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.

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.

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.

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.

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.

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.

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.

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.

Parasitic sea louse infestations on wild sea trout: separating the roles of fish farms and temperature.

BACKGROUND: The causal relation between parasitic sea lice on fish farms and sea lice on wild fish is a controversial subject. A specific scientific debate has been whether the statistical association between infestation pressure (IP) from fish farms and the number of parasites observed on wild sea trout emerges purely because of a confounding and direct effect of temperature (T). METHODS: We studied the associations between louse infestation on wild sea trout, fish farm activity and temperature in an area that practices coordinated fallowing in Nordhordland, Norway. The data were sampled between 2009 and 2016. We used negative binomial models and mediation analysis to determine to what degree the effect of T is mediated through the IP from fish farms. RESULTS: The number of attached lice on sea trout increased with the T when the IP from fish farms was high but not when the IP was low. In addition, nearly all of the effect of rising T was indirect and mediated through the IP. Attached lice remained low when neighbouring farms were in the first year of the production cycle but rose substantially during the second year. In contrast to attached lice, mobile lice were generally seen in higher numbers at lower water temperatures. Temperature had an indirect positive effect on mobile louse counts by increasing the IP which, in turn, raised the sea trout louse counts. Mobile louse counts rose steadily during the year when neighbouring farms were in the first year of the production cycle and stayed high throughout the second year. CONCLUSIONS: The estimates of the IP effect on louse counts along with the clear biennial pattern emerging due to the production cycle of fish farms clearly indicate that fish farms play an important role in the epidemiology of sea lice on wild sea trout. Furthermore, the mediation analysis demonstrates that a large proportion of the effect of T on louse counts is mediated through IP.

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.

Selection and Misclassification Biases in Longitudinal Studies.

Using imperfect tests may lead to biased estimates of disease frequency and measures of association. Many studies have looked into the effect of misclassification on statistical inferences. These evaluations were either within a cross-sectional study framework, assessing biased prevalence, or for cohort study designs, evaluating biased incidence rate or risk ratio estimates based on misclassification at one of the two time-points (initial assessment or follow-up). However, both observations at risk and incident cases can be wrongly identified in longitudinal studies, leading to selection and misclassification biases, respectively. The objective of this paper was to evaluate the relative impact of selection and misclassification biases resulting from misclassification, together, on measures of incidence and risk ratio. To investigate impact on measure of disease frequency, data sets from a hypothetical cohort study with two samples collected one month apart were simulated and analyzed based on specific test and disease characteristics, with no elimination of disease during the sampling interval or clustering of observations. Direction and magnitude of bias due to selection, misclassification, and total bias was assessed for diagnostic test sensitivity and specificity ranging from 0.7 to 1.0 and 0.8 to 1.0, respectively, and for specific disease contexts, i.e., disease prevalences of 5 and 20%, and disease incidences of 0.01, 0.05, and 0.1 cases/animal-month. A hypothetical exposure with known strength of association was also generated. A total of 1,000 cohort studies of 1,000 observations each were simulated for these six disease contexts where the same diagnostic test was used to identify observations at risk at beginning of the cohort and incident cases at its end. Our results indicated that the departure of the estimates of disease incidence and risk ratio from their true value were mainly a function of test specificity, and disease prevalence and incidence. The combination of the two biases, at baseline and follow-up, revealed the importance of a good to excellent specificity relative to sensitivity for the diagnostic test. Small divergence from perfect specificity extended quickly to disease incidence over-estimation as true prevalence increased and true incidence decreased. A highly sensitive test to exclude diseased subjects at baseline was of less importance to minimize bias than using a highly specific one at baseline. Near perfect diagnostic test attributes were even more important to obtain a measure of association close to the true risk ratio, according to specific disease characteristics, especially its prevalence. Low prevalent and high incident disease lead to minimal bias if disease is diagnosed with high sensitivity and close to perfect specificity at baseline and follow-up. For more prevalent diseases we observed large risk ratio biases towards the null value, even with near perfect diagnosis.

Farm characteristics and management routines related to cow longevity: a survey among Swedish dairy farmers.

BACKGROUND: Longevity is an important trait for increasing the profitability of dairy production. Long cow longevity is also essential to reduce the environmental impact of milk production, and to maintain positive consumer attitude. Genetic selection for increased longevity has been effective, but the phenotypic trend of longevity in Swedish dairy cows has not been improved. The objective of this study was to identify herd characteristics and management routines that are associated with the average cow longevity in a herd. To obtain this information, a questionnaire was developed and sent out to 661 Swedish dairy farmers. RESULTS: The response rate was 35%. Seventeen of the 62 characteristics investigated had either a univariable association with the outcome (days from birth to culling) at P < 0.15, or were identified as confounders in the causal diagram and were therefore considered as candidates for the multivariable analysis. Multiple imputation was used to fill in the missing data from the questionnaires, and this increased the number of usable observations in the multivariable modeling from 156 to 228. Only a few of the investigated herd characteristics and management routines were associated with average cow longevity. The results demonstrated that using herd health advisory services shortened the average longevity, while using breeding advisory services prolonged the average longevity in the herd. Furthermore, having a greater interest in animal breeding (i.e. genetic selection) decreased the longevity, and calling the veterinarian when discovering an unhealthy cow increased the average longevity. Higher age of the farmer was also associated with longer average herd longevity. CONCLUSIONS: The herd average cow longevity was only associated with some of the farm characteristics and management routines studied. The results demonstrate that the use of advisory services and farmers' attitudes could be targeted for increasing the herd longevity. Further, the results indicate that other e.g. qualitative factors influencing farmers' decisions play an important role.

Exploring milk shipment data for their potential for disease monitoring and for assessing resilience in dairy farms.

The use of routinely recorded data for research purposes and disease surveillance is an attractive proposition. However, this requires that the validity and reliability of the data be evaluated for the purpose for which they are to be used. This manuscript reports an evaluation of milk shipment data for evaluating their usefulness in disease monitoring and the resilience of organic and conventional dairy herds in Sweden. A large number of inconsistencies were observed in the data, necessitating substantial efforts to "clean" the data. Given that the selection of rules used in the cleaning process was subjective in nature, a sensitivity analysis was carried out to determine if different cleaning routines produced substantially different results. Despite the cleaning efforts we observed far more large residuals at the shipment level than expected. Thus, it was concluded that the data were too "noisy" to be used for identification of short term impacts on milk production. Resilience was evaluated by examining the residual variance in milk shipped per cow per day under the assumption that herds with high resilience would have lower residual variance. The effects on residual variance of organic status or whether or not the herd used an automatic milking system were evaluated in models in which the residual variance was stratified or not by these factors. We did not find consistent evidence to suggest that organic herds had higher resilience than conventional herds, but this could be partly due to using residual variance as the measure indicating resilience.

Diagnosing intramammary infection: Controlling misclassification bias in longitudinal udder health studies.

Using imperfect tests may lead to biased estimates of disease frequency and of associations between risk factors and disease. For instance in longitudinal udder health studies, both quarters at risk and incident intramammary infections (IMI) can be wrongly identified, resulting in selection and misclassification bias, respectively. Diagnostic accuracy can possibly be improved by using duplicate or triplicate samples for identifying quarters at risk and, subsequently, incident IMI. The objectives of this study were to evaluate the relative impact of selection and misclassification biases resulting from IMI misclassification on measures of disease frequency (incidence) and of association with hypothetical exposures. The effect of improving the sampling strategy by collecting duplicate or triplicate samples at first or second sampling was also assessed. Data sets from a hypothetical cohort study were simulated and analyzed based on a separate scenario for two common mastitis pathogens representing two distinct prevailing patterns. Staphylococcus aureus, a relatively uncommon pathogen with a low incidence, is identified with excellent sensitivity and almost perfect specificity. Coagulase negative staphylococci (CNS) are more prevalent, with a high incidence, and with milk bacteriological culture having fair Se but excellent Sp. The generated data sets for each scenario were emulating a longitudinal cohort study with two milk samples collected one month apart from each quarter of a random sample of 30 cows/herd, from 100 herds, with a herd-level exposure having a known strength of association. Incidence of IMI and measure of association with exposure (odds ratio; OR) were estimated using Markov Chain Monte Carlo (MCMC) for each data set and using different sampling strategies (single, duplicate, triplicate samples with series or parallel interpretation) for identifying quarters at risk and incident IMI. For S. aureus biases were small with an observed incidence of 0.29 versus a true incidence of 0.25IMI/100 quarter-month. In the CNS scenario, diagnostic errors in the two samples led to important selection (40IMI/100 quarter-month) and misclassification (23IMI/100 quarter-month) biases for estimation of IMI incidence, respectively. These biases were in opposite direction and therefore the incidence measure obtained using single sampling on both the first and second test (29IMI/100 quarter-month) was exactly the true value. In the S. aureus scenario the OR for association with exposure showed little bias (observed OR of 3.1 versus true OR of 3.2). The CNS scenario revealed the presence of a large misclassification bias moving the association towards the null value (OR of 1.7 versus true OR of 2.6). Little improvement could be brought using different sampling strategies aiming at improving Se and/or Sp on first and/or second sampling or using a two out of three interpretation for IMI definition. Increasing number of samples or tests can prevent bias in some situations but efforts can be spared by holding to a single sampling approach in others. When designing longitudinal studies, evaluating potential biases and best sampling strategy is as critical as the choice of test.

Infrared Thermography for the Ante Mortem Detection of Bruising in Horses Following Transport to a Slaughter Plant.

Undetected injury of horses sustained during road transport to slaughter is a welfare concern. This study evaluated digital infrared thermography (DT) for the detection of ante-mortem bruising in horses following transport to a slaughter plant. The sensitivity and specificity of DT for the detection of bruises following transport was evaluated. DT images were obtained from 93 horses (2-3 horses per load; 40 loads) at a Canadian federally approved slaughter plant. From an elevated platform 5 m from the horses, left and right lateral DT images, and one caudal pelvic area image were obtained from each horse. After slaughter the carcasses were examined for bruising (a visually discolored area on the carcass caused by damage to the blood vessels) and findings documented. Sensitivity, specificity, and predictive values were calculated for DT assessment of bruising. The prevalence of bruising on post mortem inspection was 54%. The DT approach to bruise detection at the region of interest level of 93 horses (n = 186 sides) resulted in a sensitivity of 42% and specificity of 79%. As the sensitivity was low, a more sensitive DT camera and allowing for a longer equilibration time for horses after transport may improve this approach to post transport assessment of subclinical injury.

Skeletal fluorosis in marsupials: A comparison of bone lesions in six species from an Australian industrial site.

In this study we explored the prevalence, type, location and severity of skeletal lesions in six species of Australian marsupial (Macropus giganteus, Notamacropus rufogriseus, Wallabia bicolor, Phascolarctos cinereus, Trichosurus vulpecula and Pseudocheirus peregrinus) from high and low-fluoride environments. Lesions occurred to varying extents in all species, and lesion distribution varied with biomechanical differences in gait and mastication. Bone fluoride levels increased with severity of periosteal hyperostosis. The mean bone fluoride concentration of individuals lacking hyperostosis (across all species, from both high and low-fluoride environments) was 1100±260µgF-/g dry bone, compared to 4300±1200µgF-/g and 6300±1200µgF-/g in those with mild and severe grade hyperostosis, respectively. Multivariable modelling showed that the probability of observing a lesion varied across species, anatomical location, age and bone fluoride concentration (in a non-linear manner). The pathological changes reported in the marsupials are consistent with the range of fluoride-related lesions described in other mammals, and biomechanical differences among the studied marsupial species offer some explanation for the degree of interspecific variability in prevalence, type, anatomical location, and severity of the lesions.

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).