Inferring bovine tuberculosis transmission between cattle and badgers via the environment and risk mapping.

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is one of the most challenging and persistent health issues in many countries worldwide. In several countries, bTB control is complicated due to the presence of wildlife reservoirs of infection, i.e. European badger (Meles meles) in Ireland and the UK, which can transmit infection to cattle. However, a quantitative understanding of the role of cattle and badgers in bTB transmission is elusive, especially where there is spatial variation in relative density between badgers and cattle. Moreover, as these two species have infrequent direct contact, environmental transmission is likely to play a role, but the quantitative importance of the environment has not been assessed. Therefore, the objective of this study is to better understand bTB transmission between cattle and badgers via the environment in a spatially explicit context and to identify high-risk areas. We developed an environmental transmission model that incorporates both within-herd/territory transmission and between-species transmission, with the latter facilitated by badger territories overlapping with herd areas. Model parameters such as transmission rate parameters and the decay rate parameter of M. bovis were estimated by maximum likelihood estimation using infection data from badgers and cattle collected during a 4-year badger vaccination trial. Our estimation showed that the environment can play an important role in the transmission of bTB, with a half-life of M. bovis in the environment of around 177 days. Based on the estimated transmission rate parameters, we calculate the basic reproduction ratio (R) within a herd, which reveals how relative badger density dictates transmission. In addition, we simulated transmission in each small local area to generate a first between-herd R map that identifies high-risk areas.

An observational study of ear-tagged calf mortality (1 to 100 days) on Irish dairy farms and associations between biosecurity practices and calf mortality on farms participating in a Johne's disease control program.

Postnatal mortality among replacement stock has a detrimental effect on the social, economic, and environmental sustainability of dairy production. Calf mortality rates vary between countries and show differences in temporal trends; most, however, are characterized by high levels of between-farm variability. Explaining this variation can be difficult because herd-level information on management practices relevant to calf health is often not available. The Irish Johne's Control Programme (IJCP) contains a substantial on-farm monitoring program called the Veterinary Risk Assessment and Management Plan (VRAMP). Although this risk assessment is largely focused on factors relevant to the transmission of paratuberculosis, many of its principles are good practice biocontainment policies that are also advocated for the protection of calf health. The objectives of this study were (1) to quantify mortality in ear-tagged Irish dairy calves between 2016 and 2020 using both survival and risk approaches, (2) to determine risk factors for 100-d cumulative mortality hazard in ear-tagged Irish dairy calves between 2016 and 2020, (3) to determine whether 100-d cumulative mortality hazard was higher in ear-tagged calves within herds registered in the IJCP versus those that were not registered in the IJCP and whether there were differences between these cohorts over time, and (4) within IJCP herds, to determine whether VRAMP score or changes in VRAMP score were associated with 100-d cumulative mortality hazard. Excluding perinatal mortality, the overall 100-d cumulative mortality hazard was 4.1%. Calf mortality was consistently underestimated using risk approaches that did not account for calf censoring. Cox proportional hazards models showed that cumulative mortality hazard was greater in male calves; particularly, calves born to Jersey breed dams and those with a beef breed sire. Mortality hazard increased with increasing herd size, was highest in calves born in herds that contract-reared heifers, and lowest in those born in mixed dairy-beef enterprises. Mortality hazard decreased over time with the mortality hazard in 2020 being 0.83 times that of 2016. Mortality hazard was higher in IJCP-registered herds than nonregistered herds (hazard ratio 1.06, 95% CI 1.01-1.12), likely reflecting differences in herds that enrolled in the national program. However, we detected a significant interaction between IJCP status (enrolled vs. not enrolled) and year (hazard ratio 0.96, 95% CI 0.92-1.00), indicating that the decrease in mortality hazard between 2016 and 2020 was greater in IJCP herds versus non-IJCP herds. Finally, increasing VRAMP scores (indicating higher risk for paratuberculosis transmission) were positively associated with increased calf mortality hazard. Postnatal calf mortality rates in Irish dairy herds declined between 2016 and 2020. Our study suggests that implementation of recommended biocontainment practices to control paratuberculosis in IJCP herds was associated with a reduction in calf mortality hazard.

Development of a syndromic surveillance system for Irish dairy cattle using milk recording data.

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.

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

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

Protective immunity against tuberculosis in a free-living badger population vaccinated orally with Mycobacterium bovis Bacille Calmette-Guérin.

Vaccination of badgers with Mycobacterium bovis Bacille Calmette-Guérin (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.

Is there an association between road building and bovine tuberculosis herd risk? A three time-point study in Ireland, 2011-2019.

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

Spatio-temporal models of bovine tuberculosis in the Irish cattle population, 2012-2019.

INTRODUCTION: 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.

Population Mobility Trends, Deprivation Index and the Spatio-Temporal Spread of Coronavirus Disease 2019 in Ireland.

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.

Spatial and network characteristics of Irish cattle movements.

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

Irish dairy farmers' engagement with animal health surveillance services: Factors influencing sample submission.

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.

Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland.

Control of bovine tuberculosis (bTB), caused by Mycobacterium bovis, in the Republic of Ireland costs €84 million each year. Badgers are recognized as being a wildlife source for M. bovis infection 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 of M. bovis sourced 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 similar M. bovis strains, 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.

Liver fluke in Irish sheep: prevalence and associations with management practices and co-infection with rumen fluke.

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 bovine tuberculosis cluster in north County Sligo during 2014-16.

BACKGROUND: Bovine tuberculosis (bTB, caused by infection with Mycobacterium bovis) is endemic in the Irish cattle population, and the subject of a national eradication programme since the late 1950s. During 2014, a substantial area-level bTB outbreak developing in north County Sligo, necessitating the need for an enhanced response. This paper describes this outbreak, the response that was undertaken and some lessons learned. RESULTS: In the north Sligo area between 2014 and 2016, 23 (31.9%) of restricted herds had 4 or more reactors to the single intradermal comparative tuberculin test (SICTT)/animals with bTB lesions disclosed during the restriction, and the majority (55.5%) of test-positive animals were identified as standard reactors to the SICTT. The herds restricted during 2014-16 were typically larger than other herds in the study area and introduced more animals during 2013. M. bovis was also detected in local badgers, but not deer. CONCLUSION: This paper describes a substantial outbreak in north County Sligo over a 3-year period. A coordinated area-based approach was a key feature of the outbreak, and substantial resources were applied to bring the outbreak under control. No definitive source was identified, nor reasons why a substantial number of herds were infected over a relatively short period. A coordinated regional approach was taken, and a number of lessons were learned including the need for urgency, for a team-based approach, for a consistent message when dealing with the public, for an area-based approach, for a degree of flexibility for the breakdown manager, and for molecular tools to assist in answering key questions relating to the source and spread of M. bovis to many herds during this bTB outbreak.

Sampling Methodology to Maximize the Efficient Use of National Abattoir Surveillance: Using Archived Sera to Substantiate Freedom From Bluetongue Virus Infection in Ireland.

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.

Further description of bovine tuberculosis trends in the United Kingdom and the Republic of Ireland, 2003-2015.

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.

Spatial patterns of Fasciola hepatica and Calicophoron daubneyi infections in ruminants in Ireland and modelling of C. daubneyi infection.

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.

A visual representation of cattle movement in Ireland during 2016.

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.

Trends and Predictors of Large Tuberculosis Episodes in Cattle Herds in Ireland.

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.

Validation of a spatial liver fluke model under field conditions in Ireland.

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.