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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. Department of Agriculture, Food and the Marine

Vaccination of badgers with Mycobacterium bovis Bacille Calmette-Guerin (BCG) has been shown to protect badgers against tuberculosis in experimental trials. During the 3-year County Kilkenny BCG vaccine field study, badgers were treated orally with placebo (100% in Zone A), BCG (100% in Zone C) or randomly assigned 50%: 50% treatment with BCG or placebo (Zone B). At the end of the study, 275 badgers were removed from the trial area and subjected to detailed post-mortem examination followed by histology and culture for M. bovis. Among these badgers, 83 (30.2%) were captured for the first time across the three zones, representing a non-treated proportion of the population. Analysis of the data based on the infection status of treated animals showed a prevalence of 52% (95% CI: 40%-63%) infection in Zone A (placebo), 39% (95% CI: 17%-64%) in Zone B (placebo) and 44% (95% CI: 20%-70%) in Zone B (BCG vaccinated) and 24% (95% CI: 14%-36%) in Zone C (BCG vaccinated). There were no statistically significant differences in the proportion of animals with infection involving the lung and thoracic lymph nodes, extra-thoracic infection or in the distribution and severity scores of histological lesions. Among the 83 non-treated badgers removed at the end of the study, the infection prevalence of animals in Zone A (prevalence = 46%, 95% CI: 32%-61%) and Zone B (prevalence = 44%, 95% CI: 23%-67%) was similar to the treated animals in these zones. However, in Zone C, no evidence of infection was found in any of the untreated badgers (prevalence = 0%, 95% CI: 0%-14%). This is consistent with an indirect protective effect in the non-vaccinated badgers leading to a high level of population immunity. The results suggest that BCG vaccination of badgers could be a highly effective means of reducing the incidence of tuberculosis in badger populations.

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 posteradication 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. Department of Agriculture, Food and the Marine

peer-reviewed Background Fasciola hepatica has always represented a threat to Irish livestock because the Irish climate is highly suitable for the main local intermediate host of the parasite, the snail Galba truncatula. The recent clinical emergence of infections due to Calicophoron daubneyi has raised the question of whether the two parasites, which share a niche during part of their life-cycles, interact in some way. Here, we used geographical information systems (GIS) to analyse the distribution of both parasites in cattle and sheep. We also developed the first predictive model of paramphistomosis in Ireland. Results Our results indicated that, in cattle, liver fluke infection is less common than rumen fluke infection and does not exhibit the same seasonal fluctuations. Overall, we found that cattle had a higher likelihood of being infected with rumen fluke than sheep (OR = 3.134, P < 0.01). In addition, infection with one parasite increased the odds of infection with the other in both host species. Rumen fluke in cattle showed the highest spatial density of infection. Environmental variables such as soil drainage, land cover and habitat appeared to be the most important risk factors for C. daubneyi infection, followed by rainfall and vegetation. Overall the risk of infection with this parasite was predicted to be higher in the west of the country. Conclusions This study shows differences between the infection rates and spatial patterns of bovine and ovine infections with F. hepatica and C. daubneyi in Ireland. Whether the reasons for this are due to susceptibility, exposure and/or management factors is yet to be determined. Furthermore, the rumen fluke model indicates distinct risk factors and predicted distribution to those of F. hepatica, suggesting potential biological differences between both parasite species. This work was supported by the European Union Horizon 2020 programme (PARAGONE: vaccines for animal parasites. H2020-EU.3.2. SOCIETAL CHALLENGES, under grant agreement No 635408), who provided funding for training and software access used in the analysis. The Department of Agriculture Food and the Marine - Research Stimulus Fund though the Flukeless Research Project (under project no 13/S/405), provided data employed in the modelling process.

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 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. 3 km and construction vs., P.B. was supported by the European Molecular Biology Organization (EMBO) short-term fellowship grant number 8,794 during the development of this project.

In the UK and Ireland, Bacille Calmette-Guérin (BCG) vaccination of badgers has been suggested as one of a number of strategies to control or even eradicate Mycobacterium bovis infection in badgers. In this manuscript, we present the results of a badger field trial conducted in Ireland and discuss how the novel trial design and analytical methods allowed the effects of vaccination on protection against infection and, more importantly, on transmission to be estimated. The trial area was divided into three zones North to South (A, B and C) where vaccination coverages of 0, 50 and 100%, respectively, were applied. Badgers were trapped over a 4 year period. Badgers were assigned to either placebo or vaccine treatment, with treatment allocation occurring randomly in zone B. Blood samples were collected at each capture, and serology was performed in these samples using a chemiluminescent multiplex ELISA system (Enfer test). The analysis aimed to compare new infections occurring in non-infected non-vaccinated badgers to those in non-infected vaccinated ones, while accounting for the zone in which the badger was trapped and the infection pressure to which this individual badger was exposed. In total, 440 records on subsequent trappings of individual non-infected badgers were available for analysis. Over the study period, 55 new infections occurred in non-vaccinated (out of 239 = 23.0%) and 40 in vaccinated (out of 201 = 19.9%) badgers. A Generalized Linear Model (GLM) with a cloglog link function was used for analysis. Statistical analysis showed that susceptibility to natural exposure with M. bovis was reduced in vaccinated compared to placebo treated badgers: vaccine efficacy for susceptibility, VES, was 59% (95% CI = 6.5%–82%). However, a complete lack of effect from BCG vaccination on the infectivity of vaccinated badgers was observed, i.e. vaccine efficacy for infectiousness (VEI) was 0%. Further, the basic reproduction ratio as a function of vaccination coverage (p) (i.e. R(p)) was estimated. Given that the prevalence of M. bovis infection in badgers in endemic areas in Ireland is approximately 18%, we estimated the reproduction ratio in the unvaccinated population as R(0) = 1.22. Because VEs was now known, the reproduction ratio for a fully vaccinated population was estimated as R(1) = 0.50. These results imply that with vaccination coverage in badgers exceeding 30%, eradication of M. bovis in badgers in Ireland is feasible, provided that the current control measures also remain in place. Department of Agriculture, Food and the Marine

Bovine tuberculosis (bTB) is an important zoonotic disease which has serious and sometimes fatal effects on both human and non-human animals. In many countries it is endemic in the cattle population and has a considerable economic impact through losses in productivity and impacts on trade. The incidence rate in Ireland varies by herd and location and it is hoped that statistical disease-mapping models accounting for both spatio-temporal correlation and covariates might contribute towards explaining this variation. Methods: Ireland was divided into equally sized hexagons for computational efficiency (n = 997). Different spatio-temporal random-effects models (e.g. negative binomial Besag-York-Mollié) were explored, using comprehensive data from the national bTB eradication programme to examine the association between covariates and the number of bTB cattle. Leveraging a Bayesian framework, model parameter estimates were obtained using the integrated nested Laplace approximation (INLA) approach. Exceedance probabilities were calculated to identify spatial clusters of cases. Results: Models accounting for spatial correlation significantly improved model fit in comparison to non-spatial versions where independence between regions was assumed. In our final model at hexagon level, the number of cattle (IR = 1.142, CrI: 1.108 – 1.177 per 1000), the capture of badgers (IR = 5.951, CrI: 4.482 – 7.912), percentage of forest cover (IR = 1.031, CrI: 1.020 – 1.042) and number of farm fragments (IR = 1.012, CrI: 1.009 – 1.015 per 10 fragments) were all associated with an increased incidence of bTB. Habitat suitability for badgers, percentage of dairy herds and the number of cattle movements into the herd were not. As an epidemiological tool and to suggest future work, an interactive online dashboard was developed to monitor disease progression and disseminate results to the general public. Conclusion: Accounting for spatial correlation is an important consideration in disease mapping applications and is often ignored in statistical models examining bTB risk factors. Over time, the same regions in Ireland generally show highest incidences of bTB and allocation of more resources to these areas may be needed to combat the disease. This study highlights national bTB incidence rates. Shifting from national level analysis to smaller geographical regions may help identify localised high-risk areas. Department of Agriculture, Food and the Marine

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.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. Department of Agriculture, Food and the Marine

A high-quality animal health surveillance service is required to inform policy and decision-making in food-animal disease control, to substantiate claims regarding national animal health status and for the early detection of exotic or emerging diseases. In Ireland, the Department of Agriculture, Food and the Marine provides partially subsidized testing of farm animal samples and postmortem examinations to the Irish agriculture sector (farmers) at 6 regional veterinary laboratories (RVL) throughout the country. Diagnoses and data from these submissions are recorded and reported monthly and annually to enable animal health monitoring and disease surveillance. In a passive surveillance model, both the veterinary practitioner and the farmer play a vital role in sample submission by determining which cases are sent to the laboratory for postmortem or diagnostic testing. This paper identified factors influencing Irish dairy farmers' decisions to submit carcasses to RVL. Behavioral determinants of the submission of samples where veterinary professionals are concerned has been studied previously; however, limited work has studied determinants among farmers. This study conducted qualitative analyses of decisions of Irish dairy farmers relevant to diagnostic sample submission to an RVL and to examine the herd-level characteristics of farmers that submitted cases to an RVL. The biographical narrative interpretive method was used to interview 5 case-study farmers who were classified nonsubmitters, medium, or high submitters to the postmortem service based on the proportion of on-farm mortalities submitted to the laboratory service in 2016. The data obtained from these interviews were supplemented and triangulated through dairy farmer focus groups. The data were thematically analyzed and described qualitatively. In addition, quantitative analysis was undertaken. Data for herds within the catchment area of a central RVL were extracted, and a multivariable logistic regression model was constructed to examine the relationship between herds from which carcasses were submitted to the laboratory and those from which none were submitted. Results from the analysis show that the farmer's veterinary practitioner was the primary influence on submission of carcasses to the laboratory. Similarly, the type of incident, logistical issues with transporting carcasses to the laboratory, influence of peers, presence of alternative private laboratories, and a fear of government involvement were key factors emerging from the case-study interview and focus group data. Herd size was identified in both the qualitative and quantitative analysis as a factor determining submission. In the logistic regression model, herd size and increased levels of expansion were positively correlated with the odds of submission, whereas distance from the laboratory was negatively associated with odds of submission. These results identify the main factors influencing the use of diagnostic services for surveillance of animal health, signaling how services may be made more attractive by policy makers to a potentially wider cohort of users.

Background The present study aimed to identify the national prevalence of Fasciola hepatica in Irish sheep and to conduct a risk analysis assessment based on management and treatment practices in participating flocks. Also, co-infection with rumen fluke was quantified and its association with liver fluke and management practices was assessed. Methods A total of 305 sheep flocks were selected ensuring even national representation of the sheep population. Participating farms were asked to complete a survey questionnaire on farm management practices and submit faecal samples during the winter of 2014–2015. Pooled faecal samples were analysed for the presence of F. hepatica and co-infection with rumen fluke. Apparent and true prevalence were calculated, additionally, the rate of co-infection with rumen fluke was also obtained. Correlation and regression analyses were used for assessing associations between management practices, liver fluke infection and co-infection with rumen fluke. Results The national true prevalence of F. hepatica was 50.4% (n = 305). Regional prevalence varied from 41% in the east to 52% in the south. Co-infection with rumen fluke was observed in 40% of the studied population and correlated with increased F. hepatica egg counts (OR = 2.9; P ≤ 0.001). Predominant breeds were Suffolk, Texel and Horned Mountain breeds. Beef cattle were the most frequent type of other livestock present on farms and mixed species grazing was frequently reported (73%). More than half of the flocks reported a mid-to-late lambing period (March-April). Use of mountain land for grazing was of 32%. Flukicides were most commonly used twice over the autumn-winter period. Regression analyses highlighted significant association of F. hepatica status, with the presence of other livestock on farm, frequency of flukicides used during the winter and clinical presentation of liver fluke. A significant increase in eggs per gram of faeces was observed in Charollais sheep in comparison with all other breeds. Co-infection with F. hepatica and Calicophoron daubneyi was also significantly associated with the presence of other livestock on the farm, type of flukicide used and clinical fasciolosis. Conclusions The present study provides up-to-date information on the prevalence of F. hepatica in Irish sheep and adds insight to the epidemiology of the disease. These findings will be useful for designing new holistic control measures for F. hepatica infection.

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.

International audience; We detected influenza D virus in 18 nasal swab samples from cattle in Ireland that were clinically diagnosed with respiratory disease. Specimens were obtained from archived samples received for routine diagnosis during 2014-2016. Sequencing showed that viruses from Ireland clustered with virus sequences obtained in Europe within the D/swine/OK/1334/2011 clade.

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

Bovine tuberculosis (BTB) remains as a costly disease of cattle-herds in the Republic of Ireland (ROI). This persistence is partially attributable to the presence of M. bovis infection in a wildlife reservoir, the European badger (Meles meles). Thus, both area-wide and limited-area targeted-badger-culling have been part of the ROI-BTB control/eradication program to help reduce the future incidence of a cattle-herd BTB breakdown (i.e. a "new herd-level occurrence of BTB"). However, neither badger-culling practice can be sustained as a major component in the ongoing BTB eradication program in the ROI. Vaccination of badgers with Bacille Calmette-Guerin (BCG) has been proposed as an alternative to badger culling. Thus, in 2011, a five-year non-inferiority study was implemented in seven counties in the ROI. This study was designed to compare and contrast the cattle-herd-BTB-incidence in areas where intramuscular badger vaccination would be implemented versus the cattle-herd-BTB-incidence in the remaining area of the same county where targeted-badger-culling was maintained as the standard treatment response to probable badger-sourced BTB breakdowns. Our outcome of interest was a new cattle-herd-BTB-episode (breakdown) with a total of >2 standard skin-test (SICTT) reactors detected during the episode. Treatments (badger vaccination or targeted badger culling) were cluster allocated based on where the majority of the herd owner's land was located. To assess the impact of the two treatments, we compared the incidence-risk, of our defined outcome, for cattle herds in the area under vaccination to the outcome incidence-risk for cattle herds in the remainder of the same county after 4 and 5 years of having implemented badger vaccination. A random-effects logit model with adjustment for clustering by treatment, and statistical control of herd-type, herd-size and five-year prior-BTB-episode history was used for our analyses. Although not included in the logistic model, a relative badger density metric based on the annual number of badgers captured-per-sett-night of capturing effort was developed for each treatment area; this metric indicated that relative badger density was approximately 40 % higher in vaccination areas than in the targeted badger-culling areas during our study. Overall, our study results indicated that vaccination was not inferior to targeted badger-culling in four counties and badger vaccination was deemed to produce ambivalent results in one (County Cork North) of the seven study sites in the ROI. A post-study investigation, in County Galway, where vaccination was deemed inferior to target culling, revealed that widespread purchases of cattle from a nearby cattle mart, by herd owners in the vaccination-area, was associated with the increased herd and vaccination-area risk of BTB. No single "biasing hypothesis" was evident for the apparent vaccine inferiority in the second study site (County Monaghan) where vaccination was deemed inferior to targeted culling; hence no further investigations were conducted.

Fasciola hepatica is the causative agent of fasciolosis, a global disease of a wide range of mammals, particularly sheep and cattle. Liver fluke infection causes annual losses estimated at around €2.5 billion to livestock and food industries worldwide. Various models have been developed to define risk factors and predict exposure to this liver fluke in ruminants in European countries, most of them based exclusively on data from dairy herds. The aim of this study was to validate a published theoretical baseline risk map of liver fluke exposure and cluster maps in Ireland, by including further explanatory variables and additional herd types that are spatially more widespread. Three approaches were employed: i) comparison of predicted and actual exposure; ii) comparison of cluster distribution of hotspots and coldspots; and iii) development of a new model to compare predicted spatial distribution and risk factors. Based on new survey data, the published baseline predictive map was found to have a sensitivity of 94.7%, a specificity of 5%, a positive predictive value of 60% and a negative predictive value of 38.2%. In agreement with the original model, our validation highlighted temperature and rainfall among the main risk factors. In addition, we identified vegetation indices as important risk factors. Both the previously published and our new model predict that exposure to Fasciola is higher in the western parts of Ireland. However, foci of high probability do not match completely, nor do the location of clusters of hotspots and coldspots.

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.

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

In total, 245 Cryptosporidium parvum specimens obtained from calves in 205 Irish herds between 2003 and 2005 were subtyped by sequencing the glycoprotein gene gp60 and performing multilocus analysis of seven markers. The transmission dynamics of C. parvum and the influence of temporal, spatial, parasitic, and host-related factors on the parasite (sub)populations were studied. The relationship of those factors to the risk of cryptosporidiosis was also investigated using results from 1,368 fecal specimens submitted to the veterinary laboratories for routine diagnosis during 2005. The prevalence was greatest in the northwest and midwest of the country and on farms that bought in calves. The panmixia (random mating) detected in the C. parvum population may relate to its high prevalence, the cattle density, and the frequent movement of cattle. However, local variations in these factors were reflected in the C. parvum subpopulations. This study demonstrated the importance of biosecurity in the control of bovine cryptosporidiosis (e.g., isolation and testing of calves before introduction into a herd). Furthermore, the zoonotic risk of C. parvum was confirmed, as most specimens possessed GP60 and MS1 subtypes previously described in humans.

A field trial was conducted to investigate the impact of oral vaccination of free-living badgers against natural-transmitted Mycobacterium bovis infection. For a period of three years badgers were captured over seven sweeps in three zones and assigned for oral vaccination with a lipid-encapsulated BCG vaccine (Liporale-BCG) or with placebo. Badgers enrolled in Zone A were administered placebo while all badgers enrolled in Zone C were vaccinated with BCG. Badgers enrolled in the middle area, Zone B, were randomly assigned 50:50 for treatment with vaccine or placebo. Treatment in each zone remained blinded until the end of the study period. The outcome of interest was incident cases of tuberculosis measured as time to seroconversion events using the BrockTB Stat-Pak lateral flow serology test, supplemented with post-mortem examination. Among the vaccinated badgers that seroconverted, the median time to seroconversion (413 days) was significantly longer (p = 0.04) when compared with non-vaccinated animals (230 days). Survival analysis (modelling time to seroconversion) revealed that there was a significant difference in the rate of seroconversion between vaccinated and non-vaccinated badgers in Zones A and C throughout the trial period (p = 0.015). For badgers enrolled during sweeps 1–2 the Vaccine Efficacy (VE) determined from hazard rate ratios was 36% (95% CI: -62%– 75%). For badgers enrolled in these zones during sweeps 3–6, the VE was 84% (95% CI: 29%– 97%). This indicated that VE increased with the level of vaccine coverage. Post-mortem examination of badgers at the end of the trial also revealed a significant difference in the proportion of animals presenting with M. bovis culture confirmed lesions in vaccinated Zone C (9%) compared with non-vaccinated Zone A (26%). These results demonstrate that oral BCG vaccination confers protection to badgers and could be used to reduce incident rates in tuberculosis-infected populations of badgers.

Tick-borne diseases present a major threat to both human and livestock health throughout Europe. The risk of infection is directly related to the presence of its vector. Thereby it is important to know their distribution, which is strongly associated with environmental factors: the presence and availability of a suitable habitat, of a suitable climate and of hosts. The present study models the habitat suitability for Ixodes ricinus in Ireland, where data on tick distribution are scarce. Tick habitat suitability was estimated at a coarse scale (10 km) with a multi-criteria decision analysis (MCDA) method according to four different scenarios (depending on the variables used and on the weights granted to each of them). The western part of Ireland and the Wicklow mountains in the East were estimated to be the most suitable areas for I. ricinus in the island. There was a good level of agreement between results from the MCDA and recorded tick presence. The different scenarios did not affect the spatial outputs substantially. The current study suggests that tick habitat suitability can be mapped accurately at a coarse scale in a data-scarce context using knowledge-based methods. It can serve as a guideline for future countrywide sampling that would help to determine local risk of tick presence and refining knowledge on tick habitat suitability in Ireland.

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.

SUMMARYThe reported incidence of the metastrongylid nematodeAngiostrongylus vasorum, that infects dogs and other canids, is increasing worldwide outside recognized endemic foci. This apparent expansion of the parasite's range is causing concern to veterinary clinicians as the disease caused in dogs can be life threatening and its treatment is not straightforward. The red fox is thought to be a reservoir host for dogs. To investigate the spatial distribution of infection in foxes in Ireland, the hearts and lungs of 542 foxes from all over Ireland were examined. The incidence of infection was found to be 39·9% [95% confidence interval (CI) 35·7–44·1] with positive samples occurring in each of the country's 26 counties. This report confirms that the parasite is endemic in Ireland and the overall prevalence is the second highest in Europe. This is the first survey ofA. vasoruminfection in Irish foxes and highlights the potential exposure of the Irish dog population to high risk of cross-infection. Additionally,Crenosoma vulpiswas found in seven of the foxes, a parasite not previously reported in the Irish fox.

In Ireland badgers are removed in response to tuberculosis (TB) breakdowns in cattle herds (focal culling). Prevalence studies, conducted using a detailed post mortem and bacteriological examination, showed that 36-50% of badgers were infected with Mycobacterium bovis. Focal culling forms part of the medium term national strategy for the control of bovine TB in cattle and is based on the premise that badgers in areas with herd breakdowns have a higher prevalence of infection than the badger population at large. However, the hypothesis that cattle can be used as sentinels for infection in the badger population has never been formally tested. In this study we tested the hypothesis by determining the infection prevalence in badgers in areas where there had been historically, a consistently low prevalence of infection in cattle. Low cattle TB prevalence areas were defined as those herds with ≤ 2 standard reactors in the annual round of skin testing over the preceding 5 years (Greenfield sites). Using GIS, and adjusting for variation in land use, previous culling and cattle density, 198 Greenfield sites were identified and surveyed, and 138 areas with badger setts or signs of badger activity were identified. A single badger was removed from 87 sites and all were examined using detailed post mortem and bacteriological procedures. A prevalence of M. bovis infection of 14.9% was found in the Greenfield site badgers. This prevalence was significantly lower (P

SUMMARYMycobacterium bovisinfects the wildlife species badgersMeles meleswho are linked with the spread of the associated disease tuberculosis (TB) in cattle. Control of livestock infections depends in part on the spatial and social structure of the wildlife host. Here we describe spatial association ofM. bovisinfection in a badger population using data from the first year of the Four Area Project in Ireland. Using second-order intensity functions, we show there is strong evidence of clustering of TB cases in each the four areas, i.e. a global tendency for infected cases to occur near other infected cases. Using estimated intensity functions, we identify locations where particular strains of TB cluster. Generalized linear geostatistical models are used to assess the practical range at which spatial correlation occurs and is found to exceed 6 in all areas. The study is of relevance concerning the scale of localized badger culling in the control of the disease in cattle.

Background: Schmallenberg virus (SBV) was first identified in November 2011. It is a novel Orthobunyavirus (family Bunyaviridae) whose main ill effect is congenital malformation of the musculoskeletal and central nervous systems. It is borne by Culicoides spp., and has spread extensively in western Europe. The first case of SBV in Ireland was diagnosed in October 2012. It was anticipated that once the virus emerged in Ireland that there would be wide scale or nationwide spread over the course of the 2013 vector season. The objectives of this study were to determine the seroprevalence and distribution of exposure to Schmallenberg virus in Irish cattle from November 2012 to November 2013. Methods: Samples of brain for the pathology based surveillance were collected from malformed bovine and ovine foetuses submitted for post mortem examination. These samples were tested for SBV using RT-qPCR. Three serological surveys were carried out on sera submitted for the national brucellosis eradicartion programme. A spatial analysis of both sets of data was carried out. Results: Between October 2012 and 10th May 2013, SBV was confirmed by RT-qPCR in brain tissues from malformed foetuses obtained from 49 cattle herds and 30 sheep flocks in Ireland. In national serosurveys conducted between November 2012 until November 2013 the herd-level and animal-level SBV seroprevalences in cattle were 53 and 36 % respectively for the first survey, 51 and 35 % for the second survey and 53 and 33 % for the third survey. The herd level seroprevalence in counties ranged from 0 to 100 %, with the counties in the south and southeast having the highest seroprevalence (>50 %), the midlands a moderate herd level seroprevalence (10–50 %) while northern and north western counties had a low herd level seroprevalence (0–10 %). There was close spatial agreement between the results of the two different targeted surveillance strategies. Conclusions: At the end of the 2012 vector season, there was widespread exposure to SBV among herds in southern and south eastern Ireland. During 2013, there was little or no evidence of further outward spread, unlike the situation in several other European countries. Given the lack of evidence for circulation of the virus since 2012, it is likely that the younger age cohort in herds previously exposed to SBV and substantial proportions of animals of all ages on the margins of affected areas are immunologically naïve to SBV, and would be susceptible to infection if the virus were to re-emerge.

Simon More and Guy McGrath raise issues relating to the Randomised Badger Culling Trial, that they feel warrant further discussion and study.

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 objectives of the study were to quantify the levels of badger exposure for cattle and to test the hypothesis that increased badger exposure does not increase the risk of bovine tuberculosis (BTB) in a herd. Information that became available from the targeted removal of badgers over the study period, and from a badger-removal project in county Kilkenny, during 1996-1999 was used. The specific location of cattle within each farm, and the length of time that cattle spent in each farm field during the grazing season, and in the barnyard during winter, was used to build an exposure coefficient to quantify the amount of badger exposure that cattle encountered either on pasture or in the barn. The study design was a matched case-control study in which the control herds were selected using incidence density sampling. During the 4-year study period, 543 badgers were removed and of these 96 badgers were classified as tuberculosis positive; 96 BTB herd breakdowns occurred. There was a significant association between case herds and having a higher badger sett exposure coefficient during 1996-1998. No significant association between case herds and having a higher exposure coefficient based on the number of badgers, or the number of tuberculous badgers, during September 1997-December 1999 was found.

In several EU member states, bovine spongiform encephalopathy (BSE) cases have been identified in cattle born after the reinforced ban (BARB cases), for reasons that are not entirely clear. Epidemiological investigation of these cases has proved challenging. The European Food Safety Authority recently recommended the collection of a predefined set of epidemiological data from BSE suspects and confirmed BSE cases to aid future investigations. In this study, we present an epidemiological framework and BSE investigation questionnaire to aid the investigation of suspect BSE cases, and illustrate its application during the investigation of a BSE case in Ireland in 2015. It is recommended that the framework and questionnaire are used concurrently: the framework provides structure and focus, whereas the questionnaire (with 135 questions) aids data collection. The framework focuses on confirmation and discrimination, estimating the date and location of exposure, and determining the method/source of exposure. The BSE case in Ireland in 2015 was a BARB case born in 2010. It was identified with classical BSE at an authorised knackery as part of Ireland's targeted active surveillance programme for BSE. No definitive source of infection with the BSE agent could be attributed in this case.

Badgers are a wildlife host of Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB), and an important contributor to the epidemiology of bTB in cattle in Ireland and Britain. Repeated culling of badgers in high prevalence cattle bTB areas has been used in the Republic of Ireland as one tool to reduce intra- and interspecific transmission of M. bovis. We assessed factors that influenced infection prevalence of culled badgers from 2009 to 2012 (n=4948) where spatial, temporal and intrinsic factor data were available using multivariable modelling. Prevalence appeared higher in western areas than eastern areas of Ireland and badgers were more likely to be test-positive if caught at a sett (burrow system) which was close to other infected setts (spatial clustering of infection). There was a significant positive association between badger test-status and cattle prevalence of M. bovis infection at a spatial scale of 1km around setts. Badgers were more likely to be deemed test positive if they were male (OR: 1.9) or a parous female (OR: 1.7), compared to a female who had never conceived. Our results are consistent with different groups within badger populations having differential exposures and therefore infection risk (for example, parous vs. non-parous females). Furthermore, bTB clusters within the badger population, with greater risk to badgers in setts that are closest to other infected setts. The effective scale of the association of bTB risk between badger and cattle populations may be relatively large in Ireland. Our data indicate that the overall trend in prevalence of M. bovis infection in badgers has decreased in Ireland (P

Ireland lost its official freedom from Schmallenberg virus (SBV) in October 2012. The route of introduction is uncertain, with long-distance displacement of infected Culicoides, biting midges, by suitable wind flows considered to be the most likely source. The authors investigated the potential introduction of SBV into Ireland through a Culicoides incursion event in the summer of 2012. They conducted SBV serology on archived bovine sera to identify the prospective dispersal window, then used atmospheric dispersion modelling during periods around this window to identify environmental conditions the authors considered suitable for atmospheric dispersal of Culicoides from potential infected source locations across Southern England. The authors believe that there was one plausible window over the summer of 2012, on August 10-11, based on suitable meteorological conditions. They conclude that a potential long-range transportation event of Culicoides appears to have occurred successfully only once during the 2012 vector competent season. If these incursion events remain at a low frequency, meteorological modelling has the potential to contribute cost-effectively to the alert and response systems for vectorborne diseases in the future.

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.

The advisability of evaluating the local impact of climate on herd bovine tuberculosis (bTB) occurrence has arisen due to recent climatic changes, manifested by more extreme weather events and changeable weather conditions, including changes in temperature, rainfall and vapour pressure deficit (VPD, a measure of atmospheric dryness) (Walsh 2012). Despite many studies on risk factors for herd bTB occurrence, there has been limited work evaluating the influence of weather variables. Wint and others (2002), Gilbert and others (2005) both over all of Great Britain, and Pfeiffer and others (2008, pp 86–88), in a region in southwest England found an association between the environmental variables atmospheric temperature and VPD with herd bTB occurrence, but no biological explanation was offered. In these studies, environmental variables were derived from remotely sensed data, rainfall variables were not included in the studies, and large numbers of explanatory variables were used sometimes on relatively small datasets. In this study, we conducted a preliminary evaluation of the influence of weather variables on bTB incidence in cattle herds together with well- established risk factors from 2005 to 2009 in the area of west county Wicklow (WW) in the east of Ireland. Complete data were obtained on herd- and animal-level bTB testing history from the Animal Health Computer System (AHCS), land usage from Herdfinder (each maintained by the Department of Agriculture, Food and the Marine, DAFM), and weather from Met Eireann for the period 2005–2009 at the time of study The area was chosen mainly as it has variation in weather, and herd bTB incidence was similar to the national average for the period under study. All herds registered …

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.

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 …

The principal wildlife reservoir of Mycobacterium bovis in Ireland is the European badger. Studies in the Republic of Ireland (RoI) have shown that badgers culled in association with cattle herd tuberculosis breakdowns (focal culling) have a higher prevalence of infection than the badger population at large. This observation is one rationale for the medium term national strategy of focal badger culling. A vaccination strategy for the control of bovine tuberculosis (bTB) in badgers is a preferred long-term option. The Bacillus Calmette-Guérin (BCG) vaccine has been shown to decrease disease severity in captive badgers under controlled conditions. As the vaccine has been tested in a controlled environment with precise information on infection pressure, it cannot be assumed a priori that the effects of vaccination are similar in the wild, where other environmental and/or ecological factors prevail. For this reason we have designed a vaccine field trial to assess the impact of vaccination on the incidence of TB infection in a wild badger population. The selected study area for the vaccine trial (approximately 755 square kilometers) is divided into three zones each of which has similar characteristics in terms of size, number of main badger setts, cattle herds, cattle and land classification type. Three vaccination levels (100%, 50% and 0%) will be allocated to the three zones in a way that a gradient of vaccination coverage North to South is achieved. The middle zone (zone B) will be vaccinated at a 50% coverage but zone A and C will be randomly allocated with 100% or 0% vaccination coverage. Vaccination within zone B will be done randomly at individual badger level. The objective of this paper is to describe the design of a field tuberculosis vaccination trial for badgers, the epidemiological methods that were used to design the trial and the subsequent data analysis. The analysis will enable us to quantify the magnitude of the observed vaccination effect on M. bovis transmission in badgers under field conditions and to improve our knowledge of the biological effects of vaccination on susceptibility and infectiousness.

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.

Bovine brucellosis is a major animal health problem in the Republic of Korea. Further, a number of human cases of brucellosis have recently been detected. This paper provides an overview of surveillance (to detect new cases) and control (to clear infection following case detection) of bovine brucellosis in the Republic of Korea during 2000-2006. Using data from AIMS (the national animal infectious disease data management system), we conducted separate descriptive analyses, initially using farm and then episode as our unit of interest. An episode was defined as a period of compulsory herd trading restriction, following detection of infection with Brucella abortus in one or more cattle. We also identified risk factors for two measures of disease control: episode duration (logistic generalised estimating equation model) and time to re-restriction (Cox's proportional-hazard model). There were 8530 and 52,739 reactor farms and reactor cattle, respectively, during 2000-2006. From 2004 to 2006, there was a substantial increase in the number of new outbreaks, particularly within the beef sector. The probability of a prolonged episode (>150 days) and the hazard of a second episode each increased with herd size. Further, the hazard of a second episode was higher in 2005 (compared with other years) and in the southeast of Korea (compared with other provinces). The effect of outbreak size on control varied between the beef and dairy sectors. The increase in beef cattle reactors in 2004-2006 is closely aligned to an increase in surveillance effort. Nonetheless, it is likely that this is a genuine reflection of the recent establishment and spread of brucellosis in the Korean beef cattle population. The recent increase in surveillance coverage in the beef sector is central to national eradication efforts. Current strategies to control infection following detection have generally been effective, leading to rapid clearance of infection on most farms. Control becomes problematic with increasing herd size. This work provides a detailed insight into surveillance and control of bovine brucellosis in Korea, and should assist both policy-makers and field veterinarians to improve the effectiveness of national eradication efforts.

We investigated the impact of targeted removal of badgers on the subsequent bovine tuberculosis (BTB) risk in cattle herds in county Laois, Ireland. The study period was 1989-2005. For each of 122 targeted badger-removal licenses (permit to remove badgers in the proximity of cattle herds undergoing a serious BTB episode), the herd number (index herd) for which the license was given was obtained. The herds in the proximity of the index herd were identified from another database. The main "exposure" in our study was the geographical location of herds relative to the area in which targeted badger removal was conducted. We categorized herds into five different exposure groups: herds were classified as non-exposed and denoted as group 0 (reference group) if they were located 500 m or more from the edge of any parcel of land of the index herd; group 1, was the index herds, group 2 the immediate (contiguous) neighbors of the index herd, group 3 herds were not immediate neighbors but within 150 m and group 4 herds were between 150 m and 500 m distance from the edge of any parcel of land of the index herd, respectively. We conducted a survival analysis (allowing multiple failures per herd) to compare the hazard of having a BTB episode in any of the four groups of exposed herds vs. the hazard in herds in the reference group. We controlled for other known risk factors as well taking into account a temporal component. Our analysis showed that the hazard ratio for the index herds (group 1) were non-significantly increased, indicating that there was no difference in the hazard of failing a BTB test (after the targeted badger removal was conducted) between index herds and reference herds. For the rest of the herds farther away from badger removal activities the hazards were lower than herds in areas not under badger removal. The hazard in the reference group decreased over the study period.

All the Irish cattle herds considered “clear” of bovine tuberculosis (BTB) having a single animal with a tuberculous lesion at slaughter during 2003 were identified. We performed a descriptive and logistic regression analysis to investigate whether selected risk factors had an association with the result of the herd test immediately after the tuberculous lesion was found (“Factory Lesion Test”, FLT). At the FLT, only 19.7% ( n = 338) of these 1713 herds had 1 or more standard reactors. The lesioned animal was home-bred in 46% of the “source” herds; these herds had an increased risk (23.4%) of having at least 1 standard reactor animal relative to herds with a purchased-lesioned animal (16.6%) (RR = 1.41). Our logistic models identified a number of important risk factors; two that appeared most important in predicting the FLT outcome were the time spent (residency) by the lesioned animal in the “source” herd, and the presence, or not, of the lesioned animal in a previous BTB episode in either the “source” herd, or the seller's herd in the case the lesioned animal was purchased. Our models fit the data well based on the Hosmer–Lemeshow test, however their sensitivity and specificity were very low (57% and 61% respectively). Surveillance of the cattle population for BTB using lesions found at slaughter is an essential component of an overall control program. Nonetheless, due to the poor predictability of the variables we measured, complete herd investigations are needed to help explain the FLT outcome of a herd.

This study investigated the distribution of bovine spongiform encephalopathy (BSE) in herds of cattle in Ireland over the years 1996 through 2000, prior to the introduction of widespread active surveillance. Mappings of index herds, herd density, and standardized morbidity ratios, by county, were employed to help visualize areas of potential clustering of BSE. The hypothesis of spatial clustering was tested using a spatial scan statistic applied to the location of the herd where exposure likely occurred. Both Bernoulli and Poisson spatial models indicated marked clustering of BSE herds centred on Monaghan county, with secondary clusters detected by Bernoulli approaches and some Poisson models in Wexford and Cork. The number of cases increased with time, but clear temporal-spatial clusters were rarely detected, except in the case of a cluster in Wexford. The focussed spatial scan analyses using the location of large-scale feed suppliers provided support for the hypothesis that clustering of BSE may be associated with feed source. The results of our analyses provided strong evidence in support of the hypothesis that herds, in which animals were most likely to have been exposed to the BSE agent, cluster geographically.

We investigated whether strains (restriction fragment length polymorphism, RFLP-types) of Mycobacterium bovis isolated from badgers and from cattle clustered among and within four areas in Ireland. The spatial scan test and nearest-neighbor analysis were used as the spatial cluster-detection techniques. In addition, for each of the major strains, associations between the distance to badger setts and the "centroid" of the cattle farm were assessed in a logistic model. Overall, between September 1997 and May 2000, 316 and 287 M. bovis samples, from badgers and cattle, respectively, were strain-typed. The distribution of strains in badgers, and separately in cattle, differed among areas. Within each of the four large areas, badgers and cattle tended to have similar strains; this is consistent with the sharing of M. bovis strains within an area. In more detailed within-area analyses, some spatial clusters of M. bovis strains were detected, separately, in both cattle and badgers. Almost half of the infected badger setts with a specific strain were located outside of the "detected" clusters. There was no association between the number of infected badgers with a specific M. bovis strain within 2 or 5 km distances to cattle herds, and the risk of the same strain in cattle. We speculate about the dynamic nature of badger movements, as an explanation for the absence of more clusters of most of the strains of M. bovis isolated from badgers, and its impact on trying to study transmission of M. bovis between cattle and badger.

We described the distribution of badger populations in four different areas in the Republic of Ireland. The data came from periodic targeted badger-removal and subsequent post-mortem examinations conducted between 1989 and September 1997, and from a formal badger-removal project in the same areas from 1997 through 1999. Records were complete for 2292 badgers regarding the date of capture, tuberculosis status, geographical area and specific sett from where the badgers were snared. Of 3187 setts, 2290 had no badgers recorded against them (i.e. were inactive). The badger-level prevalence of tuberculosis differed among areas (range 13-29%). Badger populations were highly clustered by sett, and this result was similar over the four study areas. The median number of badgers per active sett was 2. Tuberculous badgers also clustered within a sett. The third quartile of tuberculous badgers was 1 per active sett. The prevalence of tuberculous badgers within a sett was not related to the total number of badgers. There was little evidence of spatial clustering with only one local cluster of tuberculous setts in each of three areas, and none in the fourth area. After adjusting for the number of badgers per sett, only one area had spatial clusters identified.

This study investigated possible associations between soil types, land use and badger numbers in an area of the Irish Midlands where badger removal had been conducted during 1989-1994. For this purpose, the area was divided into approximately 2500 geo-referenced square grids of 0.5 degrees km per side. For the outcomes (setts per grid, badgers per grid and tuberculous badgers per grid), Poisson models of land use, of soil type, and a combination of these two were developed. Influential grids were removed and the models adjusted for over-dispersion in the badger outcomes. Mineral-based soils, dry and very-dry peat soils supported increased numbers of setts and badgers. High-quality pasture was the major land use (pastures often are found on mineral-based soils) and supported increased numbers of setts, badgers, and tuberculous badgers. "Natural" areas also supported more setts and broad-leaf forested areas were associated with increased tuberculous badger numbers. Discontinuous urban areas tended to decrease sett numbers per grid. Hedgerow length was not an important predictor given the information on soil type and land use. Spatial correlations existed for badger setts in 1 degrees km grids, for badger numbers in 1.5 degrees km grids, and for tuberculous badgers in 2 degrees km grids. The latter two grids have approximately the same area as the territory size used by a social group of badgers. There were no spatial correlations at the smallest (0.5 km) grid size.

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.

Selected demographic features and trends in bovine tuberculosis (BTB) from 1995 to 2010 are described for the countries of the UK and the Republic of Ireland, using standardised definitions and measures. All countries experienced a reduction in the number of cattle and herds and in the proportion of dairy herds, while average herd size increased. In general, the trends indicate a stable situation of very low BTB prevalence in Scotland and, over most of the period, a rising prevalence in England and Wales. The prevalence in the Republic of Ireland declined while Northern Ireland experienced both a rise and fall. Differences in demography, BTB programme structure and test results were noted, particularly between the island of Ireland and Great Britain. Further investigation of these differences may provide valuable insights into risk factors for BTB and optimisation of existing BTB programmes.

Bovine tuberculosis (bTB) continues to be a problem in cattle herds in Ireland and Britain. It has been suggested that failure to eradicate this disease is related to the presence of a wildlife reservoir (the badger). A large-scale project was undertaken in the Republic of Ireland during 1997–2002 to assess whether badger removal could contribute to reducing risk of cattle herd breakdowns in four areas. During the period of that “four area” study, there was a significant decrease in risk in intensively culled (removal) areas relative to reference areas. In the present study, we revisit these areas to assess if there were any residual area effects of this former intervention a decade on (2007–2012). Over the study period there was an overall declining trend in bTB breakdown risk to cattle herds. Cattle herds within former removal areas experienced significantly reduced risk of breakdown relative to herds within former reference areas or herds within non-treatment areas (OR: 0.53; P < 0.001). Increased herd breakdown risk was associated with increasing herd size (OR: 1.92-2.03; P < 0.001) and herd bTB history (OR: 2.25-2.40; P < 0.001). There was increased risk of herd breakdowns in areas with higher badger densities, but this association was only significant early in the study (PD*YEAR interaction; P < 0.001). Badgers were culled in areas with higher cattle bTB risk (targeted culling). Risk tended to decline with cumulative culling effort only in three counties, but increased in the fourth (Donegal). Culling badgers is not seen as a viable long-term strategy. However, mixed policy options with biosecurity and badger vaccination, may help in managing cattle breakdown risk. Electronic supplementary material The online version of this article (doi:10.1186/s13567-014-0109-4) contains supplementary material, which is available to authorized users.