In the Republic of Ireland, the herd-level incidence of bovine tuberculosis (bTB), caused by Mycobacterium bovis, reached 6.40% by June 29th 2025, highlighting bTB’s risk to animal health, biosecurity and the economy. The complexity of bTB epidemiology, driven by multiple host species, undetected transmission and incomplete diagnostic sensitivity, makes surveillance and control challenging. Pathogen whole-genome sequencing (WGS) can clarify transmission dynamics but is constrained by the slow, variable mutation rate of M. bovis. This pilot case study integrates WGS with epidemiological data to elucidate transmission event pathways and could be a starting point for future automation. A decision-tree framework was developed to classify likely transmission event pathways by integrating M. bovis WGS sourced from the BTBGenie research project and epidemiological data. As proof-of-concept, one farm with multiple isolates was randomly selected from a national WGS database. Twenty-eight near-identical isolates (pairwise ≤ 3 SNP divergence), from other herds, were identified across databases of the Republic of Ireland and Northern Ireland, with full metadata was available for 16 isolates. These were analysed using TracebTB, a research tool linking national animal health, movement, wildlife and land management databases. Transmission event pathways for this case herd were classified as “local area transmission” (43.75%), “within-herd transmission” (12.5%), and “cattle movement-associated transmission” (also 43.75%), divided into between-herd (25%) and within-herd (18.8%) transmission. No evidence of residual within-herd transmission was found in this herd. Homebred animals served as spatial anchors, delineating the cluster’s ‘home range’ or kernel. A spatially distant homebred case, alongside the overall home range size, suggested an undetected movement-associated transmission event, likely via undetected carriers. Integrating WGS with detailed epidemiology enables identification of probable bTB transmission event pathways, revealing undetected infections and highlighting biosecurity concerns associated with undetected carriers. The decision-tree framework provides a scalable approach for retrospective outbreak investigation, targeted surveillance, and efficient resource allocation, particularly in high-risk systems such as Controlled Finishing Units. These findings highlight the importance of transboundary collaboration in persistent bTB hotspots. Automating this approach could support validation of disease epidemiological models, guide targeted interventions, and optimising resource allocation, supporting Ireland’s goal of bTB eradication.

Since the abolition of EU milk quotas in 2015, the Irish dairy industry has expanded with a 16.6% increase in calf births since 2011. Calf losses have major implications for the economic viability and sustainability of dairy enterprises. There is a paucity of literature on mortality in calves from birth to six months, particularly at a national herd level. Previous studies have tended to focus on herd size as a risk factor for calf mortality rather than the possible influence of herd expansion. The purpose of this study is to quantify any association between dairy herd expansion and the risk of being classified as a high or low calf mortality herd based on analysis of national dairy herd identification and movement records in Ireland from 2016-2020. In calves aged under 6months, herds that expanded > 20% (OR 1.23 95% CI: 1.10-1.37, p < 0.001) and > 45% (OR 1.22, 95% CI:1.09-1.36, p = 0.001), were more likely to have > 10% herd calf mortality, compared to herds that did not increase in size. Newly established herds were more likely to have poor mortality outcomes (OR 2.44, 95% CI: 1.82-3.29, p < 0.001) compared to herds that did not increase in size. Herd expansion < 20% was not associated with mortality outcome. Herd ordinal location and herd size were significant risk factors for > 10% herd calf mortality. This study has demonstrated that herds that have expanded > 20% over five years and newly established herds were more likely to have poor mortality outcomes. It suggests that new entrants into dairy farming may benefit from targeted emphasis on herd health management. The results also highlight the value of national data as a tool to determine optimisation of farm interventions and surveillance and policy decisions to prioritise animal health and welfare.

BackgroundOvine lameness represents a significant production and welfare challenge to farmers and comprises two main categories, infectious and non-infectious lameness. The leading infectious lameness conditions are interdigital dermatitis (ID), footrot (FR) and contagious ovine digital dermatitis (CODD). The predominant types of non-infectious foot conditions include toe granulomas (TG) and shelly hoof (white line disease; SH).There is a paucity of information available as to how Irish farmers treat infectious foot lesions in sheep. This study aimed to i) Establish farmer-reported prevalence of lameness in Irish sheep flocks, ii) Assess farmers’ ability to identify infectious and non-infectious lameness types, iii) Examine the treatment methods employed by farmers for managing and treating infectious lameness in sheep.ResultsThe survey was conducted opportunistically and non-randomly. Three hundred and sixty-three valid responses were gathered. The median overall farm lameness prevalence reported was 6.0% (IQR: 4.0%–10.0%). Respondents reported ID as the most common lameness condition with a median estimated prevalence of 10.0% (IQR: 4.0 – 15.0). Respondents identified 77.9%, 76.6%, 61.7%, 67.3% and 67.0% of ID, FR, CODD, TG and SH lesions correctly, respectively. Where the respective lesion was correctly identified 95.1%, 90.2%, 49.2%, 59.7% and 68.4% reported to have seen ID, FR, CODD, TG and SH lesions, respectively on their farm previously. Antibiotic aerosol was the most frequently utilised treatment for ID (71.3% [95% CI:65.2, 76.8%]) reported by survey respondents. Antibiotic injection was reported by respondents as the most used treatment for FR (72.2% [95% CI: 65.8,78.0%]) and CODD (85.1% [95% CI: 75.8, 91.8%]). Therapeutic foot trimming was practiced by 52.9% (95% CI:46.1,59.6%) of respondents for the treatment of FR. Conclusions Interdigital dermatitis (ID) posed the greatest burden to Irish farmers, with a median farm prevalence of 10.0%, while footrot affected 90.2% of flocks (median 4.0%). Contagious ovine digital dermatitis, previously considered rare, was reported in 47% of flocks (median 3%). Farmers’ ability to correctly identify lesions varied from 79.9% for ID to 62.4% for CODD. Therapeutic foot-trimming, remain widely used within Irish flocks and was reported by 52.9% of respondents for the treatment of FR.

BackgroundBiosecurity measures are crucial to the introduction and spread of pathogens both within and between farms. External biosecurity focuses on preventing pathogens from entering or leaving the farm, while internal biosecurity aims to limit or stop the spread of pathogens within the farm. Implementing biosecurity measures not only protects animals from disease but also has positive effects on productivity, welfare and farm profitability. By reducing the need for antimicrobials, biosecurity measures also contribute to combating antimicrobial resistance. To assess and improve biosecurity, tools like Biocheck.UGent have been developed. In Ireland, the Biocheck.UGent tool has been widely used in pig farms since 2018. The aims of this study were firstly to assess temporal trends on biosecurity scores in Irish pig farms from 2018 to 2023 using the Biocheck.UGent tool and secondly to identify areas for improvement.ResultsThere was an increase in the number of annual assessments over the study period, with the majority of farms being assessed multiple times. Overall, external biosecurity scores were higher than internal scores. Improvements in the scores were observed over time for most of the subcategories for external and internal biosecurity and across the different farm types. Analysis of the subcategories within the scoring system revealed areas with lower scores, including disease management, cleaning and disinfection, and measures between compartments. Weaner-to-finisher farms tended to have lower scores compared to other farm types.ConclusionsWhile external biosecurity in Irish pig farms is generally high, there is room for improvement in internal biosecurity. This study highlights the importance of continuous efforts to improve biosecurity. The data obtained will aid in estimating the cost–benefit of implementing biosecurity measures, crucial for decision-making and better returns on investments.

BackgroundThe nutritional status in alpacas is often masked by their dense fibre coat. Its assessment is commonly approached by different body condition scores (BCS) that rely on manual palpation of defined anatomical regions. However, BCS is an important diagnostic tool to aid recognition of diseased South American camelids (SACs) and low BCS has been associated with conditions like anaemia and neutrophilia. For dose-dependent veterinary treatment, body weight (BW), that should be as accurate as possible, is required. As on-site weighing with scales is often not possible, BW can mostly only be roughly estimated. To date, it remains unclear whether BCS in alpacas provides reliable information on BW or the ratios of BW to body length commonly known as Body Mass Index (BMI) or Ponderal Index (PI). Equations to estimate BW based on body measurements are available in the literature. Nonetheless, respective equations were developed in growing alpacas or adult llamas and BCS was not included.ResultsTo compare six different BCS approaches and to examine the relationship between BCS and BW, body measurements and BCS scores were recorded in a herd of 105 alpacas. The examined BCS approaches showed significant (p < 0.05) but poor to moderate positive correlations to BW, BMI or PI. A solely visual inspection of BCS, in contrast, was not correlated with BW, BMI or PI. Equations previously developed in other studies provided an accurate estimation of BW. Multiple linear regression showed that the accuracy in predicting BW could be further increased by adding BCS data and sex.ConclusionOur observations indicate that most selected BCS approaches are not only important measures of nutritional status but can also be used to create more accurate models for BW calculation in alpacas. The study also supports the claim that a purely visual inspection of alpacas is not an adequate method to evaluate the nutritional status of these animals.

BackgroundPenile fibropapilloma is a condition caused by bovine papilloma virus and is frequently encountered in young bulls. Penile fibropapillomatosis is thought to be spread through homosexual mounting behaviour. Fibropapillomas of the penis are painful, often bleed and can impede normal intromission. Treatment may range from allowing time for slow, spontaneous regression to surgical resection but recurrence following surgery is reported by some authors.Case PresentationThirty one bulls that were presented to University College Dublin Veterinary Hospital from March 2017 to March 2023 for surgical resection of penile fibropapillomas were included in this retrospective case series. Twenty-seven of the 31 bulls (87%) were under two years of age. The majority (42%) of bulls presented were Hereford, but Angus, Charolais, Holstein-Friesian and Limousin breeds were also seen. Following examination and diagnosis of penile fibropapilloma, regional anaesthesia (xylazine-procaine epidural and internal pudendal nerve block) and standing surgical intervention (resection and cautery) was performed in each case. Phone call follow-up was performed by one author (EET) in all 31 cases and 2 cases out of the 28 that were contactable showed post-surgical recurrence of penile fibropapillomatosis (i.e., 7.1% recurrence rate).ConclusionThis case series summarises the history and presenting findings of 31 bovine penile fibropapilloma cases and describes a regional anaesthetic and standing surgical approach for successful case management.

BackgroundVirulent systemic feline calicivirus (VS-FCV) infection is an emerging disease. It is distinct from classic oronasal calicivirus infection as it manifests with unique systemic signs including severe cutaneous ulcerations, limb oedema, and high mortality, even in adequately vaccinated cats. Devastating epizootic outbreaks with hospital-acquired infections have been described in the United States, the United Kingdom, continental Europe and Australia with up to 54 cats affected in one outbreak and a mortality rate of up to 86%. This highly contagious and potentially fatal disease has not yet been reported in Ireland.Case presentationAn 11-month-old male neutered vaccinated domestic shorthair cat was presented with a 10-day history of lethargy, decreased appetite and progressively worsening pitting oedema in all four limbs. The signs were first noted after another kitten from a high-density cat shelter was introduced in to the household. Additional physical examination findings included marked pyrexia, and lingual and cutaneous ulcers. Virulent systemic feline calicivirus was diagnosed based on compatible history and clinical signs, exclusion of other causes, and calicivirus isolation by RT-PCR both in blood and oropharyngeal samples. Negative calicivirus RT-PCR in blood following resolution of the clinical signs further supported the diagnosis.ConclusionThis case represents the first known case of VS-FCV infection in Ireland. Given the severity of the clinical signs, and the high risk for epizootic outbreaks, Irish veterinarians should be aware of the disease to ensure prompt diagnosis and implementation of adequate preventive measures, in order to limit the threat that this disease represents for the wider cat population and particularly given the risk of hospital-acquired VS-FCV infection. Virulent systemic calicivirus should be suspected in cats with pyrexia of unknown origin, oedema or ulceration affecting the limbs or the face, and exposure to rescue cats from high-density households.