• Paratuberculosis sero-status and milk production, SCC and calving interval in Irish dairy herds

      Hoogendam, K; Richardson, Esther K. B.; Mee, John F (Biomed Central, 2009-04-01)
      The objective of this study was to investigate the impact of paratuberculosis sero-status on milk yield, fat, protein, somatic cell count and calving interval in Irish dairy herds. Serum from all animals over 12 months of age (n = 2,602) in 34 dairy herds was tested for antibodies to Mycobacterium avium subsp. paratuberculosis using an ELISA. Herds were categorised by sero-status into positive, non-negative and negative, where a positive herd contained two or more positive cows, a non-negative herd contained only one positive cow and a negative herd contained no positive cows. Data at animal, parity and herd-level were analysed by multiple regression using general linear models. Positive herds (mean herd size = 129 cows) and non-negative herds (81 cows) were larger than negative herds (72 cows) (P < 0.01). Negative herds had the highest economic breeding index (EBI), while positive herds had the highest estimated breeding value (EBV) for milk yield. There was no significant effect of paratuberculosis sero-status at animal, parity or herd-level on milk yield, milk fat or protein production, somatic cell count score (SCCS) or calving interval. Negative herds tended to have a lower SCCS than positive and nonnegative herds (P = 0.087). This study only examined the effects of paratuberculosis sero-status but did not examine the clinical effects of Johne's disease at the farm or dairy industry levels.
    • Pathogenomic analysis of the common bovine Staphylococcus aureus clone (ET3): emergence of a virulent subtype with potential risk to public health

      Smyth, Cyril James; Hartigan, James Patrick (University of Chicago Press, 2012-07-02)
      A common clone (ET3) of Staphylococcus aureus is responsible for a large proportion of cases of bovine mastitis and occasionally causes zoonotic infections of humans. In the present study, we report the identification of a virulent clonal subtype (ST151) of ET3, which resulted in increased tissue damage and mortality in a mouse model of mastitis. ST151 has undergone extensive diversification in virulence and regulatory‐gene content, including the acquisition of genetic elements encoding toxins not made by other ET3 strains. Furthermore, ST151 had elevated levels of RNAIII and cytolytic toxin–gene expression, consistent with the enhanced virulence observed during experimental infection. Previously, the ST151 clone was shown to be hypersusceptible to the acquisition of vancomycin‐resistance genes from Enterococcus spp. Taken together, these data indicate the emergence of a virulent subtype of the common ET3 clone, which could present an enhanced risk to public health.
    • Perinatal immuno/inflammatory responses in the presence or absence of bovine fetal infection

      Jawor, Paulina; Mee, John F; Stefaniak, Tadeusz; The National Centre for Research and Development; PBS2/A8/20/2013 (Biomed Central, 2018-11-01)
      Background It is known that the bovine fetus can mount an immune and inflammatory reaction to infection, but it is not known whether there is a contemporaneous maternal response. Nor is it known whether the response of calves which die perinatally, with or without infection, differs from that of live perinates. Hence, the objective of this study was to determine if acute phase reactant and immunoglobulin concentrations differed between calves (and their dams) in three groups: live calves (CC; n = 21) and dead calves with (PM INF+; n = 22) or without (PM INF-; n = 89) in utero infection. In calf plasma, serum amyloid A, haptoglobin, immunoglobulins M, G1 and G2 and interleukin-6 were measured. In dam serum, SAA and Hp was measured and in amniotic and abomasal fluid, IL-6 was measured. Results Live calves had higher plasma concentrations of SAA and IL-6 than dead calves with (PM INF+) or without (PM INF-) in utero infection. Calves in the PM INF-, but not PM INF+ group, had higher Hp concentrations than calves in the CC group. Calves in the PM INF+ group had higher IgG1 concentrations than calves in the PM INF- and CC groups. Except for higher IgG1 and IgG2 concentrations, biomarker values did not differ significantly between dead calves with or without in utero infection. Live calves had higher IL-6 concentrations in abomasal fluid compared to PM INF- calves. There were no significant differences in blood biomarker concentrations between dams of the three groups of calves. Amniotic fluid IL-6 concentrations were higher from the dams of control calves than the dams of uninfected calves. Conclusions Differences in biomarkers (higher Hp and IgG1; lower SAA and IL-6) between perinatal mortalities and live perinates probably reflect differences between these two groups in age at sampling (SAA and IL-6) and in utero infection (IgG1). Out of the six analytes measured in calves, only IgG1 and IgG2 were biomarkers of (chronic) in utero infection.
    • Peripheral and gastrointestinal immune systems of healthy cattle raised outdoors at pasture or indoors on a concentrate-based ration

      Lejeune, Alexandre; Monahan, Frank J; Moloney, Aidan P; Earley, Bernadette; Black, Alistair D; Campion, Deirdre P; Englishby, Tanya; Reilly, Petrina; O'Doherty, John V.; Sweeney, Torres (Biomed Central, 2010-03-31)
      Background: Despite an increasing preference of consumers for beef produced from more extensive pasture-based production systems and potential human health benefits from the consumption of such beef, data regarding the health status of animals raised on pasture are limited. The objective of this study was to characterise specific aspects of the bovine peripheral and the gastrointestinal muscosal immune systems of cattle raised on an outdoor pasture system in comparison to animals raised on a conventional intensive indoor concentrate-based system. Results: A number of in vitro functional tests of immune cells suggested subtle differences between the animals on the outdoor versus indoor production systems. There was a decrease in the number of neutrophils and monocytes engaged in phagocytosis in outdoor cattle (P < 0.01 and P < 0.05, respectively) in comparison to those indoors. Following mitogen stimulation, a lower level of interferon-γ was produced in leukocytes from the outdoor animals (P < 0.05). There was evidence of a gastrointestinal nematode infection in the outdoor animals with elevated levels of serum pepsinogen (P < 0.001), a higher number of eosinophils (P < 0.05) and a higher level of interleukin-4 and stem cell factor mRNA expression (P < 0.05) in the outdoor animals in comparison to the indoor animals. Lower levels of copper and iodine were measured in the outdoor animals in comparison to indoor animals (P < 0.001). Conclusion: Despite distinctly contrasting production systems, only subtle differences were identified in the peripheral immune parameters measured between cattle raised at pasture in comparison to animals raised on a conventional intensive indoor concentrate-based production system.
    • Physically-based, distributed, catchment modelling for estimating sediment and phosphorus loads to rivers and lakes : issues of model complexity, spatial and temporal scales and data requirements

      Nasr, Ahmed Elssidig; Bruen, Michael; Jordan, Philip; Moles, Richard; Kiely, Gerard; Byrne, Paul (Office of Public Works, 02/07/2012)
    • Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species

      De Vega, Jose J.; Teshome, Abel; Klaas, Manfred; Grant, Jim; Finnan, John; Barth, Susanne; European Union; Marie Sklodowska-Curie Actions COFUND CAROLINE; UK Research Council; FP7-KBBE-2011-5-289461; et al. (Biomed Central, 2021-03-06)
      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.
    • Pig producer perspectives on the use of meat inspection as an animal health and welfare diagnostic tool in the Republic of Ireland and Northern Ireland

      Devitt, Catherine; Boyle, Laura; Teixeira, Dayane L.; O'Connell, Niamh E.; Hawe, M.; Hanlon, A.; Department of Agriculture, Food and the Marine; RSF 11/S/107 (Biomed Central, 2016-02-09)
      Background Currently, there is growing interest in developing ante and post mortem meat inspection (MI) to incorporate measures of pig health and welfare for use as a diagnostic tool on pig farms. However, the success of the development of the MI process requires stakeholder engagement with the process. Knowledge gaps and issues of trust can undermine the effective exchange and utilisation of information across the supply chain. A social science research methodology was employed to establish stakeholder perspectives towards the development of MI to include measures of pig health and welfare. In this paper the findings of semi-structured telephone interviews with 18 pig producers from the Republic of Ireland and Northern Ireland are presented. Results Producers recognised the benefit of the utilisation of MI data as a health and welfare diagnostic tool. This acknowledgment, however, was undermined for some by dissatisfaction with the current system of MI information feedback, by trust and fairness concerns, and by concerns regarding the extent to which data would be used in the producers’ interests. Tolerance of certain animal welfare issues may also have a negative impact on how producers viewed the potential of MI data. The private veterinary practitioner was viewed as playing a vital role in assisting them with the interpretation of MI data for herd health planning. Conclusions The development of positive relationships based on trust, commitment and satisfaction across the supply chain may help build a positive environment for the effective utilisation of MI data in improving pig health and welfare. The utilisation of MI as a diagnostic tool would benefit from the development of a communication strategy aimed at building positive relationships between stakeholders in the pig industry.
    • A pilot study on the prevalence of lice in Irish beef cattle and the first Irish report of deltamethrin tolerance in Bovicola bovis

      Mckiernan, Fiona; O’Connor, Jack; Minchin, William; O’Riordan, Edward; Dillon, Alan; Harrington, Martina; Zintl, Annetta; MSD Animal Health (Biomed Central, 2021-07-05)
      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.
    • Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples.

      Mullen, Michael P.; Creevey, Christopher J.; Berry, Donagh; McCabe, Matthew; Magee, David A; Howard, Dawn J.; Killeen, Aideen P.; Park, Stephen D. E.; McGettigan, Paul; Lucy, Matt C.; et al. (Biomed Central, 2012-01-11)
      Background: The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within this axis is an attractive goal. However, large sample numbers are a pre-requisite for the identification of genetic variants underlying complex traits and although technologies are improving rapidly, high-throughput sequencing of large numbers of complete individual genomes remains prohibitively expensive. Therefore using a pooled DNA approach coupled with target enrichment and high-throughput sequencing, the aim of this study was to identify polymorphisms and estimate allele frequency differences across 83 candidate genes of the somatotrophic axis, in 150 Holstein-Friesian dairy bulls divided into two groups divergent for genetic merit for fertility. Results: In total, 4,135 SNPs and 893 indels were identified during the resequencing of the 83 candidate genes. Nineteen percent (n = 952) of variants were located within 5' and 3' UTRs. Seventy-two percent (n = 3,612) were intronic and 9% (n = 464) were exonic, including 65 indels and 236 SNPs resulting in non-synonymous substitutions (NSS). Significant (P < 0.01) mean allele frequency differentials between the low and high fertility groups were observed for 720 SNPs (58 NSS). Allele frequencies for 43 of the SNPs were also determined by genotyping the 150 individual animals (Sequenom® MassARRAY). No significant differences (P > 0.1) were observed between the two methods for any of the 43 SNPs across both pools (i.e., 86 tests in total). Conclusions: The results of the current study support previous findings of the use of DNA sample pooling and high-throughput sequencing as a viable strategy for polymorphism discovery and allele frequency estimation. Using this approach we have characterised the genetic variation within genes of the somatotrophic axis and related pathways, central to mammalian post-natal growth and development and subsequent lactogenesis and fertility. We have identified a large number of variants segregating at significantly different frequencies between cattle groups divergent for calving interval plausibly harbouring causative variants contributing to heritable variation. To our knowledge, this is the first report describing sequencing of targeted genomic regions in any livestock species using groups with divergent phenotypes for an economically important trait.
    • Polymorphisms in bovine immune genes and their associations with somatic cell count and milk production in dairy cattle

      Beecher, Christine; Daly, Mairead; Childs, Stuart; Berry, Donagh; Magee, David A; McCarthy, Tommie V; Giblin, Linda (Biomed Central, 05/11/2010)
      Background: Mastitis, an inflammation of the mammary gland, is a major source of economic loss on dairy farms. The aim of this study was to quantify the associations between two previously identified polymorphisms in the bovine toll-like receptor 2 (TLR2) and chemokine receptor 1 (CXCR1) genes and mammary health indictor traits in (a) 246 lactating dairy cow contemporaries representing five breeds from one research farm and (b) 848 Holstein-Friesian bulls that represent a large proportion of the Irish dairy germplasm. To expand the study, a further 14 polymorphisms in immune genes were included for association studies in the bull population. Results: TLR4-2021 associated (P < 0.05) with both milk protein and fat percentage in late lactation (P < 0.01) within the cow cohort. No association was observed between this polymorphism and either yield or composition of milk within the bull population. CXCR1-777 significantly associated (P < 0.05) with fat yield in the bull population and tended to associate (P < 0.1) with somatic cell score (SCS) in the cows genotyped. CD14-1908 A allele was found to associate with increased (P < 0.05) milk fat and protein yield and also tended to associate with increased (P < 0.1) milk yield. A SERPINA1 haplotype with superior genetic merit for milk protein yield and milk fat percentage (P < 0.05) was also identified. Conclusion: Of the sixteen polymorphisms in seven immune genes genotyped, just CXCR1-777 tended to associate with SCS, albeit only in the on-farm study. The lack of an association between the polymorphisms with SCS in the Holstein-Friesian data set would question the potential importance of these variants in selection for improved mastitis resistance in the Holstein-Friesian cow.
    • Post-epidemic Schmallenberg virus circulation: parallel bovine serological and Culicoides virological surveillance studies in Ireland

      Collins, Áine B; Barrett, Damien; Doherty, Michael L.; Larska, M.; Mee, John F; Teagasc Walsh Fellowship Programme; National Centre for Research and Development (NCBiR), Poland; PBS2/A8/24/2013 (Biomed Central, 2016-10-18)
      Background Schmallenberg virus (SBV) emerged in northern-Europe in 2011 resulting in an epidemic of ruminant abortions and congenital malformations throughout the continent. In the years following the epidemic there have been reports of SBV overwintering and continued circulation in several European countries. When the population-level of immunity declines in exposed regions, re-introduction of SBV could result in further outbreaks of Schmallenberg disease. The aims of this study were to determine the SBV seroprevalence in previously exposed Irish dairy herds in 2014 and to investigate if SBV continued to circulate in these herds in the three years (2013–2015) following the Irish Schmallenberg epidemic. Whole-herd SBV serosurveillance was conducted in 26 herds before (spring) and following the 2014 vector-season (winter), and following the 2015 vector-season (winter). In spring 2014, 5,531 blood samples were collected from 4,070 cows and 1,461 heifers. In winter 2014, 2,483 blood samples were collected from 1,550 youngstock (8–10 months old) and a subsample (n = 933; 288 cows, 645 heifers) of the seronegative animals identified in the spring. Youngstock were resampled in winter 2015. Culicoides spp. were collected in 10 herds during the 2014 vector-season and analysed for SBV; a total of 138 pools (3,048 Culicoides) from 6 SBV vector species were tested for SBV RNA using real-time PCR. Results In spring 2014, animal-level seroprevalence was 62.5 % (cows = 84.7 %; heifers = 0.6 %). Within-herd seroprevalence ranged widely from 8.5 %–84.1 % in the 26 herds. In winter 2014, 22 animals (0.9 %; 10 cows, 5 heifers, 7 youngstock) originating in 17 herds (range 1–4 animals/herd) tested seropositive. In winter 2015 all youngstock, including the 7 seropositive animals in winter 2014, tested seronegative suggesting their initial positive result was due to persistence of maternal antibodies. All of the Culicoides pools examined tested negative for SBV-RNA. Conclusions SBV appears to have recirculated at a very low level in these herds during 2013 and 2014, while there was no evidence of SBV infection in naïve youngstock during 2015. A large population of naïve animals was identified and may be at risk of infection in future years should SBV re-emerge and recirculate as it has done in continental Europe.
    • Predicted costs and benefits of eradicating BVDV from Ireland

      Stott, Alistair W; Humphry, Roger W; Gunn, George J; Higgins, Isabella; Hennessy, Thia; O'Flaherty, Joe; Graham, David A. (Biomed Central, 02/07/2012)
      Bovine viral diarrhoea virus (BVDV) causes an economically important endemic disease (BVD) of cattle in Ireland and worldwide. Systematic eradication by detection and removal of infectious (BVDV carrier) cattle has been successful in several regions. We therefore assessed the benefits (disease losses avoided) and costs (testing and culling regime) of a potential eradication programme in Ireland. Published bio-economic models of BVDV spread in beef suckler herds and dairy herds were adapted to estimate potential benefits of eradication in Ireland. A simple model of BVDV spread in beef finisher herds was devised to estimate the benefits of eradication in this sector. A six year eradication programme consisting of 5 inter-related virological and serological testing programmes is outlined and costed. We found that the annualised benefits of BVDV eradication in Ireland exceeded the costs by a factor of 5 in the beef suckler sector and a factor of 14 in the dairy sector. Corresponding payback periods were 1.2 and 0.5 years respectively. These results highlight the significant economic impact of BVDV on the Irish cattle industry and suggest a clear economic benefit to eradication using the proposed approach. This type of cost-benefit analysis is considered an essential prerequisite prior to undertaking an eradication campaign of this magnitude.
    • Prevalence of antibodies to Leptospira interrogans serovar hardjo in bulk tank milk from unvaccinated irish dairy herds

      Leonard, Nola; Mee, John F; Snijders, Sylvia M. E.; Mackie, Dermot (Biomed Central, 2004-04-01)
      Bulk tank milk samples, collected from 347 herds throughout the Republic of Ireland using a sampling frame based on seven milk-recording organisations, were tested by ELISA for antibodies to Leptospira interrogans serovar hardjo. These herds, which had not been vaccinated against leptospirosis within the previous five years, were categorised according to their province, milk-recording organisation and size. Two-hundred-and-seventy-three herds (79%) had a positive ELISA titre. Both the probability of a herd being seropositive and the antibody level in the herd milk sample were affected by the province (P < 0.05 and P < 0.01, respectively) and the herd size category (P < 0.05 and P < 0.01, respectively). Larger herds were significantly more likely to have positive reactions and higher mean concentrations of antibody. It was concluded that a high proportion of unvaccinated Irish dairy herds have been exposed to infection with Leptospira hardjo.
    • Prevalence of BoHV-1 seropositive and BVD virus positive bulls on Irish dairy farms and associations between bull purchase and herd status

      Martinez-Ibeas, Ana M; Power, C.; McClure, Jennifer; Sayers, Riona (Biomed Central, 2015-12-09)
      Background BVD and IBR are contagious viral diseases highly prevalent in Irish cattle. Despite their significant reproductive and economic impact very little is known about the BVD and IBR status of stock bulls (a bull used for breeding purposes). There are still a high proportion of dairy farms in Ireland that rely on the use of a bull for breeding cattle and ensuring the fertility of the bulls is of paramount importance for the efficiency of the farms. The prevalence of BoHV-1 and BVD in stock bulls in Irish dairy herds has never been investigated. The objectives of this study therefore were: (i) to provide descriptive, observational data on the use of stock bulls on Irish dairy farms; (ii) to investigate the BVD and BoHV1 status of a sub-set of stock bulls; (iii) to investigate factors associated with BVD and BoHV1 status of stock bulls and (iv) to investigate factors associated with dairy herd status for BVD and BoHV1, including any associations with the use of stock bull. A total of 529 blood samples from bulls involved in the dairy breeding process were analysed for BVD virus using RT-PCR, and BoHV-1 antibodies by ELISA test. A total of 305 different dairy herds took part in the study and the overall BVD and BoHV-1 herd status was determined by ELISA using four bulk tank milk samples over the 2009 lactation. Logistic regression was used to investigate the associations between the stock bulls and BVD and BoHV-1 herd and individual status. Results Of the 305 total participating farms, 235 farms (77 %) had at least one bull and 167 farms had purchased bulls. Two bulls (0.4 %) out of 529 tested were found positive for BVD virus and 87 (16.7 %) tested seropositive for BoHV-1. Some significant associations were identified between the purchase of bulls and both viral diseases. Purchased bulls were three times more likely to be seropositive for BoHV-1 than homebred bulls. In the same way, herds with purchased bulls were three times more likely to be classified as seropositive for BVD and four times more likely to have evidence of recent BoHV-1 circulation than farms where all the bulls were homebred. Conclusions The prevalence of BoHV-1 and BVD in stock bulls in Irish dairy herds has never been investigated. This study highlights the widespread use of stock bulls in Irish dairy herds, as well as the high rate of exchange of bulls between farms. Significant associations were found between the origin of the bull and their serological BoHV-1 status. In keeping with these results, bulls with higher number movements between farms were more likely to be seropositive for BoHV-1.
    • Prevalence of Bovine Viral Diarrhoea Virus (BVDV), Bovine Herpes Virus 1 (BHV 1), Leptospirosis and Neosporosis, and associated risk factors in 161 Irish beef herds

      Barrett, Damien; Parr, Mervyn; Fagan, John; Johnson, Alan; Tratalos, Jamie; Lively, Francis; Diskin, Michael G.; Kenny, David A.; Department of Agriculture, Food and the Marine, Ireland (Biomed Central, 2018-01-06)
      Background There are limited data available, in Ireland or elsewhere, to determine the extent of exposure to various endemic diseases among beef cows and factors associated with exposure to causative pathogens. The objectives of this study were to determine the herd and within herd prevalence of Bovine Viral Diarrhoea Virus (BVDV), Bovine Herpes Virus 1 (BHV-1), Leptospirosis and Neosporosis in a large scale study of commercial beef herds on the island of Ireland, and to examine herd level factors associated with exposure to these pathogens in these herds. Results The average number of cows tested per herd was 35.5 (median 30). Herd level seroprevalence to Bovine Herpesvirus-1(BHV-1), Bovine Viral-Diarrhoea Virus (BVDV), Leptospirosis and Neosporosis was 90%, 100%, 91% and 67%, respectively, while the mean within herd prevalence for the these pathogens was 40%, 77.7%, 65.7% and 5.7%, respectively. The study confirms that the level of seroconversion for the four pathogens of interest increases with herd size. There was also evidence that exposure to one pathogen may increase the risk of exposure to another pathogen. Conclusions Herd level seroprevalences were in excess of 90% for BVDV, BHV-1 and Leptosporosis. Larger herds were subject to increased exposure to disease pathogens. This study suggests that exposure to several pathogens may be associated with the further exposure to other pathogens.
    • Prevalence of welfare outcomes in the weaner and finisher stages of the production cycle on 31 Irish pig farms

      van Staaveren, Nienke; Calderón Díaz, Julia A.; Manzanilla, Edgar G; Hanlon, A.; Boyle, Laura; Department of Agriculture, Food and the Marine, Ireland; 11/S/107 (Biomed Central, 2018-03-27)
      Background Knowledge on the most prevalent welfare problems for pigs in different production stages is required to improve herd management plans. Thirty-one farrow-to-finish pig farms were visited between July and November 2015 to assess the welfare of pigs using the multicriteria approach of the Welfare Quality® protocol. On each farm, 6 pens were selected using proportionate stratified sampling in the first weaner (S1, 4 to 8 wks), second weaner (S2, 8 to 13 wks) and finisher stage (S3, 13 to 23 wks), excluding hospital pens. Each pen was observed for 10 min and the number of pigs affected by different welfare outcomes was recorded. The percentage of pigs affected was calculated and ranked to identify the most prevalent outcomes within each production stage. Differences between production stages were analysed using generalised linear mixed models for binomial data with pen within stage and farm as a random effect. Results Tail and ear lesions showed the highest prevalence; however, large variation was observed between farms. In S1 the most prevalent welfare outcomes (presented as median prevalence) were poor body condition (4.4%), lethargic pigs (1.5%), scouring (20.3% of pens) and huddling (3.7%). In S2 and S3 outcomes related to injurious behaviour (tail lesions: 5.9% [S2] and 10.5% [S3], ear lesions: 9.1% [S2] and 3.3% [S3], and flank lesions: 0.4% [S2] and 1.3% [S3]), lameness (0.8% [S2] and 1.1% [S3]), bursitis (3.9% [S2] and 7.5% [S3]) and hernias (1.6% [S2] and 1.8% [S3]) were more prevalent. Conclusions A large variation was observed for the recorded welfare outcomes corresponding to the different challenges pigs experience during the different stages of production on commercial pig farms. The prevalence of pigs affected by lesions caused by injurious behavior is a cause for concern and requires a collaborative approach to identify appropriate intervention strategies. This information could be used to further investigate appropriate benchmark values for different welfare outcomes that would assist the pig industry to develop appropriate health and welfare management plans to minimise welfare problems. At herd level such plans should include information on aspects of intervention, treatment, and the management of hospital pens as well as euthanasia.
    • Purging of inbreeding depression within the Irish Holstein-Friesian population

      McParland, Sinead; Kearney, Francis; Berry, Donagh (Biomed Central, 2009-01-21)
      The objective of this study was to investigate whether inbreeding depression in milk production or fertility performance has been partially purged due to selection within the Irish Holstein-Friesian population. Classical, ancestral (i.e., the inbreeding of an individual's ancestors according to two different formulae) and new inbreeding coefficients (i.e., part of the classical inbreeding coefficient that is not accounted for by ancestral inbreeding) were computed for all animals. The effect of each coefficient on 305-day milk, fat and protein yield as well as calving interval, age at first calving and survival to second lactation was investigated. Ancestral inbreeding accounting for all common ancestors in the pedigree had a positive effect on 305-day milk and protein yield, increasing yields by 4.85 kg and 0.12 kg, respectively. However, ancestral inbreeding accounting only for those common ancestors, which contribute to the classical inbreeding coefficient had a negative effect on all milk production traits decreasing 305-day milk, fat and protein yields by -8.85 kg, -0.53 kg and -0.33 kg, respectively. Classical, ancestral and new inbreeding generally had a detrimental effect on fertility and survival traits. From this study, it appears that Irish Holstein-Friesians have purged some of their genetic load for milk production through many years of selection based on production alone, while fertility, which has been less intensely selected for in the population demonstrates no evidence of purging.
    • Quantification, description and international comparison of antimicrobial use on Irish pig farms

      O’Neill, Lorcan; Rodrigues da Costa, Maria; Leonard, Finola C; Gibbons, James; Calderón Díaz, Julia A; McCutcheon, Gerard; Manzanilla, Edgar G; Department of Agriculture Food and the Marine; 15 S 676 (Biomed Central, 2020-10-12)
      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.
    • Quantitative analysis of ruminal methanogenic microbial populations in beef cattle divergent in phenotypic residual feed intake (RFI) offered contrasting diets

      Carberry, Ciara A; Kenny, David A.; Kelly, Alan K; Waters, Sinead M.; Department of Agriculture, Food and the Marine; RSF 05 224 (Biomed Central, 2014-08-22)
      Background Methane (CH4) emissions in cattle are an undesirable end product of rumen methanogenic fermentative activity as they are associated not only with negative environmental impacts but also with reduced host feed efficiency. The aim of this study was to quantify total and specific rumen microbial methanogenic populations in beef cattle divergently selected for residual feed intake (RFI) while offered (i) a low energy high forage (HF) diet followed by (ii) a high energy low forage (LF) diet. Ruminal fluid was collected from 14 high (H) and 14 low (L) RFI animals across both dietary periods. Quantitative real time PCR (qRT-PCR) analysis was conducted to quantify the abundance of total and specific rumen methanogenic microbes. Spearman correlation analysis was used to investigate the association between the relative abundance of methanogens and animal performance, rumen fermentation variables and diet digestibility. Results Abundance of methanogens, did not differ between RFI phenotypes. However, relative abundance of total and specific methanogen species was affected (P < 0.05) by diet type, with greater abundance observed while animals were offered the LF compared to the HF diet. Conclusions These findings suggest that differences in abundance of specific rumen methanogen species may not contribute to variation in CH4 emissions between efficient and inefficient animals, however dietary manipulation can influence the abundance of total and specific methanogen species.
    • Quantitative trait loci associated with different polar metabolites in perennial ryegrass - providing scope for breeding towards increasing certain polar metabolites

      Foito, Alexandre; Hackett, Christine A; Stewart, Derek; Velmurugan, Janaki; Milbourne, Dan; Byrne, Stephen L.; Barth, Susanne; Department of Agriculture, Food and the Marine, Ireland; RSF 06–346 (Biomed Central, 10/10/2017)
      Background Recent advances in the mapping of biochemical traits have been reported in Lolium perenne. Although the mapped traits, including individual sugars and fatty acids, contribute greatly towards ruminant productivity, organic acids and amino acids have been largely understudied despite their influence on the ruminal microbiome. Results In this study, we used a targeted gas-chromatography mass spectrometry (GC-MS) approach to profile the levels of 25 polar metabolites from different classes (sugars, amino acids, phenolic acids, organic acids and other nitrogen-containing compounds) present in a L. perenne F2 population consisting of 325 individuals. A quantitative trait (QTL) mapping approach was applied and successfully identified QTLs regulating seven of those polar metabolites (L-serine, L-leucine, glucose, fructose, myo-inositol, citric acid and 2, 3-hydroxypropanoic acid).Two QTL mapping approaches were carried out using SNP markers on about half of the population only and an imputation approach using SNP and DArT markers on the entire population. The imputation approach confirmed the four QTLs found in the SNP-only analysis and identified a further seven QTLs. Conclusions These results highlight the potential of utilising molecular assisted breeding in perennial ryegrass to modulate a range of biochemical quality traits with downstream effects in livestock productivity and ruminal digestion.