risk persists for extended periods following a bTB restriction, regardless of breakdown severity. There is a need for robust controls on H-herds for an extended period post de-restriction.

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. Irish Research Council Animal Health Ireland

Extending on earlier work, trends in bovine tuberculosis (bTB) from 2003 to 2015 are described for the countries of the UK and the Republic of Ireland using standardised definitions and measures. Based on measures of animal and herd incidence, there remains a stable situation of extremely low prevalence in Scotland and the Low Risk Area of England, and a higher but ongoing reduction in prevalence in the Republic of Ireland. In Northern Ireland, there has been a rising bTB trend during 2010-2015, although not to levels experienced during 2002-2004. In the High Risk Area and Edge Area of England during 2010-2015, the rising bTB trends have continued but with some recent evidence of stabilisation. In Wales, prevalence has fallen subsequent to a peak in 2008. The paper considers country-level differences in the light of key policy changes, which are presented in detail. This work is unique, and will assist policymakers when critically evaluating policy options for effective control and eradication. Ongoing updates of this analysis would be useful, providing an evidence base for country-level comparison of bTB trends into the future. The use of multivariable analytical methods should be considered, but will rely on substantial sharing of raw data across the five countries.

In Ireland, an estimated 15% of Irish soils exceed the EU threshold limit for soil Cd of 1 mg/kg. The aim was to determine the concentrations of Cd and other heavy metals (As, Hg and Pb) in kidneys collected from cattle at slaughter. Systematic sampling of eligible animals (animals that were born and reared until slaughter in the same Irish county) at the time of slaughter was conducted, until a threshold number of animals from all 26 counties and 6 age categories was reached. A predictive surface of soil Cd was generated, by kriging the Cd values of 1310 previously reported soil samples. A linear regression weighted model was developed to model kidney Cd concentration, using the risk factors of age, sex, breed, province and estimated soil Cd concentration. Kidney Cd (n = 393) concentrations varied between 0.040 and 8.630 mg/kg wet weight; while concentrations of As, Hg and Pb were low. The estimated weighted proportion of animals with a high (≥ 1 mg/kg) kidney Cd concentration was 11.25% (95% CI: 8.63–14.53%). Key predictors for high kidney Cd concentration were soil Cd, animal age and province. At a soil Cd concentration of 1.5 mg/kg, it was predicted that an age threshold to avoid exceeding a kidney Cd concentration of 1 mg/kg in most animals would be ~ 3 y in Connacht, > 4 y in Ulster, and > 5 y in Leinster and Munster. In naturally occurring areas of high Cd levels in soils in Ireland, the Cd level in bovine kidneys can exceed the current EU ML of 1 mg/kg in older animals. Kidneys of most cattle under three years of age will conform with EU requirements. Department of Agriculture, Food and the Marine

A risk factor study was conducted to identify variables associated with initial positive or inconclusive results for bovine viral diarrhoea virus (BVDV) in ear punch samples collected from calves between 1st January and 15th July 2012 (the study period) as part of the voluntary phase of the Irish national BVD eradication programme based on testing of ear tag tissue samples from calves born in participating herds. Univariable analysis indicated significant associations with the following factors: herd type; the number of cows in the herd; the number of calves born in the study period; the number of calves tested in the study period; the number of cattle purchased in 2011, between 2009 and 2011 and between 2007 and 2011; the number of tested calves whose dams had been purchased within 9 months of their calving date; and the percentage of calf mortality within 28 days of birth. The percentage of the cows in each herd that was homebred, location (province) the number of separate land parcels used by each herd, the presence of an associated sheep enterprise and the purchase of cattle through marts were not found to be significant. An initial logistic regression model was developed to model the probability of a herd having one or more BVD virus-positive or inconclusive calves. When vaccination status was initially excluded, province, log of the numbers of cows in the herd, the number of cows purchased between 2009 and 2011, the number of tested calves whose dams had been purchased within 9 months of their calving date and calf mortality were significant. When vaccination status was included, using a subset of the data based on farmers responding to a survey on vaccination status, it was retained as a significant variable along with the same variables already listed, showing a significant 2-way interaction with the log of the number of cows. There was not a significant association between an initial positive or inconclusive result and the length of time for which herds had been vaccinating. The study provides a series of key communication messages relating to both the delivery of, and benefits from, the national eradication programme.

During the last several decades in Ireland, there has been substantial scientific progress in our understanding and related policy changes in the bovine tuberculosis (bTB) eradication programme. A range of performance measurements are routinely available, each highlighting a steadily improving situation in Ireland. However, recent research has highlighted an on-going problem of residual infection, contributing to recurrent breakdowns. In light of this general improvement, but also cognisant of residual infection, a critical evaluation of changes in effectiveness of managing recurrence is particularly valuable. Therefore, the objective of the study was to compare the herd-level risk of recurrence of bTB in Ireland between 1998 and 2008. A retrospective cohort study was carried out, using a Cox proportional-hazards model, to compare the risk of restriction recurrence in herds derestricted during 1998 and 2008. These herds were observed for up to 3 years from the end of the 'index restriction'. At the univariable level, 46.4% and 34.8% of study herds derestricted in 1998 and 2008, respectively, had a subsequent breakdown during the study period (χ(2)=70.6, P

In Ireland new cases of bovine tuberculosis (bTB) are detected using both field (with the single intradermal comparative tuberculin test (SICTT)) and abattoir surveillance. Once a new case has been detected, herd restrictions, including restrictions on animal movements into and out of the herd, are implemented until the herd has passed two consecutive clear tests. While a herd is restricted, there may be several reasons why it may be desirable to introduce new stock, such as enabling routine management practices to continue ‘as near to normal’. In Ireland, introduction of animals during a bTB episode is permitted under specific conditions, with permission from the local veterinary office. The objectives of this study were (1) to provide an overview of movement events associated with each bTB episode, (2) to determine whether introduction of animals during a bTB episode is associated with increased future bTB risk and (3) to identify the practices relating to the introduction of animals that are the most risky. All herds that were not restricted at the start of 2006, but experienced a bTB episode during 2006 with 2 or more SICTT standard reactors (the eligible bTB episode) were included in the study. We calculated the number of extended eligible bTB episodes and subsequent bTB episodes that could be directly attributed to introduced animals. The main outcome of interest was the time from de-restriction of the eligible bTB episode to the start of a subsequent bTB episode or the date of the last test prior to the end of the study (31 December 2010). Cox proportional-hazard models were developed, each using a different introduction variable: introduced animals during an episode (yes/no), introduced animals prior to the first retest/first clear test, time from start of episode until first animals introduced and number of animals introduced during the episode. Only a small proportion of subsequent bTB episodes (1.8%) or extended eligible bTB episodes (2.7%) could be directly attributed to introduced animals. The results highlight an increased risk of a subsequent bTB episode among only a subset of herds that introduced animals during the eligible bTB episode. Specifically, herds that introduced animals early during the eligible bTB episode were at significantly greater future bTB risk than herds where animals were only introduced later. To illustrate, herds that introduced animals after the first retest did not have a significantly different risk compared to herds that did not introduce animals at all. In contrast, herds that did introduce animals prior to the first retest had 1.5 times higher risk of a subsequent bTB episode. Future practices concerning the introduction of animals during an episode now need to be reviewed.

In this study, we used national-level data to describe trends in on-farm intramammary antimicrobial usage in Ireland from 2003 to 2015. We calculated actual sales of intramammary tubes and the quantity of active substance sold, by year, product type [lactation or dry cow therapy (DCT)], antimicrobial group, World Health Organization antimicrobial classification, and from 2009 to 2015, prescribing route. We also estimated on-farm usage of lactation and dry cow intramammary antimicrobials using defined daily dose (DDDvet) and defined course dose (DCDvet) calculations, and dry cow coverage. Sales of tubes of antimicrobial for DCT have increased, and the estimated national dry cow coverage in 2015 was 1,022 DCDvet per 1,000 cows per year. An increase has also occurred in sales of teat sealant (2015 sales: 66.7 tubes with teat sealant for every 100 tubes with antimicrobial for DCT). In contrast, the number of tubes of antimicrobial sold for lactation use has decreased to 1,398 DDDvet and 466 DCDvet per 1,000 animals per year. Sales in intramammary tubes with at least one critically important antimicrobial (CIA) have either risen since 2007 (DCT) or fallen (lactation therapy). Increases were observed in both the number of dry cow and lactation tubes containing CIA considered of highest priority for human health. Differences between prescribing routes with respect to CIA usage were observed. This study provides detailed insight into on-farm usage of intramammary antimicrobials in Ireland. It demonstrates positive national progress but also highlights areas for review. In particular, blanket dry cow treatment in Ireland should be reconsidered. It is not possible to investigate farm-level variation in antimicrobial usage from national sales data. In several countries, measurement and benchmarking have been critical to progress in reducing antimicrobial usage in farm animal production. Central collation of data on farm-level antimicrobial use is also needed in Ireland to allow objective measurement and benchmarking of on-farm usage. More generally, standardized indicators to quantify antimicrobial usage in farm animals are urgently needed to allow country-level comparisons.

The national BVD eradication programme in Ireland started on a voluntary basis in 2012, becoming compulsory in 2013. The programme relies on accurate identification and prompt removal of BVD+ calves. However, a minority of herd owners have chosen to retain BVD+ animals (defined as still being alive more than seven weeks after the date of the initial test), typically with a view to fattening them to obtain some salvage value. During each year of the programme, additional measures have been introduced and implemented to encourage prompt removal of BVD+ animals. The objective of this study was to describe temporal trends in the retention of BVD+ calves and associated animal and herd-level risk factors during the first three years of the compulsory eradication programme in Ireland. The study population included all BVD+ calves born in Ireland in 2013–2015. A parametric survival model was developed to model the time from the initial BVD test until the animal was slaughtered/died on farm or until 31 December 2015 (whichever was earlier). A total of 29,504 BVD+ animals, from 13,917 herds, were included in the study. The proportion of BVD+ animals that were removed from the herd within 7 weeks of the initial test date increased from 43.7% in 2013 to 70.3% in 2015. BVD+ animals born in 2015 had a much lower survival time (median = 33 days) compared to the 2013 birth cohort (median = 62 days), with a year on year reduction in survival of BVD+ calves. In the initial parametric survival models, all interactions with herd type were significant. Therefore, separate models were developed for beef and dairy herds. Overall the results of the survival models were similar, with birth year, BVD+ status, herd size, county of birth and birth month consistently identified as risk factors independent of herd type (beef or dairy) or the numbers of BVD+ animals (single or multiple) in the herd. In addition, the presence of a registered mobile telephone number was identified as a risk factor in all models except for dairy herds with a single BVD+, while the sex of the BVD+ calf was only identified as a risk factor in this model. Significant progress has been made in addressing the issue of retention of BVD+ calves, however, there is a need for further improvement. A number of risk factors associated with retention have been identified suggesting areas where future efforts can be addressed.

A simple random survey was conducted in Ireland during 2005 to estimate the ELISA-prevalence of paratuberculosis, commonly called Johne's disease (JD), in the cattle population. Serum samples were collected from all 20,322 females/breeding bulls over 12 months-of-age in 639 herds. All samples were tested using a commercially available absorbed ELISA. The overall prevalence of infected herds, based on the presence of at least one ELISA-positive animal, was 21.4% (95% CI 18.4%-24.9%). Herd prevalence levels amongst dairy herds (mean 31.5%; 95% CI: 24.6%, 39.3%) was higher than among beef herds (mean 17.9%; 95% CI: 14.6%-21.8%). However, the animal level prevalence was similar. The true prevalence among all animals tested, was calculated to be 2.86% (95%CI: 2.76, 2.97) and for animals >= 2 yrs, it was 3.30% (95%CI: 3.17, 3.43). For animals in beef herds, true prevalence was 3.09% (95%CI: 2.93, 3.24), and for those in dairy herds, 2.74% (95%CI: 2.59, 2.90). The majority of herds had only one ELISA-positive infected animal. Only 6.4% (95% CI 4.7%-8.7%) of all herds had more than one ELISA-positive infected animal; 13.3% (CI 8.7%-19.7%) of dairy herds ranging from two to eight ELISA-positive infected animals; and, 3.9% beef herds (CI 2.4%-6.2%) ranging from two to five ELISA-positive infected animals. The true prevalence of herds infected and shedding Mycobacterium avium subspecies paratuberculosis is estimated to be 9.5% for all herd types; 20.6% for dairy herds; and 7.6% for beef herds. If ELISA positive animals

We examined the effect of varying levels of badger population control on the prevalence of Mycobacterium bovis infection in badgers in four counties of Ireland. In the 'Removal' and 'Buffer' areas, proactive culling was conducted to substantially reduce and subsequently maintain badger populations at a low level for five years. In the 'Reference' areas, localised reactive culling was conducted in association with herd breakdowns. The infection status of badgers was determined using bacteriology. A total of 2696 badgers were recruited into the study, and 19.0% were found to be infected with M. bovis. The two population control strategies had differing effects on the subsequent prevalence of tuberculosis in badger populations. Proactive culling led to a long term decrease in the prevalence of tuberculosis in the re-emergent populations. Although there was an overall decline in the disease prevalence, no consistent trend in disease prevalence as a result of reactive culling was observed.

Pre-movement testing for bovine tuberculosis (BTB) was compulsory in Ireland until 1996. We determined the proportion of herd restrictions (losing BTB-free status) attributable to the recent introduction of an infected bovid; described events between restoration of BTB-free status (de-restriction) and the next herd-level test for BTB; estimated the proportion of undetected infected cattle present at de-restriction; identified high-risk movements between herds (movements most likely to involve infected cattle); and determined the potential yield of infected cattle discovered (or herds that would not lose their BTB-free status) by pre-movement testing, relative to the numbers of cattle and herds tested. We used national data for all 6252 herds with a new BTB restriction in the 12 months from 1 April 2003 and 3947 herds declared BTB-free in the 12 months from 1 October 2001. We identified higher-risk animals from our logistic generalized estimating-equation models. We attributed 6-7% of current herd restrictions to the recent introduction of an infected animal. There were considerable changes to herd structure between de-restriction and the next full-herd test, and infection was detected in 10% of herds at the first assessment (full-herd test or abattoir surveillance) following de-restriction. Following movement from a de-restricted herd, the odds of an animal being positive at the next test increased with increasing time in the source herd prior to movement, increasing time between de-restriction and the next full-herd test and increasing severity of the source herd restriction. The odds decreased with increasing size of the source herd. We estimated that 15.9 destination-herd restrictions per year could be prevented for every 10,000 cattle tested pre-movement and that 3.3 destination-herd restrictions per year could be prevented for every 100 source herds tested pre-movement. The yield per pre-movement test can be increased by focusing on high-risk movements; however, this would result in a substantial decrease in the total number of potential restrictions identified.

An analysis of the molecular epidemiology of Mycobacterium bovis in badgers was made in four selected areas of the Republic of Ireland in which an intensive badger removal programme was being carried out over a period of five years. Tissue samples from 2310 badgers were cultured. Restriction fragment length polymorphism (RFLP) analysis with IS6110, polymorphic GC-rich sequence (PGRS) and direct repeat sequence (DR) probes was applied to the isolates from 398 badgers, and 52 different rflp types were identified. Most of the isolates belonged to seven predominant types, and the other 45 types were represented by few isolates. An analysis suggests that some of these 45 types may have been introduced by the inward migration of badgers and others may have been the result of genetic changes to one of the prevalent types. The badgers were divided into groups on the basis of the sett at which they were captured, and RFLP typing was applied to isolates from two or more badgers from 85 groups. Multiple RFLP types were identified among isolates from 50 of these groups, suggesting that badgers probably moved frequently between group territories.

The objective of this study was to determine the prevalence and intensity of gastrointestinal nematode, lungworm and liver fluke infection in culled cows in Ireland. Abomasa, colorectal contents and livers were collected from 30 to 68 culled beef and dairy cows during autumn 2002 and summer 2003, respectively. Ostertagia ostertagi were found in the abomasa of only three (10%) cows sampled in autumn and in 38 (57%) cows examined in summer. The majority of positive animals had low burdens of O. ostertagi but a few individuals in the group sampled during the summer had a moderate infection (5000-10,000 adult worms). A proportion of the cows in the summer group were also co-infected with small numbers of Trichostrongylus axei. Cooperia oncophora predominated in the recoveries from the larval cultures although O. ostertagi were also recovered. The overall prevalence of Dictyocaulus viviparus was 14%, based on larval identification in faecal samples. Liver fluke, or varying degrees of pathology attributable to Fasciola hepatica, were present in 65% of the livers. The results of this study extend those of previous workers, which were largely limited to dairy cows alone and which focussed on gastrointestinal nematodes and did not include simultaneous infections with lungworm and liver fluke. It was concluded, from the level of polyparasitism evident in this study, that adult cattle should be considered in preventative approaches to bovine helminthosis.

In Ireland, the herd prevalence of bovine tuberculosis has remained stable for several decades, and in common with several other countries, progress towards eradication has stalled. There is evidence in support of the potential role of infected badgers (Meles meles, a protected species) in bovine tuberculosis in Ireland and Britain. However, this evidence on its own has not been sufficient to prove disease causation. Field trials are likely to offer the best opportunity to define this role. Building on the earlier East Offaly project, our objectives were to assess the impact of badger removal on the control of tuberculosis in cattle herds in Ireland. The study was conducted from September 1997 to August 2002 in matched removal and reference areas (average area of 245.1km(2)) in four counties: Cork, Donegal, Kilkenny and Monaghan. Badger removal was intensive and proactive throughout the study period in the removal areas, but reactive (in response to severe tuberculosis outbreaks in cattle) in the reference areas. Removal intensity in the removal and reference areas during the first 2 years of the study averaged 0.57 and 0.07 badgers/km(2)/year, respectively. The outcome of interest was restriction of cattle herds due to confirmed tuberculosis, where tuberculous lesions were detected in one or more animals. Data were analysed using logistic regression (modelling the probability of a confirmed herd restriction) and survival analysis (modelling time to a confirmed herd restriction). During the study period, there was a significant difference between the removal and reference areas in all four counties in both the probability of and the time to a confirmed herd restriction due to tuberculosis. In the final year of the study, the odds of a confirmed herd restriction in the removal (as compared to the reference areas) were 0.25 in Cork, 0.04 in Donegal, 0.26 in Kilkenny and 0.43 in Monaghan. Further, the hazard ratios (removal over reference) ranged from 0.4 to 0.04 (a 60-96% decrease in the rate at which herds were becoming the subject of a confirmed restriction).

This study was undertaken to investigate the impact of the retention of calves born in one calving season and considered to be persistently infected (PI) with bovine viral diarrhoea virus (BVDV) on herd-level outcomes in the following calving season. A secondary aim was to investigate the relationship between retention and the number of BVD+ calves detected the following season. The study population included a subset of herds enrolled in the 2012 voluntary BVD eradication programme in Ireland, specifically those with a birth registered to more than 80% of the cows between 1st January and 15th July and BVDV test results available for at least 80% of these calves, during both 2012 and 2013. Calves were considered PI based on either an initial positive result without further testing (BVDPOS) or a positive result on confirmatory testing (BVDPI), collectively considered BVD+ calves. Herd-level outcomes included the BVD status of the herd, and the number of BVD+ calves born between 1st January and 15th July 2013 (the study period). There was a significant univariable association between herd BVD status in 2013 and a number of general herd factors, including location, herd type, size and number of introduced animals (overall and those pregnant at time of introduction), as well as with each of six different factors related to the retention of virus-positive calves: the number of BVD+ calves in 2012; the maximum time (days) any one BVD+ born in 2012 was retained up to September 2013; the mean time (days) BVD+ animal(s) born in 2012 were retained up to September 2013; the date (quarter/year) the last BVD+ left the herd; the presence/number of 2012-born BVD+ retained in the herd at 1st January 2013. Separate multivariable models were constructed for each retention variable. The best model fit (based on AIC) was obtained using the retention variable "date (quarter/year) last BVD+ calf left the herd", followed by "total time all BVD+ calves were retained in the herd", with (log) herd size also retained in the models. Significant differences were also found in the number of positive calves detected in positive herds in 2013 for all of the calf retention risk factors. These findings confirm an increased probability of finding a BVD+ animal in a herd following the retention of positive calves born in the previous calving season, highlighting the importance of their prompt removal.

There has been a steady reduction in the levels of bovine tuberculosis (bTB) in Ireland for some years. This paper presents a number of methods employing geographical information systems to examine how this reduction is manifested in space and time. The focus of disease mapping has traditionally been placed on identifying areas with problems. There has been limited work done in visualising improvements. The authors describe recent spatial changes in the relative incidence of bTB in Ireland across an uniform hexagonal grid, comparing the mean of the annual animal level bTB incidence during the 10-year period from 1998 to 2007 to the years 2008 to 2012. The authors map bTB incidence trends for three successive five-year periods (1998–2002, 2003–2007 and 2008–2012). Finally, the authors investigate the change in extent and severity of interpolated bTB reactor density over time.

Peer-reviewed. Released with a Creative Commons Attribution Non-Commercial No Derivatives License, 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-1 μvar) 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-1 μvar. 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-1 μvar 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-1 μvar 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-1 μvar infection and ploidy will become clearer with ongoing selection towards OsHV-1 μvar 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.

Somatic cell count (SCC) limits are a key component of national and international regulation for milk quality. As yet, very limited work has been published on SCC regulatory standards, including on the effect of different approaches to SCC data adjustment and interpretation. This study examines the effect of SCC data adjustment and interpretation, as outlined in current European Union (EU) legislation, on herd eligibility to supply raw milk for processing of dairy products for human consumption, using Irish data for illustration. The study used Irish milk-recording data as a proxy for bulk tank SCC (BTSCC) data, to calculate an unadjusted monthly SCC value for each herd during each month of participation. Subsequently, 4 data adjustments were applied, as outlined in EU and national legislation: seasonal adjustment; 3-mo rolling geometric average, without accounting for a break in the supply; 3-mo rolling geometric average, after accounting for a break in the supply; and seasonal adjustment and 3-mo rolling geometric average combined, after accounting for a break in the supply. Analyses were conducted to examine the effect, during the period from 2004 to 2010, of data adjustment on the percentage of herds with herd SCC >400,000 cells/mL. In all, 4 interpretation scenarios, incorporating different data adjustment combinations, were used to estimate herd eligibility (compliant, under warning, or suspended, as defined by legislation) to supply raw milk for processing. The 4 methods of data adjustment each led to a sizable reduction (6.7, 5.0, 5.3, and 11.1 percentage points, respectively, compared with the unadjusted data) in the percentage of herds exceeding a herd SCC of 400,000 cells/mL. Herd eligibility varied by interpretation scenarios, in particular those incorporating seasonal adjustment. The study provides new perspectives on the effect of data adjustment on herd SCC and of interpretation scenarios on herd eligibility. The results provide an illustrative, rather than definitive, picture of this effect, as national authorities use BTSCC data when determining herd eligibility, whereas this study was conducted using milk-recording data as a proxy. Some aspects of the primary EU legislation are unclear, which may lead to differences in interpretation and application. The potential impact of data adjustment and milk purchaser pricing on farm-level mastitis control in Ireland is considered.

By international standards, Ireland is a relatively small dairy producer. However, the industry plays a critical role to the national economy, accounting for approximately 3% of national gross domestic product. This paper presents insights into udder health and intramammary antibiotic usage on Irish dairy farms during 2003-2010, based on data from several sources. Three data sources were used, including data on milk recording data, intramammary antibiotic sales and animal health assessment. The milk recording data included a single unadjusted herd-level somatic cell count (SCC) value for each herd at each milk recording, being the arithmetic mean of cow-level SCC of each cow at that recording, weighted by cow-level yield. These data were used to calculate the percentage of herds each month where the unadjusted herd SCC exceeded 200,000 and 400,000 cells/mL. Two logistic generalised estimating-equations (GEE) models were developed, the outcome variable being either the probability that the monthly SCC of a herd was greater than 400,000 cells/mL or less than or equal to 200,000 cells/mL. Spring herds had a lower probability of a high SCC (> 400,000 cells/mL) during February to October compared to non-Spring herds but a higher probability between November to January. The odds of a high SCC were greater in 2005, 2006, 2009 and 2010 but less in 2007 and 2008 compared to 2004. Smaller herds had higher odds of having a high SCC compared to larger herds. We present the number of intramammary tubes and the quantity of active substance (kg) sold annually in Ireland during 2003-2010. We infer an incidence of clinical mastitis of 54.0 cases per 100 cow-years at risk, assuming 4 tubes per treatment regime, one affected quarter per cow, tubes restricted to clinical cases only and 100% of treated cases considered new cases, based on data collected on sales of in-lactation intra-mammary antibiotics. With differing assumptions, this estimate varied between 25.8 and 77.0 cases per 100 cow-years at risk. Using data on sales of dry cow therapy intra-mammary antibiotics, we also infer that most Irish dairy farmers use blanket dry cow therapy. It is important that Ireland has an objective understanding of current levels of udder health, to facilitate benchmarking and improvement into the future. Udder health is a concern on a number of Irish dairy farms. High SCC results were present throughout the year, but more marked towards the start and end of each milking season. Animal Health Ireland recently commenced a major national programme, CellCheck, in collaboration with a broad range of stakeholders, to support national SCC improvement. In this paper, relevant European and national legislation is also reviewed.

This study evaluated the impact of the Irish herd bovine tuberculosis (bTB) depopulation policy (depopulation, disinfection, contiguous testing and local badger removal where implicated) on the recurrence of bTB infection, by comparing the future risk in restocked herds following depopulation for either bTB or bovine spongiform encephalopathy (BSE) during 2003 to 2005. Each herd was assigned a ‘previous bTB risk’, based on bTB history during the five years before depopulation. Future bTB risk was estimated, using a multivariable Cox proportional hazard model for time-to-breakdown for each study herd, to identify risk factors associated with bTB. Future bTB risk varied significantly by reason for depopulation and previous bTB risk. Herds depopulated for bTB (by definition, at high bTB risk) were not significantly different from BSE herds with no or a low previous bTB risk. BSE herds with a high previous bTB risk were found to be at significantly greater future bTB risk. Herd bTB depopulation measures, as currently applied in Ireland, are shown to be effective in enabling herds to attain and retain bTB freedom following restocking. Based on the data presented, and consistent with current knowledge of the bTB epidemiology, local badger removal contributes to efforts to limit recurrence of bTB in Ireland.

JOHNE'S disease is a chronic, granulomatous enteritis of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). The ‘gold standard’ for diagnosis is individual faecal culture (IFC) of MAP. Johne's disease has been a scheduled and notifiable disease in the Republic of Ireland since 1955. The introduction of the single European market in 1992 facilitated the free movement of animals and goods within the European Union. Between 1992 and 2004, approximately 85,000 cattle (predominantly breeding stock) were imported into Ireland (Barrett and others 2006). Between 1932 and 1992, only 92 cases of Johne's disease were reported to the Irish Department of Agriculture, Fisheries and Food (DAFF) veterinary laboratory services, while between 1995 and 2002, 232 infected animals were reported (Barrett and others 2006). These observations indicate that the prevalence of Johne's disease in Ireland has increased since the introduction of the single European market. Hence, the recent epidemiology of Johne's disease in Ireland may be different from that in other countries where the disease has been endemic at a higher prevalence for longer. Although the recent prevalence (Good and others 2009) and economic impact of clinical (Barrett and others 2006) and subclinical (Hoogendam and others 2009) Johne's disease in Irish dairy herds have been reported, there are no published studies examining the risk factors for detection of MAP by IFC in Irish dairy herds. This short communication describes a case-control study aiming to identify the risk factors associated with detection of MAP by IFC in Irish dairy herds. Case herds (n=86) were defined as herds with one or more IFC-MAP-positive results in the DAFF laboratory database from samples voluntarily submitted by private veterinary practitioners between 1995 and 2007. Control herds (n=125) were defined as herds with no IFC-MAP-positive results in DAFF's laboratory database in the same period and with no ELISA-positive …

Considerable effort has been devoted to improving the existing diagnostic tests for bovine tuberculosis (single intradermal comparative tuberculin test [SICTT] and γ-interferon assay [γ-IFN]) and to develop new tests. Previously, the diagnostic characteristics (sensitivity, specificity) have been estimated in populations with defined infection status. However, these approaches can be problematic as there may be few herds in Ireland where freedom from infection is guaranteed. We used latent class models to estimate the diagnostic characteristics of existing (SICTT and γ-IFN) and new (multiplex immunoassay [Enferplex-TB]) diagnostic tests under Irish field conditions where true disease status was unknown. The study population consisted of herds recruited in areas with no known TB problems (2197 animals) and herds experiencing a confirmed TB breakdown (2740 animals). A Bayesian model was developed, allowing for dependence between SICTT and γ-IFN, while assuming independence from the Enferplex-TB test. Different test interpretations were used for the analysis: SICTT (standard and severe interpretation), γ-IFN (a single interpretation), and a range of interpretations for the Enferplex-TB (level-1 [high sensitivity interpretation] to level-5 [high specificity interpretation]). The sensitivity and specificity (95% posterior credibility intervals; 95% PCI) of SICTT[standard] relative to Enferplex-TB[level-1] and γ-IFN were 52.9-60.8% and 99.2-99.8%, respectively. Equivalent estimates for γ-IFN relative to Enferplex-TB[level-1] and SICTT were 63.1-70.1% and 86.8-89.4%, respectively. Sensitivity of Enferplex-TB[level-1] (95% PCI: 64.8-71.9%) was superior to the SICTT[standard], and specificity of the Enferplex-TB[level-5] was superior to γ-IFN (95% PCI: 99.6-100.0%). These results provide robust measures of sensitivity and specificity under field conditions in Ireland and suggest that the Enferplex-TB test has the potential to improve on current diagnostics for TB infection in cattle. The extent of that potential will be assessed in further studies.

Ireland currently obtains its avian and bovine tuberculin purified protein derivatives (PPDs) from a single source. Because problems of supply or quality cannot be discounted, it is prudent that Ireland identify alternative supplier(s) as part of a broad risk management strategy. Therefore, the aim of this study was to compare the performance of a number of different tuberculin combinations (that is, pairings of bovine and avian PPD; with different manufacturers) in the single intradermal comparative tuberculin test (SICTT), as currently performed in Ireland. The study was randomised, controlled and double-blinded. A total of 2172 cattle were used in the study. Each animal was tested using two SICTTs, the first based on the tuberculin combination in current use, and the second using one of six trial tuberculin combinations. Analyses were conducted to compare both reactor-status and skin increase. For each control/trial tuberculin combination, there was good agreement between the control and trial reactor-status. Differences in skin increases were mainly confined to animals categorised as either negative or severe inconclusive. However, the measured differences were minor, and unlikely to have a significant impact on the actual test outcome, either for individual animals or for herds. In conclusion, while further studies determining sensitivity and specificity in Ireland would have to be done in the event of a change in tuberculin PPD there should be minimal disruption of the national programme if alternative tuberculin PPDs meeting WHO, OIE and EU regulations were used. In this study, the precision of the guinea pig bio-assay to assess tuberculin potency was low and therefore Ireland should maintain its practice of periodically assessing potency in naturally infected cattle, even though this is not currently required under WHO, OIE or EU Regulations.

Background There is considerable international research regarding the link between human demographics and pet ownership. In several international studies, pet ownership was associated with household demographics including: the presence of children in the household, urban/rural location, level of education and age/family structure. What is lacking across all these studies, however, is an understanding of how these pets are spatially distributed throughout the regions under study. This paper describes the spatial distribution of pet dog and pet cat owning households on the island of Ireland. Results In 2006, there were an estimated 640,620 pet dog owning households and 215,542 pet cat owning households in Ireland. These estimates are derived from logistic regression modelling, based on household composition to determine pet dog ownership and the type of house to determine pet cat ownership. Results are presented using chloropleth maps. There is a higher density of pet dog owning households in the east of Ireland and in the cities than the west of Ireland and rural areas. However, in urban districts there are a lower proportion of households owning pet dogs than in rural districts. There are more households with cats in the urban areas, but the proportion of households with cats is greater in rural areas. Conclusions The difference in spatial distribution of dog ownership is a reflection of a generally higher density of households in the east of Ireland and in major cities. The higher proportion of ownership in the west is understandable given the higher proportion of farmers and rural dwellings in this area. Spatial representation allows us to visualise the impact of human household distribution on the density of both pet dogs and pet cats on the island of Ireland. This information can be used when analysing risk of disease spread, for market research and for instigating veterinary care.

In Ireland, new cases of bovine tuberculosis (bTB) are detected using both field and abattoir surveillance ( More and Good, 2006 ). Field surveillance is conducted through annual testing of all cattle using the single intradermal comparative tuberculin test (SICTT). An animal may be deemed a ‘standard inconclusive reactor’ (SIR) to the SICTT if the bovine response is >2 mm and between 1 and 4 mm > the avian response. The herdowner then has three choices for the management of the SIR: option 1 is to have the animal retested after a minimum period of 42 days (an inconclusive reactor retest, IRR), option 2 is to slaughter the SIR and, provided the animal has no visible lesions, have a full herd test 42 days after the SIR leaves the herd, option 3 is to slaughter the SIR and have the lymph nodes examined using histology and/or culture for bTB. In the current study, we examine the bTB risk for SIRs both at slaughter prior to the IRR and at the IRR, and the future bTB risk of TIR animals (so-called ‘transient SIRs’; SIR animals with a negative SICTT result at the subsequent IRR) that moved from the herd of disclosure within 6 months of the IRR. We also investigate factors associated with the future bTB status of SIRs at slaughter prior to the IRR and at the IRR. The study population included all SIRs identified in Ireland between 2005 and 2009 inclusive in a herd otherwise Officially TB free (OTF). Between 11.8% and 21.4% of SIRs slaughtered prior to the IRR were confirmed bTB positive at post mortem (using histology or culture if histology was not definitive), compared to 0.13–0.22% of SICTT −ve cohort animals. The post mortem bTB lesion rate of SIRs is lower than the lesion rate reported for reactor animals between 2005 and 2009 of between 34% and 39%, reflecting the doubtful infection status of these animals. Between 20.3% and 27.9% of herds were restricted at the IRR. The herd restriction rate amongst the national herd between 2005 and 2009 varied from 5.09% to 6.02%. TIRs that moved out of the disclosing herd within 6 months of the IRR were 12 times more likely to be bTB positive at the next test/slaughter compared to all animals in the national herd. The same increased risk did not apply to the SICTT −ve cohort animals that moved out of the same herds at the same time. Based on a range of measures, SIRs and TIRs are each at increased bTB risk into the future. Consequently, differential treatment of TIR animals would be justified.

Keywords: horse; equine infectious anaemia; EIA; Ireland; epidemiology; transmission; spread; outbreak investigation; veterinary hospital

Infectious bovine rhinotracheitis (IBR), caused by bovine herpes virus 1 (BoHV-1), may result in various clinical consequences, including severe respiratory disease and conjunctivitis, venereal disease and reduced reproductive performance and abortion. This paper presents the serosurveillance findings from an intake of bulls into a performance testing station in Ireland during November 2007. The herd and within-herd BoHV-1 prevalence in 53 Irish beef herds and the risk factors for infection in these herds were determined, among bulls entering a beef performance testing station in Ireland. BoHV-1 status was determined for 41 herds, of which 30 (73.2%) herds were infected and the mean within-herd BoHV-1 prevalence was 28 (± 20)%. Multivariate exact logistic modelling revealed increasing numbers of contiguous herds and decreasing percentage of males within the herd as significant risk factors associated with infected herds. These findings highlight the high prevalence of BoHV-1 infection in those Irish beef herds that submitted bulls to this performance testing station, and raise concerns regarding IBR control nationally. Deposited by bulk import

Somatic cell count (SCC) data for 480 cows in 10 Irish dairy herds from January 2001 until June 2002 were analysed. Herds were selected on the basis of a recent or ongoing history of clinical or subclinical mastitis. An individual cow SCC of 200 000 cells per ml was used as the threshold for elevation of SCC. The duration of elevated SCC prior to drying-off and the magnitude of the elevation in SCC were found to have an impact on the response to dry cow therapy (DCT). A trend also emerged indicating that increasing parity had a negative influence on the response to DCT.

The conclusion from the randomised badger culling trial was that localised badger culling not only fails to control but can actually increase the incidence of bovine tuberculosis in cattle. Professor Simon More and colleagues from University College Dublin question that conclusion, arguing that the data do not provide sufficient evidence to rule out alternative hypotheses.