An observational study of ear-tagged calf mortality (1 to 100 days) on Irish dairy farms and associations between biosecurity practices and calf mortality on farms participating in a Johne's disease control program.

Postnatal mortality among replacement stock has a detrimental effect on the social, economic, and environmental sustainability of dairy production. Calf mortality rates vary between countries and show differences in temporal trends; most, however, are characterized by high levels of between-farm variability. Explaining this variation can be difficult because herd-level information on management practices relevant to calf health is often not available. The Irish Johne's Control Programme (IJCP) contains a substantial on-farm monitoring program called the Veterinary Risk Assessment and Management Plan (VRAMP). Although this risk assessment is largely focused on factors relevant to the transmission of paratuberculosis, many of its principles are good practice biocontainment policies that are also advocated for the protection of calf health. The objectives of this study were (1) to quantify mortality in ear-tagged Irish dairy calves between 2016 and 2020 using both survival and risk approaches, (2) to determine risk factors for 100-d cumulative mortality hazard in ear-tagged Irish dairy calves between 2016 and 2020, (3) to determine whether 100-d cumulative mortality hazard was higher in ear-tagged calves within herds registered in the IJCP versus those that were not registered in the IJCP and whether there were differences between these cohorts over time, and (4) within IJCP herds, to determine whether VRAMP score or changes in VRAMP score were associated with 100-d cumulative mortality hazard. Excluding perinatal mortality, the overall 100-d cumulative mortality hazard was 4.1%. Calf mortality was consistently underestimated using risk approaches that did not account for calf censoring. Cox proportional hazards models showed that cumulative mortality hazard was greater in male calves; particularly, calves born to Jersey breed dams and those with a beef breed sire. Mortality hazard increased with increasing herd size, was highest in calves born in herds that contract-reared heifers, and lowest in those born in mixed dairy-beef enterprises. Mortality hazard decreased over time with the mortality hazard in 2020 being 0.83 times that of 2016. Mortality hazard was higher in IJCP-registered herds than nonregistered herds (hazard ratio 1.06, 95% CI 1.01-1.12), likely reflecting differences in herds that enrolled in the national program. However, we detected a significant interaction between IJCP status (enrolled vs. not enrolled) and year (hazard ratio 0.96, 95% CI 0.92-1.00), indicating that the decrease in mortality hazard between 2016 and 2020 was greater in IJCP herds versus non-IJCP herds. Finally, increasing VRAMP scores (indicating higher risk for paratuberculosis transmission) were positively associated with increased calf mortality hazard. Postnatal calf mortality rates in Irish dairy herds declined between 2016 and 2020. Our study suggests that implementation of recommended biocontainment practices to control paratuberculosis in IJCP herds was associated with a reduction in calf mortality hazard.

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.

Overpressure on fingertips prevents state estimation of the pen grip force and movement accuracy.

We tested the hypothesis that the inability to move a pen accurately in a graphic task is partly due to a decrease of afferent somatosensory information resulting from overpressure on the tactile receptors of the fingers holding the pen. To disentangle the depressed somatosensory origin from an altered motor command, we compared a condition in which the participant actively produces pressure on the pen (active grip) with a condition in which pressure is passively applied (passive grip, no grip-related motor command). We expected that the response of the somatosensory cortex to electric stimulation of the wrist's tactile nerve (i.e., SEP) would be greater in the natural pen grip (baseline condition) than in the two overpressure conditions (actively or passively induced). Fifteen adults were required to trace a geometrical shape in the three grip conditions. The SEP amplitude was not significantly different between the baseline and both overpressure conditions. However, behavioral results showed that drawing accuracy is impaired when the pressure on the pen is increased (passively or actively). Cortical source analyses revealed that the activity of the superior parietal areas (SPL) increased in both overpressure conditions. Our findings suggest that the SPL is critical for sensorimotor integration, by maintaining an internal representation of pen holding. These cortical changes might witness the impaired updating of the finger-pen interaction force for such drawing actions under visual guidance.

Numbers of close contacts of individuals infected with SARS-CoV-2 and their association with government intervention strategies.

BACKGROUND: Contact tracing is conducted with the primary purpose of interrupting transmission from individuals who are likely to be infectious to others. Secondary analyses of data on the numbers of close contacts of confirmed cases could also: provide an early signal of increases in contact patterns that might precede larger than expected case numbers; evaluate the impact of government interventions on the number of contacts of confirmed cases; or provide data information on contact rates between age cohorts for the purpose of epidemiological modelling. We analysed data from 140,204 close contacts of 39,861 cases in Ireland from 1st May to 1st December 2020. RESULTS: Negative binomial regression models highlighted greater numbers of contacts within specific population demographics, after correcting for temporal associations. Separate segmented regression models of the number of cases over time and the average number of contacts per case indicated that a breakpoint indicating a rapid decrease in the number of contacts per case in October 2020 preceded a breakpoint indicating a reduction in the number of cases by 11 days. CONCLUSIONS: We found that the number of contacts per infected case was overdispersed, the mean varied considerable over time and was temporally associated with government interventions. Analysis of the reported number of contacts per individual in contact tracing data may be a useful early indicator of changes in behaviour in response to, or indeed despite, government restrictions. This study provides useful information for triangulating assumptions regarding the contact mixing rates between different age cohorts for epidemiological modelling.

Estimation of the serial interval and proportion of pre-symptomatic transmission events of COVID- 19 in Ireland using contact tracing data.

BACKGROUND: The serial interval is the period of time between the onset of symptoms in an infector and an infectee and is an important parameter which can impact on the estimation of the reproduction number. Whilst several parameters influencing infection transmission are expected to be consistent across populations, the serial interval can vary across and within populations over time. Therefore, local estimates are preferable for use in epidemiological models developed at a regional level. We used data collected as part of the national contact tracing process in Ireland to estimate the serial interval of SARS-CoV-2 infection in the Irish population, and to estimate the proportion of transmission events that occurred prior to the onset of symptoms. RESULTS: After data cleaning, the final dataset consisted of 471 infected close contacts from 471 primary cases. The median serial interval was 4 days, mean serial interval was 4.0 (95% confidence intervals 3.7, 4.3) days, whilst the 25th and 75th percentiles were 2 and 6 days respectively. We found that intervals were lower when the primary or secondary case were in the older age cohort (greater than 64 years). Simulating from an incubation period distribution from international literature, we estimated that 67% of transmission events had greater than 50% probability of occurring prior to the onset of symptoms in the infector. CONCLUSIONS: Whilst our analysis was based on a large sample size, data were collected for the primary purpose of interrupting transmission chains. Similar to other studies estimating the serial interval, our analysis is restricted to transmission pairs where the infector is known with some degree of certainty. Such pairs may represent more intense contacts with infected individuals than might occur in the overall population. It is therefore possible that our analysis is biased towards shorter serial intervals than the overall population.

Epidemiology of age-dependent prevalence of Bovine Herpes Virus Type 1 (BoHV-1) in dairy herds with and without vaccination.

Many studies report age as a risk factor for BoHV-1 infection or seropositivity. However, it is unclear whether this pattern reflects true epidemiological causation or is a consequence of study design and other issues. Here, we seek to understand the age-related dynamics of BoHV-1 seroprevalence in seasonal calving Irish dairy herds and provide decision support for the design and implementation of effective BoHV-1 testing strategies. We analysed seroprevalence data from dairy herds taken during two Irish seroprevalence surveys conducted between 2010 and 2017. Age-dependent seroprevalence profiles were constructed for herds that were seropositive and unvaccinated. Some of these profiles revealed a sudden increase in seroprevalence between adjacent age-cohorts, from absent or low to close to 100% of seropositive animals. By coupling the outcome of our data analysis with simulation output of an individual-based model at the herd scale, we have shown that these sudden increases are related to extensive virus circulation within a herd for a limited time, which may then subsequently remain latent over the following years. BoHV-1 outbreaks in dairy cattle herds affect animals independent of age and lead to almost 100% seroconversion in all age groups, or at least in all animals within a single epidemiological unit. In the absence of circulating infection, there is a year-on-year increase in the age-cohort at which seroprevalence changes from low to high. The findings of this study inform recommendations regarding testing regimes in the context of contingency planning or an eradication programme in seasonal calving dairy herds.

Individual and herd-level milk ELISA test status for Johne's disease in Ireland after correcting for non-disease-associated variables.

Antibody-detecting tests for Mycobacterium avium ssp. paratuberculosis (MAP) have low sensitivity and imperfect specificity for detection of infection. Sensitivity increases as the disease progresses. Aside from infection status and stage of disease, several factors affect test performance. These factors have not yet been studied in dairy cows producing lower volumes of milk with higher solids concentration, such as those managed in low-input, pasture-based production systems. Furthermore, the effect of correcting for these associations on individual and herd test status is also unknown. The first objective of this study was to examine the relationship between MAP antibody response in milk and milk yield, somatic cell count (SCC), fat and protein contents, and stage of lactation in dairy cows enrolled in the national Johne's Disease Control Programme (JDCP) in Ireland. The second objective was to examine the effect of correcting the antibody response for these associations on the test status of individual cows and herds, given that individual tests are often used to define a herd's status. Data were extracted for herds in the JDCP from January 2014 to December 2015 inclusive, consisting of 42,657 milk recordings from 18,569 cows across 187 dairy herds. Two linear regression models were constructed to investigate the association between log-transformed MAP sample-to-positive ratio and milk recording data and in primi- and multiparous cows. Days in milk was modeled as a B-spline in each model, and cow and herd were included as random effects. Across both models, natural log-transformed MAP antibody response was negatively associated with milk yield, positively associated with protein and fat production, and had a curvilinear association with log-transformed SCC. The association between MAP antibody response and days in milk varied over the course of the lactation. However, when combined, these variables explained only 5.1% of the variation in the antibody response of the population. After correcting for these associations, 93 multiparous cows and 20 primiparous cows changed category (negative, suspect, or positive). When considered at the herd-test level, out of a total of 531 herd tests, 1 herd changed from negative to positive, and 5 herds changed from positive to negative. This study provides useful information to aid in the interpretation of antibody results for herds testing animals for the presence of MAP infection. At an overall population level, correction of the serological response for non-disease-associated factors has the potential to change the status of only a small number of cows. At the herd level, the proportion of herds changing status was minimal. However, depending on the implications of a herd-level serological diagnosis, consideration should be given to correcting for these non-disease-associated variables within the context of national JD control programs.

European perspectives on efforts to reduce antimicrobial usage in food animal production.

New regulations on veterinary medicines and medicated feed will substantially influence antimicrobial prescribing and usage throughout Europe into the future. These regulations have been informed by a very large body of work, including the substantial progress towards reduced antimicrobial usage in food animal production in a number of member states of the European Union (EU). This paper seeks to summarise European perspectives on efforts to reduce antimicrobial usage in food animal production. Work within the EU is informed by the global action plan of the World Health Organization, which includes a strategic objective to optimise the use of antimicrobial medicines in human and animal health. There is ongoing measurement of trends in antimicrobial usage and resistance throughout the EU, and detailed information on strategies to reduce the need to use antimicrobials in food animal production. Substantial scientific progress has been made on the measurement of antimicrobial usage, including at herd-level, and on the objective assessment of farm biosecurity. In a number of EU member states, monitoring systems for usage are well-established, allowing benchmarking for veterinarians and farms, and monitoring of national and industry-level trends. Several countries have introduced restrictions on antimicrobial prescribing and usage, including strategies to limit conflicts of interest around antimicrobial prescribing and usage. Further, a broad range of measures are being used across member states to reduce the need for antimicrobial usage in food animal production, focusing both at farm level and nationally. Veterinarians play a central role in the reduction of antimicrobial usage in farm animals. Ireland's National Action Plan on Antimicrobial Resistance 2017-20 (iNAP) provides an overview of Ireland's commitment to the development and implementation of a holistic, cross-sectoral 'One Health' approach to the problem of antimicrobial resistance. The new regulations offer an important springboard for further progress, in order to preserve the efficacy of existing antimicrobials, which are a critical international resource.

Current antimicrobial use in farm animals in the Republic of Ireland.

Antimicrobial resistance has been recognised as one of the most difficult challenges facing human and animal health in recent decades. The surveillance of antimicrobial use in animal health plays a major role in dealing with the growing issue of resistance. This paper reviews current data available on antimicrobial use in farmed animals in the Republic of Ireland, including each of the major livestock production sectors; pigs, poultry, dairy, beef and sheep. A systematic literature search was conducted to identify relevant published literature, and ongoing research was identified through the network of authors and searches of each of the research databases of the main agriculture funding bodies in Ireland. The varying quantities and quality of data available across each livestock sector underlines the need for harmonisation of data collection methods. This review highlights the progress that has been made regarding data collection in the intensive production sectors such as pigs and poultry, however, it is clear there are significant knowledge gaps in less intensive industries such as dairy, beef and sheep. To comply with European regulations an antimicrobial data collection system is due to be developed for all food-producing animals in the future, however in the short-term surveillance studies have allowed us to build a picture of current use within the Republic of Ireland. Further studies will allow us to fill current knowledge gaps and build a more comprehensive overview of antimicrobial use in farm animals in Ireland.

Can bovine TB be eradicated from the Republic of Ireland? Could this be achieved by 2030?

BACKGROUND: There has been an ongoing decline in bovine tuberculosis (TB) in the Republic of Ireland, however, TB has yet to be eradicated. Further to a recent commitment by the Irish government to eradicate TB by 2030, this paper considers two questions, 'Can bovine TB be eradicated from the Republic of Ireland?' and 'Could this be achieved by 2030?', given current knowledge from research. MAIN BODY OF THE ABSTRACT: Until very recently, Ireland has lacked key tools required for eradication. This gap has substantially been filled with the national roll-out of badger vaccination. Nonetheless, there is robust evidence, drawn from general national research, international experiences, and results of a recent modelling study, to suggest that all current strategies plus badger vaccination will not be sufficient to successfully eradicate TB from Ireland by 2030. We face a critical decision point in the programme, specifically the scope and intensity of control measures from this point forward. Adequate information is available, both from research and international experience, to indicate that these additional measures should broadly focus on adequately addressing TB risks from wildlife, implementing additional risk-based cattle controls, and enhancing industry engagement. These three areas are considered in some detail. CONCLUSION: Based on current knowledge, it will not be possible to eradicate TB by 2030 with current control strategies plus national badger vaccination. Additional measures will be needed if Ireland is to eradicate TB within a reasonable time frame. Decisions made now will have long-term implications both in terms of time-to-eradication and cumulative programme costs.

Risk factors associated with exposure to bovine respiratory disease pathogens during the peri-weaning period in dairy bull calves.

BACKGROUND: Bovine respiratory disease (BRD) remains among the leading causes of death of cattle internationally. The objective of this study was to identify risk factors associated with exposure to BRD pathogens during the peri-weaning period (day (d)-14 to d 14 relative to weaning at 0) in dairy bull calves using serological responses to these pathogens as surrogate markers of exposure. Clinically normal Holstein-Friesian and Jersey breed bull calves (n = 72) were group housed in 4 pens using a factorial design with calves of different breeds and planes of nutrition in each pen. Intrinsic, management and clinical data were collected during the pre-weaning (d - 56 to d - 14) period. Calves were gradually weaned over 14 days (d - 14 to d 0). Serological analysis for antibodies against key BRD pathogens (BRSV, BPI3V, BHV-1, BHV-4, BCoV, BVDV and H. somni) was undertaken at d - 14 and d 14. Linear regression models (for BVDV, BPI3V, BHV-1, BHV-4, BCoV and H. somni) and a single mixed effect random variable model (for BRSV) were used to identify risk factors for changes in antibody levels to these pathogens. RESULTS: BRSV was the only pathogen which demonstrated clustering by pen. Jersey calves experienced significantly lower changes in BVDV S/P than Holstein-Friesian calves. Animals with a high maximum respiratory score (≥8) recorded significant increases in H. somni S/P during the peri-weaning period when compared to those with respiratory scores of ≤3. Haptoglobin levels of between 1.32 and 1.60 mg/ml at d - 14 were significantly associated with decreases in BHV-1 S/N during the peri-weaning period. Higher BVDV S/P ratios at d - 14 were significantly correlated with increased changes in serological responses to BHV-4 over the peri-weaning period. CONCLUSIONS: Haptoglobin may have potential as a predictor of exposure to BHV-1. BRSV would appear to play a more significant role at the 'group' rather than 'individual animal' level. The significant associations between the pre-weaning levels of antibodies to certain BRD pathogens and changes in the levels of antibodies to the various pathogens during the peri-weaning period may reflect a cohort of possibly genetically linked 'better responders' among the study population.

A visual representation of cattle movement in Ireland during 2016.

The aim of this study was to create a clear visual representation of the live movements of cattle in the Republic of Ireland over the course of the year 2016. The animation created can be viewed online: https://youtu.be/PTCdPMnenBw This animation was created to be a communication tool to enable stakeholders to appreciate the extent of high risk cattle movements (farm to farm, farm to market to farm) in the Republic of Ireland and to highlight the potential role that these movements may play in the spread of infectious diseases of cattle in Ireland from one farm to another.

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.

On the neural basis of sensory weighting: Alpha, beta and gamma modulations during complex movements.

Previous studies have revealed that visual and somatosensory information is processed as a function of its relevance during movement execution. We thus performed spectral decompositions of ongoing neural activities within the somatosensory and visual areas while human participants performed a complex visuomotor task. In this task, participants followed the outline of irregular polygons with a pen-controlled cursor. At unpredictable times, the motion of the cursor deviated 120° with respect to the actual pen position creating an incongruence between visual and somatosensory inputs, thus increasing the importance of visual feedback to control the movement as suggested in previous studies. We found that alpha and beta power significantly decreased in the visual cortex during sensory incongruence when compared to unperturbed conditions. This result is in line with an increased gain of visual inputs during sensory incongruence. In parallel, we also found a simultaneous decrease of gamma and beta power in sensorimotor areas which has not been reported previously. The gamma desynchronization suggests a reduced integration of somatosensory inputs for controlling movements with sensory incongruence while beta ERD could be more specifically linked to sensorimotor adaptation processes.

The use of national-level data to describe trends in intramammary antimicrobial usage on Irish dairy farms from 2003 to 2015.

In this study, we used national-level data to describe trends in on-farm intramammary antimicrobial usage in Ireland from 2003 to 2015. We calculated actual sales of intramammary tubes and the quantity of active substance sold, by year, product type [lactation or dry cow therapy (DCT)], antimicrobial group, World Health Organization antimicrobial classification, and from 2009 to 2015, prescribing route. We also estimated on-farm usage of lactation and dry cow intramammary antimicrobials using defined daily dose (DDDvet) and defined course dose (DCDvet) calculations, and dry cow coverage. Sales of tubes of antimicrobial for DCT have increased, and the estimated national dry cow coverage in 2015 was 1,022 DCDvet per 1,000 cows per year. An increase has also occurred in sales of teat sealant (2015 sales: 66.7 tubes with teat sealant for every 100 tubes with antimicrobial for DCT). In contrast, the number of tubes of antimicrobial sold for lactation use has decreased to 1,398 DDDvet and 466 DCDvet per 1,000 animals per year. Sales in intramammary tubes with at least one critically important antimicrobial (CIA) have either risen since 2007 (DCT) or fallen (lactation therapy). Increases were observed in both the number of dry cow and lactation tubes containing CIA considered of highest priority for human health. Differences between prescribing routes with respect to CIA usage were observed. This study provides detailed insight into on-farm usage of intramammary antimicrobials in Ireland. It demonstrates positive national progress but also highlights areas for review. In particular, blanket dry cow treatment in Ireland should be reconsidered. It is not possible to investigate farm-level variation in antimicrobial usage from national sales data. In several countries, measurement and benchmarking have been critical to progress in reducing antimicrobial usage in farm animal production. Central collation of data on farm-level antimicrobial use is also needed in Ireland to allow objective measurement and benchmarking of on-farm usage. More generally, standardized indicators to quantify antimicrobial usage in farm animals are urgently needed to allow country-level comparisons.

Relative importance of herd-level risk factors for probability of infection with paratuberculosis in Irish dairy herds.

Control of paratuberculosis is challenging due to the relatively poor performance of diagnostic tests, a prolonged incubation period, and protracted environmental survival. Prioritization of herd-level interventions is not possible because putative risk factors are often not supported by risk factor studies. The objective for this study was to investigate the relative importance of risk factors for an increased probability of herd paratuberculosis infection. Risk assessment data, comprehensive animal purchase history, and diagnostic test data were available for 936 Irish dairy herds. Both logistic regression and a Bayesian ß regression on the outcome of a latent class analysis were conducted. Population attributable fractions and proportional reduction in variance explained were calculated for each variable in the logistic and Bayesian models, respectively. Routine use of the calving area for sick or lame cows was found to be a significant explanatory covariate in both models. Purchasing behavior for the previous 10 yr was not found to be significant. For the logistic model, length of time calves spend in the calving pen (25%) and routine use of the calving pen for sick or lame animals (14%) had the highest attributable fractions. For the Bayesian model, the overall R2 was 16%. Dry cow cleanliness (7%) and routine use of the calving area for sick or lame cows (6%) and had the highest proportional reduction in variance explained. These findings provide support for several management practices commonly recommended as part of paratuberculosis control programs; however, a large proportion of the observed variation in probability of infection remained unexplained, suggesting other important risks factors may exist.

Associations between paratuberculosis ELISA results and test-day records of cows enrolled in the Irish Johne's Disease Control Program.

The effect of the Mycobacterium avium ssp. paratuberculosis (MAP) ELISA status on test-day milk performance of cows from Irish herds enrolled in the pilot national voluntary Johne's disease control program during 2013 to 2015 was estimated. A data set comprising 92,854 cows and 592,623 complete test-day records distributed across 1,700 herds was used in this study. The resulting ELISA outcome (negative, inconclusive, and positive) of each cow within each year of the program was used to allocate the cow into different scenarios representing the MAP status. At MAPscenario1, all cows testing ELISA nonnegative (i.e., inconclusive and positive) were assigned a MAP-positive status; at MAPscenario2 only cows testing ELISA-positive were assigned a MAP-positive status; at MAPscenario3 only cows testing ELISA nonnegative (inconclusive or positive) and gathered exclusively from herds where at least 2 further ELISA nonnegative (inconclusive or positive) cows were found were assigned a MAP-positive status; at MAPscenario4 only cows testing ELISA-positive that were gathered exclusively from herds where at least 2 further ELISA-positive cows were found were assigned a MAP-positive status. Milk outputs based on test-day records were standardized for fat and protein contents (SMY) and the effect of MAP ELISA status on the SMY was estimated by a linear mixed effects model structure. The SMY mean difference recorded at test day between cows with a MAP-positive status and those with a MAP-negative status within MAPscenario1 was estimated at -0.182 kg/test day; the mean difference was -0.297 kg/test day for MAPscenario2; for MAPscenario3 mean difference between MAP-positive status and MAP test-negative cows was -0.209 kg/test day, and for MAPscenario4, the difference was -0.326 kg/test day.

Efficacy of washing and disinfection in cattle markets in Ireland.

BACKGROUND: Few studies have reported on the effectiveness of the washing and disinfection methods used in cattle markets in Ireland. Purchasing cattle into recipient herds poses a high biosecurity risk due to the possibility of introducing disease. In Ireland, livestock markets are an important intermediary in the movement of cattle to new herds. Thus disease control strategies need to consider the disease risk associated with moving livestock through markets. Some cattle are also moved directly from markets for slaughter at abattoirs. Washing and disinfection at markets is utilised to reduce faecal contamination in markets, thereby reducing the risk of disease spread among animals and carcass contamination at slaughter. The primary objective of this study was to assess the efficacy of standard washing and disinfection techniques at markets in Ireland in reducing bacterial contamination on internal structures. Total viable counts (TVC) of colony forming units (CFU) were used as indicators of bacterial contamination, which could include pathogens of public and animal health concern. Four hundred and seventy nine samples were taken mainly from pen floors and the TVC enumerated for each sample. RESULTS: Washing and disinfection was effective at significantly reducing TVCs on floors and metal bars of market holding pens, but residual contamination remained. Washing market pens only (no disinfection), followed by a rest period between batches of cattle (6.5 days) was as effective at reducing TVCs as washing followed by disinfection and a shorter rest period (5.5 days). CONCLUSIONS: Markets are a potential reservoir for microbial contamination with a resultant increased risk of disease spread by cattle moving through markets into new herds, and carcass contamination for cattle moving directly to slaughter. Therefore, market managers need clear advice and guidance on the development of hygiene programmes that are suitable for use in livestock markets.

An investigative framework to facilitate epidemiological thinking during herd problem-solving.

Veterinary clinicians and students commonly use diagnostic approaches appropriate for individual cases when conducting herd problem-solving. However, these approaches can be problematic, in part because they make limited use of epidemiological principles and methods, which has clear application during the investigation of herd problems. In this paper, we provide an overview of diagnostic approaches that are used when investigating individual animal cases, and the challenges faced when these approaches are directly translated from the individual to the herd. Further, we propose an investigative framework to facilitate epidemiological thinking during herd problem-solving. A number of different approaches are used when making a diagnosis on an individual animal, including pattern recognition, hypothetico-deductive reasoning, and the key abnormality method. Methods commonly applied to individuals are often adapted for herd problem-solving: 'comparison with best practice' being a herd-level adaptation of pattern recognition, and 'differential diagnoses' a herd-level adaptation of hypothetico-deductive reasoning. These approaches can be effective, however, challenges can arise. Herds are complex; a collection of individual cows, but also additional layers relating to environment, management, feeding etc. It is unrealistic to expect seamless translation of diagnostic approaches from the individual to the herd. Comparison with best practice is time-consuming and prioritisation of actions can be problematic, whereas differential diagnoses can lead to 'pathogen hunting', particularly in complex cases. Epidemiology is the science of understanding disease in populations. The focus is on the population, underpinned by principles and utilising methods that seek to allow us to generate solid conclusions from apparently uncontrolled situations. In this paper, we argue for the inclusion of epidemiological principles and methods as an additional tool for herd problem-solving, and outline an investigative framework, with examples, to effectively incorporate these principles and methods with other diagnostic approaches during herd problem-solving. Relevant measures of performance are identified, and measures of case frequencies are calculated and compared across time, in space and among animal groupings, to identify patterns, clues and plausible hypotheses, consistent with potential biological processes. With this knowledge, the subsequent investigation (relevant on-farm activities, diagnostic testing and other examinations) can be focused, and actions prioritised (specifically, those actions that are likely to make the greatest difference in addressing the problem if enacted). In our experience, this investigative framework is an effective teaching tool, facilitating epidemiological thinking among students during herd problem-solving. It is a generic and robust process, suited to many herd-based problems.

Challenges facing the veterinary profession in Ireland: 3. emergency and casualty slaughter certification.

BACKGROUND: Veterinarians are faced with significant conflicts of interest when issuing certificates for the transport and slaughter of acutely injured and casualty livestock. In a recent Policy Delphi study, emergency and casualty slaughter certification was a key concern identified by veterinary professionals in Ireland. In this case study (the third in a series of three resulting from a research workshop exploring challenges facing the veterinary profession in Ireland; the other two case studies investigate clinical veterinary services and the on-farm use of veterinary antimicrobials), we aim to provide a value-based reflection on the constraints and opportunities for best practice in emergency and casualty slaughter certification in Ireland. RESULTS: Using a qualitative focus group approach, this study gathered evidence from relevant stakeholders, namely a representative from the regulatory body, local authority veterinarians with research experience in emergency slaughter, an animal welfare research scientist, official veterinarians from the competent authority, a private veterinary practitioner, and a member of a farming organisation. Results revealed a conflict between the responsibility of private veterinary practitioners (PVPs) to safeguard the welfare of acutely injured bovines on-farm and the client's commercial concerns. As a consequence, some PVPs may feel under pressure to certify, for example, an acutely injured animal for casualty slaughter instead of recommending either on-farm emergency slaughter or disposal by the knackery service. Among Official Veterinarians, there are concerns about the pressure within processing plants to accept acutely injured livestock as casualty animals. Confusion pertaining to legislation and definition of fitness to travel also contribute to these dilemmas. CONCLUSIONS: Conflicts of interest arise due to the gap between governance and provision to facilitate on-farm emergency slaughter of livestock. Increased availability and acceptance of on-farm emergency slaughter by Food Business Operators (FBOs) would mitigate the need to certify acutely injured animals fit for transport and slaughter and thereby safeguard animal welfare. In the absence of nationwide availability and acceptance of on-farm emergency slaughter by FBOs, consideration should be given to methods to encourage all those involved in the food chain to prioritise animal welfare when in conflict with the commercial value of the animal. Training and guidelines for PVPs on the regulatory landscape and ethical decision-making should become available. The reintroduction of the fallen animal scheme should be considered to support farm animal welfare.