Post-mortem surveillance of bovine tuberculosis in Ireland: herd-level variation in the probability of herds disclosed with lesions at routine slaughter to have skin test reactors at follow-up test

Bovine Herpes Virus Type 1 (BoHV-1) seroprevalence, risk factor and Bovine Viral Diarrhoea (BVD) co-infection analysis from Ireland

Surveillance of endemic pathogens is essential for disease control, providing an evidence base for policy and advice. Bovine Herpes Virus Type 1 (BoHV-1), the causative agent of Infectious Bovine Rhinotracheitis (IBR), has been found to have high seroprevalence within the Irish cattle population. The aim of the present study was to establish seroprevalence levels for culled cattle in Ireland aged < 30 months and to establish whether BVD exposure and other factors was associated with BoHV-1 exposure. We employed random effects logit models coupled with repeated bootstrap sampling to provide robust estimates. The final dataset contained results for 5273 animals tested over two study years, 2018 and 2020. The animal-level seroprevalence of BoHV-1 was 21.43% (1130/5273; 95%CI: 20.32-22.53%). Univariable analysis suggested that BoHV-1 seropositivity risk was associated with BVDV serodiagnosis status, age, sex, year sampled, herd type, herd-size, and metrics of movement into the herd. Final random-effects multivariable models suggested increased risk associated with increasing herd size of the last herd, movements made by animals during the previous year, and the year the animal was sampled. Despite BVDV status and sex being retained in the final model, repeated bootstrap sampling of the regression model to estimate biased-corrected 95%CI suggested that these associations were not robust. The overall apparent prevalence of BoHV-1 exposure for culled cattle in Ireland declined in 2020 relative to 2018 (from 23.32 to 17.61%). Herd-size and the movement of animals were found to be important factors associated with animal-level risk, but there was less statistical support for sex-based or BVDV status associations.

The Irish bTB eradication programme: combining stakeholder engagement and research-driven policy to tackle bovine tuberculosis

A new Irish bovine tuberculosis (bTB) eradication strategy was launched in 2021. The strategy was formulated following extensive discussions with stakeholders, formal reviews of several aspects of the existing bTB policy and relevant inputs from the latest scientific research projects. A stakeholder discussion body, the TB Forum, had been established in 2018 and this continues under the new strategy, supported by three working groups (scientific, financial and implementation). The strategy sets out actions to address cattle-to-cattle and badger-to-cattle bTB transmission, along with actions to improve farm biosecurity and empower farmers to make their own choices to reduce bTB risk.Large scale vaccination of badgers has been rolled out under the new strategy, with over 20,000 km2 covered by the vaccination programme and 6,586 badgers captured in vaccination areas in 2021. Vaccination efforts have been complemented by intensive communications campaigns, including a web enabled software application ("app") enabling farmers to report the location of badger setts.Cattle which test inconclusive to the tuberculin skin test have been re-tested using a gamma interferon blood test since April 2021, enabling truly infected cattle to be identified more effectively due to the higher sensitivity of this test. An enhanced oversight process has been put in place for herds experiencing extended or repeat bTB breakdowns. Whole genome sequencing is being used to investigate links between breakdowns, with the results supporting operational decision making in case management.Communications, including biosecurity advice, are co-designed with stakeholders, in order to improve their effectiveness. A programme involving veterinary practitioners providing tailored biosecurity bTB advice to their clients was established in 2021 and was rolled out nationally during 2022.A core element of the new strategy is the continual improvement of policies in response to changing bTB risks, informed by scientific research and then implemented with stakeholder consultation.

Once bitten twice shy: Risk factors associated with bovine tuberculosis recurrence in Castilla y Leon, Spain

Persistence of bovine tuberculosis (bTB) in cattle herd remains a major challenge in disease elimination due to the ineffectual removal of all infected animals in a bTB breakdown. Characterization of herds with a higher probability of experiencing further bTB breakdowns can help to implement specific risk-based policies for disease control and eradication. Here, our aim was to identify herd- and breakdown-level risk factors in bTB infected herds in Castilla y Leon, Spain, associated with a decreased time to recurrence and an increased risk of recurrence using a mixed effects Cox proportional hazards model and a multivariable logistic regression model, respectively. Results revealed that location (province), herd size and number of incoming animals/contacts were good predictors of a decreased time to bTB recurrence and an increased risk of becoming a recurrent herd. Additionally, the duration of the previous outbreak and the number of IFN-γ herd-tests applied in it were associated with increased odds of (an early) recurrence. Risk factors identified here can be used for early identification of herds in which bTB eradication may be more challenging and that should thus be subjected to increased control efforts. The characterization of high-risk herds may help to minimize the risk of reinfection and emphasize early detection and removal of bTB positive animals in the herd.

Revisiting the relative effectiveness of slaughterhouses in Ireland to detect tuberculosis lesions in cattle (2014-2018)

Slaughterhouse or meat factory surveillance to detect factory lesions (FL) at slaughter is an important part of the bovine tuberculosis (bTB) eradication program in Ireland. The objective of this study was to quantify the effectiveness of Irish slaughterhouses or factories in submitting FL and the proportion of those submitted FL confirmed as being due to bTB in slaughtered cattle, and to identify and quantify the association of risk factors at animal, herd, and factory level with FL submission and confirmation. The data consisted of 6,611,854 animals slaughtered in Irish factories from 2014 to 2018 obtained from the Department of Agriculture, Food and Marine (DAFM), Ireland. Selected risk factors for this study included factory, year and month of slaughter, age, sex, breed, animal movement, ever inconclusive in the standard or severe skin test, herd type, herd size, and bTB history. The association of each risk factor on the FL submission and confirmation risk were analysed with univariable followed by a multivariable logistic regression with herd as random effect. Factories were ranked and compared based on the odds ratio (OR) obtained from the univariable (crude OR) and multivariable (adjusted OR) analysis. The average submission risk of all factories was 20 per 10,000 animals slaughtered, ranging from 1 to 42 per 10,000 animals slaughtered, and the average confirmation risk over all factories was 40.72%, ranging from 0.00 to 61.84%. The odds of submitting and confirming FL as bTB positive were higher in animals over eight years old compared to animals 1–2 years old (OR = 1.91, 95 CI 95% 1.77–2.06 and OR = 4.05, 95% CI 3.17–5.18, respectively), and were higher in animals that ever had inconclusive skin result based on severe interpretation (OR = 2.83, 95% CI 2.44–3.27 and OR = 4.48, 95% CI 2.66–7.54, respectively), animals originating from sucklers herds (OR = 1.08, 95% CI 1.02–1.14 and OR = 1.31, 95% CI 1.11–1.55, respectively), or herds with bTB history in the past three years (OR = 4.46, 95% CI 4.28–4.66 and OR = 319.90, 95% CI 237.98–430.04, respectively). The odds of FL submission and confirmation decreased as the herd size increased (OR = 0.95, 95% CI 0.93–0.96 and OR = 0.82, 95% CI 0.78–0.86, respectively). An inverse relationship of FL submission and confirmation was present for variable sex and inconclusive skin result with standard interpretation, where submission odds were higher in males (OR = 1.05, 95% CI 1.00–1.10) and ever inconclusive animals (OR = 74.24, 95% CI 69.39–79.43), although the confirmation odds were lower (males OR = 0.66, 95% CI 0.56–0.76; ever inconclusive OR = 0.44, 95% CI 0.36–0.54). The crude and adjusted ranking of factories did not differ greatly for FL submission, indicating that factory-related factors may contribute significantly to the submission variation between factories. However, a substantial difference between crude and adjusted confirmation ranking was present which may indicate that animal and herd-related factors were associated to variation in confirmation risk between factories.

Bovine tuberculosis in youngstock cattle: A narrative review

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, remains a high-priority global pathogen of concern. The role of youngstock animals in the epidemiology of bTB has not been a focus of contemporary research. Here we have aimed to collate and summarize what is known about the susceptibility, diagnosis, transmission (infectiousness), and epidemiology to M. bovis in youngstock (up to 1-year of age). Youngstock are susceptible to M. bovis infection when exposed, with the capacity to develop typical bTB lesions. Calves can be exposed through similar routes as adults, via residual infection, contiguous neighborhood spread, wildlife spillback infection, and the buying-in of infected but undetected cattle. Dairy systems may lead to greater exposure risk to calves relative to other production systems, for example, via pooled milk. Given their young age, calves tend to have shorter bTB at-risk exposure periods than older cohorts. The detection of bTB varies with age when using a wide range of ante-mortem diagnostics, also with post-mortem examination and confirmation (histological and bacteriological) of infection. When recorded as positive by ante-mortem test, youngstock appear to have the highest probabilities of any age cohort for confirmation of infection post-mortem. They also appear to have the lowest false negative bTB detection risk. In some countries, many calves are moved to other herds for rearing, potentially increasing inter-herd transmission risk. Mathematical models suggest that calves may also experience lower force of infection (the rate that susceptible animals become infected). There are few modeling studies investigating the role of calves in the spread and maintenance of infection across herd networks. One study found that calves, without operating testing and control measures, can help to maintain infection and lengthen the time to outbreak eradication. Policies to reduce testing for youngstock could lead to infected calves remaining undetected and increasing onwards transmission. Further studies are required to assess the risk associated with changes to testing policy for youngstock in terms of the impact for within-herd disease control, and how this may affect the transmission and persistence of infection across a network of linked herds.

Engaging With Farmers to Explore Correlates of Bovine Tuberculosis Risk in an Internationally Important Heritage Landscape: The Burren, in the West of Ireland

Bovith recene tuberculosis (bTB) continues to be a pathogen of concern in several countries globally. Analysis of areas that have higher incidences of bTB outbreaks has demonstrated how risk is not equally distributed, and local data collection, analysis and participatory engagement is required to develop tailored approaches. The Burren, an internationally important heritage landscape, has been an area of higher bTB incidence for many years in Ireland, and owing to its unique geology and farming heritage a survey was developed to engage with local farmers to gain greater insight into farming practices and bTB control to inform tailored approaches. The survey gathered data on the farm and animal management approaches being used within the Burren, including local farming techniques like the use of “winterage” (grazing exposed limestone dominated uplands). Thematic analysis of free text responses was undertaken. Quantitative data were then explored using statistical models to assess associations with recent (<3 years) self-reported bTB breakdown risk. There was a high number of responses demonstrating a high degree of willingness to engage on the issue. Thematic analysis suggested that wildlife and its management (culling and vaccination), testing quality, and its impact on the bTB scheme, and pessimism around eradication were important themes. Statistical analysis suggested that increasing bTB risk was primarily related to increasing herd-size and the percentage of herd owner's land inaccessible to those attempting to locate badger setts. There was less evidence for associations relating to the amount of time, or which season (i.e., summer), farmers utilized “winterage”. The results of the study will feed back directly to local bTB management plans and further stakeholder engagement and is an exemplar for local tailoring of national control measures in situations of high incidences of bTB outbreaks in particular areas.

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.

Future Risk of Bovine Tuberculosis (Mycobacterium bovis) Breakdown in Cattle Herds 2013-2018: A Dominance Analysis Approach

Bovine tuberculosis (bTB) remains a significant endemic pathogen of cattle herds, despite multi-decadal control programmes being in place in several countries. Understanding the risks of future bTB breakdown (BD) and the associated characteristics of herds and index breakdowns could help inform risk categorisation. Such risk categories could then contribute to tailored management and policies. Here, we estimated the future risk of herd BD for the cohort of herds that were derestricted during 2013 in Ireland using multivariable logit regression models, with a dominance analysis approach. One third of herds that were derestricted in 2013 experienced a breakdown during the follow-up five year period (1469/4459; 33%). BD length was a significant predictor of future risk, primarily driven by long BDs > 230 days relative to short BDs < 130 days (OR 95%CI: 1.157–1.851), as was having had a previous BD (OR 95%CI: 1.012–1.366). Herd-size was the dominant predictor of future risk (accounted for 46% of predicted variance), suggesting significant increase in risk of future breakdown with increasing (log) herd-size (OR 95%CI: 1.378–1.609). There was significant spatial variation in future risk across counties, and it was the second most dominant predictor of future risk (25% of predicted variance). The size of index breakdowns was not a strong predictor of future risk over a 5-year period. These findings can inform a risk-based policy development.

Development and Application of a Prioritization Tool for Animal Health Surveillance Activities in Ireland

Decisions around animal health management by stakeholders are often subject to resource limitation, therefore prioritization processes are required to evaluate whether effort is attributed appropriately. The objectives of this study were to develop and apply a surveillance prioritization process for animal health surveillance activities in Ireland. An exploratory sequential mixed research methods design was utilized. A prioritization tool was developed for surveillance activities and implemented over two phases. During the first phase, a survey was conducted which asked stakeholders to prioritize diseases/conditions by importance for Irish agriculture. In the second phase, experts identified the most important surveillance objectives, and allocated resources to the activities that they considered would best meet the surveillance objectives, for each disease/condition. This study developed a process and an accompanying user-friendly practical tool for animal disease surveillance prioritization which could be utilized by other competent authorities/governments. Antimicrobial resistance and bovine tuberculosis were ranked top of the endemic diseases/conditions in the Irish context, while African swine fever and foot and mouth disease were ranked top of the exotic diseases/conditions by the stakeholders. The study showed that for most of the diseases/conditions examined in the prioritization exercise, the respondents indicated a preference for a combination of active and passive surveillance activities. Future extensions of the tool could include prioritization on a per species basis.

Bovine Tuberculosis (Mycobacterium bovis) Outbreak Duration in Cattle Herds in Ireland: A Retrospective Observational Study

Bovine tuberculosis (bTB) outbreaks, caused by Mycobacterium bovis infection, are a costly animal health challenge. Understanding factors associated with the duration of outbreaks, known as breakdowns, could lead to better disease management policy development. We undertook a retrospective observational study (2012-2018) and employed Finite Mixture Models (FMM) to model the outcome parameter, and to investigate how factors were associated with duration for differing subpopulations identified. In addition to traditional risk factors (e.g., herd size, bTB history), we also explored farm geographic area, parcels/farm fragmentation, metrics of intensity via nitrogen loading, and whether herds were designated controlled beef finishing units (CBFU) as potential risk factors for increased duration. The final model fitted log-normal distributions, with two latent classes (k) which partitioned the population into a subpopulation around the central tendency of the distribution, and a second around the tails of the distribution. The latter subpopulation included longer breakdowns of policy interest. Increasing duration was positively associated with recent (<3 years) TB history and the number of reactors disclosed, (log) herd size, beef herd-type relative to other herd types, number of land parcels, area, being designated a CBFU ("feedlot") and having high annual inward cattle movements within the "tails" subpopulation. Breakdown length was negatively associated with the year of commencement of breakdown (i.e., a decreasing trend) and non-significantly with the organic nitrogen produced on the farm (N kg/hectare), a measure of stocking density. The latter finding may be due to confounding effects with herd size and area. Most variables contributed only moderately to explaining variation in breakdown duration, that is, they had moderate size effects on duration. Herd-size and CBFU had greater effect sizes on the outcome. The findings contribute to evidence-based policy formation in Ireland.