### Browse by

This collection contains articles published in the Open Access Biomed Central journals by Teagasc authors.

### Recent Submissions

• #### Engaging with selective dry cow therapy: understanding the barriers and facilitators perceived by Irish farmers

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

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.
• #### Genetic and economic benefits of foreign sire contributions to a domestic sheep industry; including an Ireland-New Zealand case study

Background Importation of foreign genetics is a widely used genetic improvement strategy. However, even if the foreign genetic merit is currently greater than the domestic genetic merit, differences in foreign and domestic trends mean that the long-term competitiveness of an importation strategy cannot be guaranteed. Gene flow models are used to quantify the impact that a specific subpopulation, such as foreign genetics, can have over time on the genetic or economic benefit of a domestic industry. Methods We used a deterministic recursive gene flow model to predict the commercial performance of lambs born across various subpopulations. Numerous breeding strategies were evaluated by varying market share, proportions of rams selected for mating, genetic trend, superiority of foreign genetics over domestic genetics and frequency of importation. Specifically, an Ireland-New Zealand case study was simulated to quantify the potential gain that could be made by using foreign sire contributions (New Zealand) in a domestic sheep industry (Ireland). Results Genetic and economic gains were generated from alternative breeding strategies. The ‘base scenario’ (i.e. representing the current industry) predicted an average genetic merit value of €2.51 for lambs born and an annualised cumulative benefit of €45 million (m) after 20 years. Maximum genetic (€9.45 for lambs born) and economic (annualised cumulative benefit of €180 m after 20 years) benefits were achieved by implementing the ‘PRO-intense-market scenario’ which involved shifting market share away from conservative domestic breeders and reducing the proportion of rams that were selected for mating by progressive domestic breeders from the top 40% to the top 20%, without the use of any foreign genetics. The ‘PROFOR scenario’, which considered the use of foreign and progressive domestic genetics, predicted an average genetic merit value of €7.37 for lambs born and an annualised cumulative benefit of €144 m, after 20 years. Conclusions Our results demonstrate that there is opportunity for a domestic industry to increase industry benefits without the use of foreign genetics but through an attempt to shift the market share away from conservative domestic breeders towards progressive domestic breeders. However, the importation and use of progressive foreign genetics may be an effective method to trigger a change in behaviour of conservative domestic breeders towards the use of progressive genetics.
• #### MAP, Johne’s disease and the microbiome; current knowledge and future considerations

Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne’s disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the animal, it is a huge financial burden for associated industries. Efforts to control MAP infection and Johne’s disease are complicated due to difficulties of diagnosis in the early stages of infection and challenges relating to the specificity and sensitivity of current testing methods. The methods that are available contribute to widely used test and cull strategies, vaccination programmes also in place in some countries. Next generation sequencing technologies have opened up new avenues for the discovery of novel biomarkers for disease prediction within MAP genomes and within ruminant microbiomes. Controlling Johne’s disease in herds can lead to improved animal health and welfare, in turn leading to increased productivity. With current climate change bills, such as the European Green Deal, targeting livestock production systems for more sustainable practices, managing animal health is now more important than ever before. This review provides an overview of the current knowledge on genomics and detection of MAP as it pertains to Johne’s disease.
• #### Why do Irish pig farmers use medications? Barriers for effective reduction of antimicrobials in Irish pig production

Abstract Background In addressing the threat of antimicrobial resistance, it is critical to understand the barriers to the uptake of strategies for the reduction of antimicrobial use (AMU) in the pig industry. In several EU countries, factors such as education level, habits and social pressures are recognised as affecting farmers’ decision-making process in relation to AMU. However, there is a lack of information on the Irish scenario. The aim of this study was to investigate pig farmers’ perspectives and their behaviour towards AMU to identify potential barriers to effectively reduce AMU in Irish pig production. We conducted face-to-face semi-structured interviews with 30 pig farmers, 5 pig veterinarians and 4 focus groups of pig farm personnel. We employed qualitative analyses to explore the objective of the study. Results Qualitative analysis revealed six convergent themes as potential barriers: perceptions about the need for AMU on farm, concept of animal welfare and associated management practices, legislation, culture, economics and standards of communication/type of advice-network. Overall, pig farmers believed that there is poor communication between stakeholders (i.e. farmers, vets and advisors) and a lack of reliable people to approach for advice. They considered themselves as operating responsibly in terms of AMU compared to their national and international colleagues and expressed the importance of a so-called ‘Irish solution’ to the problem of AMU because it was associated with what ‘has always been done’ and was therefore considered reliable and safe. Conclusions Barriers and challenges were in line with those identified in other EU countries highlighting similarities in behavioural and attitudinal patterns among pig farmers. Overall, farmers appeared to be more likely to rely on previous experiences or to wait for an imposed change (e.g. legislation) instead of taking personal action. Thus, considerable behavioural and attitudinal changes are needed to adopt a more responsible AMU in Irish pig production and to develop effective intervention strategies.
• #### Molecular-genetic characterization of human parvovirus B19 prevalent in Kerala State, India

Background Human parvovirus B19V is a DNA virus, and a member of the family Parvoviridae, that causes various clinical manifestations, from asymptomatic to persistent infection that is associated with different autoimmune diseases. The parvovirus B19 evolves with a very high mutation rate that is closer to those of existing RNA viruses. Globally circulating B19V is currently classified into three genotypes, but their distribution is not spatially and temporally correlated. Except for a few recent reports on B19V entry into the human host and its genetic diversity, there is a lack of sufficient studies on this virus from distinct geographical locations and no clear understanding of its evolution has been documented. Methods To better understand the evolution of the Human parvo B19V virus from India's southern part, a geographically distinct location with no reports of B19V genomes, we have screened for B19V in 456 suspected cases using VP1/2 surface marker genes, and its characteristics were studied in detail. Amongst 456 clinically suspected B19V samples, 7.2% (33/456) were found positive by nested PCR (nPCR) were subsequently validated by real-time PCR, Sanger sequencing, and metagenome analysis. Results Human parvovirus B19 infection was shown among 33 of 456 patients when tested by nPCR; 30 among these were also positive by qPCR and were subsequently confirmed by sequencing 75% nPCR positive samples and 76% qPCR positive samples were from patients with age. ≥ 50 years respectively (Additional file 1: Table S1). The complete VP1/2 gene assembly from the South Indian strain showed three novel mutations (T122A, V128I, I283V), which might significantly impact the stability and virulence of the B19V virus circulating in this part of the world. These mutations might be crucial for its adaptive evolutionary strategies facilitating the spread and infectivity potential of the virus. In maximum likelihood phylogeny of VP1/2 sequences, the South Indian B19V strain forms a separate clade closer to the existing genotype two strains circulating worldwide. Conclusion Our study contributes to a better understanding of the human parvovirus's genetic and evolutionary characteristics in South India. Also, it highlights the possibility that a positive selection pressure acting on VP1/2 could increase the survival and replication capabilities of the viruses.
• #### The effect of disinfectant ingredients on teat skin bacteria associated with mastitis in Irish dairy herds

Background Teat disinfection is an important step in the control of mastitis within a dairy herd. The objective of this study was to evaluate the effectiveness of 96 commercially available teat disinfectant products in Ireland against bacterial isolates on teat skin. Teat disinfection products were applied to the teats of seventeen Holstein–Friesian cows. A split-udder model was used where one cow received two different teat disinfection products on each day. A composite swab sample was taken of the left teats and the right teats before and after teat disinfectant application. Swab samples were plated onto 3 different selective agars to enumerate bacterial counts of streptococcal, staphylococcal and coliform isolates. Results Streptococcal isolates were the most prominent bacterial group recovered on teat swabs taken before the application of a teat disinfection product (55.0%), followed by staphylococcal isolates (41.3%) and coliform isolates (3.7%). Products were reclassified by active ingredients (n = 9) for analysis. These ingredient groups included; chlorhexidine, chlorine dioxide, diamine, iodine, iodine and lactic acid, lactic acid, lactic acid and chlorhexidine, lactic acid and hydrogen peroxide, and lactic acid and salicylic acid. The ingredient group, chlorine dioxide, resulted in comparable reductions to the iodine group for streptococcal isolates. The ingredient group, iodine combined with lactic acid, resulted in the greatest reduction of staphylococcal isolates. When observing products individually, a product containing 1.6% w/w lactic acid combined with hydrogen peroxide was the most effective at reducing streptococcal isolates on the teat skin, whereas a product containing lactic acid combined with 0.6% w/w chlorhexidine was the most effective against staphylococcal isolates. Minor differences were observed regarding the relationship between effectiveness and active ingredient concentration between products. Conclusions This study suggests that some teat disinfectant products achieve a higher reduction in bacterial levels against different specific bacterial groups on teat skin than other products. Therefore, when choosing a teat disinfectant product, the bacteria in the dairy herds’ environment should be considered. Further studies are necessary to evaluate products efficacy against new IMIs and any possible effects on teat skin condition.
• #### Effect of a single, oral administration of selenitetriglycerides, at two dose rates, on blood selenium status and haematological and biochemical parameters in Holstein-Friesian calves

Background Selenitetriglycerides are biologically active, organic forms of selenium formed as a result of the modification of selenic acid and sunflower oil. Studies in rats have shown that they are well absorbed and of low toxicity. There are no published studies on selenitetriglycerides supplementation in calves. Results In this study, selenitetriglycerides were administered once orally on the 2nd day of life at a dose of 0.5 or 1 mg Se/kg body weight to each of six Holstein-Friesian calves while six control calves were not supplemented. Blood for determination of selenium concentration, glutathione peroxidase activity, haematological parameters, aspartate aminotransferase, creatine kinase, and lactate dehydrogenase activities and glucose, total protein, albumin, triglycerides, cholesterol, urea, and creatinine concentration was collected before supplementation (day 0) and 1, 2, 5, 10 and 14 days after supplementation. Selenitetriglycerides administration increased (P < 0.01) serum selenium concentration in supplemented calves as early as day1, from a mean of 63.4 to 184.22 µg/l in calves receiving selenium at a dose of 0.5 mg/kg BW, and from 63.17 to 200.33 µg/l in calves receiving 1 mg/kg. Serum selenium concentrations remained significantly higher compared to the control group throughout the experiment. Glutathione peroxidase activity was higher in supplemented than control calves, significantly so in animals receiving the 1 mg/kg dose of Se on the 10th and 14th days (P < 0.05). There were no significant differences in the haematological and biochemical parameters between the groups. Conclusions This experiment showed that supplementation with selenitetriglycerides could significantly improve blood selenium status in calves without adverse effects on haematological or biochemical parameters. These findings are essential prerequisites for future studies on selenitetriglycerides supplementation to manage clinical selenium deficiency in calves.
• #### Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

Background The gut phageome comprises a complex phage community of thousands of individual strains, with a few highly abundant bacteriophages. CrAss-like phages, which infect bacteria of the order Bacteroidales, are the most abundant bacteriophage family in the human gut and make an important contribution to an individual’s core virome. Based on metagenomic data, crAss-like phages form a family, with four sub-families and ten candidate genera. To date, only three representatives isolated in pure culture have been reported: ΦcrAss001 and two closely related phages DAC15 and DAC17; all are members of the less abundant candidate genus VI. The persistence at high levels of both crAss-like phage and their Bacteroidales hosts in the human gut has not been explained mechanistically, and this phage-host relationship can only be properly studied with isolated phage-host pairs from as many genera as possible. Results Faeces from a healthy donor with high levels of crAss-like phage was used to initiate a faecal fermentation in a chemostat, with selected antibiotics chosen to inhibit rapidly growing bacteria and selectively enrich for Gram-negative Bacteroidales. This had the objective of promoting the simultaneous expansion of crAss-like phages on their native hosts. The levels of seven different crAss-like phages expanded during the fermentation, indicating that their hosts were also present in the fermenter. The enriched supernatant was then tested against individual Bacteroidales strains isolated from the same faecal sample. This resulted in the isolation of a previously uncharacterised crAss-like phage of candidate genus IV of the proposed Alphacrassvirinae sub-family, ΦcrAss002, that infects the gut commensal Bacteroides xylanisolvens. ΦcrAss002 does not form plaques or spots on lawns of sensitive cells, nor does it lyse liquid cultures, even at high titres. In keeping with the co-abundance of phage and host in the human gut, ΦcrAss002 and Bacteroides xylanisolvens can also co-exist at high levels when co-cultured in laboratory media. Conclusions We report the isolation and characterisation of ΦcrAss002, the first representative of the proposed Alphacrassvirinae sub-family of crAss-like phages. ΦcrAss002 cannot form plaques or spots on bacterial lawns but can co-exist with its host, Bacteroides xylanisolvens, at very high levels in liquid culture without impacting on bacterial numbers. Video abstract
• #### Bovine milk somatic cell transcriptomic response to Staphylococcus aureus is dependent on strain genotype

Background Mastitis is an economically important disease of dairy cows with Staphylococcus aureus a major cause worldwide. Challenge of Holstein-Friesian cows demonstrated that S. aureus strain MOK124, which belongs to Clonal Complex (CC)151, caused clinical mastitis, while strain MOK023, belonging to CC97, caused mild or subclinical mastitis. The aim of this study was to elucidate the molecular mechanisms of the host immune response utilising a transcriptomic approach. Milk somatic cells were collected from cows infected with either S. aureus MOK023 or MOK124 at 0, 24, 48, 72 and 168 h post-infection (hpi) and analysed for differentially expressed (DE) genes in response to each strain. Results In response to MOK023, 1278, 2278, 1986 and 1750 DE genes were found at 24, 48, 72 and 168 hpi, respectively, while 2293, 1979, 1428 and 1544 DE genes were found in response to MOK124 at those time points. Genes involved in milk production (CSN1, CSN10, CSN1S2, CSN2, a-LACTA and PRLR) were downregulated in response to both strains, with a more pronounced decrease in the MOK124 group. Immune response pathways such as NF-κB and TNF signalling were overrepresented in response to both strains at 24 hpi. These immune pathways continued to be overrepresented in the MOK023 group at 48 and 72 hpi, while the Hippo signalling, extracellular matrix interaction (ECM) and tight junction pathways were overrepresented in the MOK124 group between 48 and 168 hpi. Cellular composition analysis demonstrated that a neutrophil response was predominant in response to MOK124, while M1 macrophages were the main milk cell type post-infection in the MOK023 group. Conclusions A switch from immune response pathways to pathways involved in maintaining the integrity of the epithelial cell layer was observed in the MOK124 group from 48 hpi, which coincided with the occurrence of clinical signs in the infected animals. The higher proportion of M1 macrophages in the MOK023 group and lack of substantial neutrophil recruitment in response to MOK023 may indicate immune evasion by this strain. The results of this study highlight that the somatic cell transcriptomic response to S. aureus is dependent on the genotype of the infecting strain.
• #### A pilot study on the prevalence of lice in Irish beef cattle and the first Irish report of deltamethrin tolerance in Bovicola bovis

Background Pediculosis in cattle causes significant itching, irritation and stress to the animal, often resulting in skin damage and poor coat condition. The control of bovine pediculosis in Ireland is based predominantly on commercial insecticides belonging to one of two chemical classes, the synthetic pyrethroids and the macrocyclic lactones. In recent years, pyrethroid tolerance has been reported in a number of species of livestock lice in the United Kingdom and Australia. Results In this pilot survey, lice were detected in 16 (94%) out of 17 herds visited. Two species of lice, Bovicola bovis and Linognathus vituli were identified. In vitro contact bioassays showed evidence of deltamethrin tolerance in Bovicola bovis collected from 4 farms. This was confirmed by repeatedly assessing louse infestations on treated animals on one farm. Conclusions To our knowledge this is the first record of insecticide tolerant populations of lice in Irish cattle. The results also provide new data on the species of lice infesting beef cattle in Ireland and the prevalence and control of louse infestations in Irish beef cattle herds.
• #### Characterization and adaptation of Caldicellulosiruptor strains to higher sugar concentrations, targeting enhanced hydrogen production from lignocellulosic hydrolysates

Abstract Background The members of the genus Caldicellulosiruptor have the potential for future integration into a biorefinery system due to their capacity to generate hydrogen close to the theoretical limit of 4 mol H2/mol hexose, use a wide range of sugars and can grow on numerous lignocellulose hydrolysates. However, members of this genus are unable to survive in high sugar concentrations, limiting their ability to grow on more concentrated hydrolysates, thus impeding their industrial applicability. In this study five members of this genus, C. owensensis, C. kronotskyensis, C. bescii, C. acetigenus and C. kristjanssonii, were developed to tolerate higher sugar concentrations through an adaptive laboratory evolution (ALE) process. The developed mixed population C. owensensis CO80 was further studied and accompanied by the development of a kinetic model based on Monod kinetics to quantitatively compare it with the parental strain. Results Mixed populations of Caldicellulosiruptor tolerant to higher glucose concentrations were obtained with C. owensensis adapted to grow up to 80 g/L glucose; other strains in particular C. kristjanssonii demonstrated a greater restriction to adaptation. The C. owensensis CO80 mixed population was further studied and demonstrated the ability to grow in glucose concentrations up to 80 g/L glucose, but with reduced volumetric hydrogen productivities ( $$Q_{{{\text{H}}_{2} }}$$ Q H 2 ) and incomplete sugar conversion at elevated glucose concentrations. In addition, the carbon yield decreased with elevated concentrations of glucose. The ability of the mixed population C. owensensis CO80 to grow in high glucose concentrations was further described with a kinetic growth model, which revealed that the critical sugar concentration of the cells increased fourfold when cultivated at higher concentrations. When co-cultured with the adapted C. saccharolyticus G5 mixed culture at a hydraulic retention time (HRT) of 20 h, C. owensensis constituted only 0.09–1.58% of the population in suspension. Conclusions The adaptation of members of the Caldicellulosiruptor genus to higher sugar concentrations established that the ability to develop improved strains via ALE is species dependent, with C. owensensis adapted to grow on 80 g/L, whereas C. kristjanssonii could only be adapted to 30 g/L glucose. Although C. owensensis CO80 was adapted to a higher sugar concentration, this mixed population demonstrated reduced $$Q_{{{\text{H}}_{2} }}$$ Q H 2 with elevated glucose concentrations. This would indicate that while ALE permits adaptation to elevated sugar concentrations, this approach does not result in improved fermentation performances at these higher sugar concentrations. Moreover, the observation that planktonic mixed culture of CO80 was outcompeted by an adapted C. saccharolyticus, when co-cultivated in continuous mode, indicates that the robustness of CO80 mixed culture should be improved for industrial application.
• #### Experimental comparison of two methods to study barley responses to partial submergence

Background Crop yield is dependent on climate conditions, which are becoming both more variable and extreme in some areas of the world as a consequence of global climate change. Increased precipitation and flooding events are the cause of important yield losses due to waterlogging or (partial) submergence of crops in the field. Our ability to screen efficiently and quickly for varieties that have increased tolerance to waterlogging or (partial) submergence is important. Barley, a staple crop worldwide, is particularly sensitive to waterlogging. Screening for waterlogging tolerant barley varieties has been ongoing for many years, but methods used to screen vary greatly, from the type of soil used to the time at which the treatment is applied. This variation makes it difficult to cross-compare results. Results Here, we have devised a scoring system to assess barley tolerance to waterlogging and compare two different methods when partial submergence is applied with either water or a starch solution at an early developmental stage, which is particularly sensitive to waterlogging or partial submergence. The use of a starch solution has been previously shown to result in more reducing soil conditions and has been used to screen for waterlogging tolerance. Conclusions Our results show that the two methods provide similar results to qualitatively rank varieties as tolerant or sensitive, while also affecting plants differently, in that application of a starch solution results in stronger and earlier symptoms than applying partial submergence with water.
• #### Association between clinical respiratory signs, lung lesions detected by thoracic ultrasonography and growth performance in pre‐weaned dairy calves

Background Bovine respiratory disease (BRD) is the main cause of mortality among 1-to-5 month old calves in Ireland, accounting for approximately one-third of deaths. Despite widespread use of clinical respiratory signs for diagnosing BRD, lung lesions are detected, using thoracic ultrasonography (TUS) or following post-mortem, in calves showing no clinical signs. This highlights the limitation of clinical respiratory signs as a method of detecting sub-clinical BRD. Using 53 purchased artificially-reared male dairy calves, the objectives of this study were to: (i) characterise the BRD incidence detected by clinical respiratory signs and/or TUS, (ii) investigate the association between clinical respiratory signs and lung lesions detected by TUS, and (iii) assess the effect of BRD on pre-weaning growth. Results Clinical BRD (based on Wisconsin clinical respiratory score and/or rectal temperature > 39.6 ºC) was detected in 43 % and sonographic changes (lung lesions) were detected in 64 % of calves from purchase (23 (SD; 6.2) days of age) until weaning, 53 days post-arrival. Calves with clinical BRD were treated. Sixty-one per cent calves affected with clinical BRD had lung lesions 10.5 days (median) before detection of clinical signs. Moderate correlations (rsp 0.70; P < 0.05) were found between cough and severe lung lesions on arrival day, and between rectal temperature > 39.6 ºC and lung lesions ≥ 2 cm2 on day 7 (rsp 0.40; P < 0.05) post-arrival. Mean average daily live weight gain (ADG) of calves from purchase to weaning was 0.75 (SD; 0.10) kg; calves with or without clinical BRD did not differ in ADG (P > 0.05), whereas ADG of those with severe lung lesions (lung lobe completely consolidated or pulmonary emphysema) was 0.12 kg/d less (P < 0.05) than calves without lung lesions. Conclusions Thoracic ultrasonography detected lung consolidation in calves that did not show signs of respiratory disease. The presence of severe lung lesions was associated with reduced pre-weaning growth. These findings emphasise the importance of using TUS in addition to clinical respiratory scoring of calves for an early and accurate detection of clinical and sub-clinical BRD.
• #### Effect of space allowance and mixing on growth performance and body lesions of grower-finisher pigs in pens with a single wet-dry feeder

Background Low space allowance (SA) and mixing may result in reduced growth performance (GP) and animal welfare issues because of adverse social behaviours directed to pen mates. This could be exacerbated in pens with single space feeders owing to social facilitation of feeding behaviour. The present study aimed to investigate the effect of SA and mixing on GP and body lesions (BL) in pens with one single space wet-dry feeder. Results Two experiments were conducted on grower-finisher pigs from 10 to 21 weeks of age. In Exp1, pigs (N = 216) were assigned to three SA; 0.96 m2/pig (n = 6 pens; 10 pigs/pen; SA96), 0.84 m2/pig (n = 6; 12 pigs/pen; SA84) and 0.72 m2/pig (n = 6; 14 pigs/pen; SA72), in a randomized design. In Exp2, pigs (N = 230) were used in a 2 × 2 factorial randomized design considering SA and mixing as treatments. Pigs were assigned to two SA; 0.96 m2/pig (n = 10 pens; 10 pigs/pen; SA96) and 0.78 m2/pig (n = 10; 13 pigs/pen; SA78) and were either mixed or not at the entry to the finishing facility. GP was not affected by SA (P > 0.05) in either experiment. In Exp2, non-mixed pigs were 5.4 kg heavier (P <  0.001), gained 74 g more per day (P = 0.004), consumed 101.8 g more of feed per day (P = 0.007) and tended to have higher feed efficiency (P = 0.079) than mixed pigs from 11 to 21 weeks of age. Number of BL was affected by SA in both experiments. In Exp1, SA72 pigs had 74.4 and 97.4% more BL than SA96 and SA84 pigs at 20 weeks of age respectively (P <  0.01). In Exp2, SA78 pigs had 48.6, 43.6 and 101.3% more BL than SA96 pigs at 12, 16 and 21 weeks of age respectively (P <  0.05). Mixing did not affect the number of BL from 12 to 21 weeks of age in Exp2 (P > 0.05). Conclusion Mixing had a considerable effect on growth performance thus, strategies to avoid or mitigate mixing should be considered. Although space allowance had no effect on growth performance, high number of body lesions in the lower space allowance indicates that space allowances equal or below 0.78 m2/pig are detrimental to the welfare of pigs despite following the EU legislation.
• #### Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species

Background Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity, resilience and photosynthetic capacity at low temperature. These qualities make Miscanthus a particularly good candidate for temperate marginal land, where yields can be limited by insufficient or excessive water supply. Differences in response to water stress have been observed among Miscanthus species, which correlated to origin. In this study, we compared the physiological and molecular responses among Miscanthus species under excessive (flooded) and insufficient (drought) water supply in glasshouse conditions. Results A significant biomass loss was observed under drought conditions in all genotypes. M. x giganteus showed a lower reduction in biomass yield under drought conditions compared to the control than the other species. Under flooded conditions, biomass yield was as good as or better than control conditions in all species. 4389 of the 67,789 genes (6.4%) in the reference genome were differentially expressed during drought among four Miscanthus genotypes from different species. We observed the same biological processes were regulated across Miscanthus species during drought stress despite the DEGs being not similar. Upregulated differentially expressed genes were significantly involved in sucrose and starch metabolism, redox, and water and glycerol homeostasis and channel activity. Multiple copies of the starch metabolic enzymes BAM and waxy GBSS-I were strongly up-regulated in drought stress in all Miscanthus genotypes, and 12 aquaporins (PIP1, PIP2 and NIP2) were also up-regulated in drought stress across genotypes. Conclusions Different phenotypic responses were observed during drought stress among Miscanthus genotypes from different species, supporting differences in genetic adaption. The low number of DEGs and higher biomass yield in flooded conditions supported Miscanthus use in flooded land. The molecular processes regulated during drought were shared among Miscanthus species and consistent with functional categories known to be critical during drought stress in model organisms. However, differences in the regulated genes, likely associated with ploidy and heterosis, highlighted the value of exploring its diversity for breeding.
• #### Identifying challenges to manage body weight variation in pig farms implementing all-in-all-out management practices and their possible implications for animal health: a case study

Background Managing body weight (BW) variation is a challenge in farrow-to-finish farms implementing all-in/all-out (AIAO) production systems due to the lack of “off-site” facilities to segregate slow growing pigs (SGP). This case study investigated different approaches to managing BW variation in a farrow-to-finish commercial pig farm with a self-declared AIAO management and the possible implications for animal health. Case presentation A total of 1096 pigs (1047 pigs born within 1 week plus 49 pigs born 1 week later) were tracked until slaughter as they moved through the production stages. Piglets were individually tagged at birth and their location on the farm was recorded on a weekly basis. In total, 10.3% of pigs died during lactation. Four main cohorts of pigs were created at weaning and retrospectively identified: cohort 1 = pigs weaned at 21 days (4.5%); cohort 2 = pigs weaned at 28 days (81.0%), which was sub-divided at the end of the first nursery stage into sub-cohort 2a = pigs split at 3 weeks post-weaning (29.7%); sub-cohort 2b = pigs split at 3 weeks post-weaning from cohort 2a and split again 5 weeks post-weaning (35.5%) and sub-cohort 2c = remaining smaller size pigs from cohort 2b (10.9%); cohort 3 = pigs weaned at 35 days (2.7%) and cohort 4 = pigs weaned at 49 days (1.5%) that were later mixed with SPG, delayed pigs from other cohorts and sick/injured pigs that recovered. Four strategies to manage BW variation were identified: i) earlier weaning (cohort 1); ii) delayed weaning of SGP (cohort 3 and 4); iii) re-grading pens by BW (sub-cohorts 2a, 2b and 2c) and, iv) delayed movement of SGP to the next production stage (several pigs from all cohorts). A higher percentage of delayed pigs presented pericarditis, pleurisy and enzootic pneumonia like lesions at slaughter compared with pigs under other strategies. Conclusion A variety of management practices were implemented to minimise BW variation during the production cycle. However, several cohorts of pigs were created disrupting AIAO management. Earlier weaning should only be practiced under specific circumstances where optimal animal health and welfare are guaranteed. Delayed weaning of SGP and delaying pigs to move to the next production stage could negatively affect animal health and should be avoided.
• #### Quantification, description and international comparison of antimicrobial use on Irish pig farms

Abstract Background There is concern that the use of antimicrobials in livestock production has a role in the emergence and dissemination of antimicrobial resistance in animals and humans. Consequently, there are increasing efforts to reduce antimicrobial use (AMU) in agriculture. As the largest consumer of veterinary antimicrobials in several countries, the pig sector is a particular focus of these efforts. Data on AMU in pig production in Ireland are lacking. This study aimed to quantify AMU on Irish pig farms, to identify the major patterns of use employed and to compare the results obtained to those from other published reports and studies. Results Antimicrobial use data for 2016 was collected from 67 Irish pig farms which represented c. 35% of national production. The combined sample population consumed 14.5 t of antimicrobial by weight of active ingredient suggesting that the pig sector accounted for approximately 40% of veterinary AMU in Ireland in 2016. At farm level, median AMU measured in milligram per population correction unit (mg/PCU) was 93.9 (range: 1.0–1196.0). When measured in terms of treatment incidence (TI200), median AMU was 15.4 (range: 0.2–169.2). Oral treatments accounted for 97.5% of all AMU by weight of active ingredient and were primarily administered via medicated feed to pigs in the post weaning stages of production. AMU in Irish pig production in 2016 was higher than results obtained from the national reports of Sweden, Denmark, the Netherlands and France but lower than the United Kingdom. Conclusions Pig production in Ireland is an important consumer of veterinary antimicrobials. The quantities and patterns of AMU on Irish pig farms are comparable to pig production in other European countries but higher than some countries with more advanced AMU reduction strategies. This AMU is characterised by a high proportion of prophylactic use and is primarily administered to pigs post weaning via medicated feed. Further studies to better understand the reasons for AMU on Irish pig farms and strategies to improve health among weaner pigs will be of benefit in the effort to reduce AMU.
• #### Investigation of bovine abortion and stillbirth/perinatal mortality - similar diagnostic challenges, different approaches

Abstract This pracademic paper reviews current bovine foetopathy (abortion and stillbirth) case definitions, reporting and triage, and causes and time-of-death and proposes veterinary practitioner-focused investigative standard operating procedures (SOPs). Issues of under- and over-triage and intra-institutional SOP harmonisation are also discussed. It is proposed that an ‘observable abortion’ (120–260 days of gestation) is a more practitioner-friendly definition of abortion for reporting and benchmarking purposes and that the term ‘peristillbirth’ can replace stillbirth and perinatal mortality. Diagnosis of bovine foetopathy involves an investigative triad of the farmer, veterinary practitioner and the veterinary diagnostic laboratory. However, the poor sensitivity of abortion reporting undermines the value of currently adopted scanning/passive surveillance; parallel active surveillance/sentinel herd models should also be employed. The approach to abortion investigation differs from that of peristillbirth. The former should include collecting a herd and case history, examination and sampling of dam and cohorts and sampling of the foetus and placenta. A sample selection decision tree is provided to assist test selection. In peristillbirths, non-infectious and periparturient causes-of-death are more important hence the anamnesis must focus on peristillbirth risk factors and calving management. The foetopsy, while including the sampling menu appropriate to aborted foetuses, must also include a detailed internal and external examination of the carcass for lesions indicative of periparturient causes-of-death. In addition, for aborted foetuses the time-of-death is not important as the foetus is generally not viable; however, for the peristillbirth the time-of-death is critical as it provides useful information for the farmer to address modifiable risk factors and to alter their perinatal management. Reporting of the ultimate cause-of-death is more useful to prevent future abortions and peristillbirths though the proximate cause-of-death is often reported in the absence of a complete clinical anamnesis. Finally, the common reasons for diagnosis not reached (DNR) and the limitations of current investigative approaches are discussed.
• #### Functional analysis of bovine interleukin-10 receptor alpha in response to Mycobacterium avium subsp. paratuberculosis lysate using CRISPR/Cas9

Background The interleukin-10 receptor alpha (IL10RA) gene codes for the alpha chain of the IL-10 receptor which binds the cytokine IL-10. IL-10 is an anti-inflammatory cytokine with immunoregulatory function during the pathogenesis of many inflammatory disorders in livestock, including Johne’s disease (JD). JD is a chronic enteritis in cattle caused by Mycobacterium avium subsp. paratuberculosis (MAP) and is responsible for significant economic losses to the dairy industry. Several candidate genes including IL10RA have been found to be associated with JD. The aim of this study was to better understand the functional significance of IL10RA in the context of immune stimulation with MAP cell wall lysate. Results An IL10RA knock out (KO) bovine mammary epithelial cell (MAC-T) line was generated using the CRISPR/cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) gene editing system. These IL10RA KO cells were stimulated with the immune stimulant MAP lysate +/− IL-10, or with LPS as a positive control. In comparison to unedited cells, relative quantification of immune-related genes after stimulation revealed that knocking out IL10RA resulted in upregulation of pro-inflammatory cytokine gene expression (TNFA, IL1A, IL1B and IL6) and downregulation of suppressor of cytokine signaling 3 (SOCS3), a negative regulator of pro-inflammatory cytokine signaling. At the protein level knocking out IL10RA also resulted in upregulation of inflammatory cytokines - TNF-α and IL-6 and chemokines - IL-8, CCL2 and CCL4, relative to unedited cells. Conclusions The findings of this study illustrate the broad and significant effects of knocking out the IL10RA gene in enhancing pro-inflammatory cytokine expression and further support the immunoregulatory role of IL10RA in eliciting an anti-inflammatory response as well as its potential functional involvement during the immune response associated with JD.