Performance of various interpretations of clinical scoring systems for diagnosis of respiratory disease in dairy calves in a temperate climate using Bayesian latent class analysis.

Bovine respiratory disease (BRD) presents a challenge to farmers all over the globe not only because it can have significant impacts on welfare and productivity, but also because diagnosis can prove challenging. Several clinical scoring systems have been developed to aid farmers in making consistent early diagnosis, 2 examples being the Wisconsin (WCS) and the California (CALIF) systems. Neither of these systems were developed in or for use in a temperate environment. As environment may lead to changes in BRD presentation, the weightings and cut offs designed for one environmental presentation of BRD may not be appropriate when used in a temperate climate. Additionally, the interpretation of the scores recorded varies between studies; this may also influence conclusions. Hence, the objective of this work was to investigate the sensitivity (Se) and specificity (Sp) of these tests in a temperate climate and investigate the influence of varying the interpretation on the performance of the WCS. In this prospective study, 98 commercial spring calving dairy farms were recruited (40 randomly, 58 targeted) and visited. Thoracic ultrasound and WCS was performed on 20 randomly sampled calves between 4 and 6 weeks of age on each farm. On a subset of 32 farms, the CALIF score was also undertaken. The data were then used in a hierarchical Bayesian latent class model to estimate the Se and Sp of 5 different interpretations of the Wisconsin clinical score and one interpretation of the California clinical score. In total, 1,936 calves were examined. The Se of the Wisconsin score varied from 0.336 to 0.577 depending on the interpretation used and the Sp varied from 0.943 to 0.977. The Se of the California score was 0.529 (95% Bayesian credible interval (BCI); 0.403, 0.651) and the Sp was 0.903 (95% bci; 0.883, 0.922). In conclusion, the performance of the clinical scores in a temperate environment were similar to previously published work from more extreme climates, however the performance varied widely depending on the score interpretation. Authors should justify their usage of a particular clinical score interpretation to improve clarity in publications.

Recording antimicrobial use on Irish dairy farms: Barriers and facilitators to using technology and sharing data.

Antimicrobial use (AMU) data are essential to monitor the effect of AMU reduction strategies in animal health. The use of technology and herd recording software to record AMU will be vital to scale the collation of these data in the future. The aim of this study was to determine the barriers and facilitators to Irish dairy farmers recording their AMU using a herd recording software and sharing AMU data. Thirty-three Irish dairy farmers involved in a study on AMU monitoring were asked to record their AMU using a herd recording software over a 12-mo period. At the end of the 12-mo period, 10 of these farmers were selected to take part in semi-structured interviews exploring their opinions on recording AMU, the use of herd recording software, and sharing AMU data. Interviews were transcribed and qualitatively analyzed using inductive thematic analysis. Several barriers and facilitators to farmers recording their AMU using a herd recording software and sharing AMU data were identified. Barriers included the age and generation of the farmer, farm infrastructure, a lack of training and education, a lack of knowledge around the benefits of digital data, a lack of incentive to digitize records, and a fear of repercussions. Facilitators identified by the farmers included the benefits of having instantly available data for making herd management decisions, reduced paperwork, increased organization for inspections, and a potential positive effect on the image of the dairy industry. To increase the uptake of new technology to record AMU at farm-level, farmers will need support in terms of education and training around the software available to them and reassurance around the perceived risks of repercussions with sharing data in a digital format.

Sensitivity and specificity of mobility scoring for the detection of foot lesions in pasture-based Irish dairy cows.

Lameness is an important production disease in dairy cows worldwide and has detrimental effects on cows' welfare, production, and reproductive performance, thus affecting the sustainability of dairy farming. Timely and effective detection of lameness allows for effective treatment, minimizing progression of disease, and maximizing the prognosis of recovery. Mobility scoring (MSc) is a 4 point (0-3) visual lameness scoring system that is the industry standard in several countries. However, few studies have examined the sensitivity (Se) and specificity (Sp) of MSc to detect foot lesions. The aim of this observational study was to determine the Se and Sp of MSc to detect foot lesions in dairy cattle in a pasture-based system. Five hundred ninety-five primi- and multiparous cows were randomly selected from 12 commercial Irish dairy farms and recruited for the study. Recruited cows were mobility scored and passed through a foot-paring crate where all 4 feet were lifted for examination. The team recorded the anatomical location and severity of any foot lesions present based on appearance only. Then, based on the type and severity of the lesions present, cows were classified according to 3 case definitions case definition 1: Any lesion present; case definition 2: Moderate lesions present (excluding minor lesions expected to have a low probability of affecting gait); and case definition 3: Severe lesions present (only including lesions most likely to result in a detectable gait abnormality). Sensitivity and Sp of MSc was calculated based on a threshold of MSc ≥2, defined as impaired (MSc = 2) or severely impaired (MSc = 3) mobility for each of the 3 case definitions, at the overall level and disaggregated by parity. The overall cow-level lesion prevalence based on the case definition 1 was 0.54 with significant between-herd variation. The overall Se and Sp of MSc for the detection of foot lesions were 0.18 and 0.96, 0.35 and 0.94, 0.43 and 0.94 for the case definitions 1, 2, and 3, respectively. Our findings showed poor Se, but high Sp of MSc for the detection of cows with foot lesions in a pasture-based system.

A survey of foot disinfection practices for control of bovine digital dermatitis; evaluating solution depth, footbath hygiene, and the potential of footbaths as infection reservoirs for Treponema species.

Bovine digital dermatitis remains a widespread endemic disease of dairy cattle worldwide. Footbathing is commonly used as a control measure and has significant economic and environmental impact. There are few studies documenting footbathing practices on dairy farms, or evaluating their suitability for achieving foot disinfection. This study describes footbathing practices on 32 farms observed in the United Kingdom, Ireland, and the Netherlands. We measured solution depth throughout footbathing and observed levels below 7cm on 9/32 farms, which leads to inadequate foot coverage. Solution depth was associated with the number of cow passages, decreasing by 1.2cm for every 100 cow passages. We also describe levels of organic matter content (g/L) throughout footbathing as a proxy for footbath hygiene. Our data indicates that almost half of footbaths (15/32) became contaminated above the 20g/L threshold to which veterinary biocides are tested for efficacy, and that organic matter content is associated with the number of cow passages per liter of footbathing solution provided. A multivariable mixed model predicted that one liter of footbathing solution per cow should be sufficient to prevent excess contamination. As a further measure of hygiene, we tested a subset of footbath samples to quantify the amount of DNA present from the Treponema species which are considered instrumental in the etiology of digital dermatitis. We did not detect Treponema DNA in footbath samples, suggesting they are unlikely to act as infection reservoirs for this disease. Multivariable mixed models including farm identity as a random effect demonstrated that for both change in solution depth and organic matter content the effect of farm-level factors was large. Because of the magnitude of this farm effect, applying model predictions will not translate to adequate solution depth and hygiene on all farms. Our data highlights the importance of footbath auditing on individual farms.

Association between maternal growth in the pre-conception and early gestational period of nulliparous dairy heifers with anti-Müllerian hormone in their female offspring.

Anti-Müllerian hormone (AMH) is secreted by granulosa cells of healthy, growing follicles and is positively correlated with the ovarian reserve. Maternal and environmental factors, such as nutrition, disease, parity and endocrine disruptors, are thought to have a profound impact on ovarian reserve development during early foetal life. For genetic progress, it can be advantageous to breed dairy replacements from heifers to expedite the generation interval; however, there is some evidence that nulliparous animals produce female offspring with smaller ovarian reserves compared with multiparous animals. The objective of this prospective, observational study was to determine whether maternal growth in the pre-conception and early gestational period of nulliparous dairy heifers is associated with pre-weaning AMH concentrations in their female offspring. Our hypothesis was that excessive growth in this period would negatively impact AMH concentrations. Seasonal, pasture-based dairy heifer calves (n = 156) born from nulliparous dams, from six Irish farms, were blood sampled at an average of 60 days of age in spring 2022 and tested for AMH. Mixed-effects linear regression models were constructed with Box-Cox transformed AMH concentration as the dependent variable. The independent variables tested included maternal average daily gain (ADG) from pre-breeding examination (PBE) to pregnancy diagnosis (PD) between 30 and 60 days in calf (DIC), ADG from PBE to PD over 60 DIC and ADG between the two PDs. Calf breed and age at sampling were forced into the models, and the farm was treated as a random effect in all models. We found that as ADG increased from the pre-breeding period to their first PD visit, the AMH concentration in their offspring reduced. However, ADG explained only a small amount of the variation in AMH concentrations (marginal R2 = 0.041). In conclusion, the results of our study suggest that excessive growth prior to conception and in early gestation of nulliparous heifers could impact the ovarian reserve of their female offspring, and may imply that farmers should avoid excessive growth in the immediate pre-breeding and early gestational periods.

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.

Development of a risk assessment profile tool to determine appropriate use of SARS-CoV-2 rapid antigen detection tests for different activities and events in Ireland, since October 2021.

We describe the development of a risk assessment profile tool that incorporates data from multiple domains to help determine activities and events where rapid antigen detection tests (Ag-RDT) could be used to screen asymptomatic individuals to identify infectious cases as an additional mitigation measure to reduce transmission of SARS-CoV-2. The tool aims to stratify, in real time, the overall risk of SARS-CoV-2 transmission associated with common activities and events, and this can be matched to an appropriate Ag-RDT testing protocol.

Associations between cow-level parameters and heart rate variability as a marker of the physiological stress response in dairy cows.

To maintain and enhance cow productivity and welfare, it is important that we can accurately assess and understand how cows respond to the physiological demands of gestation and lactation. Several methods have been developed for assessing the physiological responses to stressors and for detecting distress in cattle. Heart rate (HR) variability (HRV) is a non-invasive measure of autonomic nervous system activity and consequently a component of the physiological response to stress. In cattle, HRV has been successfully used to measure autonomic responses to a variety of health conditions and management procedures. The objectives of this study were to determine whether, among commercial Holstein Friesian cows and across farms, relationships exist between cow-level factors, HR and HRV. HRV parameters were compared with production records for 170 randomly selected, Holstein-Friesian-cows on 3 commercial dairy farms. Production data included parity, days in milk (DIM), milk yield, somatic cell count (SCC), % butterfat and protein, body condition score (BCS) and genetic indices. Fixed-effect, multivariable linear regression models were constructed to examine the association between cow-level variables and HRV parameters. Statistically significant relationships were found between HR and farm, temperature and BCS, and between HRV parameters and farm, rectal temperature, BCS, DIM, and percentage butterfat. Given the significant association between farms and several of the indices measured, it is recommended that care must be taken in the interpretation of HRV studies that are conducted on animals from a single farm. The current study indicated that within clinically normal dairy cattle HRV differed with the percentage of butterfat and BCS. Based on the relationships reported previously between HRV and stress in dairy cattle these results suggest that stress may be increased early in lactation, in cows with BCS <2.75 that are producing a high percentage of butterfat milk. Future work could focus on the physiological mechanisms through which these factors and their interactions alter HRV and how such physiological stress may be managed within a commercial farm setting.

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.

Phagomagnetic separation-quantitative PCR: A rapid, sensitive and specific surveillance tool for viable Mycobacterium avium ssp. paratuberculosis in bulk tank and individual cow milk samples.

Bulk tank milk samples from 392 Northern Ireland dairy farms and individual milk from animals (n = 293) on 4 of these farms were tested by a novel phagomagnetic separation (PhMS)-quantitative (q)PCR assay able to detect and quantify viable Mycobacterium avium ssp. paratuberculosis (MAP), to demonstrate its potential utility as a milk surveillance tool. Viable MAP were detected in 26.5% of the bulk tank milks, with MAP contamination levels ranging from 1 to 8,432 MAP/50 mL of milk; less than 2% of farms had MAP contamination levels >100 MAP/50 mL in their bulk tank milk. Follow-up PhMS-qPCR testing of milk from individual animals on 4 farms that had the highest numbers of MAP in their bulk tank milks indicated that 17 to 24% of animals in each herd were shedding viable MAP in their milk. Mean MAP numbers detected ranged between 6.7 and 42.1 MAP/50 mL of milk. No significant correlation was observed between the detection of viable MAP in bulk or individual milks by PhMS-qPCR and parallel milk ELISA results, or between PhMS-qPCR results and any other milk recording results (somatic cell count, total bacterial count, % butterfat, or % protein). Viable MAP was detected by IS900 qPCR in 52 (85.2%) Pozzato broth cultures of 61 PhMS-qPCR-positive individual milks after 12 wk of incubation, suggesting few PhMS-qPCR results were false positives. The mean sensitivities of the PhMS-qPCR assay and milk ELISA applied to individual milks were estimated by Bayesian latent class analysis to be 0.7096 and 0.2665, respectively, and mean specificities were similar (0.9626 and 0.9509). Our findings clearly demonstrate that the novel PhMS-qPCR assay could be a useful milk surveillance tool for dairy processors, or a milk monitoring tool for Johne's disease control or milk quality assurance programs.

Diagnosis of respiratory disease in preweaned dairy calves using sequential thoracic ultrasonography and clinical respiratory scoring: Temporal transitions and association with growth rates.

Bovine respiratory disease (BRD) in dairy calves is a multifactorial condition, involving environmental, host, and pathogen factors. Thoracic ultrasound scoring (TUS) has recently been validated as an accurate method of detecting BRD-related lung pathology in dairy calves. Previous studies investigating the use of TUS in preweaned dairy calves have largely been based on cross-sectional data from all-year production systems. The objectives of this longitudinal observational study were to characterize the temporal transitions in TUS scores in dairy calves from pasture-based, seasonal-calving herds using sequential examinations during the preweaning period, and to investigate the relationship between the presence and temporal pattern of BRD, diagnosed by TUS or clinical respiratory scoring (CRS), and average daily gain (ADG). In spring of 2019, 317 preweaned calves from 7 commercial dairy farms were recruited at less than 4 wk old (ranging from 1-27 d of age). Each farm was examined on at least 3 occasions at 20- to 28-d intervals and housed indoors in group or individual pens. At each visit TUS scores, CRS scores based on the University of Wisconsin Calf Respiratory Score Chart (https://www.vetmed.wisc.edu/fapm/wp-content/uploads/2020/01/calf_respiratory_scoring_chart.pdf), and live weight using a dairy breed-specific weigh band were recorded. All data were recorded by the same 2 veterinarians over the course of the study. The final data set consisted of 966 TUS and CRS scores collected from 317 calves over a period of approximately 6 wk from 7 farms. The data were analyzed in multivariable, mixed effects, linear regression models, with separate models constructed for TUS and CRS scores. Random effects (intercepts) were included for calf, farm, and visit week. Additionally, a random slope was included for age at sampling by farm. Median farm TUS score ranged from 0 to 2.5 over the 3 visits (possible range: 0-5). The percentage of calves with a TUS score ≥3 (consolidation of the full thickness of 1 lung lobe), on each farm ranged from 0 to 50%. The median CRS in calves on individual farms ranged from 1 to 3 over the 3 visits (possible range: 0-12). The percentage of calves on each farm with a CRS score ≥5 (possible range: 0-12) ranged from 0 to 26%. The TUS and CRS scores were weakly correlated. The TUS was associated with reduced ADG. Calves with TUS scores ≥3 grew at 126 g/d less than unaffected calves over the 3-wk period before examination. The predicted effect on ADG was dependent on the age and duration over which the animal was affected. Calves affected later (i.e., between visits 2 and 3) had lower predicted weights at 63 d compared with calves with increased TUS scores earlier in the study period. Calves with a TUS score ≥3 at each of the 3 sampling points had the lowest weight at 63 d of age. There was no association of CRS with ADG. This study showed that in contrast to CRS, higher TUS scores are associated with lower ADG, with weight loss being more pronounced in chronic cases.

Irish dairy farmers' engagement with animal health surveillance services: Factors influencing sample submission.

A high-quality animal health surveillance service is required to inform policy and decision-making in food-animal disease control, to substantiate claims regarding national animal health status and for the early detection of exotic or emerging diseases. In Ireland, the Department of Agriculture, Food and the Marine provides partially subsidized testing of farm animal samples and postmortem examinations to the Irish agriculture sector (farmers) at 6 regional veterinary laboratories (RVL) throughout the country. Diagnoses and data from these submissions are recorded and reported monthly and annually to enable animal health monitoring and disease surveillance. In a passive surveillance model, both the veterinary practitioner and the farmer play a vital role in sample submission by determining which cases are sent to the laboratory for postmortem or diagnostic testing. This paper identified factors influencing Irish dairy farmers' decisions to submit carcasses to RVL. Behavioral determinants of the submission of samples where veterinary professionals are concerned has been studied previously; however, limited work has studied determinants among farmers. This study conducted qualitative analyses of decisions of Irish dairy farmers relevant to diagnostic sample submission to an RVL and to examine the herd-level characteristics of farmers that submitted cases to an RVL. The biographical narrative interpretive method was used to interview 5 case-study farmers who were classified nonsubmitters, medium, or high submitters to the postmortem service based on the proportion of on-farm mortalities submitted to the laboratory service in 2016. The data obtained from these interviews were supplemented and triangulated through dairy farmer focus groups. The data were thematically analyzed and described qualitatively. In addition, quantitative analysis was undertaken. Data for herds within the catchment area of a central RVL were extracted, and a multivariable logistic regression model was constructed to examine the relationship between herds from which carcasses were submitted to the laboratory and those from which none were submitted. Results from the analysis show that the farmer's veterinary practitioner was the primary influence on submission of carcasses to the laboratory. Similarly, the type of incident, logistical issues with transporting carcasses to the laboratory, influence of peers, presence of alternative private laboratories, and a fear of government involvement were key factors emerging from the case-study interview and focus group data. Herd size was identified in both the qualitative and quantitative analysis as a factor determining submission. In the logistic regression model, herd size and increased levels of expansion were positively correlated with the odds of submission, whereas distance from the laboratory was negatively associated with odds of submission. These results identify the main factors influencing the use of diagnostic services for surveillance of animal health, signaling how services may be made more attractive by policy makers to a potentially wider cohort of users.

Relative effect of milk constituents on fertility performance of milk-recorded, spring-calving dairy cows in Ireland.

Several studies have reported associations between milk composition data and fertility performance. However, no work to date has estimated the effect of milk constituents on fertility performance in cows with low milk constituent concentrations. The objective of this study was to assess the association between milk constituents, animal characteristics, and time from mating start date (MSD) to conception using survival analysis. Furthermore, we aimed to investigate the relative effect of each variable by predicting median times to conception for animals with different combinations of characteristics and milk compositions. The final data set consisted of 87,227 cow lactation records from 64,519 cows in 2,049 herds with calving dates from 2010 to 2013. Milk recording data from each lactation were used, including test day recordings at 0 to 30, 31 to 60, and 61 to 90 d in milk (DIM). The analysis was limited to spring-calving cows (i.e., animals calving from January to May inclusive). Mating start date was determined for each unique herd in each year. A cow-specific MSD (MSDcow) was defined taking into consideration the MSD for each herd and the calving date and a minimum calving to insemination interval of each herd year. The conception date for each cow was estimated using the subsequent calving date. Cows with no subsequent calving date were assumed not to have conceived. Time from MSDcow to approximate conception date was analyzed using survival analysis. Cox proportional hazard models were constructed for each of the 3 recording windows: 0 to 30, 31 to 60, and 61 to 90 DIM. A fourth model was used to assess the dynamics of milk composition over the 3 windows. To investigate the effect of these variables, model outputs were used to create parametric accelerated failure time models to predict median survival times for animals at the 10th and 90th percentiles of the variable of interest but otherwise identical across the rest of the variables. Results demonstrated that fertility breeding subindex had the largest effect on time from MSDcow to conception, with an additional 62 d open for those in the 10th percentile versus those in the 90th percentile. Of the milk constituents, milk lactose concentration had the greatest effect on MSD to conception, particularly when measured from 0 to 30 DIM. An additional 10 d open resulted from comparing those in the 10th and 90th percentiles. Milk protein concentration, although statistically significant, had a lower effect on fertility outcome when comparing cows in the 10th and 90th percentiles for this exposure variable. The greatest effect was found in the 61 to 90 DIM recording window, where cows in the 10th percentile had an additional 9 d open at the subsequent breeding season compared with those in the 90th percentile. Overall, our study shows that although the associations between milk constituents and fertility are statistically significant, their overall influence in determining MSD to conception in this study population is relatively modest, particularly compared with fertility breeding subindex, when comparing cows at the 10th and 90th percentiles. Of the milk constituents measured, milk lactose concentration measured at 0 to 30 DIM had the greatest effect in determining fertility outcome when comparing cows at the 10th and 90th percentiles. The predictive value of early-lactation test day milk composition data on hazard of pregnancy during the following breeding period, within a spring-calving context, appears to be relatively modest at the individual-cow level. Further work is required to test the usefulness of these associations at the herd level.

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.

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.

Using examination performance data and focus groups to inform teaching - a case study from final year students of veterinary medicine.

BACKGROUND: Student feedback has played an important role in the maintenance of quality and standards in higher education. Perhaps the most commonly used method to capture feedback is a series of questions or statements where students indicate their degree of satisfaction or agreement. Focus groups offer an alternative means of capturing 'richer' qualitative data relating to students' thoughts on course structure. Aside from student evaluations, student examination performance has been used as a method to evaluate the efficacy of curriculum changes at programme level. However, this data is utilised less so at a 'finer detail' level to identify specific issues with the delivery of teaching. CASE PRESENTATION: The purpose of this report was to outline the approach taken using qualitative and quantitative data to identify problems with a specific area of teaching, inform a new teaching approach and to assess the impact of those changes. Following quantitative and qualitative analysis, a practical class on dairy herd fertility performance was highlighted as an area for improvement. After the introduction of the newly formatted practical class with a greater focus on self-directed learning, there was a significant increase in the average score (p < 0.001) and a decrease in the proportion of students failing (p < 0.001) the question that assessed the analysis of dairy herd fertility data. In addition, the R-squared value between students' performance in the fertility question and their performance in the overall examination increased from 0.06 to 0.11. CONCLUSIONS: The combination of qualitative focus group data and quantitative analysis of examination performance data represent robust methods for identifying problems associated with specific aspects of veterinary teaching.

Epidemiological investigation of a severe rumen fluke outbreak on an Irish dairy farm.

Although the rumen fluke, Calicophoron daubneyi is now very common and widespread throughout Western Europe, reports of clinical cases are still rare. This study explores the epidemiological background to a severe rumen fluke outbreak in 6-month-old heifers on a dairy farm in Ireland. Sequence analysis of the cytochrome oxidase subunit 1 (Cox1) gene of the rumen fluke metacercariae on pasture failed to identify predominant, possibly pathogenic subtypes. However, estimates of metacercarial load indicated that the animals were exposed to a daily dose of about 5334 C. daubneyi metacercariae for a period of 3 weeks resulting in the build-up of very large numbers of immature worms in the small intestine. It is hypothesized that specific environmental conditions may favour this parasite over its competitor, the liver fluke, Fasciola hepatica, possibly by allowing it to emerge earlier. The possibility that C. daubneyi may be better adapted to the Irish climate than F. hepatica together with the fact that selective treatment against F. hepatica effectively frees the niche for C. daubneyi, may result in the gradual replacement of F. hepatica by C. daubneyi.

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.

The prevalence, temporal and spatial trends in bulk tank equivalent milk fat depression in Irish milk recorded herds.

BACKGROUND: Milk fat is important in terms of economic value and in its potential to provide information concerning cow diet and health. Under current milk payment schemes in Ireland farmer income is directly linked to milk fat production. METHODS: A descriptive analysis of milk fat depression (MFD) as calculated from test day milk recording data across all milk recording herds from 2004 to 2014 was undertaken. A dataset of 17 million test day records was used to calculate the prevalence of MFD in Irish milk recorded herds and to create a graphical description of the major descriptive epidemiological trends in milk fat depression in time and space in Ireland. The bulk tank equivalent (BTE) for test day milk fat was calculated for each herd and for cohorts of cows within herds using the formula; BTE milk fat = sum test day fat kg/sum test day milk kg. Milk fat depression was defined as BTE <3.3% milk fat and BTE > 3.2% milk protein. RESULTS: The annual prevalence of MFD decreased significantly over time in a linear manner until 2014. Across all years the highest prevalence of MFD occurred in April or May. The highest prevalence occurred most commonly in May, with 9.1% of herds experiencing MFD in 2014. The highest prevalence of MFD in autumn calved cohorts occurred at 181-210 days in milk whereas it occurred at days 61-90 in milk in spring calving cohorts. The stage of lactation for the most common occurrence of MFD in both the spring and autumn cohorts corresponded with the month of May. There were some notable spatial patterns regarding variations in prevalence of MFD across the country. Cohorts of cows with the highest genetic values for milk yield had the highest prevalence of MFD whereas cohorts of cows with the highest breeding values for milk fat percent had the lowest prevalence of MFD. CONCLUSIONS: A subpopulation of Irish herds experienced the condition of MFD. Descriptive analysis suggested spatial, temporal and animal level associations. This condition warrants further investigation.