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.

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.

Previous systematic reviews have highlighted the research priorities of causative agents for non-malarial febrile illnesses by counting the number of publications attributed to an agent. However, proportional morbidity rates are calculated by dividing the number of cases with a specific disease (numerator) by the total number of diagnosed fever cases (denominator) and are better indicators of the relative importance of aetiological agents in a population. Therefore, we present the leading causes of non-malarial febrile illnesses in African patients in both healthcare and community settings. Preference is given to HIV-negative patients when data could be found. We also determined summary estimates of Brucella spp., Chikungunya virus, Dengue virus, Haemophilus spp., Klebsiella spp., Leptospira spp., non-typhoidal Salmonella spp., typhoidal Salmonella spp., Staphylococcus spp., and Streptococcus spp.

The wide array of aetiological agents causing febrile illnesses on the African continent does not only complicate malaria control programs but may also hamper response to epidemic and pandemic illnesses such as Ebola and COVID-19. The harmonisation of diagnostics and study designs will reduce between-study differences, which may result in better estimates of disease burden on the continent and in the different African regions. This information is important for Pan-African surveillance and control efforts.

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.

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.

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.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-3189-6) contains supplementary material, which is available to authorized users.

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.

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.

Electronic supplementary material

The online version of this article (10.1186/s13028-018-0390-8) contains supplementary material, which is available to authorized users.

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.

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.

Comparison of fecal pooling strategies for detection of Mycobacterium avium ssp. paratuberculosis in cattle

In herds with typical moderate to low within-herd prevalence, testing for Mycobacterium avium ssp. paratuberculosis (MAP), the infectious agent of Johne's disease, will be more cost-effective if individual fecal samples are cultured in composite pools. However, sensitivity to classify a pool containing 1 or more positive individual samples as positive may depend on pool size and number of individual positive samples within a pool. Fecal samples collected from 994 dairy cows sampled at slaughter were cultured to detect MAP. Culturing was done both individually and as composite pooled samples using the TREK ESP Culture System II broth medium (Thermo Fisher Scientific, Trek Diagnostic Systems Inc., Cleveland, OH). Composite samples consisted of pools containing feces from 3, 5, 8, 10, or 15 cows. The number of individual fecal culture-positive cows within each pool ranged from 0 to 4. Culture of individual fecal samples detected MAP in 36 (3.6%) of the 994 cows. Individual samples that were detected within the first 50 d by TREK ESP Culture System II were more likely to lead to a positive pool result. In total, 840 pooled fecal samples were examined for presence of MAP, and of those, 272 pools actually contained feces from fecal culture-positive cows. The crude sensitivity (proportion of pools that contained at least 1 fecal-positive cow that tested positive) for pools of 3, 5, 8, 10, and 15 was 47, 67, 44, 59, and 39%, respectively. Across pools, an increase of the number of fecal culture-positive samples from 1 to 2 enhanced overall crude sensitivity from 44 to 71%. However, sensitivity did not further increase for pools with 3 or 4 fecal culture-positive samples (63 and 60%, respectively). Additionally, a simulation analysis assessing probability of pooled fecal samples being positive in herds of 50 and 100 cows was conducted. The simulation assumed that 1, 2, or 5 cows per herd were MAP fecal culture-positive and that pools of 5 and 10 were used. This low-prevalence herd simulation indicated that weighted mean herd probabilities of detecting a positive herd ranged between 52 and 99.3%, with the lowest probability for pools of 10 with 1 positive cow in the herd and the highest probability for pools of 5 with 5 positive cows in the herd. However, overall, pools of 5 and 10 had similar diagnostic capabilities, enabling cost savings by utilizing pools of 10.

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).

Brucellosis and Coxiella burnetii Infection in Householders and Their Animals in Secure Villages in Herat Province, Afghanistan: A Cross-Sectional Study

Background

Brucellosis and coxiellosis are known to be endemic in ruminant populations throughout Afghanistan, but information about their prevalence and factors that affect prevalence in householders and livestock under diverse husbandry systems and pastoral settings is sparse.

Methods/Principal Findings

We conducted a cross-sectional survey to investigate the seroprevalence of brucellosis and Coxiella burnetii in humans and livestock in six secure districts in Herat from 26^th December 2012–17^th January 2013. A total of 204 households with livestock were surveyed in six Kuchi and five sedentary type villages. Blood samples from 1,017 humans, 1,143 sheep, 876 goats and 344 cattle were tested for brucellosis and Q fever. About one in six households (15.7%) had at least one Brucella seropositive person, about one in eight households (12.3%) had at least one Brucella seropositive animal and about one in four (24.5%) had either seropositive animals or humans. Ninety-seven percent of households had at least one C. burnetii seropositive person and 98.5% of households had one or more C. burnetii seropositive animals. Forty- seven householders had serological evidence of exposure to both C. burnetii and Brucella and eight animals were serologically positive for both diseases. Drinking unpasteurised milk (OR 1.6), treating animals for ticks (OR 1.4), milking sheep (OR 1.4), male gender (OR 1.4) and seropositivity to Brucella (OR 4.3) were identified as risk factors for seropositivity to C. burnetii in householders. Household factors associated with households having either Brucella seropositive animals or humans were Kuchi households (OR 2.5), having ≤4 rooms in the house (OR 2.9) and not owning land (OR 2.9).

Conclusions

The results from this study provide baseline information for the planning and monitoring of future interventions against these diseases. The implementation of this study greatly improved collaboration, coordination and capability of veterinary and public health professionals from government, NGOs and donor funded projects.

Our study alerted authorities to a hitherto unrecognised high prevalence of C. burnetii infections, acted as a catalyst for the introduction of a national vaccination programme for protection of sheep and goats from brucellosis using Rev1 vaccine, demonstrated the benefits of a coordinated approach and fostered a better understanding of the nature of infection in different hosts and of the constraints for control faced by government services. A notable feature of the study was the enthusiasm and interest displayed by all of the participants throughout, from heads of government services to field personnel and villagers. Livestock owners regard zoonoses as adversities that affect their livestock and members of their households and do not partition them separately as medical or veterinary problems. Control programs need to take that perception into account and wherever possible avoid vesting ownership separately into veterinary or public health agencies.

Applying a kinetic method to an indirect ELISA measuring Ostertagia ostertagi antibodies in milk

Indirect enzyme-linked immunosorbent assays (ELISAs) are frequently run as endpoint ELISAs (e-ELISAs). However, kinetic ELISAs (k-ELISAs) have certain advantages over e-ELISAs. The objective of this study was to understand the relationship between e-ELISA and k-ELISA results. Specifically, to determine whether it was possible to run both k-ELISA and e-ELISA on the same plate and establish an appropriate time interval for k-ELISA measurements. A normalization method for k-ELISA slopes (slope ratio) is proposed. Using an indirect e-ELISA test measuring antibodies against Ostertagia ostertagi in milk from dairy cattle, we found that running a k-ELISA had no effect on optical density ratio results of an e-ELISA on the same plate, and that agreement was very strong at 10, 15, and 28 min, allowing for a reduction in the total processing time for ELISA tests.

Survival analysis of clinical mastitis data using a nested frailty Cox model fit as a mixed-effects Poisson model

Mastitis is a complex disease affecting dairy cows and is considered to be the most costly disease of dairy herds. The hazard of mastitis is a function of many factors, both managerial and environmental, making its control a difficult issue to milk producers. Observational studies of clinical mastitis (CM) often generate datasets with a number of characteristics which influence the analysis of those data: the outcome of interest may be the time to occurrence of a case of mastitis, predictors may change over time (time-dependent predictors), the effects of factors may change over time (time-dependent effects), there are usually multiple hierarchical levels, and datasets may be very large. Analysis of such data often requires expansion of the data into the counting-process format - leading to larger datasets - thus complicating the analysis and requiring excessive computing time. In this study, a nested frailty Cox model with time-dependent predictors and effects was applied to Canadian Bovine Mastitis Research Network data in which 10,831 lactations of 8035 cows from 69 herds were followed through lactation until the first occurrence of CM. The model was fit to the data as a Poisson model with nested normally distributed random effects at the cow and herd levels. Risk factors associated with the hazard of CM during the lactation were identified, such as parity, calving season, herd somatic cell score, pasture access, fore-stripping, and proportion of treated cases of CM in a herd. The analysis showed that most of the predictors had a strong effect early in lactation and also demonstrated substantial variation in the baseline hazard among cows and between herds. A small simulation study for a setting similar to the real data was conducted to evaluate the Poisson maximum likelihood estimation approach with both Gaussian quadrature method and Laplace approximation. Further, the performance of the two methods was compared with the performance of a widely used estimation approach for frailty Cox models based on the penalized partial likelihood. The simulation study showed good performance for the Poisson maximum likelihood approach with Gaussian quadrature and biased variance component estimates for both the Poisson maximum likelihood with Laplace approximation and penalized partial likelihood approaches.

Association of coagulase-negative staphylococcal species, mammary quarter milk somatic cell count, and persistence of intramammary infection in dairy cattle

This study was conducted to evaluate the association between subclinical intramammary infection (IMI) with coagulase-negative staphylococci (CNS), mammary quarter milk somatic cell count (SCC), and persistence of IMI in dairy cattle. Convenience samples of CNS isolates harvested from milk samples of subclinically infected mammary quarters collected between 4 and 2wk before drying-off, between 2wk before drying-off and the day of drying-off, within 24h after calving, between 1 and 2wk after calving, and during lactation were evaluated. Isolates were obtained from the Canadian Bovine Mastitis Research Network culture bank and were identified to the species level using rpoB gene sequencing. Cow and quarter-level data were obtained from the Canadian Bovine Mastitis Research Network database and used for statistical analyses. In addition, for mammary quarters that had more than one isolation of the same CNS species at different time points, the isolates were evaluated using pulsed-field gel electrophoresis to identify persistent IMI. Milk SCC was compared between mammary quarters infected with different CNS species and to a cohort of uninfected mammary quarters. A total of 877 isolates from 643 mammary quarters of 555 cows on 89 Canadian dairy farms were identified to the species level. Twenty different species were identified, with Staphylococcus chromogenes being the most common species identified (48% of isolates), followed by Staphylococcus simulans (19%) and Staphylococcus xylosus (10%). Of the 20 species identified, only 9 species were found in persistently infected quarters. Milk SCC was significantly higher in the CNS-infected mammary quarters than in the uninfected control quarters for 8 of the 20 species studied. Also, mean SCC differed significantly between mammary quarters infected with different CNS species. Within a given species, a high degree of variability was noted in milk SCC. These data corroborate recent data from Europe with regard to the predominance of certain species of CNS (e.g., Staph. chromogenes). In addition, some species of CNS appear to have a greater effect on milk SCC. Finally, some CNS species are associated with persistent IMI suggesting that some species (e.g., Staph. chromogenes and Staph. simulans) are better host-adapted, whereas others may have an environmental reservoir.

Time-to-event analysis of predictors for recovery from Salmonella Dublin infection in Danish dairy herds between 2002 and 2012

Salmonella Dublin infections reduce gross margins and compromise animal health and welfare in dairy cattle herds. Despite on-going control efforts in several countries the duration and risk factors of a persistent infection have been difficult to study due to a lack of suitable data. This study utilised the unique opportunity to extract systematically collected repeated bulk-tank milk antibody measurements from all the Danish dairy herds during a 10-year period to perform a time-to-event analysis of the factors that affect the duration of test-positivity and the hazards of recovery from S. Dublin at herd level. Recovery was defined as a shift from test-positive to test-negative between two year-quarters followed by at least three more test-negative year-quarters. The average duration of infection was approximately 2 years. Predictors of recovery were tested in a multivariable Cox proportional hazard model allowing herds to recover from infection multiple times over the 10-year surveillance period. The model results were based on 36,429 observations with data on all the predictors, representing 3563 herds with a total of 3246 recoveries. Sixty-seven herds (2.4%) remained test-positive throughout the study period. The rest of the 317 herds that did not have any recoveries were censored, mainly due to a cessation of milk production. Prior recovery from test-positivity turned out not to be a significant predictor of recovery in the model. The effect of the duration of infection on the conditional probability of recovery (i.e. the hazard) was time-dependent: early in the study period, long durations of infection were predictive of a low hazard of recovery. Later in the control programme the effect of duration of infection was reduced indicating a desired effect of an intensified control programme. There was an increasing tendency towards longer durations and lower hazard of recovery with: (i) increasing herd sizes, (ii) increasing bulk-tank milk somatic cell counts, (iii) increasing local prevalence within a 5 km radius, (iv) organic farming and (v) recent purchase of cattle from test-positive herds. Participation in a voluntary paratuberculosis control programme reduced the duration of infection, and there were indications that recovery from S. Dublin infection was stimulated by a centrally organised and targeted control campaign. This is the first large-scale study that investigated duration of infection and predictors of recovery from S. Dublin in cattle herds over an extended period of time. The results provide useful knowledge for the design of control programmes for S. Dublin.

Survival analysis of factors affecting incidence risk of Salmonella Dublin in Danish dairy herds during a 7-year surveillance period

A national surveillance programme for Salmonella Dublin, based on regular bulk-tank milk antibody screening and movements of cattle, was initiated in Denmark in 2002. From 2002 to end of 2009 the prevalence of test-positive dairy herds was reduced from 26% to 10%. However, new infections and spread of S. Dublin between herds continued to occur. The objective of this study was to investigate factors affecting incidence risk of S. Dublin infection in Danish dairy herds between 2003 and 2009. Herds were considered at risk when they had been test-negative for at least four consecutive year-quarters (YQs), either at the start of the study period or after recovery from infection. Survival analysis was performed on a dataset including 6931 dairy herds with 118,969 YQs at risk, in which 1523 failures (new infection events) occurred. Predictors obtained from register data were tested in a multivariable, proportional hazard model allowing for recurrence within herds. During October to December the hazard of failures was higher (hazard ratio HR=3.4, P=0.0005) than the rest of the year. Accounting for the delay in bulk-tank milk antibody responses to S. Dublin infection, this indicates that introduction of bacteria was most frequent between July and October. Purchase from test-positive cattle herds within the previous 6 months was associated with higher hazard of failures (HR=2.5, P<0.0001) compared to no purchase and purchase from test-negative herds. Increasing local prevalence, herd size and bulk-tank milk somatic cell counts were also associated with increasing hazard of failures. The effect of prior infection was time-dependent; the hazard of failures was reduced following a logarithmic decline with increasing time at risk. The hazard was markedly higher in herds with prior infections the first year after becoming at risk again, and then approached the hazard in herds without known prior infections 2-3 years after becoming test-negative. This showed that herds with prior infections need to maintain a high level of biosecurity for at least 3 years after becoming test-negative for S. Dublin to prevent recurrence. Furthermore, general recommendations for dairy herds wishing to protect their herds against S. Dublin include avoidance of purchase from and contact to test-positive herds. Large herds, herds with test-positive neighbours and herds with high somatic cell counts need to obtain and maintain a high level of biosecurity.

Culling decisions of dairy farmers during a 3-year Salmonella control study

Salmonella enterica subsp. enterica-serotypes lead to periodically increased morbidity and mortality in cattle herds. The bacteria can also lead to serious infections in humans. Consequently, Denmark has started a surveillance and control programme in 2002. The programme focuses on Salmonella Dublin which is the most prevalent and most persistent serotype in the Danish cattle population. A field study in 10 dairy herds with persistent Salmonella infections was carried out over three years to gain experience with control procedures including risk assessment, targeted control actions and test-and-cull procedures. From autumn 2003 until end of 2006 quarterly milk quality control samples from all lactating cows and biannual blood samples from all young stock above the age of three months were tested using an indirect antibody ELISA. The most recent and previous test results were used to categorise all animals into risk groups. These risk groups and all individual ELISA-results were communicated to the farmers as colour-coded lists four to six times per year. Farmers were advised to manage the risk of Salmonella transmission from cattle with repeatedly high ELISA results (flagged as "red") or cows with at least one recent moderately high ELISA result (flagged as "yellow") on the lists. Risk management included, e.g. culling or separation of the cows at calving. We analysed culling decisions using two models. For heifers a hierarchical multivariable logistic model with herd as random effect evaluated if animals with red and yellow flags had higher probability of being slaughtered or sold before first calving than animals without any risk flags. For adult cows a semi-parametric proportional hazard survival model was used to test the effect of number of red and yellow flags on hazards of culling at different time points and interactions with prevalence in the herd while accounting for parity, stage of lactation, milk yield, somatic cell count and the hierarchical structure of the data with animals clustered at herd level. This study illustrates how investigation of culling decisions made by herd managers when they have access to test-status of individual animals and overall apparent prevalence during control of an infection can lead to useful new knowledge. Overall herd managers were more likely to cull cattle with increasing number of yellow and red flags than animals with no flags. However, cattle were more likely to be culled with yellow and red flags during times with low or medium high within-herd seroprevalence than at times with high seroprevalence. These results are valuable knowledge for modelling and planning of control strategies and for making recommendations to farmers about control options.

The impact of milk handling procedures on Ostertagia ostertagi antibody ELISA test results

The impact of various milk handling stressors were analyzed using a commercially available enzyme-linked immunosorbent assay (ELISA) test measuring Ostertagia ostertagi antibodies in milk from dairy cattle (Svanovir). An indirect ELISA has the ability to determine the amount of milk production losses related to intestinal parasitism. The ELISA test recommends fresh defatted milk, however, milk collected from Dairy Herd Improvement (DHI) programs in North America undergo many stressors, including, heating, freezing and are not defatted. Normalized optical density ratios (ODRs) were compared between fresh defatted milk and milk subjected to one or more stressors with a linear mixed model accounting for differences in variation between the fresh and the frozen samples. Concordance correlation coefficients were also analyzed for comparisons to other similar studies. After accounting for random cow and container effects, the treatment factors interacted with each other (p<0.001). Biologically interesting contrasts were created to explain the interaction. The estimated difference in ODR between the milk samples handled according to recommendations of the manufacturers of Svanovir and the whole milk samples that were subjected to the most extreme treatment (heated, frozen, thawed, and re-frozen for 4 weeks) was 0.062 (p<0.001). This difference represented less than 5% of the range, and was thus considered biologically negligible. Frozen whole milk processed by DHI programs, the most likely method of collecting on-farm samples in North America, will likely yield reliable results for the indirect ELISA tests, particularly, Svanovir.

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.

Precalving factors affecting conception risk in Holstein dairy cows in tropical conditions

The objective of this study was to identify precalving nutritional risk factors that may affect variation in first service conception risk in 21 commercial Holstein dairy herds in a tropical environment (Reunion Island). The data set included 473 lactation records in 404 cows. A multivariate logistic-regression model including herd as a random effect was used to analyse the relationship between first service conception risk and energy status (body condition score, plasma glucose, insulin, cholesterol, non-esterified fatty acids and beta-hydroxybutyrate), nitrogen status (urea), hepatic function (gamma-glutamyltransferase, glutamate deshydrogenase, albumin), and mineral deficiencies (calcium, phosphorus, magnesium), adjusting systematically for factors such as breeding, season, parity, previous milk yield and fertility, calving to first service interval and type of oestrus (spontaneous versus induced). The overall mean conception risk was 0.27+/-0.02 (mean+/-S.E.M., n=473). First service conception risk was penalized by calving to 1st service interval shorter than 60 days, synchronized oestrus, previous 305-day milk yield >8000 kg (p<0.05), low blood glucose concentration in high-yielding cows (p<0.05) and combined high urea and beta-hydroxybutyrate concentrations (p<0.01). Precalving energy imbalance, revealed by low prepartum glucose concentration, was a strong nutritional predictor of low first service conception risk in high-yielding cows. Some precalving nutritional disorders potentially associated with consumption of spoiled silage which induces elevated circulating urea and beta-hydroxybutyrate have a delayed detrimental effect on conception, even if the true causes of this effect remain to be elucidated. As a conclusion, our findings should lead the breeders to pay more attention to the feeding of dry cows that is usually neglected in Reunion Island dairy farms.

Evaluation of underlying risk as a source of heterogeneity in meta-analyses: a simulation study of Bayesian and frequentist implementations of three models

Evaluation of important causes of heterogeneity among study results is an important component of any meta-analysis. For factors which can be measured (e.g. population characteristics, indicators of study quality), standard methods such as meta-regression can be used for this evaluation. The underlying risk (i.e. risk of outcome in the control population) can be viewed as a summary of the effects of unmeasured population characteristics so it is a logical candidate for evaluation as a source of heterogeneity. Unfortunately, because of its relationship with the study outcome (odds ratio or relative risk), standard methods should not be used for evaluating underlying risk as a cause of heterogeneity. Three models with different sets of underlying assumptions were evaluated in a simulation study to determine how well they performed in assessing the role of underlying risk as a source of heterogeneity. All models were fit using both Bayesian and frequentist (maximum likelihood random slopes models) estimation procedures and the results compared. Two of the models produced good results (i.e. minimal evidence of bias in parameter estimates), while the third clearly produced biased estimates of some parameters. In general, the Bayesian and frequentist approaches produced similar results. In situations in which the number of studies in a meta-analysis is small ( approximately 10), the maximum likelihood (frequentist) approach was preferable. While the bias induced by heterogeneity associated with underlying risk was generally not large, use of one of the approaches described in this paper will produce better estimates of treatment effect in situations where there is substantial heterogeneity between studies. A model based on the assumption that the number of positive events in each of the treatment and control groups are binomially distributed (Model 1) is the recommended approach.

Effect of eprinomectin pour-on treatment around calving on reproduction parameters in adult dairy cows with limited outdoor exposure

The objective of this study was to investigate if treatment of cows with eprinomectin around calving had any beneficial effects on the calving to first artificial insemination interval, calving to conception interval, and number of services per conception in totally- and semi-confined dairy herds. In totally-confined herds lactating- and dry-cows were housed throughout the summer and had no access to pasture. In semi-confined herds lactating- and dry-cows had limited outdoor exposure to a small pasture or paddock but were still fed a ration that met all their nutritional requirements. The study was carried out between February 2002 and February 2003 in 35 herds (2381 cows) located in Quebec, Ontario and Minnesota (USA) participating in a larger clinical trial. The herds kept electronic reproduction records. Cows were randomly allocated to receive eprinomectin or a placebo, with treatment being administered on or close to the day of calving. Monthly bulk tank milk samples from each farm were tested with an indirect ELISA using a crude Ostertagia ostertagi antigen and these data were averaged over the study year. The optical density ratio (ODR) values were then dichotomized into high and low using a cut-point of 0.50. Treatment effects were analyzed using Cox proportional hazards survival models with herd frailty effects for calving to conception and calving to first service intervals. Aalen's linear hazards model was used to investigate time-varying effects in the Cox models. A random effects poisson regression model was used to model the number of services per conception. Other predictor variables tested in the models were lactation number, calving season, study site, peak milk production, ODR and the lactating- and dry-cow housing variables. Overall, there was no significant effect of treatment on the three indices of reproductive performance. The effect of season of calving depended on how much time had passed since calving. Presumably this effect reflected a seasonal effect at the time of breeding. Hazard of conception in younger cows was higher than in older cows. Early bred cows tended to have a higher number of inseminations per conception than those bred late. The results of the study suggested that eprinomectin treatment at calving was not beneficial to reproduction.

Temporal and spatial analysis of the 1999 outbreak of acute clinical infectious bursal disease in broiler flocks in Denmark

The objective of this study was to describe the spatial and temporal dynamics of the 1999 outbreak of acute clinical infectious bursal disease (IBD) in broiler chicken farms in Denmark. The analysis was performed using data from all broiler farms located in the Jutland peninsula and the island of Funen (168 municipalities). The Moran's index I, K-functions and scan statistics were used to describe the dynamics of the epidemic. In addition, spatially correlated survival analyses were performed and the posterior frailties were mapped to identify areas with high or low survival times. From January to October 1999, a total of 43 farms (81 flocks) out of a total of 299 farms (2970 flocks) in 110 municipalities were infected with IBD. The outbreak developed more or less simultaneously in two regions, one in the north and the other in the center of the study area. The space-time descriptive methods suggested that the cases were more likely to occur during a short period of time and over relatively short distances, indicating that local factors facilitated the spread of the virus. For instance, the highest risk, as estimated by the K-function, was within 20 km and 20 days. The risk of transmission peaked in July and remained high until the end of the study. The spatially correlated survival analysis identified municipalities with low survival times that roughly corresponded to the clusters found using scan statistics. The analysis for the full hierarchical structure of the dataset identified variation (i.e. clustering) at the farm and municipality levels.

Evaluation of the stability of Ostertagia ostertagi ELISA microtitre plates over time using cow milk samples

The objective of this study was to assess the stability of ELISA plates prepared with one of three blocking agents and used with one of two conjugates at various time intervals after preparation of the plates. Two of the blocking agents used were commercially available: one termed stabilgaurd (stab) and one manufactured by SVANOVA Biotek AB Inc. (svan). The third blocking agent used was bovine serum albumin (bsa). A polyclonal rabbit anti-bovine IgG (poly) and an anti-bovine IgG monoclonal (mono) conjugate were used. Eighteen composite individual cow milk samples collected late in lactation (200-400 days in milk) were used in this study. An indirect microtitre plate ELISA that used the Ostertagia ostertagi antigen was used to quantify antibodies against the parasite, present in the milk samples. Each of six blocking agent/conjugate combinations (called systems) were used to test 18 milk sub-samples at 1, 4 and 24 weeks after blocking the plates. Plates blocked with stab and svan were kept at room temperature and an additional set were incubated at 37 degrees C so as to mimic long term storage (about 1 year) and tested only once at 4 weeks. Those blocked with bsa were frozen at -20 degrees C. Concordance correlation coefficients (CCC) and reproducibility were used to assess the agreement between test results conducted on the same milk sample at the various test-times using a particular system. Generally, there was good agreement between tests conducted at different times for all systems. However, the svan-mono and bsa-poly systems had the best agreement with overall CCC values of 96% and 93%, respectively. The svan-poly system had the lowest CCC of 75%. The CCC and reproducibility ranked the systems in a similar way. The high CCC between tests done using plates kept at room temperature and ones incubated at 37 degrees C, suggested that plates would be stable up to a year after blocking. The storage of plates blocked with svan and stab agents under room temperature, makes them more convenient to use and transport relative to bsa-blocked plates that have to be frozen.

Assessing the agreement between Ostertagia ostertagi ELISA tests performed using the crude adult antigen and the adult and larval stage 4 excretory/secretory antigens

The objective of this study was to determine the agreement between ELISA tests conducted using three O. ostertagia antigens: crude adult worm, larval stage 4 (L4) excretory/secretory (ES) and adult ES. This study was carried out on 289 Holstein cows from five herds in Prince Edward Island and one herd in Nova Scotia. Composite milk samples of these cows were collected (between May and September 2002) from the respective provincial laboratories and sent to the Atlantic Veterinary College where each sample was tested for antibodies to O. Ostertagi using an indirect microtitre ELISA test. Results were expressed as optical density ratio (ODR) values. Each milk sample was tested with three ELISA tests, with each test using a different O. ostertagi antigen. There was a slight rise in ODR values of both adult antigens, between May and August, with higher values obtained using the adult ES antigen. L4 ES ODR values were generally higher than those for both adult antigens during the study period, except for May. There was a more dramatic rise in L4 ES ODR values between May and August. Rises in ODR in May and end of July coincided with periods of mass maturation of L4 to adult worms. The results of the study showed that the concordance correlation coefficient (CCC) between tests performed using both ES and the crude antigens were low (crude adult versus adult ES=0.31, crude adult versus L4 ES=0.30). The highest CCC was observed between tests done using both ES antigens (CCC=0.56). Generally, the study results suggest that the antibody response (detectable by the ELISA) is mainly directed against ES antigens (especially L4) than the crude adult worm antigen.

The use of an indirect Ostertagia ostertagi ELISA to predict milk production response after anthelmintic treatment in confined and semi-confined dairy herds

An indirect Ostertagia ostertagi ELISA was used in late lactation milk samples from cows in confined and semi-confined dairy herds to determine if it could predict milk production response after endectocide treatment at calving. Holstein cows from 9 dairy farms from Prince Edward Island (PEI), 5 from central Nova Scotia and 16 from southern Ontario that were participating in a clinical trial of endectocide treatment around calving were used in this study. The cows were randomly treated with either eprinomectin pour-on endectocide or a placebo solution. Milk samples were obtained from cows late in the lactation before treatment was applied. These samples were tested for antibodies to gastrointestinal nematodes (GIN) using the indirect ELISA with the results expressed as optical density ratios (ODR). Production records were obtained from a computerized database of dairy herd improvement data. Pre-calving ODR showed a seasonal pattern. They were higher in the summer and fall and lower during the winter months. Older animals had higher pre-calving ODR values compared with younger cows. Similarly, cows from semi-confined herds had higher parasite antibody levels compared with cows from confined herds. The endectocide treatment did not affect the milk production response in the overall study population. However, the interaction effect between treatment and pre-calving ODR on milk production response after endectocide treatment was significant (P = 0.02), with some evidence of positive treatment response in cows with an ODR > 0.4. The relationship between pre-calving ODR and production response appeared to be quadratic rather than linear.

Effect of Eprinomectin Treatment at Calving on Milk Production in Dairy Herds with Limited Outdoor Exposure

The objective of this study was to determine the effect of anthelmintic treatment at calving in herds that were totally or semiconfined during the summer. In totally confined herds, lactating and dry cows were housed throughout the summer and had no access to pasture. In semiconfined herds, lactating and dry cows had limited outdoor exposure to a small pasture or paddock but were still fed a ration that met all their nutritional requirements. The study was carried out between February 2002 and February 2003 in 65 herds enrolled with DHI and distributed in 4 regions in Canada and 1 state in the United States. Cows were randomly allocated to receive eprinomectin or a placebo, with treatment being administered on or close to day of calving. In May and June 2002, 8 fecal samples were collected from each farm and fecal egg counts (FEC) were determined. Monthly bulk tank milk samples from each farm were tested with an indirect ELISA using a crude Ostertagia ostertagi antigen. Monthly test-day milk production data were recorded for 200 d after calving. In general, FEC were very low (mean = 1 egg per gram, range = 0 to 27). Mean herd bulk milk ELISA optical density ratio (ODR) values for the whole year ranged between 0.22 and 0.80. The ODR values were dichotomized into high and low using a threshold of 0.5. Treatment effects were analyzed using a linear mixed model with herd and cow as random effects. The analysis was restricted to 4789 cows (23,956 test-day records) treated between 21 d before and 7 d after calving. Overall, there was no significant effect of treatment. However, there was a tendency for an interaction between treatment and ODR, as illustrated by a larger numerical difference in treated vs. untreated cows in high-ODR herds than in low-ODR herds. However, the confidence intervals for the treatment effects (kg/d of milk per cow) in high-ODR herds (-0.33 to 1.10) and in low-ODR herds (-0.53 to 0.14) were wide and included zero. Therefore, this study failed to show a beneficial effect of eprinomectin treatment in these totally or semiconfined herds.

Estimation of specificity and sensitivity of three diagnostic tests for infectious salmon anaemia virus in the absence of a gold standard

Reverse transcriptase-polymerase chain reaction (RT-PCR), virus isolation (VI) and indirect fluorescent antibody test (IFAT) are three tests currently used by the salmon industry to identify fish infected with the infectious salmon anaemia virus (ISAV). However, very limited information is available on the sensitivity and specificity of these methods. In order to evaluate these tests in fish representing a range of farmed Atlantic salmon populations, five laboratories participated in a blind study of 400 kidney samples from four groups of fish with different prevalences of ISAV. Each laboratory used its own testing protocols. Estimates of the specificity of each test were determined directly from a population assumed to be free of infection. Indirect estimates of the sensitivity and specificity of each test were obtained using maximum likelihood estimation of a latent class model (i.e. no gold standard test result available). There was a substantial difference in sensitivity and specificity of RT-PCR among the three laboratories using this test. If only the best results for the RT-PCR tests are taken into account, the maximum likelihood estimates obtained from this study suggest RT-PCR and VI are of similar high sensitivity (range 92-100%), IFAT is the least sensitive method (range 65-76%) while the three tests have similar high specificities (range 96-100%). The results of the study suggest: (1) RT-PCR tests should be standardized before they are used as a diagnostic test for prevention and control of ISAV, (2) the sensitivity of VI was higher than expected and (3) IFAT has a low sensitivity but might be a good screening test because of its low cost.

Estimation of the repeatability and reproducibility of three diagnostic tests for infectious salmon anaemia virus

Reverse transcriptase polymerase chain reaction (RT-PCR), virus isolation (VI) and indirect fluorescent antibody tests (IFAT) are three assays currently used by the salmon industry to identify fish infected with infectious salmon anaemia virus (ISAV). However, no data are available on the repeatability (within-laboratory consistency) and reproducibility (between-laboratory consistency) of these assays and very limited information is available on the effect of freezing samples on test results. In order to evaluate these assays, five laboratories participated in a blinded study of 400 kidney samples representing four populations of farmed Atlantic salmon with different prevalence of ISAV. Each laboratory used its own testing protocols. Repeatability and reproducibility were evaluated using kappa as the measure of agreement. The effect of freezing was evaluated using the McNemar test. Freezing did not affect VI but improved the sensitivity of RT-PCR. The repeatability and reproducibility of VI was almost perfect. There was a substantial difference in repeatability of RT-PCR among the three laboratories with kappa ranging from 0.5 to 0.96. The repeatability for RT-PCR was generally low. The repeatability of IFAT was moderate when the results were analysed using 1+ and above as a positive result. The results of the study show the need to standardize the protocol and interpretation of RT-PCR.

A meta-analysis of the milk-production response after anthelmintic treatment in naturally infected adult dairy cows

Meta-analysis was used to estimate the effects of anthelmintic treatment on milk production in dairy cows. The literature search included peer-reviewed journals (both full articles and abstracts), conference proceedings and theses and included documents written in English, Spanish, French, Portuguese or Italian. The study outcome was defined as the difference in milk production (kg/cow per day) between treated and untreated cows. Random effect meta-analyses were performed on 75 trials published between 1972 and 2002. The combined estimate after controlling for publication bias and/or small-study effect was of 0.35 kg/cow per day. Significant variation among studies was detected and although several variables were associated with the study outcome, they did not significantly reduce the unexplained variability among trials. Trials reporting the use of endectocides had higher milk-production response compared with trials using older anthelmintics. Similarly, whole-herd treatment trials or trials which applied the treatment in mid-lactation or strategically throughout the year had higher response compared with calving or dry-period treatment trials. Trials reporting the results as total 305-day milk production had lower response compared with trials which measured production as daily milk weight. Primiparous cows trials had lower responses compared with multiparous cows trials.

Milk antibodies against Ostertagia ostertagi: relationships with milk IgG and production parameters in lactating dairy cattle

The present study was carried out to evaluate the relationship between milk optical density ratios (ODRs) from an indirect Ostertagia ostertagi ELISA, total milk IgG levels and milk production and then establish a correction factor to adjust ODR. Five hundred and sixty composite milk samples collected from 358 cows on four dairy herds in June and August 2002 were used in this analysis. The average ODR was 0.34. A positive correlation was found between ODR and IgG values in milk, days in milk, age and log transformed somatic cell counts (SCC). However, ODR was negatively correlated with milk production. The IgG levels and ODR values were constant from 30 to 200 days in milk. However, ODRs increased from 200 days until the end of the lactation. After controlling for age, season, herd and SCC, an increase in milk production of 13 kg/day was associated with a reduction in ODR values of 0.052. The results of the present study suggest that ODR values are not greatly influenced by production factors. ODR follow the same pattern as the IgG variation across lactation and could be adjusted in order to compare ODR values obtained from high producing cows with those obtained from low producing animals.

The effect of eprinomectin treatment at calving on reproduction parameters in adult dairy cows in Canada

A clinical trial was carried out in two provinces of Canada to investigate the effect of treatment with eprinomectin at calving on production parameters in adult dairy cattle in 1999-2000. One of the objectives of this study was to evaluate the impact of treatment on reproductive performance as measured by: calving-to-conception interval, calving-to-first service interval and number of services per conception. The ability of an indirect ELISA using a crude adult Ostertagia ostertagi antigen to predict response to treatment also was evaluated. All lactating cows in 20 dairy herds were allocated randomly to receive either eprinomectin pour-on or placebo at calving. Information on reproductive parameters was obtained from computerised cow records. Survival models were used to evaluate the effect of treatment on the two intervals and a Poisson model was used to evaluate the number of services to conception. A total of 549 cows were included in these analyses. A marginally significant treatment effect on calving-to-conception interval was observed (hazard ratio=1.24, P=0.06) but not on calving-to-first service interval. A significant reduction in the number of breedings to conception for treated animals also was observed with a longer effect in cows with short interval to first service. Milk samples from a subset of 109 late-lactation cows were tested for antibodies against O. ostertagi. The ELISA optical-density ratio (ODR) values obtained between 120 days before calving and drying off were categorised as high ODR (>or=0.5) and low ODR (<0.5). Among untreated animals, the hazard of conception was lower (hazard ratio=0.38, 95% CI=[0.19,0.75]) for high-ODR cows compared to low ODR cows suggesting that higher parasite burdens had an adverse effect on reproductive performance. Treated high-ODR cows had a hazard of conception equivalent to the hazard for all cows in the low-ODR group (indicating that treatment prevented the negative effect associated with these higher parasite burdens).

The use of negative binomial modelling in a longitudinal study of gastrointestinal parasite burdens in Canadian dairy cows

The epidemiology of bovine gastrointestinal nematodes was investigated through a 1-year (October 1999 to September 2000) longitudinal study in 38 Canadian dairy herds from 4 different provinces (Prince Edward Island, Quebec, Ontario, Saskatchewan). For each herd, fecal egg counts from 8 randomly selected animals were performed on a monthly or quarterly basis. Larval cultures were performed once, to determine the species breakdown of the parasites. All producers were interviewed regarding herd management practices. The observed fecal egg counts were low in this study, with a range from 0 to 419 nematode eggs per 5 g of feces. The mean count was 9.8 and the median was 1. Standard transformations failed to normalize the data, which followed an over-dispersed Poisson distribution. A zero inflated negative binomial model was applied to assess factors that would influence the fecal egg counts. Identified associations were: egg counts were lowest in the winter and highest in the late spring; first-lactation cattle had higher counts than older cows; if manure was spread mechanically on pastures used by lactating cattle the egg counts were higher; and if manure was spread on heifer-pastures, the adult cows had lower counts. In herds where pasture use was more extensive, the cattle had higher fecal egg counts. The difference in pasture exposure was found to be a main contributor to an observed difference in fecal egg counts among herds in the 4 provinces.