Search

Mass gathering events (MGEs) attracting local, national, or international crowds presented particular challenges in the context of the coronavirus disease 2019 (COVID-19) pandemic. Sporting, religious, music and other cultural events held during the early months of the pandemic, without social distancing or other safeguards, have been regarded as so-called ‘super spreader’ events. By the summer of 2020, MGEs were generally banned or subject to severe restrictions. Regular European sporting fixtures such as England’s Football Association and Germany’s Bundesliga matches began to return in the autumn with protective measures in place, such as matches initially held behind closed doors, and later with sub-capacity crowd limits and mandatory social distancing [1, 2, 3, 4, 5]. With protective measures in place, and proof of COVID-19 vaccination or recovery required for entry, a series of six sporting MGEs, ‘the All-Ireland Finals’ were held in the Republic of Ireland’s largest stadium, Croke Park in Dublin, during August-September 2021. This study draws on a high-resolution human population mobility dataset to quantify journeys to/from the stadium area on MGE days by destination. The anonymised, aggregated, data used is based on mobile phone usage, and consists of a series of fine-grained geographical origin-destination matrices presenting daily estimates of area to area journey numbers. With mobility from the stadium area serving as a proxy for MGE attendance, this study explores associations between MGE attendance numbers and local COVID-19 infections over subsequent five week periods. No evidence was found of association between attendance at any of the six 2021 All-Ireland MGEs and COVID-19 infections over subsequent five week periods. This finding contrasts with studies of comparable MGEs in 2020, such as English Association Football matches held during spring 2020, and German Bundesliga football matches held during autumn 2020. These differing outcomes may point to the effectiveness of transmission mitigation policies and behaviours.

This poster will present details of a novel research project which aims to assist the Irish government to mitigate the impact of various incidents on Ireland such as infectious diseases for animals, contamination of animal feedstuffs, nuclear accidents/incidents/events abroad, radioactive contamination, environmental pollution, fire, and volcanic eruptions impacting Ireland.Atmospheric dispersion modelling is the mathematical simulation of how air pollutants disperse in the atmosphere. It is performed using computer simulations which use algorithms to solve mathematical equations that govern the dispersion of airborne particles. Dispersion models estimate the downwind ambient concentration of air pollutants emitted from 1) man-made sources (e.g. industrial plants, vehicular traffic, accidental chemical/nuclear releases), and 2) natural sources (e.g. small insects, pollen, dust or volcanic ash). Dispersion models can also be used to predict future concentrations of particles under specific scenarios (e.g. pollen forecasting based on weather data, the spread of Bluetongue virus, and the spread of Foot & Mouth disease).Currently, Ireland’s national meteorological service (Met Éireann) provides numerical weather prediction data to Ireland’s Environmental Protection Agency (EPA), to simulate the dispersion of nuclear material into the atmosphere. Met Éireann supports the EPA’s modelling capability by producing a daily automated simulated nuclear release. Met Éireann performs operational Bluetongue Virus forecasting, which is sent to relevant agricultural stakeholders, and supports University College Dublin (UCD) in their modelling of Foot and Mouth disease.As climate change continues, a range of pests previously unknown in Ireland are likely to find favourable conditions here, which could potentially harm native species of plants and animals. Investigation of potential sources of these pests, and assessment of their ability to travel over large distances on prevailing winds, could help prevent losses of livestock, crops and biodiversity.To improve Ireland’s national dispersion modelling capabilities, Met Éireann propose to commence a 4-year research project in 2023 using dispersion models and high-resolution meteorological data to build forecast capacity for a range of airborne particles that can affect human, animal and plant health. Such airborne particles include bioaerosols (vector-borne diseases, pollen and fungal spores), forest fire smoke, volcanic ash plumes and Saharan dust. High-resolution meteorological data and ensemble prediction systems will be employed to identify the locations in Ireland that are likely to be affected by various aerosols under different weather conditions. Met Éireann seeks to be an authoritative source for dispersion forecasts in Ireland, which could be of significant benefit to the agriculture industry and the significant number of Irish people who suffer from asthma, hay-fever and other respiratory illnesses.

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.

Like most countries worldwide, the coronavirus disease (COVID-19) has adversely affected Ireland. The aim of this study was to (i) investigate the spatio-temporal trend of COVID-19 incidence, (ii) describe mobility trends as measured by aggregated mobile phone records, and (iii) investigate the association between deprivation index, population density and COVID-19 cases while accounting for spatial and temporal correlation. Standardised incidence ratios of cases were calculated and mapped at a high spatial resolution (electoral division level) over time. Trends in the percentage change in mobility compared to a pre-COVID-19 period were plotted to investigate the impact of lockdown restrictions. We implemented a hierarchical Bayesian spatio-temporal model (Besag, York and Mollié (BYM)), commonly used for disease mapping, to investigate the association between covariates and the number of cases. There have been three distinct “waves” of COVID-19 cases in Ireland to date. Lockdown restrictions led to a substantial reduction in human movement, particularly during the 1st and 3rd wave. Despite adjustment for population density (incidence ratio (IR) = 1.985 (1.915–2.058)) and the average number of persons per room (IR = 10.411 (5.264–22.533)), we found an association between deprivation index and COVID-19 incidence (IR = 1.210 (CI: 1.077–1.357) for the most deprived quintile compared to the least deprived). There is a large range of spatial heterogeneity in COVID-19 cases in Ireland. The methods presented can be used to explore locally intensive surveillance with the possibility of localised lockdown measures to curb the transmission of infection, while keeping other, low-incidence areas open. Our results suggest that prioritising densely populated deprived areas (that are at increased risk of comorbidities) during vaccination rollout may capture people that are at risk of infection and, potentially, also those at increased risk of hospitalisation.

Control of bovine tuberculosis (bTB), caused byMycobacterium bovis, in the Republic of Ireland costs €84 million each year. Badgers are recognized as being a wildlife source forM. bovisinfection of cattle. Deer are thought to act as spillover hosts for infection; however, population density is recognized as an important driver in shifting their epidemiological role, and deer populations across the country have been increasing in density and range. County Wicklow represents one specific area in the Republic of Ireland with a high density of deer that has had consistently high bTB prevalence for over a decade, despite control operations in both cattle and badgers. Our research used whole-genome sequencing ofM. bovissourced from infected cattle, deer and badgers in County Wicklow to evaluate whether the epidemiological role of deer could have shifted from spillover host to source. Our analyses reveal that cattle and deer share highly similarM. bovisstrains, suggesting that transmission between these species is occurring in the area. In addition, the high level of diversity observed in the sampled deer population suggests deer may be acting as a source of infection for local cattle populations. These findings have important implications for the control and ultimate eradication of bTB in Ireland.

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

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.

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.

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.

The aim of this study was to create a clear visual representation of the live movements of cattle in the Republic of Ireland over the course of the year 2016. The animation created can be viewed online: https://youtu.be/PTCdPMnenBw This animation was created to be a communication tool to enable stakeholders to appreciate the extent of high risk cattle movements (farm to farm, farm to market to farm) in the Republic of Ireland and to highlight the potential role that these movements may play in the spread of infectious diseases of cattle in Ireland from one farm to another. Department of Agriculture, Food and the Marine Department of Agriculture, Fisheries and Forestry (Australia)

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.

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

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

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.

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

Coxiella burnetii is the aetiological agent of Q fever, a zoonotic disease with a worldwide distribution whose main reservoirs are goats, sheep and cattle.1 In ruminants, infection can cause abortion and reproductive problems, with large numbers of infectious organisms shed at parturition, in milk and in urine and faeces. Infection of humans occurs mainly via the respiratory route, with airborne spread possible beyond the boundaries of the infected farm.2 In Ireland, there were six recorded human cases of Q fever in humans in 2016,3 but it is reasonable to assume that the true human incidence is considerably higher. Infection with C burnetii is common in Irish cattle herds, with previous research estimating a herd prevalence of 37.9 per cent and an animal level prevalence of 1.8 percent.4 The Irish dairy sector is currently expanding following the abolition of EU milk quotas, and the trend indicates a likely expansion of the national dairy herd for some years to come.5 For this reason, we set out to obtain a more accurate estimate of the prevalence of antibodies to C burnetii in Irish dairy herds at this transitional point. Bulk tank milk (BTM) samples were obtained under a joint industry/government scheme where the main Irish dairy processors sent BTM samples to a Department of Agriculture, Food and the Marine (DAFM) veterinary laboratory. Up to 14,464 BTM samples collected …

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.

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