Output-based assessment of herd-level freedom from infection in endemic situations: Application of a Bayesian Hidden Markov model.

Countries have implemented control programmes (CPs) for cattle diseases such as bovine viral diarrhoea virus (BVDV) that are tailored to each country-specific situation. Practical methods are needed to assess the output of these CPs in terms of the confidence of freedom from infection that is achieved. As part of the STOC free project, a Bayesian Hidden Markov model was developed, called STOC free model, to estimate the probability of infection at herd-level. In the current study, the STOC free model was applied to BVDV field data in four study regions, from CPs based on ear notch samples. The aim of this study was to estimate the probability of herd-level freedom from BVDV in regions that are not (yet) free. We additionally evaluated the sensitivity of the parameter estimates and predicted probabilities of freedom to the prior distributions for the different model parameters. First, default priors were used in the model to enable comparison of model outputs between study regions. Thereafter, country-specific priors based on expert opinion or historical data were used in the model, to study the influence of the priors on the results and to obtain country-specific estimates. The STOC free model calculates a posterior value for the model parameters (e.g. herd-level test sensitivity and specificity, probability of introduction of infection) and a predicted probability of infection. The probability of freedom from infection was computed as one minus the probability of infection. For dairy herds that were considered free from infection within their own CP, the predicted probabilities of freedom were very high for all study regions ranging from 0.98 to 1.00, regardless of the use of default or country-specific priors. The priors did have more influence on two of the model parameters, herd-level sensitivity and the probability of remaining infected, due to the low prevalence and incidence of BVDV in the study regions. The advantage of STOC free model compared to scenario tree modelling, the reference method, is that actual data from the CP can be used and estimates are easily updated when new data becomes available.

Ethical challenges facing veterinary professionals in Ireland: results from Policy Delphi with vignette methodology.

Ethics is key to the integrity of the veterinary profession. Despite its importance, there is a lack of applied research on the range of ethical challenges faced by veterinarians. A three round Policy Delphi with vignette methodology was used to record the diversity of views on ethical challenges faced by veterinary professionals in Ireland. Forty experts, comprising veterinary practitioners, inspectors and nurses, accepted to participate. In round 1, twenty vignettes describing a variety of ethically challenging veterinary scenarios were ranked in terms of ethical acceptability, reputational risk and perceived standards of practice. Round 2 aimed at characterising challenges where future policy development or professional guidance was deemed to be needed. In round 3, possible solutions to key challenges were explored. Results suggest that current rules and regulations are insufficient to ensure best veterinary practices and that a collective approach is needed to harness workable solutions for the identified ethical challenges. Challenges pertaining mostly to the food chain seem to require enforcement measures whereas softer measures that promote professional discretion were preferred to address challenges dealing with veterinary clinical services. These findings can support veterinary representative bodies, advisory committees and regulatory authorities in their decision making, policy and regulation.

Evaluation of testing strategies to identify infected animals at a single round of testing within dairy herds known to be infected with Mycobacterium avium ssp. paratuberculosis.

As part of a broader control strategy within herds known to be infected with Mycobacterium avium ssp. paratuberculosis (MAP), individual animal testing is generally conducted to identify infected animals for action, usually culling. Opportunities are now available to quantitatively compare different testing strategies (combinations of tests) in known infected herds. This study evaluates the effectiveness, cost, and cost-effectiveness of different testing strategies to identify infected animals at a single round of testing within dairy herds known to be MAP infected. A model was developed, taking account of both within-herd infection dynamics and test performance, to simulate the use of different tests at a single round of testing in a known infected herd. Model inputs included the number of animals at different stages of infection, the sensitivity and specificity of each test, and the costs of testing and culling. Testing strategies included either milk or serum ELISA alone or with fecal culture in series. Model outputs included effectiveness (detection fraction, the proportion of truly infected animals in the herd that are successfully detected by the testing strategy), cost, and cost-effectiveness (testing cost per true positive detected, total cost per true positive detected). Several assumptions were made: MAP was introduced with a single animal and no management interventions were implemented to limit within-herd transmission of MAP before this test. In medium herds, between 7 and 26% of infected animals are detected at a single round of testing, the former using the milk ELISA and fecal culture in series 5 yr after MAP introduction and the latter using fecal culture alone 15 yr after MAP introduction. The combined costs of testing and culling at a single round of testing increases with time since introduction of MAP infection, with culling costs being much greater than testing costs. The cost-effectiveness of testing varied by testing strategy. It was also greater at 5 yr, compared with 10 or 15 yr, since MAP introduction, highlighting the importance of early detection. Future work is needed to evaluate these testing strategies in subsequent rounds of testing as well as accounting for different herd dynamics and different levels of herd biocontainment.

Opportunities and constraints to improving milk quality in Ireland: enabling change through collective action.

Ireland plays a key role in contributing to the global supply of dairy produce, and increasing international demand, as well as the abolition of milk quotas in the European Union in 2015, present opportunities for the Irish milk industry. Improving milk quality is required to maximize these opportunities. National action on milk quality is spearheaded by Animal Health Ireland, yet the potential for collective action at an industry level is undermined by the inability of individual stakeholders to accept responsibility for action. In-depth qualitative interviews were conducted with n=12 stakeholder representatives. The theoretical concepts of collective action (i.e., when a group of people with a shared interest undertake some kind of voluntary common action in pursuit of that shared interest) is applied to understanding the results and identifying a collective way forward. Though consensus is apparent on the need to improve milk quality, differences exist about individual responsibility and the best way to achieve higher quality standards. The propensity for collective action is undermined by shifting responsibility to other stakeholders, stakeholder positions, trust concerns, and concerns over the commitment of other stakeholders to cooperate. Understanding how collective action works provides Animal Health Ireland with a knowledge framework in which to build stakeholder consensus. The paper concludes with practical examples of how Animal Health Ireland continues to apply this understanding by bringing individual stakeholders together to achieve milk quality improvement.

The effect of alternative testing strategies and bio-exclusion practices on Johne's disease risk in test-negative herds.

Herd classification is a key component of national Johne's disease (JD) control programs. Herds are categorized on the basis of test results, and separate sub-programs are followed for test-positive and test-negative herds. However, a test-negative herd result does not necessarily equate to JD freedom for reasons relating to disease pathogenesis and available diagnostic tests. Thus, in several countries, JD control programs define test-negative herds as having a "low risk" of infection below a specified prevalence. However, the approach is qualitative, and little quantitative work is available on herd-level estimates of probability of freedom in test-negative herds. This paper examines the effect over time of alternative testing strategies and bio-exclusion practices on JD risk in test-negative herds. A simulation model was developed in the programming language R. Key model inputs included sensitivity and specificity estimates for 3 individual animal diagnostic tests (serum ELISA, milk ELISA, and fecal culture), design prevalence, testing options, and testing costs. Key model outputs included the probability that infection will be detected if present at the design prevalence or greater (herd sensitivity; SeH), the probability that infection in the herd is either absent or at very low prevalence (i.e., less than the design prevalence; ProbF), the probability of an uninfected herd producing a false-positive result [P(False+)], and mean testing cost (HerdCost) for different testing strategies. The output ProbF can be updated periodically, incorporating data from additional herd testing and information on cattle purchases, and could form the basis for an output-based approach to herd classification. A high ProbF is very difficult to achieve, reflecting the low sensitivity of the evaluated tests. Moreover, ProbF is greatly affected by any risk of introduction of infection, decreasing in herds with poor bio-exclusion practices despite ongoing negative test results. The value of P(False+) was substantial when tests with imperfect specificity were used. Testing strategies can substantially influence testing costs but with little effect on test performance. This study illustrates an output-based approach to herd classification, with potential for national and field applications.

Animal Health Ireland: providing national leadership and coordination of non-regulatory animal health issues in Ireland.

Livestock production plays an important role in the Irish economy. Regulatory animal health issues are the responsibility of government, but until recently there has been no national coordination of non-regulatory animal health issues. This gap has recently been filled with the establishment of Animal Health Ireland (AHI), a not-for-profit, partnership-based organisation providing national leadership and coordination of non-regulatory animal health issues in Ireland. Animal Health Ireland provides benefits to livestock producers and processors by providing the knowledge, education and coordination required to establish effective control strategies, both on-farm and nationally. This paper presents a brief overview of the context for AHI, and of its establishment and initial activities. Non-regulatory animal health issues have been prioritised. A series of work programmes (each focusing on a high-priority issue) have been established. Partnership is critical to success, both for AHI as an organisation and for effective farm-level transfer of knowledge. This model for national leadership and coordination of non-regulatory animal health issues may be of relevance elsewhere.

Genetic correlations between measures of Mycobacterium bovis infection and economically important traits in Irish Holstein-Friesian dairy cows.

Mycobacterium bovis is the primary agent of tuberculosis (TB) in cattle. The failure of Ireland and some other countries to reach TB-free status indicates a need to investigate complementary control strategies. One such approach would be genetic selection for increased resistance to TB. Previous research has shown that considerable genetic variation exists for susceptibility to the measures of M. bovis infection, confirmed M. bovis infection, and M. bovis-purified protein derivative (PPD) responsiveness. The objective of this study was to estimate the genetic and phenotypic correlations between economically important traits and these measures of M. bovis infection. A total of 20,148 and 17,178 cows with confirmed M. bovis infection and M. bovis-PPD responsiveness records, respectively, were available for inclusion in the analysis. First- to third-parity milk, fat, and protein yields, somatic cell count, calving interval, and survival, as well as first-parity body condition score records, were available on cows that calved between 1985 and 2007. Bivariate linear-linear and threshold-linear sire mixed models were used to estimate (co)variance components. The genetic correlations between economically important traits and the measures of M. bovis infection estimated from the linear-linear and threshold-linear sire models were similar. The genetic correlations between susceptibility to confirmed M. bovis infection and economically important traits investigated in this study were all close to zero. Mycobacterium bovis-PPD responsiveness was positively genetically correlated with fat production (0.39) and body condition score (0.36), and negatively correlated with somatic cell score (-0.34) and survival (-0.62). Hence, selection for increased survival may indirectly reduce susceptibility to M. bovis infection, whereas selection for reduced somatic cell count and increased fat production and body condition score may increase susceptibility to M. bovis infection.

Evaluation of current equine welfare issues in Ireland: causes, desirability, feasibility and means of raising standards.

REASONS FOR PERFORMING STUDY: Significant potential threats to the health and welfare of horses exist in Ireland when supply exceeds demand and the identification system for horses is not yet robust. OBJECTIVES: To secure engagement with stakeholder groups and determine their perception of equine welfare in Ireland and encourage the development of inclusive, rather than imposed, policy solutions. METHODS: A 3 round, web-based Policy Delphi incorporating novel vignette methodology was conducted from November 2007-March 2008 to canvass opinion (in both quantitative and qualitative forms) on the perceived most significant equine welfare issues. Vignettes (narratives depicting potential compromise to equine welfare) were employed. Quantitative data were collected in the form of scoring on a 9 point Likert scale with labelled end-points, qualitative information as text subsequently analysed for themes. RESULTS: All 44 respondents completed all rounds. Major equine welfare issues were identified as welfare of horses during the disposal process and at unregulated gatherings. Assessed quantitatively on a 9 point Likert scale (0 = minimal; 8 = maximal), respondents scored the desirability and feasibility of improving standards, median 8 and 6, respectively, for both issues identified. Basic themes identified in respondents' quotes as reasons to raise equine welfare standards were ideological, protection of animal welfare, safe-guarding the reputation of the equine industry and safety (of people, horses and environment). Themes for reasons for low standards were societal norms, fiscal pressures, indolence, indifference and ignorance. Themes underpinning potential means for achieving meaningful change (solutions) were legislation, enforcement, education/training, fiscal remedies, increasing awareness and a combination of these. CONCLUSIONS: Mechanisms aimed at raising standards must be based on an understanding of motivational drivers for currently low standards. POTENTIAL RELEVANCE: The challenge is to translate the findings and this heightened awareness into meaningful change to the benefit of horses and those who care for them.

The risk of a positive test for bovine tuberculosis in cattle purchased from herds with and without a recent history of bovine tuberculosis in Ireland.

A retrospective cohort study was conducted to assess if cattle sold from Irish dairy herds within 7 months of herd de-restriction (clearance to trade) from a bovine-tuberculosis (BTB) episode had an excess risk of testing positive for BTB during the following 2 years, and to determine other risk factors associated with this outcome. If possible, a predictive metric for herds at high risk of selling future BTB-positive cattle would be generated. The unexposed cohort included all cattle sold within 7 months of the annual herd test in a random sample of dairy herds that did not test positive for BTB in 2003. The exposed cohort consisted of all cattle sold within 7 months of the date of de-restriction in all dairy herds that cleared a BTB episode in 2003. Only cattle sold from herds that were initially found to test positive for BTB using the single intradermal comparative tuberculin test (SICTT)-and not due to discovery of a BTB-positive animal at slaughter-were included as exposed cattle. To aid in the development of a predictive metric, the exposed cohort was subcategorized based on the number of reactors to the SICTT in the herd of origin during the BTB episode immediately prior to sale. The final exposure categories of 0 (unexposed), 1-7, and >or=8 total reactors were considered the unexposed, mildly exposed, and severely exposed cohorts, respectively. A multivariable logistic regression model was fit to the final BTB status of the animal using a generalized estimating equation method (GEE), assuming an exchangeable correlation structure of animals within herds, and using robust standard errors. Exposure level and the other available herd- and animal-level information were modeled. After controlling for other risk factors including the size of the herd of origin and the sex and age of the animal, the three-level exposure variable significantly improved the model (based on a change in Quasi-Akaike Information Criteria of 2.2) and demonstrated a trend of increasing risk of a future positive BTB test with increasing exposure category. The severely exposed cohort of animals had significantly higher risk of a future positive BTB test than the unexposed cohort (OR=1.78, p=0.030).

Assessment of organoleptic postmortem inspection techniques for bovine offal.

OBJECTIVE: To evaluate organoleptic postmortem inspection techniques for bovine livers and kidneys. STUDY DESIGN: At Australian export abattoirs, bovine liver and kidneys are assessed and graded by qualified meat inspectors during normal operations. Over a 12-month period at a large abattoir in eastern Australia during 1997 and 1998, a sample of these organs was reassessed independently using a range of pathological and microbiological methods. Agreement between routine inspection and independent assessment was evaluated using methods of inter-rater agreement. RESULTS: A total of 944 livers and 1374 kidneys were included in the study. All of these organs had been classified during routine inspection. The authors examined 363 livers and 329 kidneys both grossly and histologically, including 36 livers and 14 kidneys that were also subjected to microbiological examination. All other organs were only examined grossly. There was only a moderate level of agreement between the routine and independent assessment methods. For livers, the percentage agreement was 80.2%, McNemar's test of symmetry 55.2 (3 degrees of freedom, P < 0.001) and kappa 0.63. For kidneys, the percentage agreement was 67.8%, McNemar's test of symmetry 9.9 (1 df, P = 0.002) and kappa 0.35. CONCLUSIONS: The results reinforce concerns from a number of authors about organoleptic postmortem inspection. Risk assessment methodologies offer the opportunity to modify inspection techniques in a manner that is most relevant to current public health concerns.

A field trial of the effect of improved piglet management on smallholder sow productivity in the Philippines.

We conducted a randomised, controlled field trial during 1998/1999 to evaluate the hypothesis that improved piglet management would improve the reproductive performance of smallholder sows. Simple changes were introduced into the treatment herds including the construction of a heated piglet-separation pen, vitamin injections, creep feeding and early weaning. The control herds were unchanged. Data were collected from all sows in each enrolled herd over two farrowings. We enrolled 176 sows, including 170 (96 treatment and 74 control) sows that remained throughout the study period. Significant differences in the reproductive performance of treatment and control sows were recorded for interfarrowing interval (median 176 versus 220 days), average number liveborn over 2 litters (11 versus 12), and average preweaning mortality over 2 litters (0 versus 37%). Based on a discount rate of 17%, the benefit-cost ratio of the treatment was 11.1 and 12.1 over 3 and 5 years, respectively.