• Farm management factors associated with bulk tank total bacterial count in Irish dairy herds during 2006/07

      Kelly, PT; O'Sullivan, K; Berry, Donagh P.; More, Simon J; Meaney, William J; O'Callaghan, Edmond J; O'Brien, Bernadette (Biomed Central, 01/01/2009)
      Research has shown that total bacterial count (TBC), which is the bacterial growth per ml of milk over a fixed period of time, can be decreased by good hygiene and farm management practices. The objective of the current study was to quantify the associations between herd management factors and bulk tank TBC in Irish spring calving, grass-based dairy herds. The relationship between bulk tank TBC and farm management and infrastructure was examined using data from 400 randomly selected Irish dairy farms where the basal diet was grazed grass. Herd management factors associated with bulk tank TBC were identified using linear models with herd annual total bacterial score (i.e., arithmetic mean of the natural logarithm of bulk tank TBC) included as the dependent variable. All herd management factors were individually analysed in a separate regression model, that included an adjustment for geographical location of the farm. A multiple stepwise regression model was subsequently developed. Median bulk tank TBC for the sample herds was 18,483 cells/ml ranging from 10,441 to 130,458 cells/ml. Results from the multivariate analysis indicated that the following management practices were associated with low TBC; use of heated water in the milking parlour; participation in a milk recording scheme; and tail clipping of cows at a frequency greater than once per year. Increased level of hygiene of the parlour and cubicles were also associated with lower TBC. Herd management factors associated with bulk tank TBC in Irish grazing herds were generally in agreement with most previous studies from confinement systems of milk production.
    • In vivo activity of Nisin A and Nisin V against Listeria monocytogenes in mice

      Campion, Alicia; Casey, Patrick G.; Field, Des; Cotter, Paul D.; Hill, Colin; Ross, R Paul; Programme for Research in Third-Level Institutions; Irish Research Council for Science, Engineering and Technology; Enterprise Ireland; Science Foundation Ireland (Biomed Central, 01/02/2013)
      Background: Lantibiotics are post-translationally modified antimicrobial peptides, of which nisin A is the most extensively studied example. Bioengineering of nisin A has resulted in the generation of derivatives with increased in vitro potency against Gram-positive bacteria. Of these, nisin V (containing a Met21Val change) is noteworthy by virtue of exhibiting enhanced antimicrobial efficacy against a wide range of clinical and food-borne pathogens, including Listeria monocytogenes. However, this increased potency has not been tested in vivo. Results: Here we address this issue by assessing the ability of nisin A and nisin V to control a bioluminescent strain of Listeria monocytogenes EGDe in a murine infection model. More specifically, Balb/c mice were infected via the intraperitoneal route at a dose of 1 × 105 cfu/animal and subsequently treated intraperitoneally with either nisin V, nisin A or a PBS control. Bioimaging of the mice was carried out on day 3 of the trial. Animals were then sacrificed and levels of infection were quantified in the liver and spleen. Conclusion: This analysis revealed that nisin V was more effective than Nisin A with respect to controlling infection and therefore merits further investigation with a view to potential chemotherapeutic applications.
    • Farm management factors associated with bulk tank somatic cell count in Irish dairy herds

      Kelly, PT; O'Sullivan, K; Berry, Donagh P.; More, Simon J; Meaney, William J; O'Callaghan, Edmond J; O'Brien, Bernadette (Biomed Central, 01/04/2009)
      The relationship between bulk tank somatic cell count (SCC) and farm management and infrastructure was examined using data from 398 randomly selected, yet representative, Irish dairy farms where the basal diet is grazed grass. Median bulk tank SCC for the farms was 282,887 cells/ml ranging from 82,209 to 773,028 cells/ml. Two questionnaires were administered through face-to-face contact with each farmer. Herd-level factors associated with bulk tank SCC were determined using linear models with annual somatic cell score (i.e., arithmetic mean of the natural logarithm of bulk tank SCC) included as the dependent variable. All herd level factors were analysed individually in separate regression models, which included an adjustment for geographical location of the farm; a multiple regression model was subsequently developed. Management practices associated with low SCC included the use of dry cow therapy, participation in a milk recording scheme and the use of teat disinfection post-milking. There was an association between low SCC and an increased level of hygiene and frequency of cleaning of the holding yard, passageways and cubicles. Herd management factors associated with bulk tank SCC in Irish grazing herds are generally in agreement with most previous studies from confinement systems of milk production.
    • Lactobacillus ruminis strains cluster according to their mammalian gut source

      O’Donnell, Michelle M.; Harris, Hugh M B; Lynch, Denise B; Ross, R Paul; O’Toole, Paul W.; Science Foundation Ireland; 07/IN.1/B1780 (Biomed Central, 01/04/2015)
      Background Lactobacillus ruminis is a motile Lactobacillus that is autochthonous to the human gut, and which may also be isolated from other mammals. Detailed characterization of L. ruminis has previously been restricted to strains of human and bovine origin. We therefore sought to expand our bio-bank of strains to identify and characterise isolates of porcine and equine origin by comparative genomics. Results We isolated five strains from the faeces of horses and two strains from pigs, and compared their motility, biochemistry and genetic relatedness to six human isolates and three bovine isolates including the type strain 27780T. Multilocus sequence typing analysis based on concatenated sequence data for six individual loci separated the 16 L. ruminis strains into three clades concordant with human, bovine or porcine, and equine sources. Sequencing the genomes of four additional strains of human, bovine, equine and porcine origin revealed a high level of genome synteny, independent of the source animal. Analysis of carbohydrate utilization, stress survival and technological robustness in a combined panel of sixteen L. ruminis isolates identified strains with optimal survival characteristics suitable for future investigation as candidate probiotics. Under laboratory conditions, six human isolates of L. ruminis tested were aflagellate and non-motile, whereas all 10 strains of bovine, equine and porcine origin were motile. Interestingly the equine and porcine strains were hyper-flagellated compared to bovine isolates, and this hyper-flagellate phenotype correlated with the ability to swarm on solid medium containing up to 1.8% agar. Analysis by RNA sequencing and qRT-PCR identified genes for the biosynthesis of flagella, genes for carbohydrate metabolism and genes of unknown function that were differentially expressed in swarming cells of an equine isolate of L. ruminis. Conclusions We suggest that Lactobacillus ruminis isolates have potential to be used in the functional food industry. We have also identified a MLST scheme able to distinguish between strains of L. ruminis of different origin. Genes for non-digestible oligosaccharide metabolism were identified with a putative role in swarming behaviour.
    • A temporal assessment of nematode community structure and diversity in the rhizosphere of cisgenic Phytophthora infestans-resistant potatoes

      Ortiz, Vilma; Phelan, Sinead; Mullins, Ewen; European Union; KBBE.2011.3.5-01 (Biomed Central, 01/12/2016)
      Background Nematodes play a key role in soil processes with alterations in the nematode community structure having the potential to considerably influence ecosystem functioning. As a result fluctuations in nematode diversity and/or community structure can be gauged as a ‘barometer’ of a soil’s functional biodiversity. However, a deficit exists in regards to baseline knowledge and on the impact of specific GM crops on soil nematode populations and in particular in regard to the impact of GM potatoes on the diversity of nematode populations in the rhizosphere. The goal of this project was to begin to address this knowledge gap in regards to a GM potato line, cisgenically engineered for resistance to Phytophthora infestans (responsible organism of the Irish potato famine causing late blight disease). For this, a 3 year (2013, 2014, 2015) field experimental study was completed, containing two conventional genotypes (cvs. Desiree and Sarpo Mira) and a cisgenic genotype (cv. Desiree + Rpi-vnt1). Each potato genotype was treated with different disease management strategies (weekly chemical applications and corresponding no spray control). Hence affording the opportunity to investigate the temporal impact of potato genotype, disease management strategy (and their interaction) on the potato rhizosphere nematode community. Results Nematode structure and diversity were measured through established indices, accounts and taxonomy with factors recording a significant effect limited to the climatic conditions across the three seasons of the study and chemical applications associated with the selected disease management strategy. Based on the metrics studied, the cultivation of the cisgenic potato genotype exerted no significant effect (P > 0.05) on nematode community diversity or structure. The disease management treatments led to a reduction of specific trophic groups (e.g. Predacious c–p = 4), which of interest appeared to be counteracted by a potato genotype with vigorous growth phenotype e.g. cv. Sarpo Mira. The fluctuating climates led to disparate conditions, with enrichment conditions (bacterial feeding c–p = 1) dominating during the wet seasons of 2014 and 2015 versus the dry season of 2013 which induced an environmental stress (functional guild c–p = 2) on nematode communities. Conclusions Overall the functional guild indices in comparison to other indices or absolutes values, delivered the most accurate quantitative measurement with which to determine the occurrence of a specific disturbance relative to the cultivation of the studied cisgenic P. infestans-resistant potatoes.
    • Relatedness between the two-component lantibiotics lacticin 3147 and staphylococcin C55 based on structure, genetics and biological activity

      O'Connor, Eileen B; Cotter, Paul D.; O'Connor, Paula M.; O'Sullivan, Orla; Tagg, John R; Ross, R Paul; Hill, Colin (Biomed Central, 02/04/2007)
      Background: Two component lantibiotics, such as the plasmid-encoded lacticin 3147 produced by Lactococcus lactis DPC3147 and staphylococcin C55 produced by Staphylococcus aureus C55, represent an emerging subgroup of bacteriocins. These two bacteriocins are particularly closely related, exhibiting 86% (LtnA1 and C55α) and 55% (LtnA2 and C55β) identity in their component peptides. The aim of this study was to investigate, for the first time for any two component bacteriocins, the significance of the relatedness between these two systems. Results: So close is this relatedness that the hybrid peptide pairs LtnA1:C55β and C55α:LtnA2 were found to have activities in the single nanomolar range, comparing well with the native pairings. To determine whether this flexibility extended to the associated post-translational modification/processing machinery, the staphylococcin C55 structural genes were directly substituted for their lacticin 3147 counterparts in the ltn operon on the large conjugative lactococcal plasmid pMRC01. It was established that the lacticin LtnA1 post-translational and processing machinery could produce functionally active C55α, but not C55β. In order to investigate in closer detail the significance of the differences between LtnA1 and C55α, three residues in LtnA1 were replaced with the equivalent residues in C55α. Surprisingly, one such mutant LtnA1-Leu21Ala was not produced. This may be significant given the positioning of this residue in a putative lipid II binding loop. Conclusion: It is apparent, despite sharing striking similarities in terms of structure and activity, that these two complex bacteriocins display some highly dedicated features particular to either system.
    • The efficacy of thuricin CD, tigecycline, vancomycin, teicoplanin, rifampicin and nitazoxanide, independently and in paired combinations against Clostridium difficile biofilms and planktonic cells

      Mathur, Harsh; Rea, Mary C.; Cotter, Paul D; Hill, Colin; Ross, R Paul; Science Foundation Ireland; SFI/12/RC/2273 (Biomed Central, 02/06/2016)
      Background Thuricin CD is a two-component antimicrobial, belonging to the recently designated sactibiotic subclass of bacteriocins. The aim of this study was to investigate the effects of thuricin CD, as well as the antibiotics, tigecycline, vancomycin, teicoplanin, rifampicin and nitazoxanide when used independently and when combined at low concentrations on the viability of Clostridium difficile 20291 R027, TL178 R002, Liv022 R106, DPC6350 and VPI10463 biofilms and planktonic cells. Results On the basis of XTT (2,3-bis[2-methyloxy-4-nitro-5-sulphophenyl]-2H-tetrazolium-5-carboxanilide)-menadione biofilm viability assays, we found that thuricin CD was effective against biofilms of R027, Liv022 R106 and DPC6350 when used independently while nitazoxanide and rifampicin were also potent against biofilms of R027 and DPC6350, when applied on their own. Tigecycline was found to be effective against R027 and DPC6350 biofilms, whereas teicoplanin and vancomycin when used independently were only effective against DPC6350 biofilms. The efficacies of the antibiotics rifampicin, tigecycline, vancomycin and teicoplanin against C. difficile 20291 R027 biofilms were significantly potentiated when combined with thuricin CD, indicating effective antimicrobial combinations with this sactibiotic against R027 biofilms. However, the potency of nitazoxanide against R027 biofilms was significantly diminished when combined with thuricin CD, indicating an ineffective combination with this sactibiotic against R027 biofilms. Paired combinations of thuricin CD along with these five antibiotics were effective at diminishing the viability of DPC6350 biofilms. However, such combinations were largely ineffective against biofilms of TL178 R002, Liv022 R106 and VPI10463. Conclusions To the best of our knowledge, this is the first study to highlight the activity of a sactibiotic bacteriocin against biofilms and the first to reveal the potency of the antibiotics tigecycline, teicoplanin and nitazoxanide against C. difficile biofilms. On the basis of this study, it is apparent that different strains of C. difficile possess varying abilities to form biofilms and that the sensitivities of these biofilms to different antimicrobials and antimicrobial combinations are strain-dependent. Since the formation of relatively strong biofilms by certain C. difficile strains may contribute to increased cases of antibiotic resistance and recurrence and relapse of C. difficile infection, the findings presented in this study could provide alternative strategies to target this pathogen.
    • Physically-based, distributed, catchment modelling for estimating sediment and phosphorus loads to rivers and lakes : issues of model complexity, spatial and temporal scales and data requirements

      Nasr, Ahmed Elssidig; Bruen, Michael; Jordan, Philip; Moles, Richard; Kiely, Gerard; Byrne, Paul (Office of Public Works, 02/07/2012)
    • Developing an independent, generic, phosphorus modelling component for use with grid-oriented, physically-based distributed catchment models

      Nasr, Ahmed Elssidig; Taskinen, Antti; Bruen, Michael (IWA Publishing, 02/07/2012)
      Grid-oriented, physically based catchment models calculate fields of various hydrological variables relevant to phosphorous detachment and transport. These include (i) for surface transport: overland flow depth and flow in the coordinate directions, sediment load, and sediment concentration and (ii) for subsurface transport: soil moisture and hydraulic head at various depths in the soil. These variables can be considered as decoupled from any chemical phosphorous model since phosphorous concentrations, either as dissolved or particulate, do not influence the model calculations of the hydrological fields. Thus the phosphorous concentration calculations can be carried out independently from and after the hydrological calculations. This makes it possible to produce a separate phosphorous modelling component which takes as input the hydrological fields produced by the catchment model and which calculates, at each step the phosphorous concentrations in the flows. This paper summarise the equations and structure of Grid Oriented Phosphorous Component (GOPC) developed for simulating the phosphorus concentrations and loads using the outputs of a fully distributed physical based hydrological model. Also the GOPC performance is illustrated by am example of an experimental catchment (created by the author) subjected to some ideal conditions.
    • Eutrophication from agricultural sources : a comparison of SWAT, HSPF and SHETRAN/GOPC phosphorus models for three Irish catchments - Final Report

      Nasr, Ahmed Elssidig; Bruen, Michael (University College Dublin. Centre for Water Resources Research, 02/07/2012)
      Phosphorous has been implicated as the primary cause of the deterioration of surface water quality in Ireland. Extensive water quality surveys revealed that diffuse sources (runoff and subsurface flows) from agricultural land are the major contributors of phosphorus to surface waters. The mechanism of phosphorus movement from land to water can be described by a number of mathematical models that vary in modelling approaches and scales (plot, field and catchment). In this work three efficient mathematical models of diffuse source pollution in general and of phosphorus in particular have been applied, for the first time, to three Irish catchments (Clarianna (Co. Tipperary), Dripsey (Co. Cork) and Oona (Co. Tyrone)) in order to explore the suitability of these models in Irish conditions for future use in implementing the European Water Framework Directive (WFD). The models are: (i) Soil Water Assessment Tool (SWAT), (ii) Hydrological Simulation Programme FORTRAN (HSPF) and (iii) Système Hydrologique Européen TRAnsport (SHETRAN). The first two can model phosphorus production directly while the third can calculate fields of various hydrological variables relevant to phosphorous modelling. For the latter, a generic phosphorus modelling component called Grid Oriented Phosphorus Component (GOPC) has been developed here to model the phosphorus detachment and transport by taking as inputs the hydrological fields produced by any physically-based distributed catchment model such as SHETRAN. The three models have been successfully transferred to Irish conditions and this required the build up of a database consisting of topographic, land use and soil maps, water quality and weather data. The models application involved two stages. In the first stage, hydrological variables (evaporation, runoff, etc.) within the catchment domains were simulated by each of the three models. The second stage uses the outputs of the first in order to estimate the amount of phosphorus loss from the catchments. The SWAT, HSPF, and SHETRAN/GOPC models have been calibrated and then compared and assessed on the basis of their ability to fit and reproduce the flow discharges and phosphorus loads and concentrations for the three test catchments. The findings from the flow and phosphorus calibrations of SWAT and HSPF models were generally consistence with what have been found from previous studies outside Ireland. However, the simple structure of the first order kinetics method used for phosphorus modelling in HSPF has generally impeded the freedom of the phosphorus calibration which was noticeably difficult. Application of the SHETRAN model to the study catchments has illustrated the importance of carefully assigning the parameters related to the soil water modelling, particularly the parameters of the van Genuchten soil-hydraulic function, in order to obtain the best results. The GOPC performance has been found to depend significantly on the SHETRAN model which provided the required hydrological variables. The flow comparison has showed that in the three catchments, the HSPF model was the best in simulating the mean daily discharges. Moreover discharge simulation from an independent validation run of the three models in the Oona catchment have also demonstrated the superiority of the hydrological component of HSPF. However, the best calibration results for daily total phosphorus loads in the study catchments has been achieved by the SWAT model. However from the validation in the Oona catchment the HSPF has been found better than the other two models, SWAT and GOPC, in simulating the total phosphorus loads. Generally the results of total phosphorus loads from the GOPC in the three catchments were quite good and this model has reproduced some observed values better than the best model, SWAT. Simulation of the daily dissolved reactive phosphorus loads by the three models in the study catchments have showed big differences between the simulated and the observed data in most of the cases. Results for mean daily total and dissolved reactive phosphorus concentrations from the three models were not as good as the results for the loads in the three catchments.
    • Modelling phosphorus loss from agricultural catchments : a comparison of the performance of SWAT, HSPF and SHETRAN for the Clarianna catchment

      Nasr, Ahmed Elssidig; Bruen, Michael; Parkin, Geoff; Birkinshaw, Steve; Moles, Richard; Byrne, Paul (IWA Publishing, 02/07/2012)
      Much research in Europe at present has been directed at generating and assessing modelling tools for use in catchment management, driven by the requirements and schedule of the Water Framework Directive. A logical first step is to assess the suitability of existing models for this task so that any resources used in generating new models can be targeted at actual modelling needs. Crucial questions, relating to the model structure and complexity and spatial and temporal scales required must also be addressed. This paper reports a comparison of the performance and suitability of three "off-the-shelf" distributed catchment models, each with a different level of complexity, applied to modelling phosphorous losses from the Clarianna catchment in Ireland. In this paper, the performance of three such models (SWAT, HSPF and SHETRAN/GOPC) is compared, both in estimating discharges and phosphorous loads in the Clarianna catchment. The flow comparison has showed that the HSPF model was the best in simulating the mean daily discharges. However, the best calibration results for daily total phosphorus loads in the study catchment has been achieved by the SWAT model.
    • 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 (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.
    • Comparison of physically based catchment models for estimating Phosphorus losses

      Nasr, Ahmed Elssidig; Bruen, Michael (IWA publishing, 02/07/2012)
      As part of a large EPA-funded research project, coordinated by TEAGASC, the Centre for Water Resources Research at UCD reviewed the available distributed physically based catchment models with a potential for use in estimating phosphorous losses for use in implementing the Water Framework Directive. Three models, representative of different levels of approach and complexity, were chosen and were implemented for a number of Irish catchments. This paper reports on (i) the lessons and experience gained in implementing these models, (ii) compares the performances of the individual models and (iii) assesses their sensitivities to the main parameters and to spatial scales.
    • Eutrophication from agricultural sources : a comparison of SWAT, HSPF and SHETRAN/GOPC phosphorus models for three Irish catchments : executive summary

      Nasr, Ahmed Elssidig; Bruen, Michael (University College Dublin. Centre for Water Resources Research, 02/07/2012)
    • The significance of the differences in soil phosphorus representation and transport procedures in the SWAT and HSPF models and a comparison of their performance in estimating phosphorus loss from an agriculture catchment in Ireland

      Nasr, Ahmed Elssidig; Bruen, Michael; Moles, Richard; Byrne, Paul; O'Regan, Bernadette (TWRI, 02/07/2012)
      Phosphorus transported from agriculture land has been identified as a major source of water pollution in a large number of Irish catchments. Models of this process are required in order to design and assess management measures. This paper reports on the comparison and assessment of two of the most promising physically-based distributed models, SWAT and HSPF, with particular emphasis on their suitability for Irish conditions. The representation of the overall soil phosphorus cycle is similar in both models but there is a significant difference in the level of detail in describing the chemical and biochemical processes in each model. Also there are differences in modeling the mechanisms by which phosphorus is removed from the soil column and either transported in dissolved form with the runoff water or in particulate form attached to eroded or detached sediment. These differences could have a significant influence on performance when using either of the models to simulate phosphorus loss from any catchment. Both models are applied to estimating the phosphorus concentration at the outlet of the Clarianna catchment in north Tiperrary (Ireland). This catchment is small (23km2) and the landuse is mainly pasture on grey brown podozilic soils. The results of model calibration are presented along with an assessment of the usefulness of the model outputs as a water quality management tool.
    • Developing an independent, generic, phosphorus modelling component for use with grid-oriented, physically-based distributed catchment models

      Nasr, Ahmed Elssidig; Taskinen, Antti; Bruen, Michael (02/07/2012)
      Grid-oriented, physically based catchment models calculate fields of various hydrological variables relevant to phosphorous detachment and transport. These include (i) for surface transport: overland flow depth and flow in the coordinate directions, sediment load, and sediment concentration and (ii) for subsurface transport: soil moisture and hydraulic head at various depths in the soil. These variables can be considered as decoupled from any chemical phosphorous model since phosphorous concentrations, either as dissolved or particulate, do not influence the model calculations of the hydrological fields. Thus the phosphorous concentration calculations can be carried out independently from and after the hydrological calculations. This makes it possible to produce a separate phosphorous modelling component which takes as input the hydrological fields produced by the catchment model and which calculates, at each step the phosphorous concentrations in the flows. This paper summarise the equations and structure of Grid Oriented Phosphorous Component (GOPC) developed for simulating the phosphorus concentrations and loads using the outputs of a fully distributed physical based hydrological model. Also the GOPC performance is illustrated by am example of an experimental catchment (created by the author) subjected to some ideal conditions.
    • Predicted costs and benefits of eradicating BVDV from Ireland

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

      Toher, Deirdre; Downey, Gerard; Murphy, Thomas Brendan (Wiley, 02/07/2012)
      Fisher's linear discriminant analysis is one of the most commonly used and studied classification methods in chemometrics. The method finds a projection of multivariate data into a lower dimensional space so that the groups in the data are well separated. The resulting projected values are subsequently used to classify unlabeled observations into the groups. A semi-supervised version of Fisher's linear discriminant analysis is developed, so that the unlabeled observations are also used in the model fitting procedure. This approach is advantageous when few labeled and many unlabeled observations are available. The semi-supervised linear discriminant analysis method is demonstrated on a number of data sets where it is shown to yield better separation of the groups and improved classification over Fisher's linear discriminant analysis.
    • A degenerate PCR-based strategy as a means of identifying homologues of aminoglycoside and ß-lactam resistance genes in the gut microbiota

      Fouhy, Fiona; Ross, R Paul; Fitzgerald, Gerald F; Stanton, Catherine; Cotter, Paul D.; Irish Research Council; Teagasc Walsh Fellowship Programme; Science Foundation Ireland; 11/PI/1137 (Biomed Central, 05/02/2014)
      Background: The potential for the human gut microbiota to serve as a reservoir for antibiotic resistance genes has been the subject of recent discussion. However, this has yet to be investigated using a rapid PCR-based approach. In light of this, here we aim to determine if degenerate PCR primers can detect aminoglycoside and β-lactam resistance genes in the gut microbiota of healthy adults, without the need for an initial culture-based screen for resistant isolates. In doing so, we would determine if the gut microbiota of healthy adults, lacking recent antibiotic exposure, is a reservoir for resistance genes. Results: The strategy employed resulted in the identification of numerous aminoglycoside (acetylation, adenylation and phosphorylation) and β-lactam (including bla OXA, bla TEM, bla SHV and bla CTX-M) resistance gene homologues. On the basis of homology, it would appear that these genes originated from different bacterial taxa, with members of the Enterobacteriaceae being a particularly rich source. The results demonstrate that, even in the absence of recent antibiotic exposure, the human gut microbiota is a considerable reservoir for antibiotic resistance genes. Conclusions: This study has demonstrated that the gut can be a significant source of aminoglycoside and β-lactam resistance genes, even in the absence of recent antibiotic exposure. The results also demonstrate that PCR-based approaches can be successfully applied to detect antibiotic resistance genes in the human gut microbiota, without the need to isolate resistant strains. This approach could also be used to rapidly screen other complex environments for target genes.
    • Comparative genomics of lactic acid bacteria reveals a niche-specific gene set

      O'Sullivan, Orla; O'Callaghan, John; Sangrador-Vegas, Amaia; McAuliffe, Olivia; Slattery, Lydia; Kaleta, Pawel; Callanan, Michael J.; Fitzgerald, Gerald F; Ross, R Paul; Beresford, Tom (Biomed Central, 05/03/2009)
      Background: The recently sequenced genome of Lactobacillus helveticus DPC4571 1 revealed a dairy organism with significant homology (75% of genes are homologous) to a probiotic bacteria Lb. acidophilus NCFM 2. This led us to hypothesise that a group of genes could be determined which could define an organism's niche. Results: Taking 11 fully sequenced lactic acid bacteria (LAB) as our target, (3 dairy LAB, 5 gut LAB and 3 multi-niche LAB), we demonstrated that the presence or absence of certain genes involved in sugar metabolism, the proteolytic system, and restriction modification enzymes were pivotal in suggesting the niche of a strain. We identified 9 niche specific genes, of which 6 are dairy specific and 3 are gut specific. The dairy specific genes identified in Lactobacillus helveticus DPC4571 were lhv_1161 and lhv_1171, encoding components of the proteolytic system, lhv_1031 lhv_1152, lhv_1978 and lhv_0028 encoding restriction endonuclease genes, while bile salt hydrolase genes lba_0892 and lba_1078, and the sugar metabolism gene lba_1689 from Lb. acidophilus NCFM were identified as gut specific genes. Conclusion: Comparative analysis revealed that if an organism had homologs to the dairy specific geneset, it probably came from a dairy environment, whilst if it had homologs to gut specific genes, it was highly likely to be of intestinal origin. We propose that this "barcode" of 9 genes will be a useful initial guide to researchers in the LAB field to indicate an organism's ability to occupy a specific niche.