Now showing items 21-40 of 298

    • Value of simplified lung lesions scoring systems to inform future codes for routine meat inspection in pigs

      Pessoa, Joana; McAloon, Conor; Boyle, Laura; García Manzanilla, Edgar; Norton, Tomas; Rodrigues da Costa, Maria; Teagasc Walsh Scholarship Programme; Department of Agriculture, Food and the Marine; 0165; PathSurvPig 14/S/832 (Biomed Central, 2023-06-30)
      Background Across the European Union (EU), efforts are being made to achieve modernisation and harmonisation of meat inspection (MI) code systems. Lung lesions were prioritised as important animal based measures at slaughter, but existing standardized protocols are difficult to implement for routine MI. This study aimed to compare the informative value and feasibility of simplified lung lesion scoring systems to inform future codes for routine post mortem MI. Results Data on lung lesions in finisher pigs were collected at slaughter targeting 83 Irish pig farms, with 201 batches assessed, comprising 31,655 pairs of lungs. Lungs were scored for cranioventral pulmonary consolidations (CVPC) and pleurisy lesions using detailed scoring systems, which were considered the gold standard. Using the data collected, scenarios for possible simplified scoring systems to record CVPC (n = 4) and pleurisy (n = 4) lesions were defined. The measurable outcomes were the prevalence and (if possible) severity scoring at batch level for CVPC and pleurisy. An arbitrary threshold was set to the upper quartile (i.e., the top 25% of batches with high prevalence/severity of CVPC or pleurisy, n = 50). Each pair of measurable outcomes was compared by calculating Spearman rank correlations and assessing if batches above the threshold for one measurable outcome were also above it for their pairwise comparison. All scenarios showed perfect agreement (k = 1) when compared among themselves and the gold standard for the prevalence of CVPC. The agreement among severity outcomes and the gold standard showed moderate to perfect agreement (k = [0.66, 1]). The changes in ranking were negligible for all measurable outcomes of pleurisy for scenarios 1, 2 and 3 when compared with the gold standard (rs ≥ 0.98), but these changes amounted to 50% for scenario 4. Conclusions The best simplified CVPC scoring system is to simply count the number of lung lobes affected excluding the intermediate lobe, which provides the best trade-off between value of information and feasibility, by incorporating information on CVPC prevalence and severity. While for pleurisy evaluation, scenario 3 is recommended. This simplified scoring system provides information on the prevalence of cranial and moderate and severe dorsocaudal pleurisy. Further validation of the scoring systems at slaughter and by private veterinarians and farmers is needed.
    • Understanding agricultural land leasing in Ireland: a transaction cost approach

      Onofri, Laura; Trestini, Samuele; Mamine, Fateh; Loughrey, Jason (Biomed Central, 2023-06-08)
      Formal written land leasing contracts offer an alternative to land purchase for those farmers wishing to expand their land area and provide greater security relative to informal short-term rental agreements and are particularly important for beginning farmers with resources insufficient to purchase land. Formal land leasing contracts vary in terms of their duration, but there is limited understanding about the determinants of contract duration in developed countries. In this research, we use econometric techniques and transaction level data to explore the determinants of duration for agricultural land lease contracts for two regions in Ireland. Under the transaction cost economics approach, the research explores the role of legal status, price and non-price conditions in influencing the contract duration. Results indicate that the legal status of the tenant is a significant factor in influencing the duration. Provisions such as break clauses appear positively related to duration and confirm the theoretical expectation that long-term contracts create a demand for processes that enable adaptation over the course of long-term exchange.
    • Variation in the proportion of the segregating genome shared between full-sibling cattle and sheep

      Kenny, David; Berry, Donagh P.; Pabiou, Thierry; Rafter, Pierce; European Union Horizon 2020; Science Foundation Ireland; GenTore 727213; INTAQT 101000250; 16/RC/3835 (Biomed Central, 2023-04-18)
      The construction of covariance matrices that account for the genetic relationships among individuals, using pedigree or genotype data, is integral to genetic evaluations, which are now routinely used in the field of animal breeding. The objective of the present study was to estimate the standard deviation in the proportion of the segregating genome that is shared between pairs of full-sibling cattle and sheep independently. Post edits, genotype data comprising 46,069 autosomal single nucleotide polymorphisms (SNPs) were available for 4532 unique full-sibling sheep pairs, as well as for their respective parents. Post edits, genotypes from 50,493 autosomal SNPs were also available for 10,000 unique full-sibling cattle pairs, as well as their respective parents. Genomic relationship matrices were constructed for the sheep and cattle populations, separately. After accounting for both parental genomic inbreeding and the genomic relationship between both parents, the standard deviation in full-sibling cattle and sheep genomic relationships was 0.040 and 0.037 units, respectively. In addition, the intercept value from a linear regression model which regressed each full-sibling genomic relationship on both sire and dam inbreeding, as well as the genomic relationship between the parents, was 0.499 (0.001) for sheep and 0.500 (0.001) for cattle, conforming to the expectation that full-siblings, on average, share 50% of their segregating genome.
    • Behaviour change interventions for responsible antimicrobial use on farms

      Regan, Aine; Burrell, Alison; McKernan, Claire; Martin, Hannah; Benson, Tony; McAloon, Conor; Garcia Manzanilla, Edgar; Dean, Moira; Safefood (the Food Safety Promotion Board); 04–2018 (Biomed Central, 2023-04-03)
      Background In the coming years, major governance changes in the form of policy directives and regulations will catalyse major top-down change with respect to animal health on European farms in an effort to combat the OneHealth threat of antimicrobial resistance. This top-down approach must be met with bottom-up strategies to ensure target actors (namely, farmers and vets) are supported and motivated to change their practices, thus, avoiding unintended consequences of forced change. Although much behavioural research has explored the factors influencing antimicrobial practices on farms, a gap exists translating these findings into evidence-based behaviour change interventions that can be put into practice. The current study aims to fill this gap. It provides insights into identifying, understanding, and changing the behaviours of farmers and veterinarians with respect to the responsible use of antimicrobials in farming. Results Through an inter-disciplinary and multi-actor approach, the study combines scientific knowledge from the behavioural sciences and animal health sciences, coupled with tacit knowledge from a co-design, participatory approach to recommend seven behaviour change interventions that can help to support good practices amongst farmers and vets, with respect to animal health, and reduce the use of antimicrobials on farms. The behaviour change interventions include message framing; OneHealth awareness campaign; specialised communications training; on-farm visual prompts and tools; social support strategies (for both farmers and vets); and antimicrobial use monitoring. The study details each intervention with respect to their evidence base and scientific concept, grounded in behavioural science, along with stakeholder feedback on design and delivery of the interventions. Conclusions These behaviour change interventions can be taken, adapted, and put into practice by the agri-food community to support good animal health practices and responsible antimicrobial use on farms.
    • Green synthesis of nanomaterials for smart biopolymer packaging: challenges and outlooks

      Jafarzadeh, Shima; Nooshkam, Majid; Zargar, Masoumeh; Garavand, Farhad; Ghosh, Sabyasachi; Hadidi, Milad; Forough, Mehrdad (Biomed Central, 2023-02-26)
      Abstract There are several physical and chemical methods for synthesizing nanomaterials, while the most appropriate techniques involve using green chemistry and eco-friendly material. Recently, green synthesized materials for different applications have gained attention as a result of their environmental friendliness and cost-effectiveness. Applying green synthesized nanoparticles (NPS) in food packaging has been extensively investigated. Biopolymers require filler to enhance the optical, barrier, thermal, antimicrobial, and mechanical properties of packaging. Biopolymer packaging incorporated with green synthesized NPs is expected to simultaneously enhance performance while reducing environmental damage. The current review article focuses on biopolymer films with bio (green)-synthesized nanomaterials and their effectiveness in reducing the negative environmental implications of synthetic packaging. It also covers the general concepts of green synthesis of NPs, their production methods, their performance, and characterization, and discusses the potential, performance and recent developments of bio-nanocomposite films/coatings in biodegradable food packaging. Recent reports and trends provide more insight into the impact of green synthesized nanomaterials on food packaging.
    • Insights on the effects of antimicrobial and heavy metal usage on the antimicrobial resistance profiles of pigs based on culture-independent studies

      Ekhlas, Daniel; Argüello, Héctor; Leonard, Finola C.; Garcia Manzanilla, Edgar; Burgess, Catherine; Teagasc Walsh Scholarship Scheme; Spanish Ministry of Education; 2018027; BEAGAL-18–106 (Biomed Central, 2023-02-23)
      Antimicrobial resistance is a global threat to human, animal, and environmental health. In pig production, antimicrobials and heavy metals such as zinc oxide are commonly used for treatment and prevention of disease. Nevertheless, the effects of antimicrobials and heavy metals on the porcine resistome composition and the factors influencing this resistance profile are not fully understood. Advances in technologies to determine the presence of antimicrobial resistance genes in diverse sample types have enabled a more complete understanding of the resistome and the factors which influence its composition. The aim of this review is to provide a greater understanding of the influence of antimicrobial and heavy metal usage on the development and transmission of antimicrobial resistance on pig farms. Furthermore, this review aims to identify additional factors that can affect the porcine resistome. Relevant literature that used high-throughput sequencing or quantitative PCR methods to examine links between antimicrobial resistance and antimicrobial and heavy metal use was identified using a systematic approach with PubMed (NCBI), Scopus (Elsevier), and Web of Science (Clarivate Analytics) databases. In total, 247 unique records were found and 28 publications were identified as eligible for inclusion in this review. Based on these, there is clear evidence that antimicrobial and heavy metal use are positively linked with antimicrobial resistance in pigs. Moreover, associations of genes conferring antimicrobial resistance with mobile genetic elements, the microbiome, and the virome were reported, which were further influenced by the host, the environment, or the treatment itself.
    • Assessing the feasibility, fidelity and acceptability of a behaviour change intervention to improve tractor safety on farms: protocol for the BeSafe tractor safety feasibility study

      Surendran, Aswathi; McSharry, Jenny; Meredith, David; McNamara, John; Bligh, Francis; Meade, Oonagh; O’Hora, Denis; Department of Agriculture, Food and the Marine (Biomed Central, 2023-07-04)
      Background In Ireland, the agriculture sector reports the highest number of fatalities even though farmers constitute only 6% of the working population. Tractor-related behaviours are implicated in 55% of all vehicle work-related fatalities and 25% of reported injuries, and many of these occur in farmyards. There is limited research on the feasibility and acceptability of behaviour change interventions to improve tractor safety. Target behaviours that promote safe operation in farmyards, determining and addressing blind spots of tractors, were identified, and an intervention was developed following the Behaviour Change Wheel Approach. The objective of the study is to examine the feasibility, fidelity and acceptability of a behaviour change intervention to enhance the safe operation of tractors in farmyards with a particular focus on tractor blind spots. Method A single group feasibility study will be undertaken. Approximately 16 farmers from four major farm types will be recruited for the study between August and September 2022. The intervention involves an in-person demo session, facilitated discussion and personalised safety training procedure with safety goals. The study will collect data from participants at three time points: baseline (3–10 days prior to the intervention), during the intervention and at the follow-up session (7–30 days post-intervention). Quantitative data will be collected through a pre-intervention interview and feedback surveys. A pre- and post-intervention qualitative interview will also be conducted with the participants and will be supplemented with qualitative data from recruitment logs, observational memos and logs and feedback from recruiters. Evaluation of the feasibility, acceptability and fidelity of the intervention will be guided by a pre-determined feasibility checklist, fidelity framework and theoretical framework of acceptability, respectively. Interviews will be analysed using the content analysis. Discussion The current study can determine the feasibility and fidelity of delivering a systematic, theoretically driven, tailored behaviour change intervention. It will also assess whether the intervention, its ingredients and delivery are acceptable to the farming population. This study will also inform the development of a future larger trial to test the effectiveness of the intervention. Trial registration ISRCTN Identifier: ISRCTN22219089. Date applied 29 July 2022
    • Comparison of antimicrobial resistant Escherichia coli isolated from Irish commercial pig farms with and without zinc oxide and antimicrobial usage

      Ekhlas, Daniel; Sanjuán, Juan M. O.; Manzanilla, Edgar G.; Leonard, Finola C.; Argüello, Héctor; Burgess, Catherine M.; Teagasc Walsh Scholarship Programme; Spanish Ministry of Education; 2018027; BEAGAL-18-106 (Biomed Central, 2023-02-24)
      Background The prophylactic use of antimicrobials and zinc oxide (ZnO) in pig production was prohibited by the European Union in 2022 due to potential associations between antimicrobial and heavy metal usage with antimicrobial resistance (AMR) and concerns regarding environmental pollution. However, the effects of their usage on the bacterial AMR profiles on commercial pig farms are still not fully understood and previous studies examining the effect of ZnO have reported contrasting findings. The objective of this study was to examine the effects of antimicrobial and ZnO usage on AMR on commercial pig farms. Faecal and environmental samples were taken on 10 Irish commercial farms, of which 5 farms regularly used ZnO and antimicrobials (amoxicillin or sulphadiazine-trimethoprim) for the prevention of disease. The other 5 farms did not use ZnO or any other form of prophylaxis. Escherichia coli numbers were quantified from all samples using non-supplemented and supplemented Tryptone Bile X-glucuronide agar. Results In total 351 isolates were phenotypically analysed, and the genomes of 44 AmpC/ESBL-producing E. coli isolates from 4 farms were characterised using whole-genome sequencing. Phenotypic analysis suggested higher numbers of multi-drug resistant (MDR) E. coli isolates on farms using prophylaxis. Furthermore, farms using prophylaxis were associated with higher numbers of isolates resistant to apramycin, trimethoprim, tetracycline, streptomycin, and chloramphenicol, while resistance to ciprofloxacin was more associated with farms not using any prophylaxis. Thirty-four of the 44 AmpC/ESBL-producing E. coli strains harboured the blaCTX-M-1 resistance gene and were multi drug resistant (MDR). Moreover, network analysis of plasmids and analysis of integrons showed that antimicrobial and biocide resistance genes were frequently co-located on mobile genetic elements, indicating the possibility for co-selection during antimicrobial or biocide usage as a contributor to AMR occurrence and persistence on farms. Conclusions The results of this study showed evidence that antimicrobial and ZnO treatment of pigs post-weaning can favour the selection and development of AMR and MDR E. coli. Co-location of resistance genes on mobile genetic elements was observed. This study demonstrated the usefulness of phenotypic and genotypic detection of antimicrobial resistance by combining sequencing and microbiological methods.
    • HOW CAN ORGANIZATIONS SUPPORT PUBLIC ENGAGEMENT BY RESEARCH SCIENTISTS IN IRELAND? UNDERSTANDING THE PUBLIC ENGAGEMENT BEHAVIOURS AND PERCEPTIONS OF AGRI-FOOD RESEARCHERS

      Caffrey, Máire (2022-11-27)
      Science communication scholars and Research Performing Organizations advocate public engagement (PE) by scientists. EU and Irish research funders see PE as essential to deliver the full benefits of the outputs of funded research for society. PE should be a dialogue between science and society, building trust in science. Scientists are required to participate in public engagement actions. To support and encourage this, it is necessary to characterize the PE behaviors, motivations, and perceptions of scientists. Prior studies identified motivations for, and barriers to, public engagement, and found the level and type of activity is varied. There is evidence of influences from gender, career-status, age, and discipline, but it is not conclusive. There has been little study of scientists’ perceptions of PE in Ireland. To address the knowledge gap, this study surveyed Agri-food researchers in Ireland. The survey gathered data about their participation in PE, their motivations, perceived barriers, their future PE intentions, and identified training and supports needed. The data was analyzed to establish any influences of gender, career-status, age, or discipline. The aim was to establish how organizations can support, encourage, and build public engagement. These scientists have a high level of participation in Public Engagement, with high levels of largely altruistic motivations. However, they are time-poor, and unhappy with the current situation regarding institutional support. They would like PE to be recognized in career progression processes. They need relevant training. Gender, career-status, age, and discipline all influence public engagement behaviors. There is a pronounced gender effect relating to engagement with children. Senior scientists interact more with the media. Agricultural scientists are more motivated to involve the public in their research. Research organizations must recognize and value public engagement in their career assessment processes, provide training and supply supports to encourage more participation and deeper engagement
    • Financial benchmarking on dairy farms: Exploring the relationship between frequency of use and farm performance

      Ramsbottom, George; Läpple, D.; Pierce, K. M. (Elsevier, 2021-03-31)
      The importance of financial benchmarking has increased in recent years as European Union milk quota abolition has facilitated rapid change in the dairy sector. This study evaluates the association between usage frequency of a financial benchmarking tool [Profit Monitor (PM)] and farm changes on spring-calving pasture-based dairy farms. To this end, physical and financial data for 5,945 dairy farms, representing 20,132 farm years, for the years 2010 to 2018 were used. Farms were categorized by frequency of annual financial benchmarking over the 9-yr period into frequent PM users (7–9 yr), infrequent PM users (4–6 yr), low PM users (1–3 yr), and nonusers. We use a mixed model framework and econometric models to characterize farms and to explore characteristics and determinants of economic performance and user groups. The most frequent users of the financial benchmarking tool had the greatest increase in intensification (measured by change in farm stocking rate), productivity (measured by change in milk production per hectare), and financial performance (measured by change in farm gross output and net profit per hectare) across the study period. Infrequent and low PM users of the benchmarking tool were intermediate for all variables measured, whereas nonusers had the least change. Empirical results indicated that economic performance was positively associated with dairy specialization and pasture utilization for all groups. Despite considerable fluctuations over the observation period, the overall change in total farm net profit between 2010 and 2018 was greatest for the frequent PM users (an increase of 70%, or €37,639), followed by farms in the infrequent PM user category (a 71% increase corresponding to an increase of €28,008 in net profit); meanwhile, low PM user and nonuser categories showed increases of 69% (€26,270) and 42% (€10,977), respectively. The results of this study also clearly indicated the existence of a strong positive association between frequency of financial benchmarking and greater technical and financial efficiency. The econometric analysis revealed that financial benchmarking users are more likely than nonusers to have larger herds, and that regional differences exist in usage rates. Finally, the study concludes by suggesting that the development of simplified financial benchmarking technologies and their support are required to increase benchmarking frequency, which may also help to facilitate a more sustainable and resource efficient dairy industry.
    • Blood and faecal biomarkers to assess dietary energy, protein and amino acid efficiency of utilization by growing and finishing pigs

      Camp Montoro, Jordi; Solà-Oriol, David; Muns, Ramon; Gasa, Josep; Llanes, Núria; Garcia Manzanilla, Edgar; Teagasc Walsh Scholarship Scheme; 0415 (Biomed Central, 2022-07-04)
      Background Diet evaluation and optimization is a slow and expensive process and it is not possible to do it at a farm level. This study aimed to use the blood serum metabolite (BSM) and faecal volatile fatty acid (VFA) profiles as potential biomarkers to identify changes in protein, amino acid and energy dietary content in growing and finishing pig diets at farm level. Results Two studies were conducted. The first study (S1) included 20 pens of 11 pigs (87.0 ± 4.10 kg; 18 weeks old) assigned to 5 diets: control (C1), high or low crude protein (HP1 and LP1, respectively), and high or low net energy (HE1 and LE1, respectively). The second study (S2) included 28 pens of 11 pigs (41.3 ± 2.60 kg; 12 weeks old) assigned to 7 diets: control (C2), high or low crude protein (HP2 and LP2, respectively), high or low amino acid (HA2 and LA2, respectively), and high or low net energy (HE2 and LE2, respectively). Pigs were followed for 10 (S1) and 20 (S2) days, and blood and faecal samples were collected at 20 (S1) and 14 (S2) weeks of age. Data were analysed using general linear models and receiver operating characteristic curve analysis. Urea nitrogen showed the best results as a biomarker. Urea nitrogen was higher in pigs fed high protein diets, HP1 (13.6 ± 0.95 mg/dL) and HP2 (11.6 ± 0.61), compared to those fed low protein diets, LP1 (6.0 ± 0.95) and LP2 (5.2 ± 0.61; P < 0.001), showing good discrimination ability (Area under the curve (AUC) = 98.4 and 100%, respectively). These differences were not observed between diets LA2 (6.5 ± 0.61) and HA2 (8.7 ± 0.61; P > 0.05; AUC = 71.9%), which were formulated based on the ideal protein profile but with no excess of protein. Creatinine, triglycerides, branched-chain fatty acids, albumin, propionic acid, and cholesterol showed differences between at least 2 diets but only in one of the studies. Conclusions Urea nitrogen showed high accuracy to detect excess of crude protein in growing and finishing pig diets. Other biomarkers like BCFA showed promising results and need to be further studied.
    • Modelling transmission of Mycobacterium avium subspecies paratuberculosis between Irish dairy cattle herds

      Biemans, Floor; Tratalos, Jamie; Arnoux, Sandie; Ramsbottom, George; More, Simon J.; Ezanno, Pauline; Department of Agriculture, Food and the Marine; NexusMAP (Biomed Central, 2022-06-22)
      Bovine paratuberculosis is an endemic disease caused by Mycobacterium avium subspecies paratuberculosis (Map). Map is mainly transmitted between herds through movement of infected but undetected animals. Our objective was to investigate the effect of observed herd characteristics on Map spread on a national scale in Ireland. Herd characteristics included herd size, number of breeding bulls introduced, number of animals purchased and sold, and number of herds the focal herd purchases from and sells to. We used these characteristics to classify herds in accordance with their probability of becoming infected and of spreading infection to other herds. A stochastic individual-based model was used to represent herd demography and Map infection dynamics of each dairy cattle herd in Ireland. Data on herd size and composition, as well as birth, death, and culling events were used to characterize herd demography. Herds were connected with each other through observed animal trade movements. Data consisted of 13 353 herds, with 4 494 768 dairy female animals, and 72 991 breeding bulls. We showed that the probability of an infected animal being introduced into the herd increases both with an increasing number of animals that enter a herd via trade and number of herds from which animals are sourced. Herds that both buy and sell a lot of animals pose the highest infection risk to other herds and could therefore play an important role in Map spread between herds.
    • Lameness prevalence and management practices on Irish pasture-based dairy farms

      Browne, N.; Hudson, C. D.; Crossley, R. E.; Sugrue, K.; Kennedy, Emer; Huxley, J. N.; Conneely, Muireann; Teagasc Walsh Scholarship Programme; Dairy Research Ireland (Biomed Central, 2022-06-08)
      Background Lameness is a painful disease, which negatively impacts dairy cow production and welfare. The aim of this observational study was to determine herd lameness prevalence, describe current lameness management practices and identify the presence of established risk factors for lameness on Irish pasture-based dairy farms. Farms were visited once during grazing (99 farms) and again during housing (85 farms). Lameness scoring was carried out at each visit (AHDB 0–3 scale); cows were classified as lame if they scored two or three. Farm management practices and infrastructure characteristics were evaluated via farmer questionnaires and direct measurements of farm infrastructure. Results Median herd-level lameness prevalence was 7.9% (interquartile range = 5.6 – 13.0) during grazing and 9.1% (interquartile range = 4.9 – 12.0) during housing; 10.9% of cows were lame at a single visit and 3.5% were lame at both visits (chronically lame or had a repeat episode of lameness). Fifty-seven percent of farmers were not familiar with lameness scoring and only one farm carried out lameness scoring. Only 22% of farmers kept records of lame cows detected, and 15% had a lameness herd health plan. Twenty-eight percent of farmers waited more than 48 h to treat a lame cow, and 21% waited for more than one cow to be identified as lame before treating. Six percent of farmers carried out routine trimming and 31% regularly footbathed (> 12 times per year). Twelve percent put severely lame cows in a closer paddock and 8% stated that they used pain relief to treat severely lame cows. Over 50% of farms had at least one cow track measurement that was classified as rough or very rough, and cow tracks were commonly narrow for the herd size. On 6% of farms, all cubicle beds were bare concrete (no matting or bedding) and on a further 6% of farms, there was a combination of cubicles with and without matting or bedding. On 56% of farms, all pens contained less than 1.1 cubicles per cow and on 28% of farms, a proportion of pens contained less than 1.1 cubicles per cow. Conclusions Overall, this study identified infrastructure and management practices which could be improved upon. The comparatively low lameness prevalence demonstrated, compared to fully housed systems, also highlights the benefits of a pasture-based system for animal welfare; however, there remains scope for improvement.
    • Factors affecting retention of veterinary practitioners in Ireland: a cross-sectional study with a focus on clinical practice

      Ryan, Eoin G.; Beatty, Stephen H.; Gray, Elizabeth; Field, Niamh; Liston, Rory; Rhodes, Victoria; Donlon, John; Progressive Veterinary Network (Biomed Central, 2022-06-07)
      Background Retention of veterinary practitioners has arisen as a significant problem in recent years in Ireland. No prior Irish peer-reviewed publications have addressed this problem. An online questionnaire was available through social media and via email to Irish vets from January to November 2019. The aim of this survey was to ascertain the factors contributing to the problem of vet retention in Ireland. Results A total of 370 eligible responses were received. The median age of respondents was 31 and the gender balance was 250 females (68%) to 118 males (32%). The majority of respondents worked in clinical practice 322 (89%), with 138 (42.8%) in mixed practice, 115 (35.7%) in small animal practice, 49 (15.2%) solely with farm animals and 20 (6.2%) in equine practice. Fifty-four percent of respondents described themselves as likely to be leaving their current job within two years and 32.8% as being likely to leave the profession. In total, 44 variables were assessed by univariate analysis and 27 variables were significantly (P < 0.05) associated with the likelihood of a respondent leaving their current job within 2 years (LCJ2), as a proxy measure of the problem of retention. All variables significant on univariate analysis at P < 0.2 were included in a multivariable logistic regression model. Factors associated with LCJ2 included satisfaction with work-life balance (Odds Ratio (OR) 0.33); satisfaction with working hours (OR 0.2); number of years qualified (OR 0.91); position as a practice owner/partner/director (OR 0.15); and log10salary (OR 0.03). Four variables were retained in a separate multivariable linear regression model as significant (P < 0.05) predictors of log10salary. Log10salary increased with years qualified. Males had an increased salary compared to females irrespective of years qualified. Part-time employees, vets on maternity leave or postgraduate vets had a lower log10salary. Compared to veterinary employees, self-employed or locum vets had a higher log10salary. Conclusions Veterinary employers should consider salary, working hours and the facilitation of a good work-life balance in order to successfully retain veterinary employees. The significant difference in salaries currently offered to male and female vets, and the high percentage of respondents considering leaving the profession, are important findings and warrant further investigation.
    • Mycobacterium avium subspecies paratuberculosis infection in cattle – a review in the context of seasonal pasture-based dairy herds

      Field, Niamh L.; McAloon, Conor G.; Gavey, Lawrence; Mee, John F; Teagasc (Biomed Central, 2022-05-20)
      Johne’s disease is an infectious disease affecting cattle, other ruminants and non-ruminant wildlife worldwide, caused by Mycobacterium avium subspecies paratuberculosis (MAP). This review provides an up-to-date concise overview of the pathogenesis of MAP, the significance of Johne’s disease in cattle and the use of diagnostic testing at both animal and herd level in the context of seasonal pasture-based herds. While MAP can only replicate intracellularly, the bacterium is sufficiently robust to survive for months in the environment. Transmission of MAP is mostly via the faecal-oral route, however in-utero transmission in also possible. The bacteria evade the immune system by persisting in macrophages in the small intestine submucosa, with this latent stage of infection lasting, in most cases, for at least two years before bacterial shedding and clinical signs begin. The slowly progressive nature of MAP infection, poor performance of diagnostic tests and management systems that expose susceptible calves to infection make control of Johne’s disease challenging, particularly in seasonal calving herds. Testing of individual animals provides little assurance for farmers and vets due to the poor sensitivity and, in the case of ELISA, imperfect specificity of the available tests. Repeated herd-level testing is utilised by the IJCP to detect infected herds, identify high risk animals, and provide increasing confidence that test-negative herds are free of infection. The IJCP aims to control the spread of Johne’s disease in cattle in Ireland, in order to protect non-infected herds, limit the economic and animal health impact of the disease, improve calf health and reassure markets of Johne’s disease control in Ireland.
    • Antimicrobial resistance in Escherichia coli isolated from on-farm and conventional hatching broiler farms in Ireland

      Byrne, Noelle; O’Neill, Lorcan; Calderon Diaz, Julia; Garcia Manzanilla, Edgar; Vale, Ana P.; Leonard, Finola C.; Department of Agriculture, Food, and the Marine; 15 S 676 (Biomed Central, 2022-04-22)
      Background On-farm hatching (OH) systems are becoming more common in broiler production. Hatching conditions differ from conventional farms as OH chicks avoid exposure to handling, transport, post-hatch water and feed deprivation. In contrast, chicks in conventional hatching conditions (CH) are exposed to standard hatchery procedures and transported post hatching. The objectives of this pilot study were to investigate the prevalence and frequency of Escherichia coli resistant to antimicrobials, including presumptive ESBL/AmpC-producing E. coli, isolated from environmental and faecal samples from OH versus CH hatching systems, and to investigate the presence of ESBL/AmpC-producing encoding genes. Results Environmental samples were collected from one flock in 10 poultry farms (5 OH farms, 5 CH farms) on day 0 post disinfection of the facilities to assess hygiene standards. On D10 and D21 post egg/chick arrival onto the farm, samples of faeces, boot swabs and water drinker lines were collected. E. coli were isolated on MacConkey agar (MC) and MacConkey supplemented with cefotaxime (MC+). Few E. coli were detected on D0. However, on D10 and D21 E. coli isolates were recovered from faeces and boot swabs. Water samples had minimal contamination. In this study, 100% of cefotaxime resistant E. coli isolates (n=33) detected on selective media and 44% of E. coli isolates (84/192) detected on nonselective media were multidrug resistant (MDR). The antimicrobial resistance (AMR) genotype for the 15 ESBL/AmpC producing isolates was determined using multiplex PCR. Six of these were selected for Sanger sequencing of which two were positive for blaCMY-2, two for blaTEM-1 and two were positive for both genes. Conclusions There was no difference in E. coli isolation rates or prevalence of AMR found between the OH versus CH systems, suggesting that the OH system may not be an additional risk of resistant E. coli dissemination to broilers compared to the CH systems. The frequency of β-lactam resistant E. coli in boot swab and faeces samples across both OH (24/33 (73%)) and CH (9/33 (27%)) systems may indicate that hatcheries could be a reservoir and major contributor to the transmission of AMR bacteria to flocks after entry to the rearing farms.
    • Sperm DNA methylation patterns at discrete CpGs and genes involved in embryonic development are related to bull fertility

      Štiavnická, Miriama; Chaulot-Talmon, Aurélie; Perrier, Jean-Philippe; Hošek, Petr; Kenny, David A.; Lonergan, Patrick; Kiefer, Hélène; Fair, Sean; Science Foundation Ireland; 16/IA/4474 (Biomed Central, 2022-05-18)
      Background Despite a multifactorial approach being taken for the evaluation of bull semen quality in many animal breeding centres worldwide, reliable prediction of bull fertility is still a challenge. Recently, attention has turned to molecular mechanisms, which could uncover potential biomarkers of fertility. One of these mechanisms is DNA methylation, which together with other epigenetic mechanisms is essential for the fertilising sperm to drive normal embryo development and establish a viable pregnancy. In this study, we hypothesised that bull sperm DNA methylation patterns are related to bull fertility. We therefore investigated DNA methylation patterns from bulls used in artificial insemination with contrasting fertility scores. Results The DNA methylation patterns were obtained by reduced representative bisulphite sequencing from 10 high-fertility bulls and 10 low-fertility bulls, having average fertility scores of − 6.6 and + 6.5%, respectively (mean of the population was zero). Hierarchical clustering analysis did not distinguish bulls based on fertility but did highlight individual differences. Despite this, using stringent criteria (DNA methylation difference ≥ 35% and a q-value < 0.001), we identified 661 differently methylated cytosines (DMCs). DMCs were preferentially located in intergenic regions, introns, gene downstream regions, repetitive elements, open sea, shores and shelves of CpG islands. We also identified 10 differently methylated regions, covered by 7 unique genes (SFRP1, STXBP4, BCR, PSMG4, ARSG, ATP11A, RXRA), which are involved in spermatogenesis and early embryonic development. Conclusion This study demonstrated that at specific CpG sites, sperm DNA methylation status is related to bull fertility, and identified seven differently methylated genes in sperm of subfertile bulls that may lead to altered gene expression and potentially influence embryo development.
    • Ewe breed differences in the cervical transcriptome at the follicular phase of a synchronised oestrous cycle

      Abril-Parreño, Laura; Meade, Kieran G.; Krogenæs, Anette K.; Druart, Xavier; Cormican, Paul; Fair, Sean; European Research Area Network; Department of Agriculture, Food and the Marine; Teagasc; Research Council of Norway; et al. (Biomed Central, 2022-05-11)
      Background Cervical artificial insemination (AI) with frozen-thawed semen results in unacceptably low pregnancy rates internationally. The exception is in Norway, where vaginal deposition of frozen-thawed semen to a natural oestrous routinely yields pregnancy rates in excess of 70%. Previous studies by our group has demonstrated that this is due to differences in cervical sperm transport. However, a potentially important contributory factor is that ewes are inseminated to a natural oestrous in Norway but to a synchronised oestrous across most of the rest of the world. In this study, we interrogated the gene expression of the sheep cervix of four ewe breeds with known differences in pregnancy rates following cervical AI using frozen-thawed semen under the effect of exogenous hormones to synchronise the oestrous cycle. These four ewe breeds (n = 8 to 11 ewes per breed) are from two countries: Ireland (Belclare and Suffolk; medium and low fertility, respectively) and Norway (Norwegian White Sheep (NWS) and Fur; both with high fertility compared to the Irish ewe breeds). Results RNA extracted from cervical biopsies collected from these breeds was analysed by RNA-sequencing and differential gene expression analysis. Using the low-fertility Suffolk breed as a reference level; 27, 1827 and 2641 genes were differentially expressed in Belclare, Fur and NWS ewes, respectively (P <  0.05 and FC > 1.5). Gene ontology (GO) analysis revealed that Fur and NWS had an up-regulation of enriched pathways involved in muscle contraction and development compared to Suffolk. However, there was a down-regulation of the immune response pathway in NWS compared to Suffolk. In addition, GO analysis showed similar expression patterns involved in muscle contraction, extracellular matrix (ECM) development and cell-cell junction in both Norwegian ewe breeds, which differed to the Irish ewe breeds. Conclusions This novel study has identified a number of conserved and breed-specific biological processes under the effect of oestrous synchronisation that may impact cervical sperm transport during the follicular phase of the reproductive cycle.
    • Engaging with selective dry cow therapy: understanding the barriers and facilitators perceived by Irish farmers

      Huey, Sarah; Kavanagh, Michaela; Regan, Aine; Dean, Moira; McKernan, Clare; McCoy, Finola; Ryan, Eoin G.; Caballero-Villalobos, Javier; McAloon, Catherine I.; Animal Health Ireland (Biomed Central, 2021-10-23)
      Background Selective dry cow therapy (SDCT) is widely promoted in dairy farming as a method to reduce antimicrobial usage. New legislation introduced by the European Union will restrict and regulate the prophylactic and metaphylactic use of antibiotics from January 2022. Blanket dry cow therapy continues to be a practice engaged in by many farmers in Ireland and for many of these farmers, moving towards SDCT would require a significant infrastructural, behavioural and/or cultural change on their farm. Existing research has reported the important need to understand farmers’ motivations to initiate any substantial behaviour change. However, it is currently unknown what farmers know, think and believe about SDCT in Ireland. The aim of this study was to use qualitative methods to explore what barriers and facilitators farmers perceived to exist with SDCT and explore if they had chosen to implement SDCT after voluntarily participating in a funded dry cow consult with a trained veterinarian, with the objective of maximising the dry period udder health performance and moving safely to SDCT. Results In this study, 19 farmers were contacted, and telephone interviews were conducted regarding farmers’ beliefs about the consequences of SDCT. Audio recordings were professionally transcribed verbatim and analysed qualitatively using an inductive thematic analysis. The analysis identified 6 barriers and 6 facilitators to implementing SDCT. A significant fear of increasing mastitis incidence was evident that caused reluctance towards SDCT and reliance on antibiotics. Mixed perceptions on SDCT, infrastructure limitations, a perceived lack of preventive advice as well as peer influence were presented as barriers to SDCT. Farmers can build confidence when a graded approach to SDCT is implemented, which could help overcome the fear of SDCT and reliance on antibiotics. Regulatory pressure, high standards of farm hygiene and use of targeted veterinary consults were found to facilitate SDCT. Education was suggested to motivate farmers in the future uptake of SDCT. Despite cited negative influences, peer influence can be utilised to encourage the farming community. Conclusions This study prioritises areas to facilitate the major behaviour change required as a dairy industry in order to move from blanket dry cow therapy to SDCT.
    • Horn bud size of dairy-bred and suckler-bred calves at time of disbudding

      Marquette, Gabriela A.; McGee, Mark; Fisher, Andrew D.; Stanger, Kelly; Argüello, Anastasio; Earley, Bernadette; Teagasc Walsh Scholarship Programme (Biomed Central, 2021-06-16)
      Background Hot-iron disbudding is a common management procedure to prevent horn growth in calves. The study objective was to examine effect of age, breed and sex on horn bud size of dairy-bred and suckler-bred calves at time of disbudding. Results The left and right horn bud size (diameter and height in mm) of 279 calves, including dairy-bred Holstein-Friesian (Male (M) = 88) and 191 suckler-bred (86 Charolais, CH; (M = 39, Female (F) = 47), 67 Limousin, LM; (M = 32, F = 35) and 38 Simmental, SI; (M = 22, F = 16) sired)) was measured using a digital calliper at time of disbudding. Calves were retrospectively assigned to two age categories at time of disbudding: 1), 14 to 28 days (d) old and 2), 29 to 60 d old. Holstein-Friesian M calves had a greater horn bud diameter (16.97 v.14.45 mm) and height (7.79 v. 5.00 mm) compared to suckler-bred M calves (P < 0.01), with no difference (P > 0.05) among the suckler-bred calves. Suckler-bred M calves had a greater horn bud diameter (14.46 vs 13.29 mm) and height (5.01 vs 3.88 mm) compared to suckler-bred F calves (P < 0.05). The slopes of the lines of best fit show that horn bud diameter and height increased with age (P < 0.05) for HF, SI male and CH female calves while there was no relationship with age (P > 0.05) for CH and LM male calves, or for SI and LM female calves. Linear regression of age with diameter and with height for each breed and sex showed high variability in the data as indicated by R-squared values ranging from 0.003–0.41 indicating that in the case of the diameter and the height, the weight of the fitting effect was poor. Conclusions Calf age is not a good predictor of horn bud size and recommendations for the disbudding of calves should be based on horn bud size and not on age. The implications of these findings are that calves should be disbudded while horn development is still at the bud stage and when the bud is large enough to be easily palpable/visible, but not so large that disbudding could lead to severe tissue trauma.