Now showing items 21-40 of 246

    • Effect of space allowance and mixing on growth performance and body lesions of grower-finisher pigs in pens with a single wet-dry feeder

      Camp Montoro, Jordi; Boyle, Laura A; Solà-Oriol, David; Muns, Ramon; Gasa, Josep; Garcia Manzanilla, Edgar; Teagasc Walsh Scholarship Programme; 0415 (Biomed Central, 2021-01-06)
      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

      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.
    • 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

      Rodrigues da Costa, Maria; García Manzanilla, Edgar; Diana, Alessia; van Staaveren, Nienke; Torres-Pitarch, Alberto; Boyle, Laura A; Calderón Díaz, Julia A; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; 14/S/832; et al. (Biomed Central, 2021-01-11)
      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

      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.
    • Investigation of bovine abortion and stillbirth/perinatal mortality - similar diagnostic challenges, different approaches

      Mee, John F (Biomed Central, 2020-09-04)
      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

      Mallikarjunappa, Sanjay; Shandilya, Umesh K; Sharma, Ankita; Lamers, Kristen; Bissonnette, Nathalie; Karrow, Niel A; Meade, Kieran G; Teagasc Walsh Fellowship Programme; Natural Sciences and Engineering Research Council of Canada (NSERC); Semex Alliance (Canada) (2020-11-02)
      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.
    • Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle

      Lam, S.; Zeidan, J.; Miglior, F.; Suárez-Vega, A.; Gómez-Redondo, I.; Fonseca, P. A S; Guan, L. L; Waters, S.; Cánovas, A.; Ontario Ministry of Agriculture, Food, and Rural Affairs (OMAFRA); et al. (Biomed Central, 2020-10-08)
      Background Optimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy to identify genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, leading to economic benefits for beef production. This study used RNA-Seq data (GEO Accession ID: PRJEB7696 and PRJEB15314) from muscle and liver tissue, respectively, from 12 Nellore beef steers selected from 585 steers with residual feed intake measures (RFI; n = 6 low-RFI, n = 6 high-RFI). Three RNA-Seq pipelines were compared including multi-sample calling from i) non-merged samples; ii) merged samples by RFI group, iii) merged samples by RFI and tissue group. The RNA-Seq reads were aligned against the UMD3.1 bovine reference genome (release 94) assembly using STAR aligner. Variants were called using BCFtools and variant effect prediction (VeP) and functional annotation (ToppGene) analyses were performed. Results On average, total reads detected for Approach i) non-merged samples for liver and muscle, were 18,362,086.3 and 35,645,898.7, respectively. For Approach ii), merging samples by RFI group, total reads detected for each merged group was 162,030,705, and for Approach iii), merging samples by RFI group and tissues, was 324,061,410, revealing the highest read depth for Approach iii). Additionally, Approach iii) merging samples by RFI group and tissues, revealed the highest read depth per variant coverage (572.59 ± 3993.11) and encompassed the majority of localized positional genes detected by each approach. This suggests Approach iii) had optimized detection power, read depth, and accuracy of SNP calling, therefore increasing confidence of variant detection and reducing false positive detection. Approach iii) was then used to detect unique SNPs fixed within low- (12,145) and high-RFI (14,663) groups. Functional annotation of SNPs revealed positional candidate genes, for each RFI group (2886 for low-RFI, 3075 for high-RFI), which were significantly (P < 0.05) associated with immune and metabolic pathways. Conclusion The most optimized RNA-Seq pipeline allowed for more accurate identification of SNPs, associated positional candidate genes, and significantly associated metabolic pathways in muscle and liver tissues, providing insight on the underlying genetic architecture of feed efficiency in beef cattle.
    • Length of metacarpal and metatarsal bones in five Iranian sheep breeds and their associations with ungula measurements

      Azarpajouh, Samaneh; Munita, María P.; Calderón Díaz, Julia A. (2021-12-06)
      Background This study aimed to measure the length of metacarpal and metatarsal bones in five Iranian sheep breeds and to correlate the length of the bones with ungula measurements. Thoracic and pelvic limbs of 2-year-old, previously untrimmed, pastured Afshari, Moghani, Kurdi, Makoui, and Lori–Bakhtiari ewes, (n = 20 ewes per breed) were collected after slaughter. The following lengths were recorded in the metacarpal and metatarsal bones: from the margo proximalis lateralis to the lateral (L1) and medial (D1) cartilago physialis; from the margo proximalis lateralis to the margo abaxialis of the lateral (L2) and medial (D2) caput; from the cartilago physialis lateralis to the margo abaxialis of the lateral caput (X1); from the cartilago physialis medialis to the margo distalis of the caput ridge (X2) and from the margo axialis of cartilago physialis to the margo axialis of the lateral caput (X3). Additionally, measurements of the ungula including pars dorsalis length, pars mobilis lateralis and medialis height, pars dorsalis height to the ground and to the solea cornea, thickness of the solea in the pars dorsalis, pars mobilis lateralis and medialis, solea cornea length and angulus dorsalis were recorded in the medial and lateral digits of the thoracic and pelvic limbs. Data on length of the metatarsal and metacarpal bones were analysed using mixed model equations while Pearson correlations were calculated between metacarpal and metatarsal bones and ungula measurements. Results Lori- Bakhtiari and Moghani ewes had greater L1, L2, and D1 and D2 while X1, X2 and X3 was greater in Kurdi ewes (P < 0.05). Measurements such as L1, L2, D1 and D2 were greater in the metatarsal than in metacarpal bones (P < 0.05) and the opposite was observed for X1, X2 and X3 (P < 0.05). No asymmetry was observed between the lateral and medial measurements (P > 0.05). Low to moderate correlations were observed between bone and ungula measurements (P < 0.05). Conclusion Under the conditions of this study, differences in metacarpal and metatarsal bone measurements were observed between breeds but no asymmetry was observed between lateral and medial bones. Results indicate an association between metacarpal and metatarsal bones ungula measurements. This could provide baseline information for the development and/or improvement of current ungula health protocols in the studied sheep breeds.
    • Antimicrobial resistance in commensal Escherichia coli and Enterococcus spp. is influenced by production system, antimicrobial use, and biosecurity measures on Spanish pig farms

      Mencía-Ares, Oscar; Argüello, Héctor; Puente, Héctor; Gómez-García, Manuel; Manzanilla, Edgar G; Álvarez-Ordóñez, Avelino; Carvajal, Ana; Rubio, Pedro; INIA; Spanish Government (Ministerio de Educación y Formación Profesional); et al. (Biomed Central, 2021-03-19)
      Background Antimicrobial resistance (AMR) is a global public health threat consequence of antimicrobial use (AMU) in human and animal medicine. In food-producing animals factors such as management, husbandry or biosecurity may impact AMU. Organic and extensive Iberian swine productions are based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the AMR in indicator bacteria. Here, we evaluate the usefulness of commensal Escherichia coli and Enterococcus spp. isolates as AMR bioindicators when comparing 37 Spanish pig farms from both intensive and organic-extensive production systems, considering the effect of AMU and biosecurity measures, the last only on intensive farms. Results The production system was the main factor contributing to explain the AMR differences in E. coli and Enterococcus spp. In both bacteria, the pansusceptible phenotype was more common (p < 0.001) on organic-extensive farms when compared to intensive herds. The microbiological resistance in commensal E. coli was, for most of the antimicrobials evaluated, significantly higher (p < 0.05) on intensive farms. In enterococci, the lincosamides usage revealed the association between AMR and AMU, with an increase in the AMR for erythromycin (p < 0.01), quinupristin-dalfopristin (p < 0.01) and the multidrug-resistant (MDR) phenotype (p < 0.05). The biosecurity measures implemented on intensive farms influenced the AMR of these bioindicators, with a slightly lower resistance to sulfamethoxazole (p < 0.01) and the MDR phenotype (p < 0.05) in E. coli isolated from farms with better cleaning and disinfection protocols. On these intensive farms, we also observed that larger herds had a higher biosecurity when compared to smaller farms (p < 0.01), with no significant associations between AMU and the biosecurity scores. Conclusions Overall, this study evidences that the production system and, to a lesser extent, the biosecurity measures, contribute to the AMR development in commensal E. coli and Enterococcus spp., with antimicrobial usage as the main differential factor, and demonstrates the potential value of these bacteria as bioindicators on pig farms in AMR surveillance programs.
    • 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.
    • Conserved and breed-specific differences in the cervical transcriptome of sheep with divergent fertility at the follicular phase of a natural oestrus cycle

      Abril-Parreño, Laura; Meade, Kieran G.; Krogenæs, Anette K.; Druart, Xavier; Fair, Sean; Cormican, Paul; European Union; Department of Agriculture, Food and the Marine; Teagasc; Research Council of Norway; et al. (Biomed Central, 2021-10-20)
      Background The outcome of cervical artificial insemination (AI) with frozen-thawed semen in sheep is limited by the inability of sperm to traverse the cervix of some ewe breeds. Previous research has demonstrated that cervical sperm transport is dependent on ewe breed, as sperm can traverse the cervix in greater numbers in some higher fertility ewe breeds. However, the molecular mechanisms underlying ewe breed differences in sperm transport through the cervix remain unknown. In this study, we aimed to characterise the cervical transcriptome of four European ewe breeds with known differences in pregnancy rates following cervical AI using frozen-thawed semen at the follicular phase of a natural oestrous cycle. Cervical post mortem tissue samples were collected from two Irish ewe breeds (Belclare and Suffolk; medium and low fertility, respectively) and from two Norwegian ewe breeds (Norwegian White Sheep (NWS) and Fur; high fertility compared to both Irish breeds) at the follicular phase of a natural oestrous cycle (n = 8 to 10 ewes per breed). Results High-quality RNA extracted from biopsies of the mid-region of the cervix was analysed by RNA-sequencing and Gene Ontology (GO). After stringent filtering (P <  0.05 and FC > 1.5), a total of 11, 1539 and 748 differentially expressed genes (DEGs) were identified in Belclare, Fur and NWS compared to the low fertility Suffolk breed, respectively. Gene ontology analysis identified significantly enriched biological processes involved in muscle contraction, extracellular matrix (ECM) development and the immune response. Gene co-expression analysis revealed similar patterns in muscle contraction and ECM development modules in both Norwegian ewe breeds, which differed to the Irish ewe breeds. Conclusions These breed-specific biological processes may account for impaired cervical sperm transport through the cervix in sheep during the follicular phase of the reproductive cycle. This novel and comprehensive dataset provides a rich foundation for future targeted initiatives to improve cervical AI in sheep.
    • Adding value to food chain information: using data on pig welfare and antimicrobial use on-farm to predict meat inspection outcomes

      Pessoa, Joana; McAloon, Conor; Rodrigues da Costa, Maria; García Manzanilla, Edgar; Norton, Tomas; Boyle, Laura; Teagasc Walsh Scholarship Programme; Meat Industry Ireland (Biomed Central, 2021-10-14)
      Background Using Food Chain Information data to objectively identify high-risk animals entering abattoirs can represent an important step forward towards improving on-farm animal welfare. We aimed to develop and evaluate the performance of classification models, using Gradient Boosting Machine algorithms that utilise accurate longitudinal on-farm data on pig health and welfare to predict condemnations, pluck lesions and low cold carcass weight at slaughter. Results The accuracy of the models was assessed using the area under the receiver operating characteristics (ROC) curve (AUC). The AUC for the prediction models for pneumonia, dorsocaudal pleurisy, cranial pleurisy, pericarditis, partial and total condemnations, and low cold carcass weight varied from 0.54 for pneumonia and 0.67 for low cold carcass weight. For dorsocaudal pleurisy, ear lesions assessed on pigs aged 12 weeks and antimicrobial treatments (AMT) were the most important prediction variables. Similarly, the most important variable for the prediction of cranial pleurisy was the number of AMT. In the case of pericarditis, ear lesions assessed both at week 12 and 14 were the most important variables and accounted for 33% of the Bernoulli loss reduction. For predicting partial and total condemnations, the presence of hernias on week 18 and lameness on week 12 accounted for 27% and 14% of the Bernoulli loss reduction, respectively. Finally, AMT (37%) and ear lesions assessed on week 12 (15%) were the most important variables for predicting pigs with low cold carcass weight. Conclusions The findings from our study show that on farm assessments of animal-based welfare outcomes and information on antimicrobial treatments have a modest predictive power in relation to the different meat inspection outcomes assessed. New research following the same group of pigs longitudinally from a larger number of farms supplying different slaughterhouses is required to confirm that on farm assessments can add value to Food Chain Information reports.
    • Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

      Cobo-Díaz, José F.; Alvarez-Molina, Adrián; Alexa, Elena A.; Walsh, Calum J.; Mencía-Ares, Oscar; Puente-Gómez, Paula; Likotrafiti, Eleni; Fernández-Gómez, Paula; Prieto, Bernardo; Crispie, Fiona; et al. (Biomed Central, 2021-10-14)
      Background The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity. Results We identified a relatively restricted principal microbiota dominated by Pseudomonas during the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g., Acinetobacter, Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and β-dispersion of ARGs, which were predominantly assigned to Acinetobacter and associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum β-lactamase-producing Enterobacteriaceae and vancomycin-resistant Enterococcaceae was observed when cutting activities started. ARGs associated with resistance to β-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains. Conclusions The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility. Video Abstract
    • Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle

      Rafter, Pierce; Gormley, Isobel C.; Purfield, Deirdre; Parnell, Andrew C.; Naderi, Saeid; Berry, Donagh P.; Science Foundation Ireland; 14/IA/2576 (Biomed Central, 2021-10-23)
      Background The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understanding of the genetic variants that contribute to carcass merit is useful to maximize the efficiency of breeding for improved carcass merit. The objectives of the present study were two-fold: firstly, to perform genome-wide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). The LRR value of a SNP is a measure of the signal intensity of the SNP generated during the genotyping process. Results A total of 13,969, 3,954, and 2,805 detected CNVs were tested for association with the three carcass traits for the Holstein-Friesian, Charolais, and Limousin, respectively. The copy number of 16 CNVs and the LRR of 34 SNPs were associated with at least one of the three carcass traits in at least one of the three cattle breeds. With the exception of three SNPs, none of the quantitative trait loci detected in the CNV association analyses or the SNP LRR association analyses were also detected using traditional association analyses based on SNP allele counts. Many of the CNVs and SNPs associated with the carcass traits were located near genes related to the structure and function of the spliceosome and the ribosome; in particular, U6 which encodes a spliceosomal subunit and 5S rRNA which encodes a ribosomal subunit. Conclusions The present study demonstrates that CNV data and SNP LRR data can be used to detect genomic regions associated with carcass traits in cattle providing information on quantitative trait loci over and above those detected using just SNP allele counts, as is the approach typically employed in genome-wide association analyses.
    • Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms

      Mencía-Ares, Oscar; Cabrera-Rubio, Raúl; Cobo-Díaz, José F; Álvarez-Ordóñez, Avelino; Gómez-García, Manuel; Puente, Héctor; Cotter, Paul D; Crispie, Fiona; Carvajal, Ana; Rubio, Pedro; et al. (Biomed Central, 2020-11-19)
      Background The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms. Results Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms. Conclusions Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production. Video Abstract
    • A bio-economic simulation study on the association between key performance indicators and pluck lesions in Irish farrow-to-finish pig farms

      Calderón Díaz, Julia A; Rodrigues da Costa, Maria; Shalloo, Laurence; Niemi, Jarkko K; Leonard, Finola C; Crespo-Piazuelo, Daniel; Gasa, Josep; García Manzanilla, Edgar; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; et al. (Biomed Central, 2020-12-09)
      Background Pluck lesions are associated with decreased performance in grower-finisher pigs, but their economic impact needs to be further investigated. This study aimed to identify the main pluck lesions and the cut-off value for their prevalence, associated with changes in average daily gain (ADG) during the wean-to-finish period, to simulate their effects on economic performance of farrow-to-finish farms. Pigs (n = 162 ± 51.9 per farm) from 56 farrow-to-finish farms were inspected at slaughter and the prevalence of enzootic pneumonia-like lesions, pleurisy, lung scars, abscesses, pericarditis, and liver milk spots was estimated. For each farm, annual performance indicators were obtained. Regression trees analysis (RTA) was used to identify pluck lesions and to estimate cut-off values for their prevalence associated with changes in ADG. Different scenarios were simulated as per RTA results and economic and risk analyses were performed using the Teagasc Pig Production Model. Risk analysis was performed by Monte Carlo sampling using the Microsoft Excel add-in @Risk with 10,000 iterations. Results Pleurisy and lung scars were the main lesions associated with changes in ADG. Three scenarios were simulated based on RTA results: a 728 sow farrow-to-finish farm with prevalence of i) pleurisy < 25% and lung scars < 8% (LPLSC; ADG = 760 g); ii) pleurisy < 25% and lung scar ≥8% (LPHSC; ADG = 725 g) and iii) pleurisy ≥25% (HP; ADG = 671 g). The economic analysis showed increased feed and dead animals for disposal costs, and lower sales in the HP and LPHSC scenarios than in the LPLSC scenario; thereby reducing gross margin and net profit. Results from the risk analysis showed lower probability of reaching any given level of profit in the HP scenario compared with the LPHSC and LPLSC scenarios. Conclusion Under the conditions of this study, higher prevalence of pleurisy and lung scars were associated with decreased ADG during the grower-finisher period and with lower economic return in the simulated farms. These results highlight the economic benefits and importance of preventing and/or controlling respiratory disease.
    • Associations between animal and herd management factors, serological response to three respiratory pathogens and pluck lesions in finisher pigs on a farrow-to-finish farm

      Fitzgerald, Rose M; O’Shea, Helen; Manzanilla, Edgar G; Moriarty, John; McGlynn, Hugh; Calderón Díaz, Julia A; Department of Agriculture, Food and the Marine; 14/S/832 (Biomed Central, 2020-12-08)
      Background Serological screening is a common method to monitor antibody response to pathogen exposure, but results could vary due to several factors. This study aimed to quantify animal and management related factors associated with variation in antibody levels in finisher pigs at slaughter, in an Irish farrow-to-finish farm endemically infected with Actinobacillus pleuropneumonia (App), Mycoplasma hyopneumoniae (Mhyo) and swine influenza virus (SIV). A second objective was to estimate differences in antibody levels in pigs presenting pluck lesions. This was an observational study whereby pigs were managed as per routine farm practice. Data on sow parity, number of born alive (NBA) pigs per litter, cross-fostering status, birth and weaning body weight were recorded from 1016 pigs born from one farrowing batch. At slaughter, blood samples were collected for serological analysis and pigs were inspected for presence of enzootic pneumonia (EP)-like lesions, pleurisy, pericarditis and heart condemnations. Pigs were retrospectively classified into three production flows, depending on time spent in each production stage: flow 1 (F1; pigs followed the normal production flow); flow 2 (F2; pigs which were delayed by 1 week from advancing forward); and flow 3 (F3; pigs delayed by > 1 week from advancing forward). A nested case-control design was applied by matching pigs from each flow by sow parity, birth weight and NBA. Results Pigs born from primiparous sows had higher antibody levels for App than those born to parity ≥5 sows (P < 0.05) and there was no association between any of the pathogens investigated and other early life indicators (P > 0.05). Pigs in F1 had lower antibody levels for App but higher antibody levels for SIV than F2 and F3 pigs (P < 0.05). There was no association between pluck lesions and respiratory pathogens (P > 0.05), except for increased antibody levels for Mhyo when EP-like lesions were present (P = 0.006). Conclusion Results indicate that offspring from primiparous sows develop higher antibody levels for App IV toxin when exposed to this disease and that enforcement of a strict all-in/all-out production system would reduce on-farm disease circulation. A high percentage of pigs were affected with EP-like lesions which were associated with higher antibody levels for Mhyo.
    • Genetic control of temperament traits across species: association of autism spectrum disorder risk genes with cattle temperament

      Costilla, Roy; Kemper, Kathryn E; Byrne, Enda M; Porto-Neto, Laercio R; Carvalheiro, Roberto; Purfield, Deirdre C; Doyle, Jennifer L; Berry, Donagh P; Moore, Stephen S; Wray, Naomi R; et al. (Biomed Central, 2020-08-26)
      Background Temperament traits are of high importance across species. In humans, temperament or personality traits correlate with psychological traits and psychiatric disorders. In cattle, they impact animal welfare, product quality and human safety, and are therefore of direct commercial importance. We hypothesized that genetic factors that contribute to variation in temperament among individuals within a species will be shared between humans and cattle. Using imputed whole-genome sequence data from 9223 beef cattle from three cohorts, a series of genome-wide association studies was undertaken on cattle flight time, a temperament phenotype measured as the time taken for an animal to cover a short-fixed distance after release from an enclosure. We also investigated the association of cattle temperament with polymorphisms in bovine orthologs of risk genes for neuroticism, schizophrenia, autism spectrum disorders (ASD), and developmental delay disorders in humans. Results Variants with the strongest associations were located in the bovine orthologous region that is involved in several behavioural and cognitive disorders in humans. These variants were also partially validated in independent cattle cohorts. Genes in these regions (BARHL2, NDN, SNRPN, MAGEL2, ABCA12, KIFAP3, TOPAZ1, FZD3, UBE3A, and GABRA5) were enriched for the GO term neuron migration and were differentially expressed in brain and pituitary tissues in humans. Moreover, variants within 100 kb of ASD susceptibility genes were associated with cattle temperament and explained 6.5% of the total additive genetic variance in the largest cattle cohort. The ASD genes with the most significant associations were GABRB3 and CUL3. Using the same 100 kb window, a weak association was found with polymorphisms in schizophrenia risk genes and no association with polymorphisms in neuroticism and developmental delay disorders risk genes. Conclusions Our analysis showed that genes identified in a meta-analysis of cattle temperament contribute to neuron development functions and are differentially expressed in human brain tissues. Furthermore, some ASD susceptibility genes are associated with cattle temperament. These findings provide evidence that genetic control of temperament might be shared between humans and cattle and highlight the potential for future analyses to leverage results between species.
    • Microbiome definition re-visited: old concepts and new challenges

      Berg, Gabriele; Rybakova, Daria; Fischer, Doreen; Cernava, Tomislav; Vergès, Marie-Christine C; Charles, Trevor; Chen, Xiaoyulong; Cocolin, Luca; Eversole, Kellye; Corral, Gema H; et al. (Biomed Central, 2020-06-30)
      Abstract The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term “microbiome.” Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract
    • Anthelmintic resistance among gastrointestinal nematodes of cattle on dairy calf to beef farms in Ireland

      Kelleher, Anne C; Good, Barbara; de Waal, Theo; Keane, Orla M; Teagasc Walsh Fellowship Programme (Biomed Central, 2020-07-01)
      Background The control of gastrointestinal nematodes (GIN) of cattle in pasture-based production systems such as Ireland is highly dependent on the availability of efficacious anthelmintics. There is very little information available on the efficacy of the broad-spectrum anthelmintics against GIN of cattle in Ireland and the aim of this study was to determine the prevalence of anthelmintic resistance on dairy calf to beef farms. Results GIN burden was monitored on thirty-six recruited farms by performing herd level faecal egg counts (FEC) every 2 weeks. Of these, nine farms were lost from the study as calves were treated with an anthelmintic for Dictyocaulus viviparus, two were lost as they treated for GIN, one dropped out of the study and on one the herd FEC did not reach the threshold for carrying out the Faecal Egg Count Reduction Test (FECRT). On the remaining 23 farms, once the herd FEC reached 100 eggs per gram, a FECRT was carried out. Pre and post-treatment larval cultures were also performed to identify the GIN to genus level. The efficacy of fenbendazole, levamisole, ivermectin and moxidectin was evaluated on 15, 11, 16 and 11 farms respectively. Resistance to fenbendazole was identified on 9 farms (60%) with resistance suspected on a further farm. Resistance to levamisole, ivermectin and moxidectin was detected on 2 (18%), 16 (100%) and 8 (73%) farms respectively. The predominant genera detected pre and post-treatment were Cooperia and Ostertagia with both genera detected post-treatment with fenbendazole and ivermectin. Due to the low proportion of Ostertagia spp. pre-treatment, the efficacy of levamisole or moxidectin against this genus could not be reliably established. Conclusions Anthelmintic resistance was widespread on the sampled dairy calf to beef farms in Ireland with resistance to benzimidazole, levamisole, ivermectin and moxidectin detected.