• 16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

      Fouhy, Fiona; Clooney, Adam G; STANTON, CATHERINE; Claesson, Marcus J.; Cotter, Paul D.; European Union; Science Foundation Ireland; 603038; SFI/12/RC/2273; SFI/11/PI/1137 (Biomed Central, 24/06/2016)
      Background Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the community. Numerous factors, including DNA extraction method, primer sequences and sequencing platform employed, can affect the accuracy of the results achieved. The aim of this study was to determine the impact of these three factors on 16S rRNA gene sequencing results, using mock communities and mock community DNA. Results The use of different primer sequences (V4-V5, V1-V2 and V1-V2 degenerate primers) resulted in differences in the genera and species detected. The V4-V5 primers gave the most comparable results across platforms. The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. Data generated from DNA extracted using the 2 extraction methods were very similar. Conclusions Microbiota compositional data differed depending on the primers and sequencing platform that were used. The results demonstrate the risks in comparing data generated using different sequencing approaches and highlight the merits of choosing a standardised approach for sequencing in situations where a comparison across multiple sequencing runs is required.
    • A comparison of SWAT, HSPF and SHETRAN/GOPC for modelling phosphorus export from three catchments in Ireland

      Nasr, Ahmed Elssidig; Bruen, Michael; Jordan, Philip; Moles, Richard; Kiely, Gerard; Byrne, Paul; Environmental Protection Agency; Teagasc; Teagasc (Elsevier, 02/07/2012)
      Recent extensive water quality surveys in Ireland revealed that diffuse phosphorus (P) pollution originating from agricultural land and transported by runoff and subsurface flows is the primary cause of the deterioration of surface water quality. P transport from land to water can be described by mathematical models that vary in modelling approach, complexity and scale (plot, field and catchment). Here, three mathematical models (SWAT, HSPF and SHETRAN/GOPC) of diffuse P pollution have been tested in three Irish catchments to explore their suitability in Irish conditions for future use in implementing the European Water Framework Directive. After calibrating the models, their daily flows and total phosphorus (TP) exports are compared and assessed. The HSPF model was the best at simulating the mean daily discharge while SWAT gave the best calibration results for daily TP loads. Annual TP exports for the three models and for two empirical models were compared with measured data. No single model is consistently better in estimating the annual TP export for all three catchments.
    • 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.
    • Alterations in hepatic miRNA expression during negative energy balance in postpartum dairy cattle

      Fatima, Attia; Waters, Sinead M.; O'Boyle, Padraig; Seoighe, Cathal; Morris, Dermot G.; Teagasc Walsh Fellowship Programme (Biomed Central, 2014-01-15)
      Background Negative energy balance (NEB), an altered metabolic state, occurs in early postpartum dairy cattle when energy demands to support lactation exceed energy intake. During NEB the liver undergoes oxidative stress and increased breakdown of fatty acids accompanied by changes in gene expression. It is now known that micro RNAs (miRNA) can have a role in mediating such alterations in gene expression through repression or degradation of target mRNAs. miRNA expression is known to be altered by metabolism and environmental factors and miRNAs are implicated in expression modulation of metabolism related genes. Results miRNA expression was profiled in the liver of moderate yielding dairy cattle under severe NEB (SNEB) and mild NEB (MNEB) using the Affymetrix Gene Chip miRNA_2.0 array with 679 probe sets for Bos-taurus miRNAs. Ten miRNAs were found to be differentially expressed using the ‘samr’ statistical package (delta = 0.6) at a q-value FDR of < 12%. Five miRNAs including miR-17-5p, miR-31, miR-140, miR-1281 and miR-2885 were validated using RT-qPCR, to be up-regulated under SNEB. Liver diseases associated with these miRNAs include non-alcoholic fatty liver (NAFLD) and hepatocellular carcinoma (HCC). miR-140 and miR-17-5p are known to show differential expression under oxidative stress. A total of 32 down-regulated putative target genes were also identified among 418 differentially expressed hepatic genes previously reported for the same animal model. Among these, GPR37 (G protein-coupled receptor 37), HEYL (hairy/enhancer-of-split related with YRPW motif-like), DNJA1, CD14 (Cluster of differentiation 14) and GNS (glucosamine (N-acetyl)-6-sulfatase) are known to be associated with hepatic metabolic disorders. In addition miR-140 and miR-2885 have binding sites on the most down-regulated of these genes, FADS2 (Fatty acid desaturase 2) which encodes an enzyme critical in lipid biosynthesis. Furthermore, HNF3-gamma (Hepatocyte nuclear factor 3-gamma), a hepatic transcription factor (TF) that is involved in IGF-1 expression regulation and maintenance of glucose homeostasis is a putative target of miR-31. Conclusions This study shows that SNEB affects liver miRNA expression and these miRNAs have putative targets in hepatic genes down-regulated under this condition. This study highlights the potential role of miRNAs in transcription regulation of hepatic gene expression during SNEB in dairy cattle. Background Negative energy balance (NEB), an altered metabolic state, occurs in early postpartum dairy cattle when energy demands to support lactation exceed energy intake. During NEB the liver undergoes oxidative stress and increased breakdown of fatty acids accompanied by changes in gene expression. It is now known that micro RNAs (miRNA) can have a role in mediating such alterations in gene expression through repression or degradation of target mRNAs. miRNA expression is known to be altered by metabolism and environmental factors and miRNAs are implicated in expression modulation of metabolism related genes. Results miRNA expression was profiled in the liver of moderate yielding dairy cattle under severe NEB (SNEB) and mild NEB (MNEB) using the Affymetrix Gene Chip miRNA_2.0 array with 679 probe sets for Bos-taurus miRNAs. Ten miRNAs were found to be differentially expressed using the ‘samr’ statistical package (delta = 0.6) at a q-value FDR of < 12%. Five miRNAs including miR-17-5p, miR-31, miR-140, miR-1281 and miR-2885 were validated using RT-qPCR, to be up-regulated under SNEB. Liver diseases associated with these miRNAs include non-alcoholic fatty liver (NAFLD) and hepatocellular carcinoma (HCC). miR-140 and miR-17-5p are known to show differential expression under oxidative stress. A total of 32 down-regulated putative target genes were also identified among 418 differentially expressed hepatic genes previously reported for the same animal model. Among these, GPR37 (G protein-coupled receptor 37), HEYL (hairy/enhancer-of-split related with YRPW motif-like), DNJA1, CD14 (Cluster of differentiation 14) and GNS (glucosamine (N-acetyl)-6-sulfatase) are known to be associated with hepatic metabolic disorders. In addition miR-140 and miR-2885 have binding sites on the most down-regulated of these genes, FADS2 (Fatty acid desaturase 2) which encodes an enzyme critical in lipid biosynthesis. Furthermore, HNF3-gamma (Hepatocyte nuclear factor 3-gamma), a hepatic transcription factor (TF) that is involved in IGF-1 expression regulation and maintenance of glucose homeostasis is a putative target of miR-31. Conclusions This study shows that SNEB affects liver miRNA expression and these miRNAs have putative targets in hepatic genes down-regulated under this condition. This study highlights the potential role of miRNAs in transcription regulation of hepatic gene expression during SNEB in dairy cattle.
    • The altered gut microbiota in adults with cystic fibrosis

      Burke, D.G.; Fouhy, Fiona; Harrison, M. J; Rea, Mary; Cotter, Paul D.; O'Sullivan, Orla; STANTON, CATHERINE; Hill, Cian J; Shanahan, Fergus; Plant, Barry J.; et al. (Biomed Central, 09/03/2017)
      Background Cystic Fibrosis (CF) is an autosomal recessive disease that affects the function of a number of organs, principally the lungs, but also the gastrointestinal tract. The manifestations of cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction in the gastrointestinal tract, as well as frequent antibiotic exposure, undoubtedly disrupts the gut microbiota. To analyse the effects of CF and its management on the microbiome, we compared the gut microbiota of 43 individuals with CF during a period of stability, to that of 69 non-CF controls using 454-pyrosequencing of the 16S rRNA gene. The impact of clinical parameters, including antibiotic therapy, on the results was also assessed. Results The CF-associated microbiome had reduced microbial diversity, an increase in Firmicutes and a reduction in Bacteroidetes compared to the non-CF controls. While the greatest number of differences in taxonomic abundances of the intestinal microbiota was observed between individuals with CF and the healthy controls, gut microbiota differences were also reported between people with CF when grouped by clinical parameters including % predicted FEV1 (measure of lung dysfunction) and the number of intravenous (IV) antibiotic courses in the previous 12 months. Notably, CF individuals presenting with severe lung dysfunction (% predicted FEV1 ≤ 40%) had significantly (p < 0.05) reduced gut microbiota diversity relative to those presenting with mild or moderate dysfunction. A significant negative correlation (−0.383, Simpson’s Diversity Index) was also observed between the number of IV antibiotic courses and gut microbiota diversity. Conclusions This is one of the largest single-centre studies on gut microbiota in stable adults with CF and demonstrates the significantly altered gut microbiota, including reduced microbial diversity seen in CF patients compared to healthy controls. The data show the impact that CF and it's management have on gut microbiota, presenting the opportunity to develop CF specific probiotics to minimise microbiota alterations.
    • The altered gut microbiota in adults with cystic fibrosis

      Burke, D.G.; Fouhy, Fiona; Harrison, M. J; Rea, Mary; Cotter, Paul D.; O'Sullivan, Orla; STANTON, CATHERINE; Hill, Cian J; Shanahan, Fergus; Plant, Barry J.; et al. (Biomed Central, 09/03/2017)
      Background Cystic Fibrosis (CF) is an autosomal recessive disease that affects the function of a number of organs, principally the lungs, but also the gastrointestinal tract. The manifestations of cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction in the gastrointestinal tract, as well as frequent antibiotic exposure, undoubtedly disrupts the gut microbiota. To analyse the effects of CF and its management on the microbiome, we compared the gut microbiota of 43 individuals with CF during a period of stability, to that of 69 non-CF controls using 454-pyrosequencing of the 16S rRNA gene. The impact of clinical parameters, including antibiotic therapy, on the results was also assessed. Results The CF-associated microbiome had reduced microbial diversity, an increase in Firmicutes and a reduction in Bacteroidetes compared to the non-CF controls. While the greatest number of differences in taxonomic abundances of the intestinal microbiota was observed between individuals with CF and the healthy controls, gut microbiota differences were also reported between people with CF when grouped by clinical parameters including % predicted FEV1 (measure of lung dysfunction) and the number of intravenous (IV) antibiotic courses in the previous 12 months. Notably, CF individuals presenting with severe lung dysfunction (% predicted FEV1 ≤ 40%) had significantly (p < 0.05) reduced gut microbiota diversity relative to those presenting with mild or moderate dysfunction. A significant negative correlation (−0.383, Simpson’s Diversity Index) was also observed between the number of IV antibiotic courses and gut microbiota diversity. Conclusions This is one of the largest single-centre studies on gut microbiota in stable adults with CF and demonstrates the significantly altered gut microbiota, including reduced microbial diversity seen in CF patients compared to healthy controls. The data show the impact that CF and it's management have on gut microbiota, presenting the opportunity to develop CF specific probiotics to minimise microbiota alterations.
    • Analysis of Johne’s disease ELISA status and associated performance parameters in Irish dairy cows

      Kennedy, Aideen E.; Byrne, Nicky; Garcia, A. B; O'Mahony, James A.; Sayers, Riona; Irish Dairy Levy Research Trust (2016-03-02)
      Background Infection with Mycobacterium avium subspecies paratuberculosis (MAP) has been associated with reductions in milk production in dairy cows and sub optimal fertility. The aim of this study was to highlight the production losses associated with testing MAP ELISA positive in Irish dairy cows. Secondary objectives included investigation of risk factors associated with testing MAP ELISA positive. A survey of management practices on study farms was also conducted, with examination of associations between management practices and herd MAP status. Blood samples were collected from 4188 breeding animals on 22 farms. Samples were ELISA tested using the ID Screen Paratuberculosis Indirect Screening Test. Production parameters examined included milk yield, milk fat, milk protein, somatic cell count, and calving interval. The association between MAP ELISA status and production data was investigated using multi-level mixed models. Logistic regression was used to identify risk factors for testing JD blood ELISA positive at individual cow level and to identify associations between farm management practices and herd MAP status. Results Data were available for 3528 cows. The apparent prevalence recorded was 7.4 %. Mixed model analysis revealed no statistically significant association between testing MAP ELISA positive and dairy cow production parameters. Risk factors associated with testing positive included larger sized herds being over twice more likely to test positive than smaller herds (OR 2.4 P = <0.001). Friesians were less likely to test positive relative to other breeds. A number of study farmers were engaged in management practices that have previously been identified as high risk for MAP transmission e.g., 73.1 % pooled colostrum and 84.6 % of study farmers used the calving area to house sick animals throughout the year. No significant associations however, were identified between farm management practices and herd MAP status. Conclusion No production losses were identified; however an apparent prevalence of 7.4 % was recorded. With the abolition of EU milk quotas herd size in Ireland is expanding, as herds included in this study were larger than the national average, results may be indicative of future JD levels if no JD control programmes are implemented to minimise transmission.
    • 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.
    • Anthelmintic-resistant nematodes in Irish commercial sheep flocks- the state of play

      Good, Barbara; Hanrahan, James P; de Waal, Daniel Theodorus; Patten, Thomas; Kinsella, Andrew; Lynch, Ciaran Oliver (Biomed Central, 2012-12-22)
      Anthelmintic resistance has been reported in most sheep producing countries. Prior to the mid 1990s, reports of anthelmintic resistance in Ireland were sparse and focused on benzimidazole, one of the three classes of anthelmintic available during this period. This evidence for efficacy issues on Irish farms combined with awareness that anthelmintic resistance was increasingly being reported in other countries prompted the need for more comprehensive investigations on Irish farms. Faecal egg count reduction and micro-agar larval development tests were employed to investigate resistance to benzimidazole, levamisole and macrocyclic lactone. There is compelling evidence for resistance to both benzimidazole (>88% of flocks) and levamisole (>39% of flocks). Resistance of nematode populations to macrocyclic lactone was suspected on a small number of farms (11%) but needs to be confirmed. The recent introduction of two new classes of anthelmintics, after over a 25 year interval, together with the evidence that anthelmintic resistance is reported within a relatively short time following the introduction of a new anthelmintic compound means that the challenge to the industry is immediate. Actions are urgently required to manage anthelmintic resistance so as to prolong the lifespan of anthelmintics.
    • 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.
    • Antimicrobial resistance in Escherichia coli isolated from on-farm and conventional hatching broiler farms in Ireland

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

      Sweeney, Torres; Lejeune, Alexandre; Moloney, Aidan; Monahan, Frank J; Gettigan, Paul M; Downey, Gerard; Park, Stephen D. E.; Ryan, Marion T; Department of Agriculture, Food and the Marine (Biomed Central, 2016-09-21)
      Background Differences between cattle production systems can influence the nutritional and sensory characteristics of beef, in particular its fatty acid (FA) composition. As beef products derived from pasture-based systems can demand a higher premium from consumers, there is a need to understand the biological characteristics of pasture produced meat and subsequently to develop methods of authentication for these products. Here, we describe an approach to authentication that focuses on differences in the transcriptomic profile of muscle from animals finished in different systems of production of practical relevance to the Irish beef industry. The objectives of this study were to identify a panel of differentially expressed (DE) genes/networks in the muscle of cattle raised outdoors on pasture compared to animals raised indoors on a concentrate based diet and to subsequently identify an optimum panel which can classify the meat based on a production system. Results A comparison of the muscle transcriptome of outdoor/pasture-fed and Indoor/concentrate-fed cattle resulted in the identification of 26 DE genes. Functional analysis of these genes identified two significant networks (1: Energy Production, Lipid Metabolism, Small Molecule Biochemistry; and 2: Lipid Metabolism, Molecular Transport, Small Molecule Biochemistry), both of which are involved in FA metabolism. The expression of selected up-regulated genes in the outdoor/pasture-fed animals correlated positively with the total n-3 FA content of the muscle. The pathway and network analysis of the DE genes indicate that peroxisome proliferator-activated receptor (PPAR) and FYN/AMPK could be implicit in the regulation of these alterations to the lipid profile. In terms of authentication, the expression profile of three DE genes (ALAD, EIF4EBP1 and NPNT) could almost completely separate the samples based on production system (95 % authentication for animals on pasture-based and 100 % for animals on concentrate- based diet) in this context. Conclusions The majority of DE genes between muscle of the outdoor/pasture-fed and concentrate-fed cattle were related to lipid metabolism and in particular β-oxidation. In this experiment the combined expression profiles of ALAD, EIF4EBP1 and NPNT were optimal in classifying the muscle transcriptome based on production system. Given the overall lack of comparable studies and variable concordance with those that do exist, the use of transcriptomic data in authenticating production systems requires more exploration across a range of contexts and breeds.
    • Are some teat disinfectant formulations more effective against specific bacteria isolated on teat skin than others?

      Fitzpatrick, Sarah R; Garvey, Mary; Flynn, Jim; Jordan, Kieran; Gleeson, David E; Dairy Research Ireland; Teagasc Walsh Fellowship Programme; 2016054 (Biomed Central, 2019-04-25)
      The use of pre- and post-milking teat disinfectants can reduce teat bacterial load and aid in the collection of high-quality milk. The objective of this study was to compare the reduction in bacteria populations on teat skin after the application of different commercial teat disinfectant products. Ten teat disinfectant products were applied to the teats of 10 Holstein–Friesian cows. One cow received one teat disinfectant product at each sampling point before cluster application for milking. A composite swab sample was taken of the 4 teats of each cow before and after teat disinfectant application. Swab samples were placed on three different selective agars to enumerate bacterial counts of staphylococcal, streptococcal and coliforms isolates on teat skin. Staphylococcal isolates were the most prominent bacterial group recovered on teat swabs (49%), followed by streptococcal (36%) and coliform (15%) isolates before the application of disinfectant. The average bacterial reductions on teat skin were shown to be 76%, 73% and 60% for staphylococcal, streptococcal and coliform isolates, respectively. All of the teat disinfectant products tested reduced teat bacterial load for all three bacterial groups. Product 4 containing 0.6% w/w diamine was the most effective against bacterial populations of staphylococcal and streptococcal isolates on teat skin with a reduction of 90% and 94%, respectively. Whereas product 10, which contained 0.5% w/w iodine, resulted in the highest reduction in coliforms on teat skin with a reduction of 91%. Results from this study suggest that specific bacterial population loads on teats can be reduced using different teat disinfectant formulations.
    • Assessment of factors affecting flood forecasting accuracy and reliability. Carpe Diem Centre for Water Resources Research : Deliverable 10.3

      Bruen, Michael; Nasr, Ahmed Elssidig; Yang, Jianqing; Parmentier, Benoit (University College Dublin. Departmetn of Civil Engineering, 2012-07-02)
      In Deliverable 10.1, a optimal methodology for combining precipitation information from raingauges, radar and NWP models (in this case HIRLAM) was described. It was based on an artificial neural network combination model, fitted to historic data, and operating on one-dimensional time-series of discharges. In this report, this new methodology is tested by applying it to (i) a rural catchment (Dargle)and (ii) a small urban catchment (CityWest). The results are compared with measured discharge series in both cases. Various measures of performance, applied to both the entire discharge series and also to the peaks-only are reported for various combinations of lead-time, spatial resolution and numbers of neurons in the hidden layer of the ANN model.
    • Association between clinical respiratory signs, lung lesions detected by thoracic ultrasonography and growth performance in pre‐weaned dairy calves

      Cuevas-Gómez, Inmaculada; McGee, Mark; Sánchez, José M; O’Riordan, Edward; Byrne, Nicky; McDaneld, Tara; Earley, Bernadette; US-Ireland DAFM grant; 2018US-IRL200 (Biomed Central, 2021-03-25)
      Background Bovine respiratory disease (BRD) is the main cause of mortality among 1-to-5 month old calves in Ireland, accounting for approximately one-third of deaths. Despite widespread use of clinical respiratory signs for diagnosing BRD, lung lesions are detected, using thoracic ultrasonography (TUS) or following post-mortem, in calves showing no clinical signs. This highlights the limitation of clinical respiratory signs as a method of detecting sub-clinical BRD. Using 53 purchased artificially-reared male dairy calves, the objectives of this study were to: (i) characterise the BRD incidence detected by clinical respiratory signs and/or TUS, (ii) investigate the association between clinical respiratory signs and lung lesions detected by TUS, and (iii) assess the effect of BRD on pre-weaning growth. Results Clinical BRD (based on Wisconsin clinical respiratory score and/or rectal temperature > 39.6 ºC) was detected in 43 % and sonographic changes (lung lesions) were detected in 64 % of calves from purchase (23 (SD; 6.2) days of age) until weaning, 53 days post-arrival. Calves with clinical BRD were treated. Sixty-one per cent calves affected with clinical BRD had lung lesions 10.5 days (median) before detection of clinical signs. Moderate correlations (rsp 0.70; P < 0.05) were found between cough and severe lung lesions on arrival day, and between rectal temperature > 39.6 ºC and lung lesions ≥ 2 cm2 on day 7 (rsp 0.40; P < 0.05) post-arrival. Mean average daily live weight gain (ADG) of calves from purchase to weaning was 0.75 (SD; 0.10) kg; calves with or without clinical BRD did not differ in ADG (P > 0.05), whereas ADG of those with severe lung lesions (lung lobe completely consolidated or pulmonary emphysema) was 0.12 kg/d less (P < 0.05) than calves without lung lesions. Conclusions Thoracic ultrasonography detected lung consolidation in calves that did not show signs of respiratory disease. The presence of severe lung lesions was associated with reduced pre-weaning growth. These findings emphasise the importance of using TUS in addition to clinical respiratory scoring of calves for an early and accurate detection of clinical and sub-clinical BRD.
    • Association of bovine leptin polymorphisms with energy output and energy storage traits in progeny tested Holstein-Friesian dairy cattle sires

      Giblin, Linda; Butler, Stephen T.; Kearney, Breda M.; Waters, Sinead M.; Callanan, Michael J.; Berry, Donagh; Department of Agriculture, Food and the Marine, Ireland; Irish Dairy Levy Research Trust; Teagasc Walsh Fellowship Programme; RSF-06-0353; et al. (Biomed Central, 29/07/2010)
      Background: Leptin modulates appetite, energy expenditure and the reproductive axis by signalling via its receptor the status of body energy stores to the brain. The present study aimed to quantify the associations between 10 novel and known single nucleotide polymorphisms in genes coding for leptin and leptin receptor with performance traits in 848 Holstein-Friesian sires, estimated from performance of up to 43,117 daughter-parity records per sire. Results: All single nucleotide polymorphisms were segregating in this sample population and none deviated (P > 0.05) from Hardy-Weinberg equilibrium. Complete linkage disequilibrium existed between the novel polymorphism LEP-1609, and the previously identified polymorphisms LEP-1457 and LEP-580. LEP-2470 associated (P < 0.05) with milk protein concentration and calf perinatal mortality. It had a tendency to associate with milk yield (P < 0.1). The G allele of LEP-1238 was associated (P < 0.05) with reduced milk fat concentration, reduced milk protein concentration, longer gestation length and tended to associate (P < 0.1) with an increase in calving difficulty, calf perinatal mortality and somatic cells in the milk. LEP-963 exhibited an association (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and gestation length. It also tended to associate with milk yield (P < 0.1). The R25C SNP associated (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and length of gestation. The T allele of the Y7F SNP significantly associated with reduced angularity (P < 0.01) and reduced milk protein yield (P < 0.05). There was also a tendency (P < 0.1) for Y7F to associate with increased body condition score, reduced milk yield and shorter gestation (P < 0.1). A80V associated with reduced survival in the herd (P < 0.05). Conclusions Several leptin polymorphisms (LEP-2470, LEP-1238, LEP-963, Y7F and R25C) associated with the energetically expensive process of lactogenesis. Only SNP Y7F associated with energy storage. Associations were also observed between leptin polymorphisms and calving difficulty, gestation length and calf perinatal mortality. The lack of an association between the leptin variants investigated with calving interval in this large data set would question the potential importance of these leptin variants, or indeed leptin, in selection for improved fertility in the Holstein-Friesian dairy cow.
    • Association of genetic polymorphisms related to Johne’s disease with estimated breeding values of Holstein sires for milk ELISA test scores

      Mallikarjunappa, Sanjay; Schenkel, Flavio S; Brito, Luiz F; Bissonnette, Nathalie; Miglior, Filippo; Chesnais, Jacques; Lohuis, Michael; Meade, Kieran G; Karrow, Niel A; Semex Alliance; et al. (Biomed Central, 2020-05-27)
      Background Johne’s disease (JD) is a chronic intestinal inflammatory disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) infection in ruminants. Since there are currently no effective vaccine or treatment options available to control JD, genetic selection may be an alternative strategy to enhance JD resistance. Numerous Single Nucleotide Polymorphisms (SNPs) have been reported to be associated with MAP infection status based on published genome-wide association and candidate gene studies. The main objective of this study was to validate these SNPs that were previously identified to be associated with JD by testing their effect on Holstein bulls’ estimated breeding values (EBVs) for milk ELISA test scores, an indirect indicator of MAP infection status in cattle. Results Three SNPs, rs41810662, rs41617133 and rs110225854, located on Bos taurus autosomes (BTA) 16, 23 and 26, respectively, were confirmed as significantly associated with Holstein bulls’ EBVs for milk ELISA test score (FDR < 0.01) based on General Quasi Likelihood Scoring analysis (GQLS) analysis. Single-SNP regression analysis identified four SNPs that were associated with sire EBVs (FDR < 0.05). This includes two SNPs that were common with GQLS (rs41810662 and rs41617133), with the other two SNPs being rs110494981 and rs136182707, located on BTA9 and BTA16, respectively. Conclusions The findings of this study validate the association of SNPs with JD MAP infection status and highlight the need to further investigate the genomic regions harboring these SNPs.
    • 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.
    • Atypical Listeria innocua strains possess an intact LIPI-3

      Clayton, Evelyn M; Daly, Karen M.; Guinane, Caitriona M.; Hill, Colin; Cotter, Paul D.; Ross, R Paul; Enterprise Ireland; Science Foundation Ireland; 06/IN.1/B98; 10/IN.1/B3027 (Biomed Central, 08/03/2014)
      Background: Listeria monocytogenes is a food-borne pathogen which is the causative agent of listeriosis and can be divided into three evolutionary lineages I, II and III. While all strains possess the well established virulence factors associated with the Listeria pathogenicity island I (LIPI-1), lineage I strains also possess an additional pathogenicity island designated LIPI-3 which encodes listeriolysin S (LLS), a post-translationally modified cytolytic peptide. Up until now, this pathogenicity island has been identified exclusively in a subset of lineage I isolates of the pathogen Listeria monocytogenes. Results: In total 64 L. innocua strains were screened for the presence of LIPI-3. Here we report the identification of an intact LIPI-3 in 11 isolates of L. innocua and the remnants of the cluster in several others. Significantly, we can reveal that placing the L. innocua lls genes under the control of a constitutive promoter results in a haemolytic phenotype, confirming that the cluster is capable of encoding a functional haemolysin. Conclusions: Although the presence of the LIPI-3 gene cluster is confined to lineage I isolates of L. monocytogenes, a corresponding gene cluster or its remnants have been identified in many L. innocua strains.