Now showing 1 - 10 of 21
  • Publication
    Modelling transmission of Mycobacterium avium subspecies paratuberculosis between Irish dairy cattle herds
    Bovine paratuberculosis is an endemic disease caused by Mycobacterium avium subspecies paratuberculosis (Map). Map is mainly transmitted between herds through movement of infected but undetected animals. Our objective was to investigate the effect of observed herd characteristics on Map spread on a national scale in Ireland. Herd characteristics included herd size, number of breeding bulls introduced, number of animals purchased and sold, and number of herds the focal herd purchases from and sells to. We used these characteristics to classify herds in accordance with their probability of becoming infected and of spreading infection to other herds. A stochastic individual-based model was used to represent herd demography and Map infection dynamics of each dairy cattle herd in Ireland. Data on herd size and composition, as well as birth, death, and culling events were used to characterize herd demography. Herds were connected with each other through observed animal trade movements. Data consisted of 13 353 herds, with 4 494 768 dairy female animals, and 72 991 breeding bulls. We showed that the probability of an infected animal being introduced into the herd increases both with an increasing number of animals that enter a herd via trade and number of herds from which animals are sourced. Herds that both buy and sell a lot of animals pose the highest infection risk to other herds and could therefore play an important role in Map spread between herds.
  • Publication
    Evaluation of national surveillance methods for detection of Irish dairy herds infected with Mycobacterium avium ssp. paratuberculosis
    The aim of this study was to evaluate the utility and cost-effectiveness of a range of national surveillance methods for paratuberculosis in Irish dairy herds. We simulated alternative surveillance strategies applied to dairy cattle herds for the detection of Mycobacterium avium ssp. paratuberculosis (MAP)-infected herds (case-detection) or for estimation of confidence of herd freedom from infection (assurance testing). Strategies simulated included whole-herd milk or serum serology, serology on cull cows at slaughter, bulk milk tank serology, environmental testing, and pooled fecal testing. None of the strategies evaluated were ideal for widespread national case-detection surveillance. Herd testing with milk or serum ELISA or pooled fecal testing were the most effective methods currently available for detection of MAP-infected herds, with median herd sensitivity >60% and 100% herd specificity, although they are relatively expensive for widespread use. Environmental sampling shows promise as an alternative, with median herd sensitivity of 69%, but is also expensive unless samples can be pooled and requires further validation under Irish conditions. Bulk tank milk testing is the lowest cost option and may be useful for detecting high-prevalence herds but had median herd sensitivity <10% and positive predictive value of 85%. Cull cow sampling strategies were also lower cost but had median herd sensitivity <40% and herd positive predictive values of <50%, resulting in an increased number of test-positive herds, each of which requires follow-up herd testing to clarify status. Possible false-positive herd testing results associated with prior tuberculosis testing also presented logistical issues for both cull cow and bulk milk testing. Whole-herd milk or serum ELISA testing are currently the preferred testing strategies to estimate confidence of herd freedom from MAP in dairy herds due to the good technical performance and moderate cost of these strategies for individual herd testing. Cull cow serology and bulk tank milk sampling provide only minimal assurance value, with confidence of herd freedom increasing only minimally above the prior estimate. Different testing strategies should be considered when deciding on cost-effective approaches for case-detection compared with those used for building confidence of herd freedom (assurance testing) as part of a national program.
      150Scopus© Citations 21
  • Publication
    Decision support beyond total savings—Eligibility and potential savings for individual participants from changes in the national surveillance strategy for bovine viral diarrhoea (BVD) in Ireland
    Surveillance and management of livestock diseases is often evaluated with reference to expected sector-wide costs. In contrast, we calculate losses or savings for individual herd owners of a change in monitoring strategy during a national cattle disease eradication programme: bovine viral diarrhoea (BVD) in Ireland. The alternative strategy differs in how the disease is identified; by its sample- rather than census-based approach; and by its greater cost per test. We examined the costs faced by each breeding herd if testing were conducted using serology on a sample of young stock, in contrast to the current method of tissue-tag testing of all newborn calves. Following best knowledge of the likely costs, the following input values were used: i) €2.50 per test for tissue-tag testing and €7.66 for serology, ii) serology conducted on a sample of 10 young stock per management group from either the 6–12 month or 9–18 month cohorts; iii) 3 scenarios for the number of management groups: one per herd (M∞), one per 100 cows (M100) and one per 50 cows (M50). We found that many herds would often not be able to supply a suitable sample of young stock for serology or would face higher testing costs than when using tissue tag testing. The largest number (25%) of herds would benefit from participating in the change if sampling were done in October. These could annually save between €2.1 million under M∞ and €0.8 million under M50 (€108 - €49 per herd). However, analysing herd-level data we found that 90% of all Irish breeding herds would save less than €1.42 per cow or €99 in total per annum under M∞ and €0.59 per cow or €36 in total under M50. In a sensitivity analysis, we allowed serology costs to vary between €2 and €10 per animal. Herds at the 10 t h percentile of most savings made from switching would save at most €155 (M∞ at €2 per serology test) but would not save anything under M50 at costs ≥ €10. We conclude that, under these assumptions, the expected reduction in testing costs for the majority of beneficiaries would barely outweigh the practical implications of the strategy switch or the risks to the eradication programme associated with sample based surveillance. This study does not assess the cost-effectiveness of alternatives post-eradication.
      296Scopus© Citations 3
  • Publication
    Sampling Methodology to Maximize the Efficient Use of National Abattoir Surveillance: Using Archived Sera to Substantiate Freedom From Bluetongue Virus Infection in Ireland
    In recent years, there has been increasing recognition of the value of multiple data sources available to fulfill surveillance objectives, and the use of these has been applied to address many questions relating to animal health surveillance. In Ireland, we face a slightly different problem, namely, best use of an existing surveillance resource (serological samples collected over many years from cull cows at slaughter), which has been used to substantiate freedom from Brucella abortus following its successful eradication in 2009. In this study, we evaluate a sampling methodology to use this resource to substantiate freedom from bluetongue virus (BTV) infection. An examination of the degree to which cull cows were resident in the same herd throughout the midge biting season showed that, of 50,640 samples collected between 17 October and 23 December 2016, 80.2% were from animals resident in the same herd between 01 April 2016 and 2 months prior to their slaughter date, 74.1% for 1 month prior, 70.1% for 2 weeks prior, 66.4% for 1 week prior, and 56.4% up to 1 day prior to slaughter. An examination was made of the degree to which individual samples within the same 88-well frozen storage block came from geographically clustered herds, whether from a concentration of animals from the same herd in a single block, or from clustering around the slaughterhouse where the samples were taken. On the basis of these analyses, a sampling strategy was derived aimed at minimizing the number of storage blocks which needed to be thawed, whilst ensuring a large enough and representative sample, geographically stratified according to the bovine population of 51 squares, each 45 × 45 km, covering the entirety of Ireland. None of the 503 samples tested were positive for BTV, providing reassurance of national BTV freedom. More broadly, the study demonstrates the use of abattoir-based serological samples collected for one large scale surveillance programme in surveillance for other bovine infections.
      295Scopus© Citations 3
  • Publication
    A systematic framework of modelling epidemics on temporal networks
    We present a modelling framework for the spreading of epidemics on temporal networks from which both the individual-based and pair-based models can be recovered. The proposed temporal pair-based model that is systematically derived from this framework offers an improvement over existing pair-based models by moving away from edge-centric descriptions while keeping the description concise and relatively simple. For the contagion process, we consider the susceptible–infected–recovered (SIR) model, which is realized on a network with time-varying edges. We show that the shift in perspective from individual-based to pair-based quantities enables exact modelling of Markovian epidemic processes on temporal tree networks. On arbitrary networks, the proposed pair-based model provides a substantial increase in accuracy at a low computational and conceptual cost compared to the individual-based model. From the pair-based model, we analytically find the condition necessary for an epidemic to occur, otherwise known as the epidemic threshold. Due to the fact that the SIR model has only one stable fixed point, which is the global non-infected state, we identify an epidemic by looking at the initial stability of the model.
      117Scopus© Citations 3
  • Publication
    Model to simulate the spread of Mycobacterium avium subsp. paratuberculosis (Map) within and between herds via trade movements between dairy herds
    Model to simulate the spread of Mycobacterium avium subsp. paratuberculosis (Map) within and between herds via trade movements between dairy herds. Control measures can be applied: - trade movements rewiring to foster exchanges between herds of the same status (according to within-herd prevalence) (w option) - hygiene, by decreasing calf exposure to bacterial environment (e option) - early culling of high shedders (k option). Model is mechanistic (infection dynamics) and data-driven (movements and demography), stochastic, discrete-time and individual-based. Requirements: C++ compiler: g++ (tested version: 7.2.0) => sudo apt install g++. Warning: standard library C++11 is required. tclap (version 1.2.1): sudo apt install libtclap-dev.
  • Publication
    Using an epidemiological framework and bovine spongiform encephalopathy investigation questionnaire to investigate suspect bovine spongiform encephalopathy cases: an example from a bovine spongiform encephalopathy case in Ireland in 2015
    In several EU member states, bovine spongiform encephalopathy (BSE) cases have been identified in cattle born after the reinforced ban (BARB cases), for reasons that are not entirely clear. Epidemiological investigation of these cases has proved challenging. The European Food Safety Authority recently recommended the collection of a predefined set of epidemiological data from BSE suspects and confirmed BSE cases to aid future investigations. In this study, we present an epidemiological framework and BSE investigation questionnaire to aid the investigation of suspect BSE cases, and illustrate its application during the investigation of a BSE case in Ireland in 2015. It is recommended that the framework and questionnaire are used concurrently: the framework provides structure and focus, whereas the questionnaire (with 135 questions) aids data collection. The framework focuses on confirmation and discrimination, estimating the date and location of exposure, and determining the method/source of exposure. The BSE case in Ireland in 2015 was a BARB case born in 2010. It was identified with classical BSE at an authorised knackery as part of Ireland's targeted active surveillance programme for BSE. No definitive source of infection with the BSE agent could be attributed in this case.
      242Scopus© Citations 3
  • Publication
    The Irish cattle population structured by enterprise type: overview, trade & trends
    Background: The cattle sector is the most important economic production unit of the Irish farming and agri-food sector. Despite its relevance, there has been limited quantitative information about the structure of differing cattle production types and of the connections between them. This paper addresses this gap by providing, for the first time, an overview of the Irish cattle population structured by enterprise type. Methods & Results: We collected data from the cattle register for the period 2015 to 2019 and assigned registered herds to one of 18 different herd types using a recently published herd type classification approach. This allows, for the first time, to exploring changes in enterprise types and subtypes over time, and describing the movements between these subtypes and from these subtypes to slaughter. Conclusions: The overview and associated classification presented in this study will form the basis for a number of future comparative studies, including cross-sectoral assessments of profitability, estimation of the extent of animal health losses on Irish cattle farms or structural analysis of Greenhouse Gas (GHG) emissions across production systems.
      78Scopus© Citations 1
  • Publication
    Combining expert knowledge and machine-learning to classify herd types in livestock systems
    A detailed understanding of herd types is needed for animal disease control and surveillance activities, to inform epidemiological study design and interpretation, and to guide effective policy decision-making. In this paper, we present a new approach to classify herd types in livestock systems by combining expert knowledge and a machine-learning algorithm called self-organising-maps (SOMs). This approach is applied to the cattle sector in Ireland, where a detailed understanding of herd types can assist with on-going discussions on control and surveillance for endemic cattle diseases. To our knowledge, this is the first time that the SOM algorithm has been used to differentiate livestock systems. In compliance with European Union (EU) requirements, relevant data in the Irish livestock register includes the birth, movements and disposal of each individual bovine, and also the sex and breed of each bovine and its dam. In total, 17 herd types were identified in Ireland using 9 variables. We provide a data-driven classification tree using decisions derived from the Irish livestock registration data. Because of the visual capabilities of the SOM algorithm, the interpretation of results is relatively straightforward and we believe our approach, with adaptation, can be used to classify herd type in any other livestock system.
      91Scopus© Citations 8
  • Publication
    The bovine tuberculosis cluster in north County Sligo during 2014-16
    Background: Bovine tuberculosis (bTB, caused by infection with Mycobacterium bovis) is endemic in the Irish cattle population, and the subject of a national eradication programme since the late 1950s. During 2014, a substantial area-level bTB outbreak developing in north County Sligo, necessitating the need for an enhanced response. This paper describes this outbreak, the response that was undertaken and some lessons learned. Results: In the north Sligo area between 2014 and 2016, 23 (31.9%) of restricted herds had 4 or more reactors to the single intradermal comparative tuberculin test (SICTT)/animals with bTB lesions disclosed during the restriction, and the majority (55.5%) of test-positive animals were identified as standard reactors to the SICTT. The herds restricted during 2014–16 were typically larger than other herds in the study area and introduced more animals during 2013. M. bovis was also detected in local badgers, but not deer. Conclusion: This paper describes a substantial outbreak in north County Sligo over a 3-year period. A coordinated area-based approach was a key feature of the outbreak, and substantial resources were applied to bring the outbreak under control. No definitive source was identified, nor reasons why a substantial number of herds were infected over a relatively short period. A coordinated regional approach was taken, and a number of lessons were learned including the need for urgency, for a team-based approach, for a consistent message when dealing with the public, for an area-based approach, for a degree of flexibility for the breakdown manager, and for molecular tools to assist in answering key questions relating to the source and spread of M. bovis to many herds during this bTB outbreak.
      204Scopus© Citations 1