• Labour efficiency on-farm

      O'Brien, Bernadette; Gleeson, David E; O'Donovan, K.; Ruane, D.; Kinsella, J.; Mee, John F; Boyle, Laura; McNamara, John G. (Teagasc, 2007-01-01)
      Improvements in milking efficiency have a greater influence than any other aspect of the dairy farmers work on overall farm labour inputs (Whipp, 1992). In order to facilitate the examination of milking process labour inputs, the milking process may be divided into the following three components: herding pre and post milking (transfer of cows to and from the milking parlour); milking (milking tasks / work routines within the parlour); and washing (washing of milking machine and yard). Meanwhile, within milking specifically, the number of cows milked per operator per hour is the best measure of both the performance of the operator and the milking installation (Clough, 1978). This is affected by the following three factors: the milking times of the cows, the number and arrangement of the milking units, and the operator’s work routine (Whipp, 1992). The addition of extra milking units will only increase milking performance if the operator has idle time during milking (Hansen, 1999).
    • Land Drainage - A farmer’s practical guide to draining grassland in Ireland

      Tuohy, Patrick; Fenton, Owen; O'Loughlin, James; Humphreys, James (Teagasc, 30/07/2013)
      No drainage work should be carried out before the drainage characteristics of the soil are established by a site and soil test pit investigation. • Two types of drainage system exist: a groundwater drainage system and a shallow drainage system. The design of the system depends entirely on the drainage characteristics of the soil. • Distinguishing between the two types of drainage systems essentially comes down to whether or not a permeable layer is present (at a workable depth) that will allow the flow of water with relative ease. If such a layer is evident, a piped drain system at that depth is likely to be effective. If no such layer is found during soil test pit investigations, it will be necessary to improve the drainage capacity of the soil. This involves a disruption technique such as moling, gravel moling or subsoiling in tandem with collector drains. • Drains are not effective unless they are placed in a free draining soil layer or complimentary measures (mole drainage, subsoiling) are used to improve soil drainage capacity. If water is not moving through the soil in one or other of these two ways, the water table will not be lowered. • Outfall level must not dictate the drainage system depth. If a free draining layer is present, it must be utilised. • Drain pipes should always be used for drains longer than 30 m. If these get blocked it is a drainage stone and not a drainage pipe issue. • Drainage stone should not be filled to the top of the field trench except for very limited conditions (the bottom of an obvious hollow). Otherwise it is an extremely expensive way of collecting little water. • Most of the stone being used for land drainage today is too big. Clean aggregate in the 10–40 mm (0.4 to 1.5 inch approx) grading band should be used. Generally you get what you pay for. • Subsoiling is not effective unless a shallow impermeable layer is being broken or field drains have been installed prior to the operation. Otherwise it will not have any long-term effect and may do more harm than good. • Most land drainage systems are poorly maintained. Open drains should be clean and as deep as possible and field drains feeding into them should be regularly rodded or jetted.
    • Leukocyte profile, gene expression, acute phase response, and metabolite status of cows with sole hemorrhages

      O'Driscoll, Keelin; McCabe, Matthew; Earley, Bernadette; Marie Curie Intra-European Fellowship; 252611 (Elsevier, 2017-08-23)
      Sole hemorrhages result from disruption to normal claw horn formation and are caused by a variety of internal and external factors. Evidence suggests that they are painful, although they do not usually cause clinical lameness and are difficult to detect by observing cow gait. Little is known about how or whether sole hemorrhages affect the cow systemically. This study compared hematology profile, leukocyte gene expression, and physiological responses of cows with no/mild hemorrhages (category 1; n = 17), moderate hemorrhages (category 2; n = 18), and severe hemorrhages (category 3; n = 12). At approximately 100 d in milk, all cows in the study herd (n = 374) were locomotion scored before hoof examination. The cows included in the study were not clinically lame and had no other hoof disorder. Blood samples were taken from all cows within 24 h of selection. Leukocyte counts were obtained using an automated cell counter, cortisol and dehydroepiandrosterone (DHEA) concentration by ELISA, and plasma haptoglobin, urea, total protein, creatine kinase and glucose were analyzed on a clinical chemistry analyzer. Expression of 16 genes associated with lameness or stress were estimated using real-time quantitative PCR. Data from cows within each category were compared using the Mixed procedure in SAS (version 9.3; SAS Institute Inc., Cary, NC). Fixed effects included hemorrhage severity category and lactation number, with days in milk and body condition score included as covariates. Locomotion score worsened as sole hemorrhage category worsened. Locomotion score of category 1 cows tended to be lower than that of category 2 cows and was lower than that of category 3 cows. The locomotion score of category 3 cows was also greater than that of categories 1 and 2 combined. Category had no effect on leukocyte number, on any of the individual leukocyte cell numbers or percentages, cortisol or DHEA concentration, cortisol:DHEA ratio, or relative expression of any of the genes investigated, and we detected no differences in plasma glucose, protein, or creatine kinase concentrations between categories. However, category 3 cows had greater plasma concentrations of haptoglobin and tended to have lesser concentrations of plasma urea than category 1 and 2 cows. The differences in gait between cows with no or minor sole hemorrhages and cows with severe hemorrhages indicate that hemorrhages may be associated with discomfort or pain. Nevertheless, the only physiological measure that changed with increasing locomotion score was plasma haptoglobin concentration. Haptoglobin has previously been found to be elevated in lame cows, and thus shows promise as a marker for limb pain.
    • Leveraging Social Network Analysis for Characterizing Cohesion of Human-Managed Animals

      Vimalajeewa, Dixon; Balasubramaniam, Sasitharan; O'Brien, Bernadette; Kulatunga, Chamil; Berry, Donagh P.; Science Foundation Ireland; Department of Agriculture, Food and the Marine; European Union; 13/1A/1977; 16/RC/3835; et al. (Institute of Electrical and Electronics Engineers (IEEE), 2019-04)
      Social network analysis (SNA) is a technique to study behavioral dynamics within a social group. In SNA, it is an open question whether it is possible to characterize animal-level behaviors by using group-level information. Also, it was believed that the combined use of SNA would provide a more comprehensive understanding of social dynamics. In light of these two factors, here we explain an approach to evaluate animal importance to a group by considering the variability in group-level structural information, which is computed by joining the animal- and group-level SNA measures node centrality and network entropy, respectively. Moreover, two other metrics, animal social interaction range and nearest-neighbor frequency matrix, which represent a social affiliation of each animal within the group, are computed to help address the general challenges in graph-based SNA and, thereby, improve the precision of animal importance measures. Finally, we derive the joint distribution of animal importance of the group in detecting atypical social behaviors. The approach is tested using tracking data of dairy cows. The reliability of the derived animal importance was superior to the already existing animal importance measures. To illustrate the usability of the animal importance metric, a simulation study was conducted to identify sick and estrus animals in a group. The social affiliation of sick cows was less when compared to healthy cows. Also, their individual distributions of animal importance were shifted toward the left of the mean of the animal importance distributions of healthy cows. Consequently, the joint distribution of animal importance of the group exhibited a bimodal distribution with a left tailored shape. The behavior of cows in estrus was opposite to that of sick cows. Moreover, with the increasing number of sick and estrus cows in the group, respectively, the group entropy decreased with larger variance and slightly increased with less variance. Therefore, the entropy-based animal importance metric has superior performances when evaluating animal importance to the group compared to the existing metrics. It can be used for generating alerts for the early detection of atypical social behaviors associated with, for instance, animal health, veterinary, and welfare.
    • Linkage between predictive transmitting ability of a genetic index, potential milk production, and a dynamic model

      Ruelle, Elodie; Delaby, Luc; Shalloo, Laurence; Department of Agriculture, Food and the Marine; 11/S/132 (Elsevier, 2019-01-26)
      With the increased use of information and communication technology–based tools and devices across traditional desktop computers and smartphones, models and decision-support systems are becoming more accessible for farmers to improve the decision-making process at the farm level. However, despite the focus of research and industry providers to develop tools that are easy to adopt by the end user, milk-production prediction models require substantial parameterization information for accurate milk production simulations. For these models to be useful at an individual animal level, they require the potential milk yield of the individual animals (and possibly potential fat and protein yields) to be captured and parameterized within the model to allow accurate simulations of the interaction of the animal with the system. The focus of this study was to link 3 predicted transmitting ability (PTA) traits from the Economic Breeding Index (PTA for milk yield, fat, and protein) with potential index parameters for milk, fat, and protein required as inputs to a herd-based dynamic milk model. We compiled a data set of 1,904 lactations that included different experiments conducted at 2 closed sites during a 14-yr period (2003–2016). The treatments implied different stocking rates, concentrate supplementation levels, calving dates, and genetic potential. The first step, using 75% of the data randomly selected, was to link the milk, fat, and protein yields achieved within each lactation to their respective PTA value, stocking rate, parity, and concentrate supplementation level. The equations generated were transformed to correspond to inputs to the pasture-based herd dynamic milk model. The equations created were used in conjunction with the model to predict milk, fat, and protein production. Then, using the remaining 25% data of the data set, the simulations were compared against the actual milk produced during the experiments. When the model was tested, it was capable of predicting the lactation milk, fat, and protein yield with a relative prediction error of <10% at the herd level and <13% at the individual animal level.
    • Linking Hydro-Geophysics and Remote Sensing Technology for Sustainable Water and Agricultural Catchment Management

      O'Leary, Dave; Fenton, Owen; Mellander, Per-Erik; Tuohy, Patrick; Brown, C.; Daly, E. (2019-05)
      The acquisition of sub-surface data for agricultural purposes is traditionally achieved by in situ point sampling in the top 2m over limited target areas (farm scale ~ km2) and time periods. This approach is inadequate for integrated regional (water catchment ~ 100 km2) scale management strategies which require an understanding of processes varying over decadal time scales in the transition zone (~ 10’s m) from surface to bedrock. With global food demand expected to increase by 100% by 2050, there are worldwide concerns that achievement of production targets will be at the expense of water quality. In order to overcome the limitations of the traditional approach, this research programme will combine airborne and ground geophysics with remote sensing technologies to access hydrogeological and soil structure information on Irish Soils at multiple spatial scales. It will address this problem in the context of providing tools for the sustainable management of agricultural intensification envisioned in Food Harvest 2020 and Food Wise 2025 and considering the EU Habitats and Water Framework Directives (WFD), Clean Air Policy and Soil Thematic Strategies. The work will use existing ground based geophysical and hydrogeological data from Teagasc Agricultural Catchment Programme (ACP) and Heavy Soil sites co-located ground and airborne electromagnetic data. Neural Networks training and Machine learning approaches will supplement traditional geophysical workflows. Work will then focus on upscaling results from ACP to WFD catchment scale. This upscaling will require modification of traditional satellite remote sensing conceptual frameworks to analyse heterogeneous, multi-temporal data streams.
    • Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation

      Bowen, Jenna M.; Cormican, Paul; Lister, Susan J.; McCabe, Matthew S.; Duthie, Carol-Anne; Roehe, Rainer; Dewhurst, Richard J.; Teagasc Walsh Fellowship Programme; AHDB Beef and Lamb; the Scottish Government; et al. (Public Library of Science (PLoS), 2020-04-24)
      Ruminant methane production is a significant energy loss to the animal and major contributor to global greenhouse gas emissions. However, it also seems necessary for effective rumen function, so studies of anti-methanogenic treatments must also consider implications for feed efficiency. Between-animal variation in feed efficiency represents an alternative approach to reducing overall methane emissions intensity. Here we assess the effects of dietary additives designed to reduce methane emissions on the rumen microbiota, and explore relationships with feed efficiency within dietary treatment groups. Seventy-nine finishing steers were offered one of four diets (a forage/concentrate mixture supplemented with nitrate (NIT), lipid (MDDG) or a combination (COMB) compared to the control (CTL)). Rumen fluid samples were collected at the end of a 56 d feed efficiency measurement period. DNA was extracted, multiplexed 16s rRNA libraries sequenced (Illumina MiSeq) and taxonomic profiles were generated. The effect of dietary treatments and feed efficiency (within treatment groups) was conducted both overall (using non-metric multidimensional scaling (NMDS) and diversity indexes) and for individual taxa. Diet affected overall microbial populations but no overall difference in beta-diversity was observed. The relative abundance of Methanobacteriales (Methanobrevibacter and Methanosphaera) increased in MDDG relative to CTL, whilst VadinCA11 (Methanomassiliicoccales) was decreased. Trimethylamine precursors from rapeseed meal (only present in CTL) probably explain the differences in relative abundance of Methanomassiliicoccales. There were no differences in Shannon indexes between nominal low or high feed efficiency groups (expressed as feed conversion ratio or residual feed intake) within treatment groups. Relationships between the relative abundance of individual taxa and feed efficiency measures were observed, but were not consistent across dietary treatments.
    • Live animal measurements, carcass composition and plasma hormone and metabolite concentrations in male progeny of sires differing in genetic merit for beef production

      Clarke, Anne Marie; Drennan, Michael J; McGee, Mark; Kenny, David A.; Evans, R. D.; Berry, Donagh (Cambridge University Press, 2009-07)
      In genetic improvement programmes for beef cattle, the effect of selecting for a given trait or index on other economically important traits, or their predictors, must be quantified to ensure no deleterious consequential effects go unnoticed. The objective was to compare live animal measurements, carcass composition and plasma hormone and metabolite concentrations of male progeny of sires selected on an economic index in Ireland. This beef carcass index (BCI) is expressed in euros and based on weaning weight, feed intake, carcass weight and carcass conformation and fat scores. The index is used to aid in the genetic comparison of animals for the expected profitability of their progeny at slaughter. A total of 107 progeny from beef sires of high (n = 11) or low (n = 11) genetic merit for the BCI were compared in either a bull (slaughtered at 16 months of age) or steer (slaughtered at 24 months of age) production system, following purchase after weaning (8 months of age) from commercial beef herds. Data were analysed as a 2 × 2 factorial design (two levels of genetic merit by two production systems). Progeny of high BCI sires had heavier carcasses, greater (P < 0.01) muscularity scores after weaning, greater (P < 0.05) skeletal scores and scanned muscle depth pre-slaughter, higher (P < 0.05) plasma insulin concentrations and greater (P < 0.01) animal value (obtained by multiplying carcass weight by carcass value, which was based on the weight of meat in each cut by its commercial value) than progeny of low BCI sires. Regression of progeny performance on sire genetic merit was also undertaken across the entire data set. In steers, the effect of BCI on carcass meat proportion, calculated carcass value (c/kg) and animal value was positive (P < 0.01), while a negative association was observed for scanned fat depth pre-slaughter and carcass fat proportion (P < 0.01), but there was no effect in bulls. The effect of sire expected progeny difference (EPD) for carcass weight followed the same trends as BCI. Muscularity scores, carcass meat proportion and calculated carcass value increased, whereas scanned fat depth, carcass fat and bone proportions decreased with increasing sire EPD for conformation score. The opposite association was observed for sire EPD for fat score. Results from this study show that selection using the BCI had positive effects on live animal muscularity, carcass meat proportion, proportions of high-value cuts and carcass value in steer progeny, which are desirable traits in beef production.
    • A Live Bio-Therapeutic for Mastitis, Containing Lactococcus lactis DPC3147 With Comparable Efficacy to Antibiotic Treatment

      Kitching, Michael; Mathur, Harsh; Flynn, James; Byrne, Noel; Dillon, Pat; Sayers, Riona; Rea, Mary; Hill, Colin; Ross, R. Paul; Enterprise Ireland; et al. (Frontiers Media SA, 2019-09-27)
      Bovine mastitis is an ongoing significant concern in the dairy and agricultural industry resulting in substantial losses in milk production and revenue. Among the predominant etiological agents of bovine mastitis are Staphylococcus aureus, Streptococcus uberis, Streptococcus dysgalactiae, and Escherichia coli. Currently, the treatment of choice for bovine mastitis involves the use of commercial therapeutic antibiotic formulations such as TerrexineTM, containing both kanamycin and cephalexin. Such antibiotics are regularly administered in more than one dose resulting in the withholding of milk for processing for a number of days. Here, we describe the optimization of a formulation of Lactococcus lactis DPC3147, that produces the two-component bacteriocin lacticin 3147, in a liquid paraffin-based emulsion (formulation hereafter designated ‘live bio-therapeutic’) for the first time and compare it to the commercial antibiotic formulation TerrexineTM, with a view to treating cows with clinical/sub-clinical mastitis. Critically, in a field trial described here, this ‘ready-to-use’ emulsion containing live L. lactis DPC3147 cells exhibited comparable efficacy to TerrexineTM when used to treat mastitic cows. Furthermore, we found that the L. lactis cells within this novel emulsion-based formulation remained viable for up to 5 weeks, when stored at 4, 22, or 37◦C. The relative ease and cost-effective nature of producing this ‘live bio-therapeutic’ formulation, in addition to its enhanced shelf life compared to previous aqueous-based formulations, indicate that this product could be a viable alternative therapeutic option for bovine mastitis. Moreover, the singledose administration of this ‘live bio-therapeutic’ formulation is a further advantage, as it can expedite the return of the milk to the milk pool, in comparison to some commercial antibiotics. Overall, in this field trial, we show that the live bio-therapeutic formulation displayed a 47% cure rate compared to a 50% cure rate for a commercial antibiotic control, with respect to curing cows with clinical/sub-clinical mastitis. The study suggests that a larger field trial to further demonstrate efficacy is warranted.
    • Liver fluke in Irish sheep: prevalence and associations with management practices and co-infection with rumen fluke

      Munita, Maria Pia; Rea, Rosemary; Martinez-Ibeas, Ana Maria; Byrne, Noel; McGrath, Guy; Munita-Corbalan, Luis Enrique; Sekiya, Mary; Mulcahy, Grace; Sayers, Ríona G.; Department of Agriculture, Food and the Marine; et al. (Springer Science and Business Media LLC, 2019-11-06)
      Background: The present study aimed to identify the national prevalence of Fasciola hepatica in Irish sheep and to conduct a risk analysis assessment based on management and treatment practices in participating focks. Also, co-infection with rumen fuke was quantifed and its association with liver fuke and management practices was assessed. Methods: A total of 305 sheep focks were selected ensuring even national representation of the sheep population. Participating farms were asked to complete a survey questionnaire on farm management practices and submit faecal samples during the winter of 2014–2015. Pooled faecal samples were analysed for the presence of F. hepatica and coinfection with rumen fuke. Apparent and true prevalence were calculated, additionally, the rate of co-infection with rumen fuke was also obtained. Correlation and regression analyses were used for assessing associations between management practices, liver fuke infection and co-infection with rumen fuke. Results: The national true prevalence of F. hepatica was 50.4% (n=305). Regional prevalence varied from 41% in the east to 52% in the south. Co-infection with rumen fuke was observed in 40% of the studied population and corre‑ lated with increased F. hepatica egg counts (OR=2.9; P≤0.001). Predominant breeds were Sufolk, Texel and Horned Mountain breeds. Beef cattle were the most frequent type of other livestock present on farms and mixed species grazing was frequently reported (73%). More than half of the focks reported a mid-to-late lambing period (MarchApril). Use of mountain land for grazing was of 32%. Flukicides were most commonly used twice over the autumnwinter period. Regression analyses highlighted signifcant association of F. hepatica status, with the presence of other livestock on farm, frequency of fukicides used during the winter and clinical presentation of liver fuke. A signifcant increase in eggs per gram of faeces was observed in Charollais sheep in comparison with all other breeds. Co-infec‑ tion with F. hepatica and Calicophoron daubneyi was also signifcantly associated with the presence of other livestock on the farm, type of fukicide used and clinical fasciolosis. Conclusions: The present study provides up-to-date information on the prevalence of F. hepatica in Irish sheep and adds insight to the epidemiology of the disease. These fndings will be useful for designing new holistic control meas‑ ures for F. hepatica infection.
    • Liver fluke in Irish sheep: prevalence and associations with management practices and co-infection with rumen fluke.

      Munita, Maria Pia; Rea, Rosemary; Martinez-Ibeas, Ana Maria; Byrne, Noel; McGrath, Guy; Munita-Corbalan, Luis Enrique; Sekiya, Mary; Mulcahy, Grace; Sayers, Riona; Department of Agriculture, Food and the Marine (Biomed Central, 2019-11-06)
      Background The present study aimed to identify the national prevalence of Fasciola hepatica in Irish sheep and to conduct a risk analysis assessment based on management and treatment practices in participating flocks. Also, co-infection with rumen fluke was quantified and its association with liver fluke and management practices was assessed. Methods A total of 305 sheep flocks were selected ensuring even national representation of the sheep population. Participating farms were asked to complete a survey questionnaire on farm management practices and submit faecal samples during the winter of 2014–2015. Pooled faecal samples were analysed for the presence of F. hepatica and co-infection with rumen fluke. Apparent and true prevalence were calculated, additionally, the rate of co-infection with rumen fluke was also obtained. Correlation and regression analyses were used for assessing associations between management practices, liver fluke infection and co-infection with rumen fluke. Results The national true prevalence of F. hepatica was 50.4% (n = 305). Regional prevalence varied from 41% in the east to 52% in the south. Co-infection with rumen fluke was observed in 40% of the studied population and correlated with increased F. hepatica egg counts (OR = 2.9; P ≤ 0.001). Predominant breeds were Suffolk, Texel and Horned Mountain breeds. Beef cattle were the most frequent type of other livestock present on farms and mixed species grazing was frequently reported (73%). More than half of the flocks reported a mid-to-late lambing period (March-April). Use of mountain land for grazing was of 32%. Flukicides were most commonly used twice over the autumn-winter period. Regression analyses highlighted significant association of F. hepatica status, with the presence of other livestock on farm, frequency of flukicides used during the winter and clinical presentation of liver fluke. A significant increase in eggs per gram of faeces was observed in Charollais sheep in comparison with all other breeds. Co-infection with F. hepatica and Calicophoron daubneyi was also significantly associated with the presence of other livestock on the farm, type of flukicide used and clinical fasciolosis. Conclusions The present study provides up-to-date information on the prevalence of F. hepatica in Irish sheep and adds insight to the epidemiology of the disease. These findings will be useful for designing new holistic control measures for F. hepatica infection.
    • Liver transcriptome profiling of beef steers with divergent growth rate, feed intake, or metabolic body weight phenotypes

      Mukiibi, Robert; Vinsky, Michael; Keogh, Kate; Fitzsimmons, Carolyn; Stothard, Paul; Waters, Sinéad M; Li, Changxi; Alberta Livestock and Meat Agency; Alberta Agriculture and Forestry; Genome Alberta; et al. (Oxford University Press (OUP), 2019-10-04)
      Average daily gain (ADG) and daily dry matter intake (DMI) are key determinants of beef industry profitability. These traits together with metabolic body weight (MWT) are combined as component traits to calculate residual feed intake (RFI), a common measure of feed efficiency in beef cattle. Recently, there have been significant efforts towards molecular genetic characterization of RFI through transcriptomic studies in different breeds and tissues. However, molecular mechanisms of RFI component traits still remain predominately unexplored. Therefore, in the current study, we investigated the hepatic transcriptomic profiles and their associations with ADG, DMI, and MWT in Angus, Charolais, and Kinsella Composite (KC) populations through global RNAseq analyses. In each population and for each trait, 12 steers with extreme phenotypes (n = 6 low and n = 6 high) were analyzed for differential gene expression. These animals were from 20 beef steers of each Angus, Charolais, and KC breed population that were initially selected for a transcriptome study of RFI. At a false discovery rate <0.05 and fold change >1.5, we identified 123, 102, and 78 differentially expressed (DE) genes between high- and lowADG animals of Angus, Charolais, and KC populations, respectively. For DMI, 108, 180, and 156 DE genes were identified between high- and low-DMI from Angus, Charolais, and KC populations, respectively, while for MWT, 80, 82, and 84 genes were differentially expressed between high- and low-MWT animals in Angus, Charolais, and KC populations, respectively. The identified DE genes were largely breed specific (81.7% for ADG, 82.7% for DMI, and 83% for MWT), but were largely involved in the same biological functions across the breeds. Among the most enriched biological functions included metabolism of major nutrients (lipids, carbohydrates, amino acids, vitamins, and minerals), small molecule biochemistry, cellular movement, cell morphology, and cell-to-cell signaling and interaction. Notably, we identified multiple DE genes that are involved in cholesterol biosynthesis, and immune response pathways for the 3 studied traits. Thus, our findings present potential molecular genetic mechanisms and candidate genes that influence feed intake, growth, and MWT of beef cattle.
    • Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) prevalence in humans in close contact with animals and measures to reduce on-farm colonisation

      Crespo-Piazuelo, Daniel; Lawlor, Peadar G.; Irish Health Research Board; JPIAMR-2017–1-A (Biomed Central, 2021-08-06)
      Since the 1940s, Staphylococcus aureus has adapted to the use of different antimicrobials to treat infections. Although S. aureus can act as a commensal bacterium, some strains are facultative pathogens and acquiring them can be fatal. In particular, treating infections caused by S. aureus with acquired antimicrobial resistance is problematic, as their treatment is more difficult. Some of these S. aureus variants are methicillin-resistant S. aureus (MRSA) with prevalence across the globe in health-care facilities, community settings and on livestock farms. Apart from humans, MRSA can colonise other animal species, and because of this, resistance to new antimicrobials can appear and jump between species. Livestock and companion animals are particularly important in this regard considering the relatively high usage of antimicrobials in these species. There is a risk to humans who come into direct contact with animals acquiring MRSA but there is also the risk of animals acquiring MRSA from colonised humans. In this review, we summarise studies conducted worldwide to characterise the prevalence of MRSA in veterinarians, farmers and other personnel who come into close contact with animals. Finally, alternative treatment, preventive measures and on-farm strategies to reduce MRSA introduction to a farm and carriage within a herd are discussed.
    • Long-term effects of prior diets, dietary transition and pregnancy on adipose gene expression in dairy heifers

      Waerp, Hilde K.; Waters, Sinead M.; McCabe, Matthew S.; Cormican, Paul; Salte, Ragnar; The Research Council of Norway; 199448 (Public Library of Science (PLoS), 2019-07-03)
      Adipose tissue is highly involved in whole-body metabolism and is the main site for lipid synthesis, storage and mobilization in ruminants. Therefore, knowledge about adipose tissue responses to different diets is important, especially in growing heifers as the feeding regimes of replacement heifers affect their future success as dairy cows. However, at gene expression level such knowledge is limited. As part of a larger feed trial, adipose tissue biopsies from 24 Norwegian Red heifers were collected at 12 months of age (12MO) and at month seven of gestation (PREG) and analyzed by next-generation mRNA sequencing. Between these two sampling points, all heifers had gone through a successful conception and a feed change from four dietary treatments of high or low energy (HE/LE) and protein (HP/LP) content (treatments LPHE, HPHE, LPLE and HPLE) to a low-energy, low-protein pregnancy feed given to all animals. Gene expression differences between different feed treatments at 12MO are described in an earlier publication from our group. The main objectives of this study were to investigate the long-term effects of diets differing in protein and energy density level on gene expression in adipose tissue of growing replacement dairy heifers. To achieve this, we examined the post-treatment effects between the treatment groups at month seven of gestation; 6 months after the termination of experimental feeding, and the long-term gene expression changes occurring in the adipose tissue between 12MO and PREG. Post-treatment group comparisons showed evidence of long-term effects of dietary treatment on adipose gene expression. Differences between protein treatments were smaller than between energy treatments. Adipose gene expression changes from 12MO to PREG were much larger for the HE than the LE treatments and seemed to mostly be explained by the characteristics of the diet change. 97 genes displayed a unidirectional expression change for all groups from 12MO to PREG, and are considered to be treatment-independent, possibly caused by pregnancy or increased age. This study provides candidate genes and key regulators for further studies on pregnancy preservation (TGFB1, CFD) and metabolic regulation and efficiency (PI3K, RICTOR, MAP4K4,) in dairy cattle.
    • Long-term effects of prior diets, dietary transition and pregnancy on adipose gene expression in dairy heifers

      Wærp, Hilde K. L.; Waters, Sinead M.; McCabe, Matthew S.; Cormican, Paul; Salte, Ragnar; Research Council of Norway; TINE SA Norwegian dairies; Felleskjøpet agricultural cooperative; Animalia AS; 199448 (Public Library of Science (PLoS), 2019-07-03)
      Adipose tissue is highly involved in whole-body metabolism and is the main site for lipid synthesis, storage and mobilization in ruminants. Therefore, knowledge about adipose tissue responses to different diets is important, especially in growing heifers as the feeding regimes of replacement heifers affect their future success as dairy cows. However, at gene expression level such knowledge is limited. As part of a larger feed trial, adipose tissue biopsies from 24 Norwegian Red heifers were collected at 12 months of age (12MO) and at month seven of gestation (PREG) and analyzed by next-generation mRNA sequencing. Between these two sampling points, all heifers had gone through a successful conception and a feed change from four dietary treatments of high or low energy (HE/LE) and protein (HP/LP) content (treatments LPHE, HPHE, LPLE and HPLE) to a low-energy, low-protein pregnancy feed given to all animals. Gene expression differences between different feed treatments at 12MO are described in an earlier publication from our group. The main objectives of this study were to investigate the long-term effects of diets differing in protein and energy density level on gene expression in adipose tissue of growing replacement dairy heifers. To achieve this, we examined the post-treatment effects between the treatment groups at month seven of gestation; 6 months after the termination of experimental feeding, and the long-term gene expression changes occurring in the adipose tissue between 12MO and PREG. Post-treatment group comparisons showed evidence of long-term effects of dietary treatment on adipose gene expression. Differences between protein treatments were smaller than between energy treatments. Adipose gene expression changes from 12MO to PREG were much larger for the HE than the LE treatments and seemed to mostly be explained by the characteristics of the diet change. 97 genes displayed a unidirectional expression change for all groups from 12MO to PREG, and are considered to be treatment-independent, possibly caused by pregnancy or increased age. This study provides candidate genes and key regulators for further studies on pregnancy preservation (TGFB1, CFD) and metabolic regulation and efficiency (PI3K, RICTOR, MAP4K4,) in dairy cattle.
    • Long-term stability of RNA in post-mortem bovine skeletal muscle, liver and subcutaneous adipose tissues

      Bahar, Bojlul; Monahan, Frank J; Moloney, Aidan P; Schmidt, Olaf; MacHugh, David E; Sweeney, Torres; National Development Plan 2000-2006; Teagasc Walsh Fellowship Programme (Biomed Central, 2007-11-29)
      Background: Recovering high quality intact RNA from post-mortem tissue is of major concern for gene expression studies in animals and humans. Since the availability of post-mortem tissue is often associated with substantial delay, it is important that we understand the temporal variation in the stability of total RNA and of individual gene transcripts so as to be able to appropriately interpret the data generated from such studies. Hence, the objective of this experiment was to qualitatively and quantitatively assess the integrity of total and messenger RNA extracted from bovine skeletal muscle, subcutaneous adipose tissue and liver stored at 4°C at a range of time points up to 22 days post-mortem. These conditions were designed to mimic the environment prevailing during the transport of beef from the abattoir to retail outlets. Results: The 28S and 18S rRNA molecules of total RNA were intact for up to 24 h post-mortem in liver and adipose tissues and up to 8 days post-mortem in skeletal muscle. The mRNA of housekeeping genes (GAPDH and ACTB) and two diet-related genes (RBP5 and SCD) were detectable up to 22 days post-mortem in skeletal muscle. While the mRNA stability of the two housekeeping genes was different in skeletal muscle and liver, they were similar to each other in adipose tissue. After 22 days post-mortem, the relative abundance of RBP5 gene was increased in skeletal muscle and in adipose tissue and decreased in liver. During this period, the relative abundance of SCD gene also increased in skeletal muscle whereas it decreased in both adipose tissue and liver. Conclusion: Stability of RNA in three tissues (skeletal muscle, subcutaneous adipose tissue and liver) subjected to long-term post-mortem storage at refrigeration temperature indicated that skeletal muscle can be a suitable tissue for recovering biologically useful RNA for gene expression studies even if the tissue is subjected to post-mortem storage for weeks, whereas adipose tissue and liver should be processed within 24 hours post-mortem.
    • Longitudinal study of the effect of rubber slat mats on locomotory ability, body, limb and claw lesions, and dirtiness of group housed sows

      Calderon Diaz, Julia; Fahey, A. G.; KilBride, A. L.; Green, L. E.; Boyle, Laura A; Teagasc Walsh Fellowship Programme (Oxford University Press (OUP), 2013-08-01)
      This study evaluated the influence of floor type on sow welfare with particular focus on lameness, claw lesions (CL), and injuries. The study used 164 gilts housed in groups of 8 from AI to 110 d of pregnancy in pens with concrete (n = 84) slatted floor left uncovered or covered by 10-mm rubber slat mats (n = 80) through 2 parities. Lameness (0 = normal to 5 = severe), limb (0 = normal to 6 = severe) and body (0 = normal to 5 = severe) lesions, and manure on the body (MOB; score 0 to 2) were recorded at AI, 24 to 72 h postmixing, between 50 and 70 d of pregnancy, and 2 wk before farrowing. Claw lesions (score 0 = normal to 3 = severe) were recorded at AI and between 50 and 70 d of pregnancy. The dirtiness and wetness of the floors was scored weekly (score 0 = clean to 4 = >75% of the pen soiled/wet). Data from the first and second parities were analyzed separately. Sows were categorized as nonlame (score ≤ 1) or lame (score ≥ 2). Median (Me) scores were calculated for CL and body and limb lesions and were classified as less than or equal to the median or greater than the median lesion scores. Sows on rubber slat mats had a reduced risk of lameness during both parities (P < 0.01) compared with sows on concrete. They also had an increased risk of scores greater than the median for toe overgrowth (Me = 2 and Me = 3 in the first and second parity, respectively) and heel sole crack (HSC; Me = 3) during both parities (P < 0.01) and for cracks in the wall (CW; Me = 4) and white line damage (WL; Me = 4; P < 0.01) in the first and second parity, respectively. There was a reduced risk of lameness in sows with scores greater than the median for HSC (P = 0.05) in the first parity and WL (Me = 3; P < 0.01) and CW (Me = 3; P < 0.05) in the second parity. Wounds (Me = 3) and severe lesions (Me = 0) on the limbs with scores greater than the median were associated with an increased risk of lameness (P < 0.01) in the first and second parity, respectively. Sows on rubber slat mats had a reduced risk of scores greater than the median for swellings (Me = 4) and wounds (P < 0.01) during both parities. Pens with rubber slat mats were dirtier than uncovered pens (P < 0.01); however, there was no association between MOB and flooring type. There was also no association between body lesion score and flooring type. In this study, CL were not associated with an increased risk of lameness. Therefore, even though rubber slat mats were associated with an increased risk of CL, they improved the welfare of group housed sows by reducing the risk of lameness and limb lesions.
    • Low numbers of ovarian follicles ≥3 mm in diameter are associated with low fertility in dairy cows

      Mossa, F.; Walsh, S.W.; Butler, Stephen T.; Berry, Donagh; Carter, F.; Lonergan, P.; Smith, G.W.; Ireland, J.J.; Evans, A.C.O. (American Dairy Science Association, 2012-05-01)
      The total number of ovarian follicles ≥3 mm in diameter (antral follicle count, AFC) during follicular waves varies among cattle of similar age, but AFC is highly repeatable within individuals. We hypothesized that lower AFC could be associated with reduced fertility in cattle. The AFC was assessed by ultrasonography for 2 d consecutively during the first wave of follicular growth of the estrous cycle, 4.6 ± 1.43 d (mean ± SD) after estrus, in 306 Holstein-Friesian dairy cows approximately 70 d postpartum. Cows were classified into 3 groups based on AFC: low (AFC ≤15), intermediate (AFC = 16 to 24), and high (AFC ≥25). During the cycle in which AFC was assessed and in subsequent cycles, cows were artificially inseminated (AI) following detection of estrus, and pregnancy status was assessed using ultrasonography. Cows with high AFC had 3.34 times greater odds of being pregnant at the end of the breeding season compared with cows with low AFC; the odds of a successful pregnancy at first service were 1.75 times greater in the intermediate compared with the low group. The predicted probability of a successful pregnancy by the end of the breeding period (length of breeding season was 86 ± 16.3 d) was 94, 88, and 84% for the high, intermediate, and low AFC groups, respectively. No difference was evident among groups in 21-d submission rate (proportion of all cows detected in estrus and submitted for AI in the first 21 d of the breeding season), but the interval from calving to conception was shorter in the high (109.5 ± 5.1 d) versus low (117.1 ± 4 d) group, and animals with intermediate AFC received fewer services during the breeding season (2.3 ± 0.1) compared with animals with low AFC (2.7 ± 0.1). Lactating cows with ≤15 ovarian follicles have lower reproductive performance compared with cows with higher numbers of follicles, but the existence of a positive association between high numbers of ovarian follicles and fertility is yet to be established.
    • Low numbers of ovarian follicles ≥3 mm in diameter are associated with low fertility in dairy cows

      Mossa, F.; Walsh, Siobhán; Butler, Stephen T.; Berry, Donagh; Carter, Fiona; Lonergan, Patrick; Smith, George W.; Ireland, James J.; Evans, Alex C.O. (Elsevier for American Dairy Science Association, 2012-04-24)
      The total number of ovarian follicles ≥3 mm in diameter (antral follicle count, AFC) during follicular waves varies among cattle of similar age, but AFC is highly repeatable within individuals. We hypothesized that lower AFC could be associated with reduced fertility in cattle. The AFC was assessed by ultrasonography for 2 d consecutively during the first wave of follicular growth of the estrous cycle, 4.6 ± 1.43 d (mean ± SD) after estrus, in 306 Holstein-Friesian dairy cows approximately 70 d postpartum. Cows were classified into 3 groups based on AFC: low (AFC ≤15), intermediate (AFC = 16 to 24), and high (AFC ≥25). During the cycle in which AFC was assessed and in subsequent cycles, cows were artificially inseminated (AI) following detection of estrus, and pregnancy status was assessed using ultrasonography. Cows with high AFC had 3.34 times greater odds of being pregnant at the end of the breeding season compared with cows with low AFC; the odds of a successful pregnancy at first service were 1.75 times greater in the intermediate compared with the low group. The predicted probability of a successful pregnancy by the end of the breeding period (length of breeding season was 86 ± 16.3 d) was 94, 88, and 84% for the high, intermediate, and low AFC groups, respectively. No difference was evident among groups in 21-d submission rate (proportion of all cows detected in estrus and submitted for AI in the first 21 d of the breeding season), but the interval from calving to conception was shorter in the high (109.5 ± 5.1 d) versus low (117.1 ± 4 d) group, and animals with intermediate AFC received fewer services during the breeding season (2.3 ± 0.1) compared with animals with low AFC (2.7 ± 0.1). Lactating cows with ≤15 ovarian follicles have lower reproductive performance compared with cows with higher numbers of follicles, but the existence of a positive association between high numbers of ovarian follicles and fertility is yet to be established.
    • Low-density genotype panel for both parentage verification and discovery in a multi-breed sheep population

      Berry, Donagh; McHugh, Noirin; Wall, E.; McDermott, K.; O’Brien, A.C.; Department of Agriculture, Food and the Marine (Teagasc, 2019-03-01)
      The generally low usage of artificial insemination and single-sire mating in sheep, compounded by mob lambing (and lambing outdoors), implies that parentage assignment in sheep is challenging. The objective here was to develop a low-density panel of single nucleotide polymorphisms (SNPs) for accurate parentage verification and discovery in sheep. Of particular interest was where SNP selection was limited to only a subset of chromosomes, thereby eliminating the ability to accurately impute genome-wide denser marker panels. Data used consisted of 10,933 candidate SNPs on 9,390 purebred sheep. These data consisted of 1,876 validated genotyped sire–offspring pairs and 2,784 validated genotyped dam–offspring pairs. The SNP panels developed consisted of 87 SNPs to 500 SNPs. Parentage verification and discovery were undertaken using 1) exclusion, based on the sharing of at least one allele between candidate parent–offspring pairs, and 2) a likelihood-based approach. Based on exclusion, allowing for one discordant offspring–parent genotype, a minimum of 350 SNPs was required when the goal was to unambiguously identify the true sire or dam from all possible candidates. Results suggest that, if selecting SNPs across the entire genome, a minimum of 250 carefully selected SNPs are required to ensure that the most likely selected parent (based on the likelihood approach) was, in fact, the true parent. If restricting the SNPs to just a subset of chromosomes, the recommendation is to use at least a 300-SNP panel from at least six chromosomes, with approximately an equal number of SNPs per chromosome.