The paradox of predation studies.

Understanding the causal relationships that contribute to mortality in populations is a priority for epidemiology, animal husbandry and ecology. Of all the sources of mortality in nature, predation is perhaps the most important, while simultaneously being one of the most difficult to study and understand. In this opinion piece, we use the epidemiological concept of the sufficient-component cause model to outline why we believe that predation studies often misrepresent predators as sufficient cause of death (or natural mortality) in ecological studies. This is pivotal in conservation biology because such studies have often led to demands for predator removal throughout the world. We use the sufficient-component cause model to illustrate the paradox that multiple studies, each studying singular putative causes of mortality (including predation), will sum to more than 100% mortality when added together. We suggest that the sufficient-component framework should be integrated into both fundamental and applied ecology to better understand the role of predators in natural ecosystems.

Chronic excess fluoride uptake contributes to degenerative joint disease (DJD): Evidence from six marsupial species.

One of the manifestations of chronic fluoride toxicosis in mammals is skeletal fluorosis, which can include lesions of degenerative joint disease (DJD). Although DJD lesions have been less commonly studied than bone or dental lesions in relation to the pathology and epidemiology of fluoride toxicosis, there have been multiple independent studies in various species that have concluded that there appears to be an effect. The mechanisms by which fluoride affects the joints are not clear, but our data provide evidence that chronic excess dietary fluoride intake contributes to DJD. Our study is the first to specifically address the association between fluoride exposure and DJD in multiple species of free-ranging mammals. We describe levels of DJD in six marsupial species (Macropus giganteus, Notamacropus rufogriseus, Wallabia bicolor, Phascolarctos cinereus, Trichosurus vulpecula and Pseudocheirus peregrinus) inhabiting high and low fluoride environments. Lesions occurred to varying extents in all species, and lesion distribution varied with biomechanical differences in gait. In addition, we show an association (independent of age) between increasing bone fluoride concentration (as a measure of fluoride exposure) and increasing prevalence of moderate and severe DJD in five species of marsupial, which we propose does not persist at the highest levels of fluoride exposure due to selective survival bias.

Prevalence and risk factors for gastrointestinal parasites in small-scale pig enterprises in Central and Eastern Uganda.

In Eastern Africa, small-scale pig keeping has emerged as a popular activity to generate additional household income. Infections of pigs with gastrointestinal helminths can limit production output, increase production costs, and pose zoonotic risks. A cross-sectional, community-based study in three districts in Eastern and Central Uganda examined the prevalence of gastrointestinal helminthes and associated risk factors in 932 randomly sampled pigs. Using the combined sedimentation-flotation method, 61.4 % (58.2-64.5 %, 95 % confidence interval [CI]) tested positive for one or more gastrointestinal helminths, namely, strongyles (57.1 %, 95 % CI), Metastrongylus spp. (7.6 %, 95 % CI), Ascaris suum (5.9 %, 95 % CI), Strongyloides ransomi (4.2 %, 95 % CI), and Trichuris suis (3.4 %, 95 % CI). Coccidia oocysts were found in 40.7 % of all pigs sampled (37.5-44.0 %, 95 % CI). Significant differences across the three districts were observed for the presence of A. suum (p < 0.001), Metastrongylus spp. (p = 0.001), S. ransomi (p = 0.002), and coccidia oocysts (p = 0.05). All animals tested negative for Fasciola spp. and Balantidium coli. Thirty-five variables were included in univariable analyses with helminth infection as the outcome of interest. A causal model was generated to identify relationships among the potential predictors, and consequently, seven variables with p ≤ 0.15 were included in a multivariable analysis for helminth infection. The final regression models showed that routine management factors had a greater impact on the prevalence of infection than regular, preventive medical treatment or the level of confinement. Factors that negatively correlated with gastrointestinal infection were the routine removal of manure and litter from pig pens (p ≤ 0.05, odds ratio [OR] = 0.667) and the routine use of disinfectants (p ≤ 0.05, OR = 0.548).

Evaluation of environmental fecal culture for Mycobacterium avium subspecies paratuberculosis detection in dairy herds and association with apparent within-herd prevalence.

This study evaluated test characteristics of environmental culture (EC) for the detection of Mycobacterium avium subspecies paratuberculosis (MAP) in 32 herds over a 2-year period. Individual fecal samples were collected every 6 mo and environmental samples every 3 mo. Individual fecal culture was performed on samples from positive pools. Samples were cultured in broth, with confirmatory polymerase chain reaction performed on positive fecal samples. Repeated measures were accounted for using GEE logistic models. Relative to a MAP herd-status based on all pooled fecal culture results collected during the study, sensitivity of a set of 6 EC-samples collected from prescribed locations within the herd environment (EC-6) was 71% [95% confidence interval (CI): 49% to 86%] and specificity was 99% (95% CI: 95% to 100%). Sensitivity of EC increased as apparent within-herd fecal culture prevalence (aWHP) increased. The estimated aWHP increased as the proportion of positive EC-samples within an EC-6 set increased. Environmental culture is an acceptable tool for herd diagnosis of MAP in low-prevalence herds.

Évaluation de la culture fécale environnementale pour la détection deMycobacterium aviumsous-espèceparatuberculosisdans les troupeaux laitiers et l'association avec la prévalence apparente dans les troupeaux. Cette étude a évalué les caractéristiques des tests de cultures environnementales (CE) pour la détection de Mycobacterium avium sous-espèce paratuberculosis (MAP) dans 32 troupeaux pendant une période de deux ans. Des échantillons fécaux individuels ont été prélevés tous les 6 mois et des échantillons environnementaux tous les 3 mois. La culture fécale individuelle a été réalisée sur des échantillons provenant des échantillons regroupés positifs. Les échantillons ont été cultivés dans du bouillon et l'amplification en chaîne par la polymérase de confirmation a été réalisée sur des échantillons fécaux positifs. Des mesures répétées ont été enregistrées à l'aide de modèles logistiques d'équations généralisées d'estimation. En rapport avec un statut de troupeau pour MAP fondé sur tous les résultats des cultures fécales regroupées prélevées durant l'étude, la sensibilité d'un groupe de 6 échantillons-CE prélevés dans les lieux prescrits au sein de l'environnement du troupeau (CE-6) était de 71 % [intervalle de confiance (IC) de 95 %: de 49 % à 86 %] et la spécificité était de 99 % (IC de 95 %: de 95 % à 100 %). La sensibilité de CE a augmenté au fur et à mesure que la prévalence apparente de la culture fécale dans le troupeau (PaCF) montait. La PaCF estimée augmentait tandis que la proportion d'échantillons CE positifs dans le groupe CE-6 montait. La culture environnementale est un outil acceptable pour le diagnostic de MAP chez le troupeau pour les troupeaux avec une faible prévalence.(Traduit par Isabelle Vallières).

Effectiveness of emamectin benzoate for treatment of Lepeophtheirus salmonis on farmed Atlantic salmon Salmo salar in the Bay of Fundy, Canada.

Emamectin benzoate (an avermectin chemotherapeutant administered to fish as an in-feed treatment) has been used to treat infestations of sea lice Lepeophtheirus salmonis on farmed Atlantic salmon Salmo salar in the Bay of Fundy, New Brunswick, Canada, since 1999. This retrospective study examined the effectiveness of 114 emamectin benzoate treatment episodes from 2004 to 2008 across 54 farms. Study objectives were to establish whether changes in the effectiveness of emamectin benzoate were present for this period, examine factors associated with treatment outcome, and determine variables that influenced differences in L. salmonis abundance after treatment. The analysis was carried out in 2 parts: first, trends in treatment effectiveness and L. salmonis abundance were explored, and second, statistical modelling (linear and logistic regression) was used to examine the effects of multiple variables on post-treatment abundance and treatment outcome. Post-treatment sea lice abundance increased in the later years examined. Mean abundance differed between locations in the Bay of Fundy, and higher numbers were found at farms closer to the mainland and lower levels were found in the areas around Grand Manan Island. Treatment effectiveness varied by geographical region and decreased over time. There was an increased risk for unsuccessful treatments in 2008, and treatments applied during autumn months were more likely to be ineffective than those applied during summer months.

Bulk tank milk selenium and its association with milk production parameters in Canadian dairy herds.

An observational study was conducted in 63 Canadian dairy farms to evaluate the association of bulk tank milk selenium (Se) concentration (BTSe) with average daily milk yield, milk fat and milk protein, bulk tank somatic cell count (BTSCC), and the probability of being a Staphylococcus aureus-positive herd. Bulk tank milk samples collected between March 2007 and February 2008 were evaluated for BTSCC, S. aureus culture status, and BTSe. Mean BTSe was 0.51 ± 0.15 µmol/L; no herds were classified as deficient or marginal based on BTSe. Bulk tank milk Se was unconditionally associated with milk production; however, adjusting by region indicated a confounding effect of this variable. There was no relationship between BTSe and BTSCC. Higher values of BTSe were associated with lower risk of being a S. aureus-positive herd, possibly as a result of a more robust udder immune response, or as a result of providing Se at a higher rate as one component of an udder health program that reduces risk of being S. aureus positive.

Design and analysis of a structured questionnaire to assess the probability of elimination of Rhipicephalus microplus from farms in a subtropical area.

In areas in which R. microplus may be eliminated from farms, it is essential to evaluate the infestation situation and the biosecurity measures available when deciding whether or not to undertake an elimination effort. Multiple questionnaires have been developed to evaluate the cattle tick situation on farms, however, the validity of those questionnaires has not been evaluated. This study aimed to develop a standardized and validated questionnaire to estimate the likelihood of cattle tick elimination from farms. A list of items (topics) to be covered was sent to 25 experts for their evaluation, with 11 responding. Based on the selected items, thirty-five closed questions were developed and evaluated through a cognitive interview process with 8 veterinarians and 5 farmers. Subsequently, a focus group evaluation was carried out with 30 farmers and a pretest of the revised questionnaire was performed with 94 farmers. A test, re-test evaluation was carried out in a subset of the pretest respondents after two-weeks. The questionnaire took approximately 10 min to complete. The ability of the questionnaire to reliably produce a score reflecting the expected probability of a farm eliminating ticks was evaluated through the use of a two-parameter logistic item-response theory model. A subset of questions related to a unidimensional latent variable were identified. This set of items appeared to have good ability to predict which farms were more likely to achieve the elimination, although the evaluation of that predictive ability was beyond the scope of this work.

Strengthening causal inference from randomised controlled trials of complex interventions.

Researchers conducting randomised controlled trials (RCTs) of complex interventions face design and analytical challenges that are not fully addressed in existing guidelines. Further guidance is needed to help ensure that these trials of complex interventions are conducted to the highest scientific standards while maximising the evidence that can be extracted from each trial. The key challenge is how to manage the multiplicity of outcomes required for the trial while minimising false positive and false negative findings. To address this challenge, we formulate three principles to conduct RCTs: (1) outcomes chosen should be driven by the intent and programme theory of the intervention and should thus be linked to testable hypotheses; (2) outcomes should be adequately powered and (3) researchers must be explicit and fully transparent about all outcomes and hypotheses before the trial is started and when the results are reported. Multiplicity in trials of complex interventions should be managed through careful planning and interpretation rather than through post hoc analytical adjustment. For trials of complex interventions, the distinction between primary and secondary outcomes as defined in current guidelines does not adequately protect against false positive and negative findings. Primary outcomes should be defined as outcomes that are relevant based on the intervention intent and programme theory, declared (ie, registered), and adequately powered. The possibility of confirmatory causal inference is limited to these outcomes. All other outcomes (either undeclared and/or inadequately powered) are secondary and inference relative to these outcomes will be exploratory.

Longitudinal Study of Selected Bacterial Zoonoses in Small Ruminants in Tana River County, Kenya.

Brucellosis, Q fever, and leptospirosis are priority zoonoses worldwide, yet their epidemiology is understudied, and studies investigating multiple pathogens are scarce. Therefore, we selected 316 small ruminants in irrigated, pastoral, and riverine settings in Tana River County and conducted repeated sampling for animals that were initially seronegative between September 2014 and June 2015. We carried out serological and polymerase chain reaction tests and determined risk factors for exposure. The survey-weighted serological incidence rates were 1.8 (95% confidence intervals [CI]: 1.3-2.5) and 1.3 (95% CI: 0.7-2.3) cases per 100 animal-months at risk for Leptospira spp. and C. burnetii, respectively. We observed no seroconversions for Brucella spp. Animals from the irrigated setting had 6.83 (95% CI: 2.58-18.06, p-value = 0.01) higher odds of seropositivity to C. burnetii than those from riverine settings. Considerable co-exposure of animals to more than one zoonosis was also observed, with animals exposed to one zoonosis generally having 2.5 times higher odds of exposure to a second zoonosis. The higher incidence of C. burnetii and Leptospira spp. infections, which are understudied zoonoses in Kenya compared to Brucella spp., demonstrate the need for systematic prioritization of animal diseases to enable the appropriate allocation of resources.

A systematic review and meta-analysis of the aetiological agents of non-malarial febrile illnesses in Africa.

BACKGROUND: The awareness of non-malarial febrile illnesses (NMFIs) has been on the rise over the last decades. Therefore, we undertook a systematic literature review and meta-analysis of causative agents of non-malarial fevers on the African continent. METHODOLOGY: We searched for literature in African Journals Online, EMBASE, PubMed, Scopus, and Web of Science databases to identify aetiologic agents that had been reported and to determine summary estimates of the proportional morbidity rates (PMr) associated with these pathogens among fever patients. FINDINGS: A total of 133 studies comprising 391,835 patients from 25 of the 54 African countries were eligible. A wide array of aetiologic agents were described with considerable regional differences among the leading agents. Overall, bacterial pathogens tested from blood samples accounted for the largest proportion. The summary estimates from the meta-analysis were low for most of the agents. This may have resulted from a true low prevalence of the agents, the failure to test for many agents or the low sensitivity of the diagnostic methods applied. Our meta-regression analysis of study and population variables showed that diagnostic methods determined the PMr estimates of typhoidal Salmonella and Dengue virus. An increase in the PMr of Klebsiella spp. infections was observed over time. Furthermore, the status of patients as either inpatient or outpatient predicted the PMr of Haemophilus spp. infections. CONCLUSION: The small number of epidemiological studies and the variety of NMFI agents on the African continent emphasizes the need for harmonized studies with larger sample sizes. In particular, diagnostic procedures for NMFIs should be standardized to facilitate comparability of study results and to improve future meta-analyses. Reliable NMFI burden estimates will inform regional public health strategies.

The use of item response theory models to evaluate scales designed to measure knowledge of, and attitudes toward, antibiotic use and resistance in Swedish dairy producers.

Scales are frequently used to quantify latent traits that can not be measured directly (eg knowledge of a subject, attitude toward an issue, severity of a clinical condition). Historically, little attention has been paid within veterinary medical sciences to evaluating how well these scales perform. In this study methods that can be used in this evaluation were reviewed and applied to scales quantifying two unmeasurable traits: knowledge of, and attitudes toward, antibiotic use and resistance in Swedish dairy farms. Items (questionnaire questions) that did not fit well with the assumed unmeasurable trait were identified and removed. Item response theory models were applied to the remaining items to determine how well they contributed to the scale using item characteristic curves and a variety of information functions. A graphical evaluation of the fit of the models to the data was then carried out. For the knowledge scale, the evaluation identified a number of items which did not fit well with the scale. It subsequently demonstrated that the scale did a good job of discriminating among producers with below average knowledge, but had very little ability to separate average producers from those with a high level of knowledge. Similarly, the attitude scale did well at discriminating among producers with an average or poor attitude toward reducing their own antibiotic use, but had little ability to distinguish among those with above average attitudes. Item response theory models are valuable for determining how well items contribute to predicting an individual's value of the latent variable and whether or not there are "gaps" in the scale which are not measured well. Guidelines for the use of these methods in the development or refinement of scales are presented. Their post-hoc use to verify the performance of scales in preparation for subsequent analyses is also discussed.

Seroprevalence and Risk Factors of Brucella Infection in Dairy Animals in Urban and Rural Areas of Bihar and Assam, India.

This study assessed seropositivity of Brucella infection in dairy animals and risk factors associated with it. The cross-sectional study used multi-stage, random sampling in the states of Bihar and Assam in India. In total, 740 dairy animals belonging to 534 households of 52 villages were covered under this study. Serological testing was conducted by indirect enzyme-linked immunosorbent assay (iELISA). Animal-level Brucella seropositivity was found to be 15.9% in Assam and 0.3% in Bihar. Seropositivity in urban areas (18.7%) of Assam was found to be higher than in rural areas (12.4%). Bihar was excluded from the risk factor analysis, as only one Brucella seropositive sample was detected in the state. A total of 30 variables were studied for assessing risk factors, of which 15 were selected for multivariable regression analyses following a systematic process. Finally, only three risk factors were identified as statistically significant. It was found that animals belonging to districts having smaller-sized herds were less likely (p < 0.001) to be Brucella seropositive than animals belonging to districts having larger-sized herds. Furthermore, the chance of being Brucella seropositive increased (p = 0.007) with the increase in age of dairy animals, but decreased (p = 0.072) with the adoption of artificial insemination (AI) for breeding. We speculated that the identified risk factors in Assam likely explained the reason behind lower Brucella seropositivity in Bihar, and therefore any future brucellosis control program should focus on addressing these risk factors.

Who let the dogs out? Exploring the spatial ecology of free-roaming domestic dogs in western Kenya.

The spatial ecology of free-roaming dogs determines their role in the transmission of zoonoses. This study describes the geographic range of and identifies sites frequently visited by free-roaming domestic dogs in western Kenya. Eight sites in Busia county, western Kenya, were selected. At each site, ten dog-keeping households were recruited, a questionnaire was administered, and a GPS logger was fixed around the neck of one dog in each household. Loggers were programmed to capture the dog's position every minute, for five consecutive days. Individual summaries of GPS recordings were produced, and the daily distance traveled was calculated. 50% and 95% utilization distribution isopleths were produced, and the area within these isopleths was extracted to estimate the size of the core and extended Home Ranges (HRs), respectively. Linear regression analyses were performed to identify factors associated with the movement parameters. The centroid points of the 10, 50, and 90% isopleths were reproduced, and the corresponding sites identified on the ground. Seventy-three dogs were included in the final analyses. The median daily distance traveled was 13.5km, while the median core and extended HRs were 0.4 and 9.3 ha, respectively. Older dogs had a larger extended HR and traveled more daily, while the effect of sex on dog movement depended on their neutering status. Dogs spent most of their time at their household; other frequently visited sites included other household compounds, fields, and rubbish dumps. One of the centroids corresponded to a field located across the international Kenya-Uganda border, emphasizing the fluidity across the border in this ecosystem. Multiple dogs visited the same location, highlighting the heterogeneous contact networks between dogs, and between dogs and people. The field data presented are of value both in understanding domestic dog ecology and resource utilization, and in contextualizing infectious and parasitic disease transmission models.

Impact of participatory training of smallholder pig farmers on knowledge, attitudes and practices regarding biosecurity for the control of African swine fever in Uganda.

We evaluated the impact of a participatory training of pig farmers on knowledge, attitude and practices (KAP) of biosecurity relating to ASF control in two districts of Uganda using a randomized control trial (RCT). A total of 830 pig farmers from 32 villages were included in the study, with 425 farmers receiving training, while 405 did not. An item response theory model was used to assess the impact of the training on farmer's KAP. Logistic regression models were used to assess the factors that affected knowledge gain and change in attitude and practices after training. Focus group discussions (FGD) were carried out with selected farmers from the treatment group at the end of the intervention, to share their experiences and discuss potential factors that could hinder adoption of biosecurity in their communities. Results of the regression analyses showed that there was a significant effect of biosecurity training (p = .038) on gain in knowledge after 12 months, but there were limited changes in farmer's attitude and practice at 12 and 28 months after training. Pig production domain (peri-urban/urban production), group membership, gender (male) and education of the farmer positively influenced knowledge gain and attitude of farmers towards biosecurity. This paper provides empirical evidence on the impact of training intervention on biosecurity practices for disease prevention or control. In addition, it breaks down the components of the biosecurity practices and documents the specific challenges to its uptake by the farmers. It therefore relaxes the assumption of knowledge constraint as a barrier to uptake. The results clearly show that knowledge is not the binding constraint to uptake of the biosecurity interventions.

Antimicrobial Use in Extensive Smallholder Livestock Farming Systems in Ethiopia: Knowledge, Attitudes, and Practices of Livestock Keepers.

Antimicrobial resistance (AMR) is a major public health threat, and inappropriate antimicrobial use (AMU) in food animal production can contribute to the global burden of AMR in humans. This study was conducted to understand knowledge, attitude, and practice (KAP) of smallholder livestock owners regarding antimicrobial use, residue, and resistance in three agro-ecological zones and production systems in Ethiopia. A cross-sectional study based on structured interviews was conducted. Twenty-one items were used to assess farmers' KAP. Item response theory (IRT) model and Cronbach's alpha were used to assess the KAP measurement scales. Inferential analyses were used to compare the differences in the practices in terms of the farm and socio-economic characteristics. There was a difference in the type of antimicrobials reported use between agro-ecological zones and production systems. Pastoralists most commonly used antibiotics (86.7%) followed by anthelminthics (70.8%). Overall, tetracyclines (36.4%), aminoglycosides (31.3%), and trimethoprim-sulfonamides (6.2%) were the most frequently used classes of antibiotics across the study sites. Human preparation antibiotics (tetracyclines) were also being used for veterinary purposes by 18.5% of pastoralist households. About 81.6% of livestock owners surveyed reported to have access to veterinary drugs although access varied between agro-ecological zones and production system. About 72.3% of pastoralists administered antibiotics by not following through the full treatment course. Moreover, 70% of respondents were not aware of the recommended withdrawal periods of milk and meat after antibiotic treatment. It was noticed that around 80 and 70% of respondents had a tendency to give doses higher or lower than recommended of antimicrobials, respectively. The study confirms the need for interventions to increase knowledge among smallholder farmers to improve the way antimicrobials in general and antibiotics in particular are used in these settings. In addition, professional involvement, supervision, and guidance can also lead to more efficient antimicrobial use by smallholder livestock owners. The study also highlights the need for research into the development of usable tools that measure antibiotic knowledge and attitudes.

Risk Factors for Brucella Seroprevalence in Peri-Urban Dairy Farms in Five Indian Cities.

Brucellosis is endemic among dairy animals in India, contributing to production losses and posing a health risk to people, especially farmers and others in close contact with dairy animals or their products. Growing urban populations demand increased milk supplies, resulting in intensifying dairy production at the peri-urban fringe. Peri-urban dairying is under-studied but has implications for disease transmission, both positive and negative. In this cross-sectional study, five Indian cities were selected to represent different geographies and urbanization extent. Around each, we randomly selected 34 peri-urban villages, and in each village three smallholder dairy farms (defined as having a maximum of 10 dairy animals) were randomly selected. The farmers were interviewed, and milk samples were taken from up to three animals. These were tested using a commercial ELISA for antibodies against Brucella abortus, and factors associated with herd seroprevalence were identified. In all, 164 out of 1163 cows (14.1%, 95% CI 12.2-16.2%) were seropositive for Brucella. In total, 91 out of 510 farms (17.8%, 95% CI 14.6-21.4%) had at least one positive animal, and out of these, just seven farmers stated that they had vaccinated against brucellosis. In four cities, the farm-level seroprevalence ranged between 1.4-5.2%, while the fifth city had a seroprevalence of 72.5%. This city had larger, zero-grazing herds, used artificial insemination to a much higher degree, replaced their animals by purchasing from their neighbors, were less likely to contact a veterinarian in case of sick animals, and were also judged to be less clean. Within the high-prevalence city, farms were at higher risk of being infected if they had a young owner and if they were judged less clean. In the low-prevalence cities, no risk factors could be identified. In conclusion, this study has identified that a city can have a high burden of infected animals in the peri-urban areas, but that seroprevalence is strongly influenced by the husbandry system. Increased intensification can be associated with increased risk, and thus the practices associated with this, such as artificial insemination, are also associated with increased risk. These results may be important to identify high-risk areas for prioritizing interventions and for policy decisions influencing the structure and development of the dairy industry.

Quantitative epidemiology: progress and challenges.

This manuscript is derived from a presentation at the 2006 AVEPM--Schwabe Symposium which honoured the 2006 recipient of the Calvin Schwabe Award--Dr. S. Wayne Martin. Throughout his career, Dr. Martin was instrumental in furthering the development of quantitative epidemiology. This manuscript highlights some of the recent advances in quantitative methods used in veterinary epidemiology and identifies some of the challenges we still face in the use of these methods. Areas discussed are: methods for analyzing hierarchical data, Bayesian methods, survival analysis and integrating causal thinking and statistical analyses.

Using pseudogold standards and latent-class analysis in combination to evaluate the accuracy of three diagnostic tests.

We previously reported our use of latent-class models to estimate the sensitivity (Se) and specificity (Sp) for each of three tests used to monitor farmed salmon for infectious salmon anaemia virus (ISAv). Those tests were reverse-transcriptase polymerase chain reaction (RT-PCR), virus isolation (VI), and an indirect immunofluorescent-antibody test (IFAT). We used tissues from 403 salmon from four populations presumed to have different prevalence of ISAv. However, no formal evaluation of the assumptions of conditional independence and constant accuracy had been carried out. In our present study, we "adjusted" that and used two pseudogold standards (a composite reference standard and a study pseudogold), as indicative of the true health status of each fish. The assumption of constant accuracy across populations was evaluated using separate random-effects logistic-regression models for fish classified as D+ or D- (disease positive or negative, according to the pseudogold standards) with study population included in the model to determine if it affected the probability of a positive test result. Where there was evidence of variation in test accuracy across populations, the issue was further investigated using separate latent-class models with informative priors for each study population. Our results suggested that only one PCR test had an accuracy that varied across populations. The assumption of conditional independence among tests was first evaluated using log-linear models of D+ and D- fish with significant interaction between test results indicative of conditional dependence. Latent-class models which incorporated up to two pairs of between-test dependencies were also fit using Bayesian methods. The two approaches showed considerable evidence of dependence between IFAT and VI and some evidence of dependence between one PCR and IFAT. Results obtained from both maximum-likelihood models and from Bayesian analyses of models allowing for conditional dependence between two pairs of tests were consistent with those obtained with the pseudogold standards. The results suggest that pseudogold standards can help in choosing a correct dependence structure and should be used in combination with latent-class models.

Description of empirical movement data from Canadian swine herds with an application to a disease spread simulation model.

We report the methods and findings of a survey of Canadian swine producers summarizing farm-types at-risk of foreign animal disease (FAD) and the routine movement of animals, semen and workers among swine farms, as observed during a 42-day period. Of the 311 producers who returned completed questionnaires, 17% represented swine-herds with no swine or semen movement on or off the farm during the 42 days, 57% were sow herds or farrow-to-finish herds with limited movement onto the farm but movement off the farm, and 26% were swine-herds with movements on and off the farm. A substantial number of premises (>50% in some provinces) with swine also kept other animal species on the same premises. We applied the empirical movement data from the survey in a stochastic simulation model to estimate the number of herds infected and the basic regional distribution of infection that could be expected to occur if the FAD was not detected and routine movements were permitted to occur up to 42 days after infection with a FAD of a single randomly selected herd. Forty-five percent of the simulations did not involve spread beyond the index farm, whereas 34.8% involved spread among five or more farms after 42 days of routine movement.

Relationships among milk urea-nitrogen, dietary parameters, and fecal nitrogen in commercial dairy herds.

Our study objective was to determine the ability of milk urea-nitrogen concentrations ([MUN]) to predict fecal nitrogen concentrations ([Fecal N]) in commercial dairy herds. A total of 83 dairy herds were each visited 3 times within 48 h after a monthly herd milk test. For each farm visit, forages were sampled for nutrient analyses, which were entered into a computerized ration evaluator, and fecal samples were taken per rectum from each of 6 cows (2 early-, 2 mid-, and 2 late-lactation). Fecal samples were pooled, mixed, and analyzed for nitrogen content. Fecal nitrogen concentrations were compared with the routinely measured nutritional parameters from the ration evaluation, and the herd average [MUN] for the previous milk test date using mixed linear regression analyses. Total protein supplied in the ration was significantly positively associated with [Fecal N], but herd average [MUN] was not associated (P > 0.10) with [Fecal N].