Sample size calculations for Bayesian prediction of bovine viral-diarrhoea-virus infection in beef herds

We used a Bayesian classification approach to predict the bovine viral-diarrhoea-virus infection status of a herd when the prevalence of persistently infected animals in such herds is very small (e.g. <1%). An example of the approach is presented using data on beef herds in Wyoming, USA. The approach uses past covariate information (serum-neutralization titres collected on animals in 16 herds) within a predictive model for classification of a future observable herd. Simulations to estimate misclassification probabilities for different misclassification costs and prevalences of infected herds can be used as a guide to the sample size needed for classification of a future herd.     

Mathematical modelling of pseudorabies virus (syn. Aujeszky's disease virus) outbreaks aids eradication programmes: a review

Pseudorabies virus will be eradicated from the Netherlands if a typical infectious pig (Rind) infects, on average, less than one other pig. In this review, we used a stochastic SIR model to estimate Rind using data from the field and from experiments. Rind in sow herds was estimated to be significantly less than 1 and in rearing and finishing pigs Rind was higher than 1. However, if Rind is higher than 1, PRV can still be eradicated if one infectious herd infects less than one other herd during the period that the herd is infectious(Rherd <1). Some future developments in Dutch pig husbandry (e.g. group-housing of sows) and possible risks after halting vaccination are also quantitatively evaluated.     

Pig and herd level prevalence of Toxoplasma gondii in Ontario finisher pigs in 2001, 2003, and 2004

The objective of this study was to estimate the apparent and true prevalence of exposure to Toxoplasma gondii in Ontario finisher pigs. During the study period (2001 to 2004), sera from 6048 pigs were tested with a commercial enzyme-linked immunosorbent assay (ELISA); 103 farms were included 1 to 3 times in the study. True prevalence was estimated using a Bayesian approach. Apparent prevalence at the pig level was 1.59% [95% confidence interval (CI): 0.45, 2.99] in 2001, 0.06% (95% CI: 0.00, 0.46) in 2003, and 0.26% (95% CI: 0.00, 0.82) in 2004. Apparent prevalence at the herd-level was 13.7% (95% CI: 7.5, 22.3) in 2001; 1.25% (95% CI: 0.03, 6.77) in 2003, and 3.75% (95% CI: 0.78, 10.6) in 2004. Similarly, posterior Bayesian estimates of true prevalence at the pig level were 1.7% [95% probability interval (PI): 1.2, 2.2] in 2001, 0.2% (95% PI: 0.04, 0.4) in 2003, and 0.3% (95% PI: 0.1, 0.7) in 2004. At the herd level, posterior estimates of prevalence were 11.6% (95% PI: 7.4, 16.8) in 2001, 0% (95% PI: 0.0, 2.5) in 2003, and 1.2% (95% PI: 0.0, 5.0) in 2004 when a herd cut-point > or = 1 was used. Exposure to T. gondii in finishing pig farms in Ontario appears to be infrequent.     

Importance of claw quality in cattle: Review and recommendations to achieve genetic improvement. Report of the E.A.A.P. working group on “claw quality in cattle”

The objective of this report is to review results of research and to discuss recommendations to achieve genetic improvement of claw quality. High claw quality is defined as a low susceptibility for claw disorders and a low need for footcare. The economic importance of claw problems is considerable, with about 25% of dairy cows treated per year. Direct effects are costs of trimming, veterinary costs and forced culling (2–3%). Indirect costs are decreased milk production or daily gain, lower fertility, decrease of herd life, and lower salvage value.Lameness problems are mainly localized in the claws and can have a traumatic, systemic or infectious origin. The claw quality is a product of claw shape, characteristics of the horn and anatomy of the inner structure of the claw. Environmental factors like housing systems, management and nutrition give considerable herd effects. Improvement of claw quality in the short term can be achieved by managemental procedures that will reduce foot and leg problems in confinement.Genetic improvement can give a contribution in the long term. Genetic variation in claw traits and claw disorders are recorded between and within breeds. Heritabilities and additive genetic variation for claw shape measurements (e.g. claw length, claw angle) are high enough to obtain genetic change in these traits. Claw measurements are partly symptoms but also predisposition factors for claw disorders like sole ulcers. Shorter and steeper hind leg claws are favourable predispositions.Veterinary records on claw and leg disorders after treatment yield very low heritabilities. Claw judgements should be replaced by more effective measurements because of low h² and low correlation to claw disorders.Implementation of genetic improvement based on measurements of claw shape (angle, length) may start with a progeny test of 30–50 daughters in first lactation of the most promising A.I. bulls in milk production. Relationships of claw characteristics of young bulls with those of their parents and daughters is recommended for further analysis.     

Observer agreement on pen level prevalence of clinical signs in finishing pigs

Four observers performed a standard clinical examination of finisher pigs in two commercial finisher herds. In herd 1, 600 finisher pigs in 44 pens were examined. The observers assessed clinical signs of lameness, umbilical hernia and tail bite according to a standardized procedure. The prevalence of the clinical signs was estimated at the pen level. The procedure was repeated after 3 months in another herd, where 730 finisher pigs in 69 pens were examined. The agreement between observer pairs was assessed using prevalence-adjusted bias-adjusted kappa (PABAK) and proportionate-agreement estimates (P_pos and P_neg).

Observer bias was present despite training and standardization of the participating observers. The highest pen level agreement for the observer pairs was found for pens that had one or more pigs with tail bite (PABAK = 0.82–1.00) and umbilical hernia (PABAK = 0.77–1.00). The agreement was fair-to-moderate for identification of pens holding one or more lame pigs (PABAK = 0.27–0.71). In general, the average agreement of observer pairs on absence of clinical signs (P_neg) was higher than for presence (P_pos). The observer bias varied between observer pairs and with the clinical signs.     

Spatial clustering of swine influenza in Ontario on the basis of herd-level disease status with different misclassification errors

This approach maximizes sensitivity of serology-based monitoring systems by considering spatial clustering of herds classified as false positive by herd testing, allowing outbreaks to be detected in an early phase. The primary objective of this study was to determine whether swine herds infected with influenza viruses cluster in space, and if so, where they cluster. The secondary objective was to investigate the combining of a multivariate spatial scan statistic with herd test results to maximize the sensitivity of the surveillance system for swine influenza. We tested for spatial clustering of swine influenza using the Cuzick–Edwards test as a global test. The location of the most likely spatial clusters of cases for each subtype and strain in a sample of 65 sow and 72 finisher herds in 2001 (Ontario, Canada), and 76 sow herds in 2003 (Ontario, Canada) was determined by a spatial scan statistic in a purely spatial Bernoulli model based on single and multiple datasets.

A case herd was defined by true herd-disease status for sow or finisher herds tested for H1N1, and by apparent herd-disease status for sow herds tested for two H3N2 strains (A/Swine/Colorado/1/77 (Sw/Col/77) and A/Swine/Texas/4199-2/98 (Sw/Tex/98)). In sow herds, there was no statistically significant clustering of H1N1 influenza after adjustment for pig-farm density. Similarly, spatial clustering was not found in finisher herds. In contrast, clustering of H3N2 Sw/Col/77 (prevalence ratio = 12.5) and H3N2 Sw/Tex/98 (prevalence ratio = 15) was identified in an area close to a region with documented isolation of avian influenza isolates from pigs.

For the H1N1 subtype tested by ELISA, we used an approach that minimized overall misclassification at the herd level. This could be more applicable for detecting clusters of positive farms when herd prevalence is moderate to high than when herd prevalence is low. For the H3N2 strains we used an approach that maximized herd-level sensitivity by minimizing the herd cut-off. This is useful in situations where prevalence of the pathogen is low. The results of applying a multivariate spatial scan statistic approach, led us to generate the hypothesis that an unknown variant of influenza of avian origin was circulating in swine herds close to an area where avian strains had previously been isolated from swine. Maximizing herd sensitivity and linking it with the spatial information can be of use for monitoring of pathogens that exhibit the potential for rapid antigenic change, which, consequently, might then lead to diminished cross-reactivity of routinely used assays and lower test sensitivity for the newly emerged variants. Veterinary authorities might incorporate this approach into animal disease surveillance programs that either substantiate freedom from disease, or are aimed at detecting early incursion of a pathogen, such as influenza virus, or both.     

Forecasting clinical disease in pigs: comparing a naive and a Bayesian approach

In veterinary practice the clinician often evaluates and predicts herd health status over time according to clinical criteria. In this paper, we modeled three different clinical signs among pigs based on longitudinal clinical observations in 15 pig herds. We compared and discussed the outputs from two different approaches for making clinical forecasts in a herd: a naive approach using a simple time series model with previous disease observations as predictors and a Bayesian state space models approach, in which the time lag variable entered into the random component of the model. We used the Markov chain Monte Carlo technique to calculate posterior distributions of the forecasts. For the herd specific forecasts the results showed that there were only minor differences between the forecasts from the simple time series model and the median forecasts from the Bayesian model. However, the credibility intervals from the Bayesian model were wider than the forecasts from the simple model and, therefore the Bayesian model encompassed the variability in the forecasts better. Compared to the statistical model, the simple time series would be easier to implement in a practical setting. However, the latter lacks the inherent “generality” from the statistical model that allows the user to make statements about the distribution of the herds and to predict disease status based on the “average” correlation among the herds. The applicability of the Bayesian approach within a clinical decision-making framework was discussed, with special emphasis on the use of prior information and clinical forecasting.     

A biological network describing infection with Mycoplasma hyopneumoniae in swine herds

We have made a biological model based on a Bayesian network for risk factors for infection with Mycoplasma hyopneumoniae (Mycoplasma) in slaughter pigs; prevalence of infection is based on veterinary examinations. The model is a probabilistic/stochastic determination based on the inherent biological uncertainty of the severity of infection with Mycoplasma and the derived stochastic effects on productivity for the herd. The conditional probabilities in the Bayesian network are based on published studies and expert opinions. We used the model to calculate how the risk factors and our evidence about the herd influenced our view on the severity of Mycoplasma, and how our view changed when we had more veterinary evidence. We also show how one can use the model to deal with conflicting examinations.     

Genetic parameters and genotype x environment interaction for feed efficiency traits in steers fed grower and finisher diets

The objective of this study was to examine the genetic parameters and genetic correlations of feed efficiency traits in steers (n = 490) fed grower or finisher diets in 2 feeding periods. A bivariate model was used to estimate phenotypic and genetic parameters using steers that received the grower and finisher diets in successive feeding periods, whereas a repeated animal model was used to estimate the permanent environmental effects. Genetic correlations between the grower-fed and finisher-fed regimens were 0.50 ± 0.48 and 0.78 ± 0.43 for residual feed intake (RFI) and G:F, respectively. The moderate genetic correlation between the 2 feeding regimens may indicate the presence of a genotype × environment interaction for RFI. Permanent environmental effects (expressed in percentage of phenotypic variance) were detected in the grower-fed steers for ADG (38%), DMI (30%), RFI (18%), and G:F (40%) and also in the finisher-fed steers for ADG (28%), DMI (35%), metabolic mid-weight (23%), and RFI (10%). Heritability estimates were 0.08 ± 0.10 and 0.14 ± 0.15 for the grower-fed steers and 0.42 ± 0.16 and 0.40 ± 17 for the finisher-fed steers for RFI and G:F, respectively. The dependency of the RFI on the feeding regimen may have serious implications when selecting animals in the beef industry. Because of the higher cost of grains, feed efficiency in the feedlot might be overemphasized, whereas efficiency in the cow herd and the backgrounding segments may have less emphasis. These results may also favor the retention (for subsequent breeding) of cows whose steers were efficient in the feedlot sector. Therefore, comprehensive feeding trials may be necessary to provide more insight into the mechanisms surrounding genotype × environment interaction in steers.     

Infectious and rearing-system related risk factors for chronic pleuritis in slaughter pigs

Chronic pleuritis (CP) in Danish pigs for slaughter is by far the most frequent finding at the routine post-mortem meat inspection. An initial investigation published in 1990 demonstrated infectious and management-related risk factors. Serological testing for additional infectious agents, as well as the need to consider the effect of disease clustering at the herd level, required a re-analysis of the data.

Our re-analysis used a representative sample of 4800 pigs originating from 623 Danish herds. Each pig was examined for the presence of CP and progressive atrophic rhinitis (PAR). The gender of the pig, the weight of the carcass, and the herd of origin were also recorded. Individual blood samples were examined for seropositivity for Actinobacillus pleuropneumoniae (AP) serotypes 2, 6, 7, 12, Haemophilus parasuis, Mycoplasma hyopneumoniae (MYC) and swine influenza (SI). Herd-level information retrieved through a questionnaire included health status, production type, herd size (i.e. pigs per year) and vaccination procedures.

Associations between CP and infectious, individual and herd-related factors were investigated by logistic regression with random effects. Among pigs from herds with conventional health status, seropositivity for AP serotypes 2 and 6, and MYC had odds ratios (ORs) of CP of 9.0, 1.6 and 1.8, respectively. Neither seropositivity for AP serotype 7 nor SI were associated with CP by themselves, but interacted: OR of CP of 5.3 (1.8) when present at the same time among pigs exhibiting (not exhibiting) PAR. An association of PAR with CP was found, and PAR interacted with AP serotype 7: OR=10.0 (4.3) when both factors were present among pigs exposed (non-exposed) to SI. The OR (0.97) for an increase of carcass weight by 1 kg was negligible.

In pigs from specific pathogen-free (SPF) herds, seropositivity for MYC and herd size were associated with CP. Moreover, for a herd size of 1000 pigs, CP was associated with exposure to MYC by an OR of 3.3 (decreasing to 1.9 when the herd size was increased by 1000). Farrow-to-finish as opposed to finishing herd had an OR of CP of 3.2.

In conventional herds, seropositivity for AP serotype 2 and MYC were associated with 51% and 29% of the occurrence of CP. In SPF herds, farrow-to-finish as opposed to finishing herds was associated with 47% of the occurrence of CP. Seropositivity for MYC was associated with 33% (39%) of the occurrence of CP in herds with a size > (≤) 1500 pigs.     

Genetic parameters for claw health and feet and leg conformation traits in Finnish Ayrshire cows

Genetic parameters for different claw disorders, overall claw health and feet and leg conformation traits were estimated for Finnish Ayrshire cows. The merged data set with records of claw health and feet and leg conformation traits consisted of 105 000 observations from 52 598 Finnish Ayrshire cows between 2000 and 2010. The binary claw health data and the linearly scored conformation data were analysed using an animal model and restricted maximum likelihood method by applying the statistical package ASReml. Binomial logistic models with mixed effects were used to estimate genetic parameters for sole haemorrhages, chronic laminitis, white‐line separation, sole ulcer, interdigital dermatitis, heel horn erosion, digital dermatitis, corkscrew claw and overall claw health. Estimated heritabilities for different claw disorders using a binomial logistic model ranged from 0.01 to 0.20. Estimated heritability for overall claw health using a binomial logistic model was 0.08. Estimated heritabilities for feet and leg conformation traits ranged from 0.07 to 0.39. The genetic correlations between claw health and feet and leg conformation traits ranged from ?0.40 to 0.42. All phenotypic correlations were close to zero. The moderate genetic correlation, together with higher heritability of feet and leg conformation traits, showed that RLSV (rear leg side view) is a useful indicator trait to be used together with claw trimming information to increase the accuracy of breeding values for claw health in genetic evaluation.     

Use of a Bayesian risk-mapping technique to estimate spatial risks for mare reproductive loss syndrome in Kentucky

OBJECTIVE: To estimate spatial risks associated with mare reproductive loss syndrome (MRLS) during 2001 among horses in a specific study population and partition the herd effects into those attributable to herd location and those that were spatially random and likely attributable to herd management. Animals-Pregnant broodmares from 62 farms in 7 counties in central Kentucky. PROCEDURE: Veterinarians provided the 2001 abortion incidence proportions for each farm included in the study. Farms were georeferenced and data were analyzed by use of a fully Bayesian risk-mapping technique. RESULTS: Large farm-to-farm variation in MRLS incidence proportions was identified. The farm-to-farm variation was largely attributed to spatial location rather than to spatially random herd effects. CONCLUSIONS AND CLINICAL RELEVANCE: Results indicate that there are considerable data to support an ecologic cause and potential ecologic risk factors for MRLS. Veterinary practitioners with more detailed knowledge of the ecology in the 7 counties in Kentucky that were investigated may provide additional data that would assist in the deduction of the causal factor of MRLS via informal geographic information systems analyses and suggest factors for inclusion in further investigations.     

Effect of dietary calcium and phosphorus level sequences on performance, structural soundness and bone characteristics of growing-finishing swine

The effects of feeding various dietary Ca:P level sequences on gain and feed efficiency, leg structural soundness and bone indices of growing-finishing swine were evaluated as an incomplete 3 X 3 factorial arrangement of treatments in a split-plot design. A total of 664 pigs were fed one of three total dietary Ca:P levels (.52:.40, .65:.50, .80:.60%) from 19-kg to 56-kg body weights followed by one of three Ca:P levels (.45:.32, .52:.40, .65:.50%) to market weight. The .80:.60% and .65:.50% Ca:P mineral sequence was not evaluated. Diets were formulated to 14.5% crude protein using a corn-soybean meal mixture with proportions of dicalcium phosphate and limestone altered to attain the desired dietary Ca:P levels. Maximum gains occurred at the .65:.50% and .52:.40% Ca:P level during the grower (P less than .01) and finisher (P less than .01) periods, respectively. No grower X finisher phase pig gain or feed intake interaction resulted, providing evidence of no carry-over response on these measurements from the grower to the finisher period. Serum P concentration increased and plateaued at the same dietary Ca:P level, as did rate of gain at both 56-kg and 95-kg body weights. Leg soundness subjectively evaluated at 56-kg and 95-kg body weights revealed no effect of dietary Ca:P level on soundness scores at 56 kg, but at 95-kg body weight, the interaction between grower and finisher diets was significant. Percentage bone ash of the humerus, shaft thickness and bending moment of the femur increased as dietary Ca:P level increased at both 56-kg and 95-kg body weights.(ABSTRACT TRUNCATED AT 250 WORDS)     

Eradication of porcine reproductive and respiratory syndrome virus by serum inoculation of na?ve gilts

The acclimatization program included exposure to serum and recovery. A continuous flow unit (nursery to finishing) from the same farm was selected as a potential source of porcine reproductive and respiratory syndrome virus (PRRSV). Negative gilts were inoculated 5 d after arrival by intramuscular injection of serum from selected animals. There was a significant reduction in seroprevalence in the sow herd 1 y after implementation of the gilt inoculation program (P < 0.05). At that time, all of the tested nursery pigs were negative for PRRSV. The fully segregated finisher population had a significant reduction in the frequency of PRRSV positive animals (P < 0.05) by enzyme-linked immunosorbent assay (ELISA), with all animals testing negative by the end of the study. However a persistent seroconversion was observed in the partially segregated finisher pigs (P > 0.05). In conclusion, the gilt serum inoculation program achieved sow herd stabilization, as defined by the production of negative weaned pigs and this resulted in the eradication of PRRSV in the fully segregated flow.     

Herd risk factors associated with sero-prevalence of Maedi-Visna in the Manitoba sheep population

Disease associated with Maedi-Visna infection results in substantial economic losses in affected sheep producing areas of the world. A survey was conducted to estimate herd and individual seroprevalence in the province of Manitoba and evaluate risk factors for seropositive herds. Of 2207 sheep sampled from 77 selected sheep flocks, the animal level seroprevalence was 2.47% and herd level seroprevalence was 25.10%. The herd-level factors of presence of clinical skin disease, herd size of > 70, history of musculoskeletal/lameness abnormalities, and the purchase of new stock (> 50) in the last 1 to 5 y, showed significant associations with seropositive herd status. The study documented a remarkable stability of low seroprevalence in the province over a 20-year period in the absence of a systematic disease control program.     

Streptococcal meningitis in pigs: field trial to study the prophylactic effect of trimethoprim/sulphadiazine medication in feed

Half the progeny in a 200-sow herd (2045 pigs) was given feed medicated with 500 g/tonne of a 1:5 trimethoprim/sulphadiazine mixture from three to nine weeks of age. The other half (1989) acted as controls. The trial lasted 12 months. No difference was observed between the two groups in the incidence of streptococcal meningitis and the morbidity and mortality from all disease causes during the growing/fattening periods did not differ significantly. The main diseases encountered were pneumonia (7.24 per cent), streptococcal meningitis (5.12 per cent), leg and foot disorders (3.34 per cent) and the after-effects of vices (1.86 per cent). The resistance of faecal coliforms to trimethoprim was studied during the six-week period of trimethoprim/sulphadiazine feeding. Faecal coliforms in both medicated and non-medicated groups developed almost 100 per cent resistance. However, resistance developed more slowly in the untreated pigs. The medicated pigs showed a small overall improvement in feed conversion rate up to 18 weeks of age mainly because of a marked improvement between three and six weeks.     

Herd-level prevalence of Mycobacterium avium subsp. paratuberculosis infection in United States dairy herds in 2007

Testing of composite fecal (environmental) samples from high traffic areas in dairy herds has been shown to be a cost-effective and sensitive method for classification of herd status for Mycobacterium avium subsp. paratuberculosis (MAP). In the National Animal Health Monitoring System's (NAHMS) Dairy 2007 study, the apparent herd-level prevalence of MAP was 70.4% (369/524 had ≥1 culture-positive composite fecal samples out of 6 tested). Based on these data, the true herd-level prevalence (HP) of MAP infection was estimated using Bayesian methods adjusting for the herd sensitivity (HSe) and herd specificity (HSp) of the test method. The Bayesian prior for HSe of composite fecal cultures was based on data from the NAHMS Dairy 2002 study and the prior for HSp was based on expert opinion. The posterior median HP (base model) was 91.1% (95% probability interval, 81.6 to 99.3%) and estimates were most sensitive to the prior for HSe. The HP was higher than estimated from the NAHMS Dairy 1996 and 2002 studies but estimates are not directly comparable with those of prior NAHMS studies because of the different testing methods and criteria used for herd classification.     

Genetic evaluation of dairy cattle for conformation traits using random regression models

Random regression models were applied to eight conformation traits (i.e. stature, rump angle, thurl width, rear leg set, rear udder width, rear udder height, udder depth, and fore udder attachment) of Holstein cows from the northeastern United States. Covariates for fixed and random regressions included age and age‐squared for six of the traits, and two additional covariates were included for rear udder width and rear udder height. Other effects in the model were herd—year‐classifier and months in milk. Fixed covariates were nested within year of birth of the cow. Variance components were estimated using Bayesian theory and Gibbs sampling procedure. Estimated breeding values from the random regression models were compared to two single trait models. The first model utilized only the first classification record of the cow in first lactation, and the second model utilized all classifications of the cow in a simple repeatability model. Additive genetic merit for conformation traits changed with the age of the animal. Some traits were affected by age more than others. The single trait, single record model and the simple repeatability model were not appropriate in predicting breeding values at mature ages for rear udder width and rear udder height.     

Predicted costs and benefits of eradicating BVDV from Ireland

Bovine viral diarrhoea virus (BVDV) causes an economically important endemic disease (BVD) of cattle in Ireland and worldwide. Systematic eradication by detection and removal of infectious (BVDV carrier) cattle has been successful in several regions. We therefore assessed the benefits (disease losses avoided) and costs (testing and culling regime) of a potential eradication programme in Ireland. Published bio-economic models of BVDV spread in beef suckler herds and dairy herds were adapted to estimate potential benefits of eradication in Ireland. A simple model of BVDV spread in beef finisher herds was devised to estimate the benefits of eradication in this sector. A six year eradication programme consisting of 5 inter-related virological and serological testing programmes is outlined and costed. We found that the annualised benefits of BVDV eradication in Ireland exceeded the costs by a factor of 5 in the beef suckler sector and a factor of 14 in the dairy sector. Corresponding payback periods were 1.2 and 0.5 years respectively. These results highlight the significant economic impact of BVDV on the Irish cattle industry and suggest a clear economic benefit to eradication using the proposed approach. This type of cost-benefit analysis is considered an essential prerequisite prior to undertaking an eradication campaign of this magnitude.