Survey of farm, parlour and milking management, parlour technologies, SCC control strategies and farmer demographics on Irish dairy farms

BACKGROUND

This cross-sectional study describes a survey designed to fill knowledge gaps regarding farm management practices, parlour management practices and implemented technologies, milking management practices, somatic cell count (SCC) control strategies, farmer demographics and attitudes around SCC management on a sample of Irish dairy farms.

RESULTS

We categorized 376 complete responses by herd size quartile and calving pattern. The average respondent herd was 131 cows with most (82.2%) operating a seasonal calving system. The median monthly bulk tank somatic cell count for seasonal calving systems was 137,000 cells/ml (range 20,000 - 1,269,000 cells/ml), 170,000 cells/ml for split-calving systems (range 46,000 - 644,000 cells/ml) and 186,000 cells/ml for 'other' herds (range 20,000 - 664,000 cells/ml). The most common parlour types were swing-over herringbones (59.1%) and herringbones with recording jars (22.2%). The average number of units across herringbone parlours was 15, 49 in rotary parlours and two boxes on automatic milking system (AMS) farms. The most common parlour technologies were in-parlour feeding systems (84.5%), automatic washers on the bulk tank (72.8%), automatic cluster removers (57.9%), and entrance or exit gates controlled from the parlour pit (52.2%). Veterinary professionals, farming colleagues and processor milk quality advisors were the most commonly utilised sources of advice for SCC management (by 76.9%, 50.0% and 39.2% of respondents respectively).

CONCLUSIONS

In this study, we successfully utilised a national survey to quantify farm management practices, parlour management practices and technology adoption levels, milking management practices, SCC control strategies and farmer demographics on 376 dairy farms in the Republic of Ireland. Rotary and AMS parlours had the most parlour technologies of any parlour type. Technology add-ons were generally less prevalent on farms with smaller herds. Despite finding areas for improvement with regard to frequency of liner changes, glove-wearing practices and engagement with bacteriology of milk samples, we also found evidence of high levels of documentation of mastitis treatments and high use of post-milking teat disinfection. We discovered that Irish dairy farmers are relatively content in their careers but face pressures regarding changes to the legislation around prudent antimicrobial use in their herds.

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.

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.

The impact of changing the cut-off threshold of the interferon-gamma (IFN-γ) assay for diagnosing bovine tuberculosis in Ireland

In Ireland, the interferon-gamma (IFN-γ) assay is routinely used as an ancillary test interpreted in parallel with the single intradermal comparative tuberculin test (SICTT) to maximize the detection of bovine tuberculosis (bTB) infected animals. Up until 2018, a positive test result was recorded in the IFN-γ ELISA assay following whole blood stimulation with purified protein derivative (PPD)-bovine (B), PPD-avian (A) and nil sample (N), using the interpretation criteria, B-N > 50 optical density units (OD), B > 100 and B-A > 0. Following a review of available data, the threshold of the B-A component changed to B-A > 80. As predicting the impact of changing the cut-off thresholds for the IFN-γ test de novo is challenging, the aims of this study were to follow animals that initially tested negative using the new IFN-γ assay interpretation criteria and investigate their future risk of disclosure with bTB, with a focus on animals that otherwise would have been removed when using the older interpretation criteria (0 < B-A ≤ 80). Enrolled animals (n = 28,669 cattle from 527 herds) were followed up for two years (2019-2021), or to point of bTB detection or death. At the end of follow-up, 1151 (4.0%) of enrolled animals were bTB cases. The majority of these cases were diagnosed using SICTT (80.5%). The cumulative number of positive animals that would have been removed if the old cut-off (0 < B-A ≤ 80) was used amounted to 1680 cattle (5.9% of the enrolled cohort). Of these, 127 (7.5%) were diagnosed with bTB during follow-up. In contrast, 1024 of the 1151 cattle which subsequently tested positive during the study period following a negative IFN-γ test would not have been identified with the old or new IFN-γ cut-off criteria. Survival analysis showed that animals that would have been removed under the old interpretation criteria were at increased risk of a positive diagnosis with bTB during follow-up compared to other test negative animals. A newly developed risk prediction model (using a Cox proportional hazard model) showed that age, animal number of SICTT tests, number of inconclusive SICTT tests, B-A (IFN-γ assay), B-N (IFN-γ assay), animals from store herds and the percentage of the rest of the herd that were positive during the breakdown were statistically significantly associated with bTB detection. However, inclusion of the IFN-γ OD variables did not show added value in terms of prediction performance of the model.

Recording Antimicrobial Use on Irish Dairy Farms: Barriers & Facilitators to Using Technology and Sharing Data

Antimicrobial use (AMU) data are essential to monitor the impact 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 digitalise 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 impact 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.

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.

Comparison between two scoring methods to assess tail damage of docked pig carcasses during postmortem inspection in Ireland

Background

Tail inspection in the abattoir is a tool to help determine the welfare status of pigs. However, methodologies vary widely. Moreover, meat inspection is moving from palpation and incision towards visual-only (VIS) examination. This study investigated whether a VIS examination was sufficient to detect tail damage compared to handling (HAND), which ensures examination of all aspects of the tail.

Method

The severity of tail skin damage (0 [undamaged] - 4 [partial/full loss of tail]) and presence/absence of bruises was scored using both methods after scalding/dehairing of 5498 pig carcasses.

Results

There was a good relationship between methods when evaluating tail skin damage (sensitivity, 82.48%; specificity, 99.98%; accuracy, 98.98%; correlation ρ = 0.84). The results were similar for the presence of bruises (sensitivity, 74.98%; specificity, 99.09%; accuracy, 89.94%; correlation ρ = 0.79). However, the percentage of tails classified as undamaged was higher using VIS (69.9%) than HAND (63.55%) examination. Conversely, VIS detected fewer mild lesions (score 1 - 13.64%; score 2 - 11.73%) than HAND (score 1 - 15.21%; score 2 - 15.53%). A higher percentage of bruises was detected using HAND than VIS (37.96% vs. 29.03%).

Conclusions

Visual evaluation is a valid alternative to handling evaluation of carcass tail damage and bruising.

A systematic review of the relationship between housing environmental factors and bovine respiratory disease in preweaned calves - Part 1: Ammonia, air microbial count, particulate matter and endotoxins

Bovine respiratory disease (BRD) is one of the leading causes of mortality and morbidity in calves across diverse management systems. Despite expert opinion often citing the influence of housing environment on the level of respiratory disease in calf groups, there have been few reviews of environmental factors that predispose to BRD. This systematic review was undertaken to identify the measurable environmental variables associated with respiratory disease in housed preweaned calves. To achieve this Pubmed, CAB Direct and Scopus databases were searched. To be considered for inclusion, publications had to be fully published in English, published before 24 November, 2022 and include at least one measurable/ manipulated environmental variable and a standardized method of BRD detection. Twelve publications were included in this review. These examined a wide range of risk factors including air microbial count (four publications), air particulate matter (one publication); air endotoxins (one publication) and air ammonia (four publications). From the included publications, a statistically significant relationship to BRD was identified in 2/4 examining air microbial count, 1/1 examining air particulate matter, 1/1 examining air endotoxins and 2/4 examining air ammonia. This review indicated a paucity of evidence from the peer-review literature demonstrating a significant association between the many investigated exposure factors and BRD occurrence. An optimal environment for housed calves could not be clearly identified in this review.

A systematic review of the relationship between housing environmental factors and bovine respiratory disease in preweaned calves - Part 2: Temperature, relative humidity and bedding

Bovine respiratory disease (BRD) is a challenge in all housed farming systems that raise calves. Farm to farm variation in BRD prevalence can be partially attributed to variation in host immunity, pathogens and housing environment. Unlike host immunity and BRD pathogens, housing environment has not been well investigated. The objective of this systematic review was to identify the measurable environmental variables associated with BRD in housed preweaned calves. Pubmed, CAB Direct and Scopus databases were searched. To be considered for inclusion publications had to be published in English, before 24 November, 2022 and include at least one measurable/ manipulated environmental variable and a standardized method of BRD detection. In total 12 publications were included in this review. In this second part of the systematic review the environmental variables identified were; temperature (9 publications); relative humidity (8 publications); bedding (5 publications); ventilation (1 publication); air CO2 concentration (1 publication) and air velocity (4 publications). Of the publications that were examined a statistically significant relationship to BRD was identified in 4/9 publications examining temperature, 3/8 examining relative humidity, 2/4 examining air velocity, 2/5 examining bedding, 0/1 examining ventilation rates and 0/1 examining CO2 concentration. From this review it is clear high airspeed at calf level should be avoided as should deep, wet pack bedding. The relationship between BRD prevalence and both high and low temperature requires more investigation to identify temperature thresholds associated with increased risk of BRD as well as the most influential modifiers. An optimal environment for housed calves could not be clearly identified in this review.

Determining the clinical utility of a single pre-breeding examination for predicting subsequent reproductive performance in seasonal pasture-based dairy heifers

Heifers that conceive early in the breeding season are key to the maintenance of a compact calving pattern in seasonal dairy herds. The purpose of this prospective observational study was to determine whether a single pre-breeding examination is useful in predicting future reproductive and calving performance in dairy heifers. This evaluation was based on a matrix of easily measurable variables which could be applied to seasonal, pasture-based dairy heifers. The matrix variables were; body weight (≥55% mature body weight at mating start date), body condition score (≥3.5), and the presence of a corpus luteum. Seasonal, pasture-based dairy heifers (n = 572) on six commercial dairy farms were examined at an average of 28 days prior to the breeding season. At this examination, they were classified as READY (meeting all three of the above criteria), INTERMEDIATE (meeting one or two of the above criteria) or PROBLEM (meeting none of the above criteria) based on the matrix and then exposed to a routine artificial insemination (AI) breeding period followed by bull breeding depending on individual farm management. Subsequent pregnancy status was determined by transrectal ultrasonography initially at 30-60 days in calf (DIC), and confirmed at over 60 DIC. After the breeding season, 519 (96%) of heifers were determined to be pregnant, of which 345 (64%) became pregnant within the first three weeks of the breeding season. Farmers collected calving data; including calving difficulty score, from the heifers the following spring. A logistic regression model was used to analyse the association between the matrix categories and the following outcomes: reproductive (21 day submission rate, 1st AI conception rate, 3 wk and 6 wk in calf rate) and calving (assistance and dystocia). Heifers classified as PROBLEM had significantly lower odds of conceiving to the first AI serve and of becoming pregnant within the first three and six weeks of the breeding season (P ≤ 0.05). In conclusion, the proposed matrix could be practically useful for classifying heifers prior to the breeding season.

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.

Prevalence of respiratory disease in Irish preweaned dairy calves using hierarchical Bayesian latent class analysis

Introduction

Bovine respiratory disease (BRD) has a significant impact on the health and welfare of dairy calves. It can result in increased antimicrobial usage, decreased growth rate and reduced future productivity. There is no gold standard antemortem diagnostic test for BRD in calves and no estimates of the prevalence of respiratory disease in seasonal calving dairy herds.

Methods

To estimate BRD prevalence in seasonal calving dairy herds in Ireland, 40 dairy farms were recruited and each farm was visited once during one of two calving seasons (spring 2020 & spring 2021). At that visit the prevalence of BRD in 20 calves between 4 and 6 weeks of age was determined using thoracic ultrasound score (≥3) and the Wisconsin respiratory scoring system (≥5). Hierarchical Bayesian latent class analysis was used to estimate the calf-level true prevalence of BRD, and the within-herd prevalence distribution, accounting for the imperfect nature of both diagnostic tests.

Results

In total, 787 calves were examined, of which 58 (7.4%) had BRD as defined by a Wisconsin respiratory score ≥5 only, 37 (4.7%) had BRD as defined by a thoracic ultrasound score of ≥3 only and 14 (1.8%) calves had BRD based on both thoracic ultrasound and clinical scoring. The primary model assumed both tests were independent and used informed priors for test characteristics. Using this model the true prevalence of BRD was estimated as 4%, 95% Bayesian credible interval (BCI) (1%, 8%). This prevalence estimate is lower or similar to those found in other dairy production systems. Median within herd prevalence varied from 0 to 22%. The prevalence estimate was not sensitive to whether the model was constructed with the tests considered conditionally dependent or independent. When the case definition for thoracic ultrasound was changed to a score ≥2, the prevalence estimate increased to 15% (95% BCI: 6%, 27%).

Discussion

The prevalence of calf respiratory disease, however defined, was low, but highly variable, in these seasonal calving dairy herds.

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.

Growth rates of contract-reared versus home-reared replacement dairy heifers

Successful heifer rearing is dependent on achieving optimal average daily gain (ADG) targets to calve for the first time at 24 months. Whilst dairy farmers internationally have traditionally managed their heifers on-farm to achieve these targets, recent dairy herd expansion within Europe has resulted in increased demand for labour-saving heifer-rearing strategies, such as off-farm contractrearing. However, loss of direct influence on the day-to-day management decisions affecting the ability of heifers to grow adequately to achieve this age of first calving may represent a potential barrier to uptake. Hence, the aim of this longitudinal observational study was to compare the growth rates of contract- vs home-reared heifers. Approximately 6 500 heifers from 120 commercial Irish dairy farms were enrolled in a 3-year study. For 65 of these farms, heifers were reared at a contract-rearing facility. For the remaining 55 farms, heifers were reared on their home farm. Over the course of 20 months from birth until precalving, heifers were examined and weighed at four farm visits. The relationship between several independent variables (farm type, herd size, heifer breed, economic breeding index (EBI) and health events) and ADG at different time points was investigated and analysed utilising linear mixed models. Overall ADG for heifers throughout the rearing period was 0.71 kg/day. There was a significant association between farm type and ADG for all five linear ADG models; home-reared heifers grew, on average, 0.025, 0.039, 0.11 and 0.059 kg/day more than contract-reared heifers between visit 1 and visit 4 (overall ADG), visit 1 and visit 2, visit 2 and visit 3 and visit 1 and visit 3, respectively. The occurrence of diarrhoea during farm visit 2 (median age 8.5 months) was associated with a significant reduction in ADG between visit 3 and visit 4. Calf-hood disease (diarrhoea, respiratory disease or navel ill) was not associated with the growth rate during any of the subsequent visit periods. While home-reared heifers had greater ADG during four of the five periods studied, median heifer ADG in both cohorts exceeded the minimum published target weight gains at each developmental stage required for heifers to reach puberty, conceive at 15 months and calve for the first time at 24 months. Importantly, there was wide variation both within enterprises and between farms. It was concluded that while the absolute difference in daily growth rates of home- and contract-reared heifers was minimal, when considered in the context of the entire heifer-rearing period, these growth rate differences have the potential to impact the future reproductive and milk production performance of heifers.

Seroprevalence of Mycoplasma bovis in bulk milk samples in Irish dairy herds and risk factors associated with herd seropositive status

Mycoplasma bovis is a serious disease of cattle worldwide; mastitis, pneumonia, and arthritis are particularly important clinical presentations in dairy herds. Mycoplasma bovis was first identified in Ireland in 1994, and the reporting of Mycoplasma-associated disease has substantially increased over the last 5 years. Despite the presumed endemic nature of M. bovis in Ireland, there is a paucity of data on the prevalence of infection, and the effect of this disease on the dairy industry. The aim of this observational study was to estimate apparent herd prevalence for M. bovis in Irish dairy herds using routinely collected bulk milk surveillance samples and to assess risk factors for herd seropositivity. In autumn 2018, 1,500 herds out of the 16,858 herds that submitted bulk tank milk (BTM) samples to the Department of Agriculture testing laboratory for routine surveillance were randomly selected for further testing. A final data set of 1,313 sampled herds with a BTM ELISA result were used for the analysis. Testing was conducted using an indirect ELISA kit (ID Screen Mycoplasma bovis). Herd-level risk factors were used as explanatory variables to determine potential risk factors associated with positive herd status (reflecting past or current exposure to M. bovis). A total of 588 of the 1,313 BTM samples were positive to M. bovis, providing an apparent herd prevalence of 0.45 (95% CI: 0.42, 0.47) in Irish dairy herds in autumn 2018. Multivariable analysis was conducted using logistic regression. The final model identified herd size, the number of neighboring farms, in-degree and county as statistically significant risk factors for herd BTM seropositivity to M. bovis. The results suggest a high apparent herd prevalence of seropositivity to M. bovis, and evidence that M. bovis infection is now endemic in the Irish dairy sector. In addition, risk factors identified are closely aligned to what we would expect of an infectious disease. Awareness raising and education about this important disease is warranted given the widespread nature of exposure and likely infection in Irish herds. Further work on the validation of diagnostic tests for herd-level diagnosis should be undertaken as a matter of priority.

Mycobacterium avium subspecies paratuberculosis infection in cattle - a review in the context of seasonal pasture-based dairy herds

Johne’s disease is an infectious disease affecting cattle, other ruminants and non-ruminant wildlife worldwide, caused by Mycobacterium avium subspecies paratuberculosis (MAP). This review provides an up-to-date concise overview of the pathogenesis of MAP, the significance of Johne’s disease in cattle and the use of diagnostic testing at both animal and herd level in the context of seasonal pasture-based herds. While MAP can only replicate intracellularly, the bacterium is sufficiently robust to survive for months in the environment. Transmission of MAP is mostly via the faecal-oral route, however in-utero transmission in also possible. The bacteria evade the immune system by persisting in macrophages in the small intestine submucosa, with this latent stage of infection lasting, in most cases, for at least two years before bacterial shedding and clinical signs begin. The slowly progressive nature of MAP infection, poor performance of diagnostic tests and management systems that expose susceptible calves to infection make control of Johne’s disease challenging, particularly in seasonal calving herds. Testing of individual animals provides little assurance for farmers and vets due to the poor sensitivity and, in the case of ELISA, imperfect specificity of the available tests. Repeated herd-level testing is utilised by the IJCP to detect infected herds, identify high risk animals, and provide increasing confidence that test-negative herds are free of infection. The IJCP aims to control the spread of Johne’s disease in cattle in Ireland, in order to protect non-infected herds, limit the economic and animal health impact of the disease, improve calf health and reassure markets of Johne’s disease control in Ireland.

Implementation of compact calving at the farm level: A qualitative analysis of farmers operating pasture-based dairy systems in Ireland

Pasture-based dairy systems aim to maximize the proportion of grazed pasture in the cow's diet by having a compact calving season that coincides with the onset of the grass growing season. In Ireland, where pasture-based systems are dominant, a key performance indicator that reflects the degree of compact calving is referred to as 6-wk calving rate (6-wk CR). Although the industry target is 90%, the national average 6-wk CR in Ireland is currently 67%. The aim of this study was to use qualitative research to understand in depth farmers' experiences in implementing a high 6-wk CR. Ten case-study dairy farmers were interviewed using the biographical narrative interpretive method. We identified 5 broad and often interrelated themes evoked by farmers regarding 6-wk CR: the "good" farmer; support networks; free time and family time; simplicity of a structured system; and profitability and monetary gain. The findings of this study identify complexities and challenges at farm level when it comes to increasing 6-wk CR, such as increased workload and challenges associated with large numbers of male calves born during a condensed calving season. Benefits experienced by farmers as a result of increasing 6-wk CR included increased days in milk and consequently improved cash flow as well as increased grass utilization. Our findings are of interest to researchers and extension agents involved in programs concerned with reproductive management in pasture-based dairy systems.

Potential Application of SARS-CoV-2 Rapid Antigen Diagnostic Tests for the Detection of Infectious Individuals Attending Mass Gatherings - A Simulation Study

Rapid Antigen Diagnostic Tests (RADTs) for the detection of SARS-CoV-2 offer advantages in that they are cheaper and faster than currently used PCR tests but have reduced sensitivity and specificity. One potential application of RADTs is to facilitate gatherings of individuals, through testing of attendees at the point of, or immediately prior to entry at a venue. Understanding the baseline risk in the tested population is of particular importance when evaluating the utility of applying diagnostic tests for screening purposes. We used incidence data from January and from July-August 2021, periods of relatively high and low levels of infection, to estimate the prevalence of infectious individuals in the community at particular time points and simulated mass gatherings by sampling from a series of age cohorts. Nine different illustrative scenarios were simulated, small (n = 100), medium (n = 1,000) and large (n = 10,000) gatherings each with 3 possible age constructs: mostly younger, mostly older or a gathering with equal numbers from each age cohort. For each scenario, we estimated the prevalence of infectious attendees, then simulated the likely number of positive and negative test results, the proportion of cases detected and the corresponding positive and negative predictive values, and the cost per case identified. Our findings suggest that for each reported case on a given day, there are likely to be 13.8 additional infectious individuals also present in the community. Prevalence ranged from 0.26% for "mostly older" events in July-August, to 2.6% for "mostly younger" events in January. For small events (100 attendees) the expected number of infectious attendees ranged from <1 across all age constructs of attendees in July-August, to 2.6 for "mostly younger" events in January. For large events (10,000 attendees) the expected number of infectious attendees ranged from 27 (95% confidence intervals 12 to 45) for mostly older events in July-August, to 267 (95% confidence intervals 134 to 436) infectious attendees for mostly younger attendees in January. Given rapid changes in SARS-CoV-2 incidence over time, we developed an RShiny app to allow users to run updated simulations for specific events.

Reproductive tract disease in Irish grazing dairy cows: Retrospective observational study examining its association with reproductive performance and accuracy of 2 diagnostic tests

The detection of reproductive tract disease (RTD) 3 wk postpartum is important because of its effect on subsequent reproductive outcomes. Numerous methods for the diagnosis of RTD are described, some of which are more practical and instantaneous in terms of diagnosis. Two of these methods involve identification of purulent vaginal discharge (PVD) and evidence of ultrasonographic uterine changes indicative of endometritis (UE). The objectives of our retrospective observational study were (1) to assess the association of PVD or UE score at the prebreeding examination (PBE) with the hazard of pregnancy within the subsequent breeding season; (2) to determine the test sensitivity (Se) and specificity (Sp) at the point of sampling of both tests using a Bayesian latent class model; and (3) to determine the effect of varying positivity thresholds on test accuracy. To achieve these objectives, we analyzed an initial data set of 5,049 PBE from 2,460 spring-calved cows in 8 herds between 2014 and 2018. Each PBE was conducted once between 25 and 86 d in milk. At each PBE, vaginal discharge was obtained with a Metricheck device (Simcro) whereas uterine contents were assessed using transrectal ultrasonography. Purulent vaginal discharge was scored on a scale of 0 to 3 depending on discharge character, and UE was scored on a scale of 0 to 4 depending on the presence and consistency of intraluminal fluid. Cows with scores of ≥2 in either test had received treatment. Fertility data were available from 4,756 PBE after data exclusion. The association between PVD or UE score at the PBE and subsequent hazard of pregnancy was analyzed using a Cox proportional hazards model. Cows with a PVD score of 2 or 3 were less likely to conceive than cows with a PVD score 0 [score 2 hazard ratio (HR) = 0.74; 95% confidence interval (CI): 0.59-0.94; score 3 HR = 0.65; 95% CI: 0.51-0.84]. Cows with a UE score of 1, 2, 3, or 4 were less likely to conceive than cows with a UE score of 0 (score 1 HR = 0.82; 95% CI: 0.73-0.93; score 2 HR = 0.79; 95% CI: 0.62-1.00; score 3 HR = 0.43; 95% CI: 0.43-0.90; score 4 HR = 0.39; 95% CI: 0.26-0.58). To determine the Se and Sp of PVD or UE score for diagnosis of RTD at the time of PBE, a Bayesian latent class model was fitted on 2,460 individual cow PBE. Flat priors were used for the Se and Sp of UE, whereas informative priors were used for PVD Se (mode = 65%, 5th percentile = 45%) and Sp (mode = 90%, 5th percentile = 80%) and RTD prevalence (mode = 20%, 5th percentile = 10%). Posterior estimates (median and 95% Bayesian probability intervals; BPI) were obtained using 'rjags' (R Studio). The optimal test thresholds (PVD and UE score ≥1) were selected by assessing the effect of different thresholds on test estimates and using a misclassification cost analysis. Based on these, median (95% BPI) Se for PVD and UE score ≥1 were 44% (29-60%) and 67% (33-100%), respectively. Median Sp for PVD and UE score ≥1 were 90% (86-93%) and 91% (86-93%), respectively. Higher scores in both tests were associated with impaired fertility, and UE scoring with a threshold of ≥1 had the highest test Se and Sp estimates although test Se was conditional on days in milk when the PBE occurred.

Characteristics (sensitivity and specificity) of herd-level diagnostic tests for Mycobacterium avium subspecies paratuberculosis in cattle - A systematic review

Diagnostic tests for Johne's disease in cattle are characterised by poor sensitivity and often imperfect specificity at the animal level. Because farmers and veterinarians have limited assurance or confidence from results of testing individual animals for Mycobacterium avium subsp. paratuberculosis (MAP), control programmes based on whole herd-level testing provide the best framework for classifying herds. At the herd level, there is a diverse range of testing options for MAP based on both direct and indirect testing of individual and pooled samples. The most common measures of herd test performance, herd sensitivity (HSe) and herd specificity (HSp), are important for decision-making in herd test selection, for estimating prevalence and as inputs for simulation studies. This systematic review investigated the results of herd test evaluations for MAP in cattle, through a comprehensive search of the literature and a systematic four-stage screening process to identify relevant publications. Forty-six publications with relevant results were eligible for inclusion in the final review, containing evaluations of whole-herd ELISA serological testing, bulk milk tank ELISA, culture, PCR and phage testing, pooled faecal testing and environmental sample testing. Data extracted from each publication included sample populations, methods of analysis, reference tests, cut-off points, HSe and HSp. Direct comparisons between the reported HSe and HSp estimates of different studies is challenging due to the variations in herd prevalence and test protocols used. The data in this systematic review will benefit decision-makers and researchers and highlights knowledge gaps requiring further research.

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.

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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-021-12318-y.

The Effect of Contract-Rearing on the Health Status of Replacement Dairy Heifers

The aim of this study was to compare the health status of contract- vs. conventionally reared replacement dairy heifers over a 2-year period. A total of 120 dairy farmers were enrolled in the study in spring 2018: 55 farmers were rearing their own heifers (control farmers; CFs), and 65 were sending heifers to a contract-rearing farm (source dairy farmers; SDFs). Between spring 2018 and autumn 2019, approximately 5500 replacement heifers from these farms were monitored for signs of ill health during four farm visits using a modified version of the Wisconsin calf health scoring system. Additionally, faecal and nasal swabs were taken from a proportion of heifers with clinical signs of diarrhoea and respiratory disease to determine the associated aetiological agents. Results indicate few differences in the health status and pathogen exposure status of home-reared versus contract-reared heifers. Additionally, the number of source dairy farms represented and commingling of heifers from multiple origins at the rearing unit were not associated with an increased incidence of respiratory disease or diarrhoea among contract-reared heifers. It was concluded that contract-rearing did not result in adverse health outcomes for replacement dairy heifers. This is the first study to demonstrate this finding in a robust, longitudinal, herd-level population study.

A survey of biosecurity and health management practices on Irish dairy farms engaged in contract-rearing

A survey was conducted to investigate potential differences in biosecurity and health management practices on Irish dairy farms that sent their heifers for contract-rearing (source dairy farms, SDF; n = 62) and those rearing their own heifers (control farms, CF; n = 50). Participating farmers were surveyed by postal questionnaire between September and November 2018. The overall response rate was 93%. Results show that structurally, SDF were larger, less fragmented, and more specialized than CF. Outsourcing of labor-intensive activities to external contractors was more common among SDF than CF, exposing them to potentially increased biosecurity risks associated with animal movements, use of shared equipment, and increased frequency of farm visitors. The majority of SDF sent heifers to a single-origin rearing facility (70%), with heifers most commonly arriving at the rearing unit between 2 and 4 mo (53%) and returning to the dairy farm between 18 and 21 mo of age (56%). Despite the increased biosecurity risk associated with contract-rearing, implementation of disease prevention measures was not superior on SDF compared with CF. For both farm types, there was scope for improvement to visitor biosecurity protocols, quarantine procedures, colostrum feeding practices, and hygiene of calving areas. This research provides an overview of the demographics and farm management practices implemented by dairy farmers engaged in contract-rearing of replacement heifers, and will serve to inform farmers, veterinary advisors, and policy makers.

Estimation of the true prevalence of inaccurate artificial inseminations in Irish milk recording dairy cows using a Bayesian latent class analysis

Inaccurate artificial insemination (IAI) refers to an artificial insemination (AI) that is performed when a cow is not in oestrus. IAIs have economic impacts on the dairy industry through of semen wastage or iatrogenic pregnancy loss. However, few studies have quantified the prevalence of IAIs in a population. The primary objective of this prospective study was to estimate the cow-level true prevalence of IAIs in Irish milk recording dairy herds using a latent class model with a Bayesian framework. Milk samples were collected at a milk recording laboratory from 576 dairy cows in 125 herds who had received an AI on the same day they were sampled for routine milk constituent analysis. Milk progesterone (MP4) analysis was conducted on these samples using radioimmunoassay to determine the progesterone concentration. Fertility data (i.e., subsequent calving date) was retrospectively obtained from the Irish National Cattle Breeding Federation for milk sampled cows and an apparent conception (AC) to the sample AI was determined based on an estimated gestational range of 270-290 days. Both tests (MP4 and AC) were used in a latent class model to estimate the true prevalence of IAI. For the MP4 test, a concentration of ≥ 5 ng/mL in whole milk was deemed to be test positive while for the AC test, a cow that did not conceive to the sampled AI was deemed test positive. Prior information for prevalence of IAI was obtained from a literature review while MP4 sensitivity (Se) and specificity (Sp) were obtained from expert opinion. Non-informative priors were used for the Se and Sp of the AC test. Posterior inferences (median and 95 % Bayesian probability intervals; BPI) were obtained using the 'rjags' package in the R statistical software. In the final model, median cow-level true prevalence of IAI was 4.4 % (BPI; 1.7-9.0 %). Median Se and Sp estimates for MP4, were 83.0 % (BPI; 65.0-96.2 %) and were 97.4 % (BPI; 94.6-99.6 %), respectively. Median Se and Sp estimates for AC, were 64.8 % (BPI; 44.5-88.6 %) and 49.8 % (BPI; 45.3-54.1 %), respectively. The present study estimates that the overall cow-level true prevalence of IAI in Irish dairy cows is relatively low. This is the first study to report the cow-level true prevalence of IAI using a Bayesian latent class model.

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.

Outcome analysis of 95 harness racehorses with confirmed dorsal displacement of the soft palate treated with laryngeal tie-forward surgery

BACKGROUND

The laryngeal tie-forward (LTF) procedure is commonly used to treat intermittent dorsal displacement of the soft palate (iDDSP). There is a wide range in reported efficacy of treating horses with and without a definitive diagnosis of iDDSP.

OBJECTIVES

To evaluate the racing performance of harness racehorses in which iDDSP had been definitely diagnosed and treated solely with the LTF procedure.

STUDY DESIGN

Retrospective case series.

METHODS

Ninety-five harness racehorses were treated with LTF for confirmed iDDSP. A definite diagnosis of iDDSP was made with high-speed treadmill or overground endoscopy. Upper respiratory tract (URT) disorders, short-term complications, and horses returning for recurrence of URT problems were recorded. Performance before and after LTF was assessed by reviewing career race records and comparing performance index (PI), and racing speed marks from the baseline, preoperative, and postoperative periods. The effect of basihyoid-cricoid (BC) net distance shortened on racing performance was assessed.

RESULTS

Postoperatively, PI increased in 36/54 (67%, 95% CI 54%-79%) of experienced racehorses, and 44/67 (66%, 54%-77%) established or improved their racing speed mark relative to the preoperative period. As a group, PI decreased by a mean (SE) of 0.9 (0.17) points (P < .001) prior to diagnosis/surgery. Postoperatively, PI increased by 0.5 (0.16) points (P = .003), and racing speed improved by 0.83 (0.22) s (P < .001). Twenty-five percent (17%-34%) and 49% (39%-60%) of horses did not demonstrate a decline in PI and racing speed prior to diagnosis, respectively. Net BC distance shortening did not affect performance postoperatively. Twenty of 95 horses (21%, 13%-29%) had confirmed recurrence of iDDSP 46-708 days postoperatively.

MAIN LIMITATIONS

Not all horses were evaluated with exercising endoscopy postoperatively. Racehorses inevitably develop other racing-related problems which confound studies of this nature.

CONCLUSIONS

This study provides scientific support for the use of LTF to treat iDDSP in harness racehorses although iDDSP seems to affect harness racehorses differently as individuals.

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.

The effect of dairy heifer pre-breeding growth rate on first lactation milk yield in spring-calving, pasture-based herds

Optimising heifer growth rate may offer an opportunity to improve lifetime milk yield per cow, enhancing the environmental and economic efficiency of dairy farming operations. The effect of dairy heifer pre-breeding average daily weight gain (ADG_PB) on first lactation milk yield was investigated. This observational study employed a data set comprising 265 Holstein-Friesian, or Holstein-Friesian-cross-Jersey heifers from seven commercial, spring-calving, pasture-based dairy herds, where the major component of the diet was grazed grass. These were weighed at birth and prior to breeding and ADG_PB was calculated. Milk recordings were performed throughout the heifers' first lactation and 305-day yield figures calculated from these records. Yields were corrected to 4% fat and 3.1% protein to create standardised 305-day milk yield (SMY), which was the outcome of interest. Median ADG_PB was 0.72 kg/day. Median 305-day yield was 5 967 kg. Linear regression was used to investigate the effect of weight and genetic, age and first calving factors on SMY. Pre-breeding average daily weight gain, age at first calving and predicted transmitting abilities for milk protein production and calving interval were all significant in the final model, which also included the random effects of farm and month of calving within year. ADG_PB was quadratically related to first lactation SMY, with an ADG_PB of 0.82 kg/day corresponding to the maximum predicted SMY. The model predicted that a heifer growing at 0.82 kg/day would produce 1 120 kg more SMY than a heifer growing at 0.55 kg/day, 218 kg more than a heifer growing at 0.7 kg/day and 103 kg more than a heifer growing at 0.90 kg/day. Manipulation of heifer growth rate may offer a viable method of increasing first lactation milk yield.

Cow-level prevalence and risk factors for estrus detection inaccuracy in seasonal calving pasture-based dairy cows

High submission rates and pregnancies per AI are essential to ensure compact calving is achieved in seasonal calving pasture-based systems. Estrus detection inaccuracy (EDI) is one area that negatively impacts pregnancies per AI as it increases the inseminations per pregnancy with little probability of conception, while also having the potential to disrupt established pregnancies. The aims of this cross-sectional study were to provide cow-level estimates of EDI prevalence and determine cow-level risk factors for EDI in seasonal calving pasture-based systems. A total of 1071 milk samples were obtained from 984 cows on 19 farms in spring 2018 and analyzed by radioimmunoassay to determine the progesterone concentration at the time of artificial insemination. Based on a validation study on a subset of cows, an inaccurate estrus detection was described as a concentration of progesterone in foremilk of ≥3 ng/ml which corresponded to a composite milk progesterone value of 5 ng/ml. To investigate selected risk factors for EDI, we conducted statistical analyses using two multivariate logistic regression models, stratifying by insemination number (first versus repeat). The overall prevalence of EDI was 4.7% with a prevalence of 3.3% of EDI at first insemination and 14.1% at repeat insemination. Absence of a mounting abrasion (Adjusted odds ratio (AOR) = 3.0) was a significant risk factor for EDI on first insemination while abnormal preceding repeat interval (AOR = 9.5), the absence of an observed standing estrus (AOR = 12.5) and the absence of a mounting abrasion (AOR = 4.1) were significant risk factors for EDI on repeat insemination. The results indicate that cow-level estimated prevalence of EDI in a selection of pasture-based herds was low at first insemination but higher for repeat insemination. It confirms that certain cow-level risk factors existed for EDI, thus providing preliminary evidence for potential future investigation into the targeted use of on-farm progesterone assays in pasture-based herds.

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.

Johne's disease in Irish dairy herds: considerations for an effective national control programme

The Irish dairy industry has established a reputation for the production of safe and healthy dairy products and is seeking to further expand its export market for high value dairy products. To support its reputation, stakeholders aim to control Johne’s disease. To assist decision-makers determine the most appropriate design for an Irish programme, a narrative review of the scientific literature on the epidemiology of Johne’s disease, and selected control programmes throughout the world was undertaken. Two modelling studies specifically commissioned by Animal Health Ireland to assess testing methods used to demonstrate confidence of freedom in herds and to evaluate a range of possible surveillance strategies provided additional information. The majority of control programmes tend to be voluntary, because of the unique epidemiology of Johne’s disease and limited support for traditional regulatory approaches. While acknowledging that test performance and sub-clinical sero-negative shedders contributes to the spread of infection, a range of socio-political issues also exist that influence programme activities. The paper provides a rationale for the inclusion of a Veterinary Risk Assessment and Management Plan (VRAMP), including voluntary whole herd testing to identify infected herds and to support assurance-based trading through repeated rounds of negative testing, national surveillance for herd-level case-detection, and improved understanding of biosecurity management practices. Identification and promotion of drivers for industry and producer engagement in Ireland is likely to guide the future evolution of the Irish Johne’s Control Programme (IJCP) and further enhance its success. The provision of training, education and extension activities may encourage farmers to adopt relevant farm management practices and help them recognize that they are ultimately responsible for their herd’s health and biosecurity.

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.

Herb species inclusion in grazing swards for dairy cows-A systematic review and meta-analysis

A systematic review and meta-analysis were conducted to estimate the effect of herb species on milk production and urinary nitrogen (UN) excretion from grazing dairy cows. Grazing swards consisting of herb species grown with either a grass species or a grass and legume (multispecies swards) were compared with non-herb-containing swards consisting of a grass species grown as a monoculture or grass-legume swards (simple swards). A literature search was completed using the online databases CAB Direct, Web of Science, and Google Scholar, using the search strategy "dairy cow", "herb OR forb OR phorb", and "grazing". Milk production data, variance, and sample size were required for eligibility. In all, 116 studies were identified. Following eligibility screening, 11 papers from 6 journals, published between 2006 and 2018, were available for analysis. Studies were from New Zealand (N = 7), Australia (N = 3), and the United States (N = 1). The population was either Holstein Friesian or Holstein Friesian × Jersey dairy cows, with a range in mean daily milk yield (MY) from 12.1 kg to 34.7 kg (mean = 18.6 kg). A total of 25 comparisons were used for milk production analysis, with 324 and 284 cows included in multispecies and simple sward groups respectively. Data analysis was conducted in R using a random effects, robust variance estimation model (R Foundation for Statistical Computing, Vienna, Austria). Heterogeneity was reported using the I² statistic. Milk production was significantly increased. Analysis of MY resulted in a weighted mean difference (WMD) of +1.20 kg/d (95% CI = 0.90, 1.49; I² = 4%). Fat and protein kg were also significantly increased (WMD +0.06 kg/d; CI = 0.01, 0.11). Urinary nitrogen excretion was estimated from milk urea nitrogen when reported (n = 6). A WMD of -28.1 g of N/d (95% CI = -81.1, 24.9) was generated, with heterogeneity high among studies (I² = 75%). This meta-analysis shows the potential benefits of multispecies swards. Although we saw no significant difference in UN excretion, an increase in milk production was found.

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 (MSD_cow) 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 MSD_cow 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 MSD_cow 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.

Cow-level risk factors for reproductive tract disease diagnosed by 2 methods in pasture-grazed dairy cattle in Ireland

The cow-side diagnosis of reproductive tract disease (RTD) involves identifying the presence of purulent vaginal discharge (PVD) and ultrasonographic endometritis (UE). The objectives of our study were to obtain prevalence estimates for RTD diagnosed by 2 methods (PVD and UE scoring) and to investigate the risk factors for increased probability of RTD if these methods are used in isolation or in combination. Our retrospective observational cohort study tested the hypothesis that RTD assessed by 2 methods would have similar risk factors, and that those would be mainly cow- and calving-related factors. We analyzed data from 5,049 pre-breeding examinations (PBE) from 2,460 spring-calved cows on 8 farms between 2014 and 2018. Cow-related details assessed were days in milk at PBE, breed, lactation number, dry period length, body condition score at calving and PBE, 305-d milk yield, predicted transmitting ability for production and fertility, the presence of a corpus luteum at PBE, and positive diagnosis the previous year. Calving details assessed were type of sire, calf sex, twinning, stillbirth, calving difficulty score, and retained fetal membranes. We conducted statistical analyses using 4 multivariable logistic regression models to identify the risk of RTD diagnosed by (1) PVD in isolation, (2) UE in isolation, (3) the presence of either PVD or UE; and (4) the presence of both PVD and UE. We accounted for herd, cow, and year as random effects in all 4 models. The overall prevalence of RTD in models 1, 2, 3, and 4 were 7.5, 6.7, 11.6, and 2.6%, respectively. Days in milk at PBE, the interaction between days in milk and retained fetal membranes, twinning, and the predicted transmitting ability for calving interval were consistently significant risk factors for positive scores in all 4 models. Considerable calving difficulty [adjusted odds ratio (AOR) = 13.64], Holstein Friesian dam breed (AOR = 2.58), first lactation (AOR = 2.39), and body condition score at PBE (AOR = 1.64) were risk factors for a positive PVD score but not for a positive UE score. Fifth lactation (AOR = 1.69), a beef-sired calf (AOR = 1.46), and the absence of a corpus luteum at PBE (AOR = 1.57) were risk factors for a positive UE score but not for a positive PVD score. These results support the hypothesis that most of the risk factors for PVD and UE are the same but some are distinctly different, implying that in some instances the 2 methods diagnose separate components of the RTD complex.

The effect of growth rate on reproductive outcomes in replacement dairy heifers in seasonally calving, pasture-based systems

The effect of average daily gain (ADG) on reproductive outcomes in replacement dairy heifers was investigated. All heifers were managed in the typical Irish spring calving, pasture-based system, where the herd calves in 1 block between January and April and the majority of the diet comprises grazed grass. Heifer calves (n = 399) from 7 herds were weighed at birth and at the beginning of the breeding season, and ADG was calculated. Service dates and pregnancy diagnosis results were recorded, and conception dates were calculated. Days open (DO) was defined as the number of days between the beginning of the breeding season and conception. Genetic data were retrieved from the Irish Cattle Breeding Federation database. A Cox proportional hazard model was constructed to identify variables with a significant effect on DO. An accelerated failure time model was used to predict survival curves and median survival times for different combinations of the significant variables. The ADG ranged from 0.41 to 0.91 kg/d, with a median of 0.70 kg/d. Frailty effect of farm within year, maintenance subindex of the economic breeding index, and ADG had a significant effect on DO. Derived from the final accelerated failure time model, the predicted median DO for a heifer with an ADG of 0.40, 0.70, or 0.90 kg/d aged 443 d at the beginning of the breeding season and with a maintenance subindex in the second tercile were 27, 16, and 11 d, respectively.

A review of paratuberculosis in dairy herds - Part 2: On-farm control

Bovine paratuberculosis is a chronic infectious disease of cattle, caused by Mycobacterium avium subspecies paratuberculosis (MAP). This is the second in a two-part review of the epidemiology and control of paratuberculosis in dairy herds. Several negative production effects associated with MAP infection have been described, but perhaps the most significant concern in relation to the importance of paratuberculosis as a disease of dairy cattle is the potential link with Crohn's disease in humans. Milk is considered a potential transmission route to humans and it is recognised that pasteurisation does not necessarily eliminate the bacterium. Therefore, control must also include reduction of the levels of MAP in bulk milk supplied from dairy farms. There is little field evidence in support of specific control measures, although several studies seem to show a decreased prevalence associated with the implementation of a combined management and test-and-cull programme. Improvements in vaccination efficacy and reduced tuberculosis (TB) test interference may increase uptake of vaccination as a control option. Farmer adoption of best practice recommendations at farm level for the control of endemic diseases can be challenging. Improved understanding of farmer behaviour and decision making will help in developing improved communication strategies which may be more efficacious in affecting behavioural change on farm.

A review of paratuberculosis in dairy herds - Part 1: Epidemiology

Bovine paratuberculosis is a chronic infectious disease of cattle caused by Mycobacterium avium subspecies paratuberculosis (MAP). This is the first in a two-part review of the epidemiology and control of paratuberculosis in dairy herds. Paratuberculosis was originally described in 1895 and is now considered endemic among farmed cattle worldwide. MAP has been isolated from a wide range of non-ruminant wildlife as well as humans and non-human primates. In dairy herds, MAP is assumed to be introduced predominantly through the purchase of infected stock with additional factors modulating the risk of persistence or fade-out once an infected animal is introduced. Faecal shedding may vary widely between individuals and recent modelling work has shed some light on the role of super-shedding animals in the transmission of MAP within herds. Recent experimental work has revisited many of the assumptions around age susceptibility, faecal shedding in calves and calf-to-calf transmission. Further efforts to elucidate the relative contributions of different transmission routes to the dissemination of infection in endemic herds will aid in the prioritisation of efforts for control on farm.

Evaluation of national surveillance methods for detection of Irish dairy herds infected with Mycobacterium avium ssp. paratuberculosis

The aim of this study was to evaluate the utility and cost-effectiveness of a range of national surveillance methods for paratuberculosis in Irish dairy herds. We simulated alternative surveillance strategies applied to dairy cattle herds for the detection of Mycobacterium avium ssp. paratuberculosis (MAP)-infected herds (case-detection) or for estimation of confidence of herd freedom from infection (assurance testing). Strategies simulated included whole-herd milk or serum serology, serology on cull cows at slaughter, bulk milk tank serology, environmental testing, and pooled fecal testing. None of the strategies evaluated were ideal for widespread national case-detection surveillance. Herd testing with milk or serum ELISA or pooled fecal testing were the most effective methods currently available for detection of MAP-infected herds, with median herd sensitivity >60% and 100% herd specificity, although they are relatively expensive for widespread use. Environmental sampling shows promise as an alternative, with median herd sensitivity of 69%, but is also expensive unless samples can be pooled and requires further validation under Irish conditions. Bulk tank milk testing is the lowest cost option and may be useful for detecting high-prevalence herds but had median herd sensitivity <10% and positive predictive value of 85%. Cull cow sampling strategies were also lower cost but had median herd sensitivity <40% and herd positive predictive values of <50%, resulting in an increased number of test-positive herds, each of which requires follow-up herd testing to clarify status. Possible false-positive herd testing results associated with prior tuberculosis testing also presented logistical issues for both cull cow and bulk milk testing. Whole-herd milk or serum ELISA testing are currently the preferred testing strategies to estimate confidence of herd freedom from MAP in dairy herds due to the good technical performance and moderate cost of these strategies for individual herd testing. Cull cow serology and bulk tank milk sampling provide only minimal assurance value, with confidence of herd freedom increasing only minimally above the prior estimate. Different testing strategies should be considered when deciding on cost-effective approaches for case-detection compared with those used for building confidence of herd freedom (assurance testing) as part of a national program.

Modeling of alternative testing strategies to demonstrate freedom from Mycobacterium avium ssp. paratuberculosis infection in test-negative dairy herds in the Republic of Ireland

In light of the various adverse effects of Johne's disease on animal productivity and the debate on the role of its causative organism, Mycobacterium avium ssp. paratuberculosis, in the etiology of Crohn's disease, major dairy-producing countries around the world have implemented national control programs aimed at reducing the prevalence of this infection in cattle. A pilot control program was initiated in Ireland in 2013, with a key objective to provide farmers with test-negative dairy herds with tools and knowledge to increase their confidence of freedom over time. The aim of this study was to estimate the confidence of freedom obtained in test-negative Irish dairy herds over time with various sampling scenarios and to evaluate the cost-effectiveness of alternative scenarios for achieving an acceptable level of confidence of freedom in herds with no evidence of infection. A stochastic model was developed to simulate repeated annual testing of individual animals using ELISA and confirmatory assays over a period of 20 yr. Two scenarios modeled the current herd-screening options, whereas 14 alternative scenarios explored the effect of varying parameters from the current testing strategies, such as the frequency of testing, the eligibility criteria for selecting animals, the type of assay, the probability of introduction, and the assay sensitivity. Results showed that the current testing strategy with milk twice a year or serum once a year in all animals over 2 yr old provided the highest annual herd sensitivity, with a median value of 55%. Although the median confidence of freedom increased over time for all scenarios, the time required to reach 90 and 95% confidence of freedom was highly variable between scenarios. Under the testing scenario where serum tests were used once a year, the confidence of freedom reached 90% after 4 yr and 95% after 7 yr of testing. Some of the alternative scenarios achieved an acceptable level of confidence of freedom in a reasonable timeframe and at lesser cost than the current testing strategies. The results of this work are used to provide recommendations for the next phases of the program.

Low accuracy of Bayesian latent class analysis for estimation of herd-level true prevalence under certain disease characteristics-An analysis using simulated data

Estimation of the true prevalence of infected individuals involves the application of a diagnostic test to a population and adjusting according to test performance, sensitivity and specificity. Bayesian latent class analysis for the estimation of herd and animal-level true prevalence, has become increasingly used in veterinary epidemiology and is particularly useful in incorporating uncertainty and variability into analyses in a flexible framework. However, the approach has not yet been evaluated using simulated data where the true prevalence is known. Furthermore, using this approach, the within-herd true prevalence is often assumed to follow a beta distribution, the parameters of which may be modelled using hyperpriors to incorporate both uncertainty and variability associated with this parameter. Recently however, the authors of the current study highlighted a potential issue with this approach, in particular, with fitting the distributions and a tendency for the resulting distribution to invert and become clustered at zero. Therefore, the objective of the present study was to evaluate commonly specified models using simulated datasets where the herd-level true prevalence was known. The specific purpose was to compare findings from models using hyperpriors to those using a simple beta distribution to model within-herd prevalence. A second objective was to investigate sources of error by varying characteristics of the simulated dataset. Mycobacterium avium subspecies paratuberculosis infection was used as an example for the baseline dataset. Data were simulated for 1000 herds across a range of herd-level true prevalence scenarios, and models were fitted using priors from recently published studies. The results demonstrated poor performance of these latent class models for diseases characterised by poor diagnostic test sensitivity and low within-herd true prevalence. All variations of the model appeared to be sensitive to the prior and tended to overestimate herd-level true prevalence. Estimates were substantially improved in different infection scenarios by increasing test sensitivity and within-herd true prevalence. The results of this study raise questions about the accuracy of published estimates for the herd-level true prevalence of paratuberculosis based on serological testing, using latent class analysis. This study highlights the importance of conducting more rigorous sensitivity analyses than have been carried out in previous analyses published to date.

The Herd-Level Sensitivity of Abattoir Surveillance for Bovine Tuberculosis: Simulating the Effects of Current and Potentially Modified Meat Inspection Procedures in Irish Cattle

The European Food Safety Authority (EFSA) has published a series of opinions to assess the impact of changing from the current meat inspection procedures (CMI) to visual-only inspection (VOI) procedures. Concern has been raised that changes from CMI to VOI would adversely affect the effectiveness of surveillance for bovine tuberculosis (bTB) in EU member states, both for countries with and without official status of bTB freedom (OTF and non-OTF countries, respectively). This study was conducted to estimate the impact of a change from CMI to VOI in abattoirs on herd-level detection sensitivity in Ireland, a non-OTF country. Using national Irish data, we identified all herds that sold at least one animal to slaughter during 2010-12 whilst unrestricted for bTB. For each of these herds, we calculated the number of cattle sent to slaughter whilst unrestricted, the number of factory lesion tests (FLT) that had been performed, and estimated the apparent within-herd prevalence (APwh). A FLT is a whole-herd test conducted in a herd following the confirmation of bTB in an animal at slaughter. We considered five different inspection scenarios, each based on meat inspection and bacteriology in series, including current meat inspection (CMI) and four visual-only inspection scenarios (VOI2, VOI3, VOI4, VOI5) with reducing inspection sensitivities. Separately for each inspection scenario, a simulation model was used to estimate the herd-level detection sensitivity and the number of bTB-herds (that is, herds that sent at least one animal detected with M. bovis to slaughter when unrestricted during 2010-12) that would and would not be detected. The simulated mean herd-level detection sensitivity estimates were 0.24 for CMI, and 0.16, 0.12, 0.10 and 0.08 for VOI2-5, assuming a 2-, 3-, 4- and 5-fold decrease, respectively, in the animal-level detection sensitivity of VOI relative to that of CMI. The estimated number of non-detected bTB-herds is substantial with CMI, and increases in the series of VOI scenarios with decreasing herd-level detection sensitivity. If VOI were introduced without alternative surveillance means to compensate for the decrease in animal-level inspection sensitivity, such changes might jeopardise bTB surveillance, control and eradication programmes in cattle herds of non-OTF countries, including Ireland.

Diagnostic potential of the peptide-mediated magnetic separation (PMS)-phage assay and PMS-culture to detect Mycobacterium avium subsp. paratuberculosis in bovine milk samples

Controlling the spread of Johne's disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP), in domestic livestock is challenging. Current diagnostic methods lack sufficient sensitivity to detect subclinically infected animals, and thus, better diagnostic methods are needed. This study was carried out to investigate the diagnostic potential of two novel peptide-mediated magnetic separation (PMS)-based tests-a PMS-phage assay and PMS-culture-both of which have been developed and optimized to detect viable MAP cells in bovine milk. Individual milk samples (50 ml) were obtained from 105 "non-infected" and 40 "MAP-infected" animals (classified as such on the basis of prior faecal culture and serum-ELISA results) in three dairy herds and tested in parallel by the PMS-phage assay and PMS-culture. Diagnostic sensitivity (DSe) and specificity (DSp) of the PMS-phage and PMS-culture methods were determined relative to the MAP infection status of the animal contributing the milk sample. The PMS-based tests applied individually showed moderate DSe (PMS-culture 0.250 and PMS-phage assay 0.325) and high DSp (0.962 and 1.000, respectively). When results of the two PMS-based tests were combined, DSe increased substantially to 0.525, and the DSp was calculated to be 0.962. It was concluded that combined application of the PMS-phage assay and PMS-culture provided the most complete picture regarding the presence of viable MAP in bovine milk samples. A comprehensive validation of the PMS-based assays relative to currently used diagnostic methods (faecal culture and serum-ELISA) would be the next step in assessment of the diagnostic potential of these novel PMS-based methods.

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 β 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.