Absence of effects of widespread badger culling on tuberculosis in cattle.

Government policy in England aims for the elimination of bovine tuberculosis (bTB). This policy includes culling of European badger (Meles meles) to reduce cattle TB incidence. The rationale is based on a field trial, the Randomised Badger Culling Trial (RBCT) 1998-2005, which reported a substantial decrease in bTB herd incidence where badger culling had been implemented, in comparison to untreated control areas. The RBCT was undertaken because previous studies of reductions in badgers by culling, reported a possible association between bTB in badger and cattle, but none could directly show causation. The effect of intensive widespread (proactive) culling in the RBCT was reported in 2006 in the journal Nature. Analysis of an extensive badger removal programme in England since 2013 has raised concerns that culling has not reduced bTB herd incidence. The present study re-examined RBCT data using a range of statistical models. Most analytical options showed no evidence to support an effect of badger culling on bTB herd incidence 'confirmed' by visible lesions and/or bacterial culture post mortem following a comparative intradermal skin test (SICCT). However, the statistical model chosen by the RBCT study was one of the few models that showed an effect. Various criteria suggest that this was not an optimal model, compared to other analytical options available. The most likely explanation is that the RBCT proactive cull analysis over-fitted the data with a non-standard method to control for exposure giving it a poor predictive value. Fresh appraisal shows that there was insufficient evidence to conclude RBCT proactive badger culling affected bTB breakdown incidence. The RBCT found no evidence of an effect of culling on 'total' herd incidence rates. Total herd incidences include those confirmed as bTB at necropsy and those herds where there was at least one animal animal positive to the comparative intradermal skin test, the standard diagnostic test used for routine surveillance, but not confirmed at necropsy. This was also the case using the more suitable statistical models. Use only of 'confirmed' herd incidence data, together with a more recent (2013) published perception that RBCT data presented 'a strong evidence base….with appropriate detailed statistical or other quantitative analysis' should be reconsidered. The results of the present report are consistent with other analyses that were unable to detect any disease control benefits from badger culling in England (2013-2019). This study demonstrates one form of potential driver to the reproducibility crisis, in this case with disease control management in an increasingly intensified livestock industry.

A combined microphysiological-computational omics approach in dietary protein evaluation.

Food security is under increased pressure due to the ever-growing world population. To tackle this, alternative protein sources need to be evaluated for nutritional value, which requires information on digesta peptide composition in comparison to established protein sources and coupling to biological parameters. Here, a combined experimental and computational approach is presented, which compared seventeen protein sources with cow's whey protein concentrate (WPC) as the benchmark. In vitro digestion of proteins was followed by proteomics analysis and statistical model-based clustering. Information on digesta peptide composition resulted in 3 cluster groups, primarily driven by the peptide overlap with the benchmark protein WPC. Functional protein data was then incorporated in the computational model after evaluating the effects of eighteen protein digests on intestinal barrier integrity, viability, brush border enzyme activity, and immune parameters using a bioengineered intestine as microphysiological gut system. This resulted in 6 cluster groups. Biological clustering was driven by viability, brush border enzyme activity, and significant differences in immune parameters. Finally, a combination of proteomic and biological efficacy data resulted in 5 clusters groups, driven by a combination of digesta peptide composition and biological effects. The key finding of our holistic approach is that protein source (animal, plant or alternative derived) is not a driving force behind the delivery of bioactive peptides and their biological efficacy.

Associations between preconception macronutrient intake and birth weight across strata of maternal BMI.

INTRODUCTION: Maternal nutrition during pregnancy is linked with birth outcomes including fetal growth, birth weight, congenital anomalies and long-term health through intra-uterine programming. However, a woman's nutritional status before pregnancy is a strong determinant in early embryo-placental development, and subsequently outcomes for both mother and child. Therefore, the aim of this study was to investigate the association between dietary macronutrient intake in the preconception period with birth weight. METHODS: We studied a group of 1698 women from the Dutch Perined-Lifelines linked birth cohort with reliable detailed information on preconception dietary macronutrient intake (using a semi quantitative food frequency questionnaire) and data available on birth weight of the offspring. Birth weight was converted into gestational age adjusted z-scores, and macronutrient intake was adjusted for total energy intake using the nutrient residual method. Preconception BMI was converted into cohort-based quintiles. Multivariable linear regression was performed, adjusted for other macronutrients and covariates. RESULTS: Mean maternal age was 29.5 years (SD 3.9), preconception BMI: 24.7 kg/m2 (SD 4.2) and median daily energy intake was 1812 kcal (IQR 1544-2140). Mean birth weight was 3578 grams (SD 472). When adjusted for covariates, a significant association (adjusted z score [95% CI], P) between polysaccharides and birth weight was shown (0.08 [0.01-0.15], 0.03). When linear regression analyses were performed within cohort-based quintiles of maternal BMI, positive significant associations between total protein, animal protein, fat, total carbohydrates, mono-disaccharides and polysaccharides with birth weight were shown in the lowest quintile of BMI independent of energy intake, intake of other macronutrients and covariates. CONCLUSION: Out of all macronutrients studied, polysaccharides showed the strongest association with birth weight, independent of energy intake and other covariates. Our study might suggest that specifically in women with low preconception BMI a larger amount of macronutrient intake was associated with increased birth weight. We recommend that any dietary assessment and advise during preconception should be customized to preconception weight status of the women.

Offspring Birth Weight Is Associated with Specific Preconception Maternal Food Group Intake: Data from a Linked Population-Based Birth Cohort.

The preconception period has been recognized as one of the earliest sensitive windows for human development. Maternal dietary intake during this period may influence the oocyte quality, as well as placenta and early embryonic development during the first trimester of pregnancy. Previous studies have found associations between macronutrient intake during preconception and pregnancy outcomes. However, as food products consist of multiple macro- and micronutrients, it is difficult to relate this to dietary intake behavior. Therefore, the aim of this study was to investigate the association between intake of specific food groups during the preconception period with birth weight, using data from the Perined-Lifelines linked birth cohort. The Perined-Lifelines birth cohort consists of women who delivered a live-born infant at term after being enrolled in a large population-based cohort study (The Lifelines Cohort). Information on birth outcome was obtained by linkage to the Dutch perinatal registry (Perined). In total, we included 1698 women with data available on birth weight of the offspring and reliable detailed information on dietary intake using a semi-quantitative food frequency questionnaire obtained before pregnancy. Based on the 2015 Dutch Dietary Guidelines and recent literature 22 food groups were formulated. Birth weight was converted into gestational age-adjusted z-scores. Multivariable linear regression was performed, adjusted for intake of other food groups and covariates (maternal BMI, maternal age, smoking, alcohol, education level, urbanization level, parity, sex of newborn, ethnicity). Linear regression analysis, adjusted for covariates and intake of energy (in kcal) (adjusted z score [95% CI], P) showed that intake of food groups "artificially sweetened products" and "vegetables" was associated with increased birth weight (resp. (ß = 0.001 [95% CI 0.000 to 0.001, p = 0.002]), (ß = 0.002 [95% CI 0.000 to 0.003, p = 0.03])). Intake of food group "eggs" was associated with decreased birth weight (ß = -0.093 [95% CI -0.174 to -0.013, p = 0.02]). Intake in food groups was expressed in 10 g per 1000 kcal to be able to draw conclusions on clinical relevance given the bigger portion size of the food groups. In particular, preconception intake of "artificially sweetened products" was shown to be associated with increased birth weight. Artificial sweeteners were introduced into our diets with the intention to reduce caloric intake and normalize blood glucose levels, without compromising on the preference for sweet food products. Our findings highlight the need to better understand how artificial sweeteners may affect the metabolism of the mother and her offspring already from preconception onwards.

Bayesian Network Modeling Applied to Feline Calicivirus Infection Among Cats in Switzerland.

Bayesian network (BN) modeling is a rich and flexible analytical framework capable of elucidating complex veterinary epidemiological data. It is a graphical modeling technique that enables the visual presentation of multi-dimensional results while retaining statistical rigor in population-level inference. Using previously published case study data about feline calicivirus (FCV) and other respiratory pathogens in cats in Switzerland, a full BN modeling analysis is presented. The analysis shows that reducing the group size and vaccinating animals are the two actionable factors directly associated with FCV status and are primary targets to control FCV infection. The presence of gingivostomatitis and Mycoplasma felis is also associated with FCV status, but signs of upper respiratory tract disease (URTD) are not. FCV data is particularly well-suited to a network modeling approach, as both multiple pathogens and multiple clinical signs per pathogen are involved, along with multiple potentially interrelated risk factors. BN modeling is a holistic approach-all variables of interest may be mutually interdependent-which may help to address issues, such as confounding and collinear factors, as well as to disentangle directly vs. indirectly related variables. We introduce the BN methodology as an alternative to the classical uni- and multivariable regression approaches commonly used for risk factor analyses. We advise and guide researchers about how to use BNs as an exploratory data tool and demonstrate the limitations and practical issues. We present a step-by-step case study using FCV data along with all code necessary to reproduce our analyses in the open-source R environment. We compare and contrast the findings of the current case study using BN modeling with previous results that used classical regression techniques, and we highlight new potential insights. Finally, we discuss advanced methods, such as Bayesian model averaging, a common way of accounting for model uncertainty in a Bayesian network context.

Introducing a drift and diffusion framework for childhood growth research.

Background: Growth trajectories are highly variable between children, making epidemiological analyses challenging both to the identification of malnutrition interventions at the population level and also risk assessment at individual level. We introduce stochastic differential equation (SDE) models into child growth research. SDEs describe flexible dynamic processes comprising: drift - gradual smooth changes - such as physiology or gut microbiome, and diffusion - sudden perturbations, such as illness or infection. Methods: We present a case study applying SDE models to child growth trajectory data from the Haydom, Tanzania and Venda, South Africa sites within the MAL-ED cohort. These data comprise n=460 children aged 0-24 months. A comparison with classical curve fitting (linear mixed models) is also presented. Results: The SDE models offered a wide range of new flexible shapes and parameterizations compared to classical additive models, with performance as good or better than standard approaches. The predictions from the SDE models suggest distinct longitudinal clusters that form distinct 'streams' hidden by the large between-child variability. Conclusions: Using SDE models to predict future growth trajectories revealed new insights in the observed data, where trajectories appear to cluster together in bands, which may have a future risk assessment application. SDEs offer an attractive approach for child growth modelling and potentially offer new insights.

A Pharmacokinetic Study of an Ibuprofen Topical Patch in Healthy Male and Female Adult Volunteers.

The pharmacokinetics of a novel locally applied ibuprofen topical patch was evaluated. Healthy subjects (n = 28) were administered a 200-mg ibuprofen patch every 24 hours for 5 days, and steady-state pharmacokinetics was determined. The amount of ibuprofen remaining in the patch following each patch removal was also assessed. The maximum steady-state drug concentration and area under the concentration curve from time 0 on day 5 (t = 0) to the 24-hours sample on day 6 were 514 ng/mL (95% CI 439 to 603 ng/mL) and 9.78 kg·h/mL (95% CI 8.43 to 11.4 kg·h/mL), respectively. Maximum ibuprofen concentration on day 5 occurred at 20 hours post-patch application. No evidence of drug accumulation was observed, and steady state was achieved between days 2 and 5. Ibuprofen levels attenuated rapidly to baseline within 24 hours after treatment discontinuation. The amount of ibuprofen remaining in the patch was high (≥80%). Treatment-emergent adverse events were generally mild, with the most prevalent being headache (n = 6; 21.4%). Only 4 TEAEs were considered related to the ibuprofen patch: paresthesia (n = 1), headache (n = 2), and pruritic rash (n = 1). The study found that the systematic absorption of ibuprofen from a 200-mg patch was low and that the levels of ibuprofen leaving the patch over a 24-hour period are consistent with levels required for therapeutic relief as shown in other studies.

Efficacy and tolerability of a new ibuprofen 200mg plaster in patients with acute sports-related traumatic blunt soft tissue injury/contusion.

BACKGROUND: Ibuprofen is used for the treatment of non-serious pain. This study assessed the efficacy and safety of a new ibuprofen plaster for the treatment of pain associated with acute sports impact injuries/contusions. METHODS: In this randomised, double-blind, multi-centre, placebo controlled, parallel group study, adults (n = 130; 18-58 years of age) diagnosed with acute sports-related blunt soft tissue injury/contusion were randomized to receive either ibuprofen 200 mg plaster or placebo plaster. Plasters were administered once daily for five consecutive days. The primary assessment was area under the visual analogue scale (VAS) of pain on movement (POM) over 0 to three days (VAS AUC0-3d). Other endpoints included algometry AUC from 0 to three days (AUC0-3d) and 0 to five days (AUC0-5d), to evaluate improvement of sensitivity at the injured site, and patient and investigator global assessment of efficacy. Safety was monitored throughout the study. RESULTS: The ibuprofen plaster resulted in superior reduction in AUC0-3d compared with placebo; the Least Squares (LS) mean difference was 662.82 mm*h in favour of the ibuprofen 200mg plaster (P = 0.0011). The greater improvement in VAS AUC of POM was also observed after 12 h, 24 h, and five days of therapy. Tenderness also significantly improved with the ibuprofen plaster compared with placebo; LS mean difference in algometry/tenderness AUC0-3d was 1.87 N/cm2*d and AUC0-5d was 1.87 N/cm2*d (P values ≤0.0004). At all study timepoints, a greater percentage of patients and investigators rated the effectiveness of the ibuprofen 200 mg plaster as good/excellent than the placebo plaster. Treatment-emergent adverse events for the ibuprofen plaster were few (≤1.5%) and were mild in severity. CONCLUSIONS: The results of this study indicate 200 mg plaster is effective and safe for the treatment of pain due to acute sports-related traumatic blunt soft tissue injury/contusion in adults.

The current and future burden of late-onset dementia in the United Kingdom: Estimates and interventions.

INTRODUCTION: We estimate the burden of late-onset dementia in the United Kingdom through to 2025 and assess the impact of potential interventions. METHODS: We compute disability adjusted life years (DALYs) through to 2025 and consider three interventions, all assumed launched in 2018; (1) an optimistic limiting case of a 100% preventive intervention with immediate uptake of 100% of the population at risk; (2) an intervention which delays onset by 5 years, linear uptake to 50% after 5 years; (3) as (2) but uptake 75% after 5 years. RESULTS: By 2025, the DALY burden will have increased by 42% from the Global Disease Burden 2010 estimate. Intervention results: (1) a 9% decrease by 2025; (2) a 33% increase; and (3) a 28% increase. DISCUSSION: At current prevalence rates, the ability of an intervention to offset the projected increase in DALY burden of dementia in the United Kingdom by 2025 appears low.

Latent porcine circovirus type 2-infected domestic pigs: A potential infection model for the effective development of vaccines against latent or chronic virus induced diseases.

Until recently, knowledge of the pathogenicity of Circoviridae and Anelloviridae family members was limited. Our previous discoveries provided clues toward resolving this issue based on studies of the latent nature of porcine circovirus type 2 (PCV2) genotype group members. We developed a conventional pig infection model that indicated that weaners already harbored latent PCV2 infection in the thymus, which enabled the viruses to specifically modulate the maturation of T-helper cells. This finding raised the possibility that the thymi of normal fetuses were already infected with PCV2. The present findings further substantiate our hypothesis that PCV2 masquerades as the host by infecting fetuses before they acquire immune-competence. We provide the first demonstration that all domestic pig fetuses preferentially harbor latent PCV2-infected cells in their thymi. These PCV2-infected cells are different from thymocytes and are located in the medulla of the fetal thymus. These latent PCV2-infected cells in fetuses are found at the same location and share characteristics with the infected cells observed in adolescent pigs. Moreover, fetuses also harbor these infected cells in other lymph system organs. We provide the first demonstration that the fetal thymus virus pools are minimally affected by sow vaccination, highlighting the immune-privileged character of this organ. Furthermore, we found a striking reduction in virus-infected cells in the fetal spleen and an increase in PCV2-infected cells in the fetal intestine of anti-PCV2-vaccinated mothers. These data indicate that specific immune response interactions occur between mothers and their progeny that are not dependent on the humoral immunity of the mother and cannot be attributed to the rudimentary humoral responses of the fetuses because these pig fetuses do not have any PCV2-specific antibodies. These shifts in our understanding of the PCV2-infected cell pool will lead to different avenues in the search for effective vaccination strategies against latent and chronic pathogens.

T-cell reprogramming through targeted CD4-coreceptor and T-cell receptor expression on maturing thymocytes by latent Circoviridae family member porcine circovirus type 2 cell infections in the thymus.

Although porcine circovirus type 2 (PCV2)-associated diseases have been evaluated for known immune evasion strategies, the pathogenicity of these viruses remained concealed for decades. Surprisingly, the same viruses that cause panzootics in livestock are widespread in young, unaffected animals. Recently, evidence has emerged that circovirus-like viruses are also linked to complex diseases in humans, including children. We detected PCV2 genome-carrying cells in fetal pig thymi. To elucidate virus pathogenicity, we developed a new pig infection model by in vivo transfection of recombinant PCV2 and the immunosuppressant cofactor cyclosporine A. Using flow cytometry, immunofluorescence and fluorescence in situ hybridization, we found evidence that PCV2 dictates positive and negative selection of maturing T cells in the thymus. We show for the first time that PCV2-infected cells reside at the corticomedullary junction of the thymus. In diseased animals, we found polyclonal deletion of single positive cells (SPs) that may result from a loss of major histocompatibility complex class-II expression at the corticomedullary junction. The percentage of PCV2 antigen-presenting cells correlated with the degree of viremia and, in turn, the severity of the defect in thymocyte maturation. Moreover, the reversed T-cell receptor/CD4-coreceptor expression dichotomy on thymocytes at the CD4(+)CD8(interm) and CD4SP cell stage is viremia-dependent, resulting in a specific hypo-responsiveness of T-helper cells. We compare our results with the only other better-studied member of Circoviridae, chicken anemia virus. Our data show that PCV2 infection leads to thymocyte selection dysregulation, adding a valuable dimension to our understanding of virus pathogenicity.

Estimating diagnostic test accuracies for Brachyspira hyodysenteriae accounting for the complexities of population structure in food animals.

For swine dysentery, which is caused by Brachyspira hyodysenteriae infection and is an economically important disease in intensive pig production systems worldwide, a perfect or error-free diagnostic test ("gold standard") is not available. In the absence of a gold standard, Bayesian latent class modelling is a well-established methodology for robust diagnostic test evaluation. In contrast to risk factor studies in food animals, where adjustment for within group correlations is both usual and required for good statistical practice, diagnostic test evaluation studies rarely take such clustering aspects into account, which can result in misleading results. The aim of the present study was to estimate test accuracies of a PCR originally designed for use as a confirmatory test, displaying a high diagnostic specificity, and cultural examination for B. hyodysenteriae. This estimation was conducted based on results of 239 samples from 103 herds originating from routine diagnostic sampling. Using Bayesian latent class modelling comprising of a hierarchical beta-binomial approach (which allowed prevalence across individual herds to vary as herd level random effect), robust estimates for the sensitivities of PCR and culture, as well as for the specificity of PCR, were obtained. The estimated diagnostic sensitivity of PCR (95% CI) and culture were 73.2% (62.3; 82.9) and 88.6% (74.9; 99.3), respectively. The estimated specificity of the PCR was 96.2% (90.9; 99.8). For test evaluation studies, a Bayesian latent class approach is well suited for addressing the considerable complexities of population structure in food animals.

Transarticular fixation with cortical screws combined with dorsal laminectomy and partial discectomy as surgical treatment of degenerative lumbosacral stenosis in 17 dogs: clinical and computed tomography follow-up.

OBJECTIVE: To describe clinical outcome and technical outcome assessed using computed tomography (CT) in dogs with degenerative lumbosacral stenosis (DLSS) treated by dorsal laminectomy, partial discectomy, and transarticular screw fixation. STUDY DESIGN: Retrospective observational case series. ANIMALS: Dogs with DLSS (n = 17). METHODS: Dogs with neurologic and magnetic resonance imaging (MRI) findings compatible with DLSS treated by dorsal laminectomy, partial discectomy and transarticular screw fixation were enrolled. Pre- and postoperative neurologic status was compared. Lumbosacral (LS) angle in extension and misalignment in preoperative MRI were compared with the postoperative CT. Residual mobility of the LS joint after fixation was also evaluated. Status of screws, presence of new bone formation over screw heads/articular facets and presence of adjacent segment disease (ASD) were assessed. RESULTS: Median CT follow-up was 12 months. Clinical improvement was seen in 13 dogs, 2 dogs had intermittent LS pain, and 2 dogs needed revision surgery. In 5 dogs, screws were either pulled out or broken. Reduction of LS angle in extension and misalignment was achieved. Residual mobility of the LS segment was present and ASD was not recognized. CONCLUSIONS: Transarticular screw fixation in dogs with DLSS is associated with a considerable number of technical failures and does not result in rigid stabilization; however, this did not significantly adversely influence clinical outcome.

Dynamics of the force of infection: insights from Echinococcus multilocularis infection in foxes.

Characterizing the force of infection (FOI) is an essential part of planning cost effective control strategies for zoonotic diseases. Echinococcus multilocularis is the causative agent of alveolar echinococcosis in humans, a serious disease with a high fatality rate and an increasing global spread. Red foxes are high prevalence hosts of E. multilocularis. Through a mathematical modelling approach, using field data collected from in and around the city of Zurich, Switzerland, we find compelling evidence that the FOI is periodic with highly variable amplitude, and, while this amplitude is similar across habitat types, the mean FOI differs markedly between urban and periurban habitats suggesting a considerable risk differential. The FOI, during an annual cycle, ranges from (0.1,0.8) insults (95% CI) in urban habitat in the summer to (9.4, 9.7) (95% CI) in periurban (rural) habitat in winter. Such large temporal and spatial variations in FOI suggest that control strategies are optimal when tailored to local FOI dynamics.

High-resolution manometric evaluation of the effects of cisapride and metoclopramide hydrochloride administered orally on lower esophageal sphincter pressure in awake dogs.

OBJECTIVE: To evaluate the effects of cisapride and metoclopramide hydrochloride administered orally on the lower esophageal sphincter (LES) resting pressure in awake healthy dogs. ANIMALS: 6 adult Beagles. PROCEDURES: Each dog was evaluated after administration of a single dose of cisapride (0.5 mg/kg), metoclopramide (0.5 mg/kg), or placebo (empty gelatin-free capsule) in 3 experiments performed at 3-week intervals. To measure LES pressure, a high-resolution manometry catheter equipped with 40 pressure sensors spaced 10 mm apart was used. For each experiment, LES pressure was recorded during a 20-minute period with a virtual electronic sleeve emulation before treatment (baseline) and at 1, 4, and 7 hours after drug or placebo administration. A linear mixed-effects model was used to test whether the 3 treatments affected LES pressure differently. RESULTS: In the cisapride, metoclopramide, and placebo experiments, median baseline LES pressures were 29.1, 30.5, and 29.0 mm Hg, respectively. For the cisapride, metoclopramide, and placebo treatments, median LES pressures at 1 hour after administration were 44.4, 37.8, and 36.6 mm Hg, respectively; median LES pressures at 4 hours after administration were 50.7, 30.6, and 31.1 mm Hg, respectively; and median LES pressures at 7 hours after administration were 44.3, 28.5, and 33.3 mm Hg, respectively. The LES pressures differed significantly only between the placebo and cisapride treatments. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggested that orally administered cisapride may be of benefit in canine patients for which an increase in LES pressure is desirable, whereas orally administered metoclopramide did not affect LES resting pressures in dogs.

Applying Bayesian network modelling to understand the links between on-farm biosecurity practice during the 2007 equine influenza outbreak and horse managers' perceptions of a subsequent outbreak.

Australia experienced its first ever outbreak of equine influenza in August 2007. Horses on 9359 premises were infected over a period of 5 months before the disease was successfully eradicated through the combination of horse movement controls, on-farm biosecurity and vaccination. In a previous premises-level case-control study of the 2007 equine influenza outbreak in Australia, the protective effect of several variables representing on-farm biosecurity practices were identified. Separately, factors associated with horse managers' perceptions of the effectiveness of biosecurity measures have been identified. In this analysis we applied additive Bayesian network modelling to describe the complex web of associations linking variables representing on-farm human behaviours during the 2007 equine influenza outbreak (compliance or lack thereof with advised personal biosecurity measures) and horse managers' perceptions of the effectiveness of such measures in the event of a subsequent outbreak. Heuristic structure discovery enabled identification of a robust statistical model for 31 variables representing biosecurity practices and perceptions of the owners and managers of 148 premises. The Bayesian graphical network model we present statistically describes the associations linking horse managers' on-farm biosecurity practices during an at-risk period in the 2007 outbreak and their perceptions of whether such measures will be effective in a future outbreak. Practice of barrier infection control measures were associated with a heightened perception of preparedness, whereas horse managers that considered their on-farm biosecurity to be more stringent during the outbreak period than normal practices had a heightened perception of the effectiveness of other measures such as controlling access to the premises. Past performance in an outbreak setting may indeed be a reliable predictor of future perceptions, and should be considered when targeting infection control guidance to horse owners and managers.

Improving epidemiologic data analyses through multivariate regression modelling.

: Regression modelling is one of the most widely utilized approaches in epidemiological analyses. It provides a method of identifying statistical associations, from which potential causal associations relevant to disease control may then be investigated. Multivariable regression - a single dependent variable (outcome, usually disease) with multiple independent variables (predictors) - has long been the standard model. Generalizing multivariable regression to multivariate regression - all variables potentially statistically dependent - offers a far richer modelling framework. Through a series of simple illustrative examples we compare and contrast these approaches. The technical methodology used to implement multivariate regression is well established - Bayesian network structure discovery - and while a relative newcomer to the epidemiological literature has a long history in computing science. Applications of multivariate analysis in epidemiological studies can provide a greater understanding of disease processes at the population level, leading to the design of better disease control and prevention programs.

Identifying associations in Escherichia coli antimicrobial resistance patterns using additive Bayesian networks.

While the genesis of antimicrobial resistance (AMR) in animal production is a high profile topic in the media and the scientific community, it is still not well understood. The epidemiology of AMR is complex. This complexity is demonstrated by extensive biological and evolutionary mechanisms which are potentially impacted by farm management and husbandry practices - the risk factors. Many parts of this system have yet to be fully described. Notably, the occurrence of multiple resistance patterns is the rule rather than exception - the multivariate problem. A first essential step in the development of any comprehensive risk factor analysis - whose goal is the prevention or reduction of AMR - is to describe those associations between different patterns of resistance which are systematic. That is, have sufficient statistical support for these patterns to be considered robust features of the underlying epidemiological system, and whose presence must therefore be incorporated into any risk factor analysis of AMR for it to be meaningful with respect to the farm environment. Presented here is a case study that seeks to identify systematic associations between patterns of resistance to 13 different antimicrobials in Escherichia coli isolates obtained from composite finisher (>80 kg) pig faecal samples obtained from Canada's five major pork producing provinces. The use of a Bayesian network analysis approach allowed us to identify many systematic associations between individual antimicrobial resistances. Sixteen of these resistances are corroborated with existing literature. These associations are distributed between several important classes of antimicrobials including the ß-lactams, folate biosynthesis inhibitors, tetracyclines, aminoglycosides and quinolones. This study presents an exciting first step towards the larger and far more ambitious goal of developing generic and holistic risk factor analyses for on-farm occurrence of AMR. Analyses of this nature would combine multivariate response variables (joint patterns of resistance) with multi-factorial causal factors from within the livestock production environment thereby permitting a more complete understanding of the epidemiology of antimicrobial resistance.

Untangling the complex inter-relationships between horse managers' perceptions of effectiveness of biosecurity practices using Bayesian graphical modelling.

On-farm biosecurity practices have been promoted in many animal industries to protect animal populations from infections. Current approaches based on regression modelling techniques for assessing biosecurity perceptions and practices are limited for analysis of the interrelationships between multivariate data. A suitable approach, which does not require background knowledge of relationships, is provided by Bayesian network modelling. Here we apply such an approach to explore the complex interrelationships between the variables representing horse managers' perceptions of effectiveness of on-farm biosecurity practices. The dataset was derived from interviews conducted with 200 horse managers in Australia after the 2007 equine influenza outbreak. Using established computationally intensive techniques, an optimal graphical statistical model was identified whose structure was objectively determined, directly from the observed data. This methodology is directly analogous to multivariate regression (i.e. multiple response variables). First, an optimal model structure was identified using an exact (exhaustive) search algorithm, followed by pruning the selected model for over-fitting by the parametric bootstrapping approach. Perceptions about effectiveness of movement restrictions and access control were linked but were generally segregated from the perceptions about effectiveness of personal and equipment hygiene. Horse managers believing in the effectiveness of complying with movement restrictions in stopping equine influenza spread onto their premises were also more likely to believe in the effectiveness of reducing their own contact with other horses and curtailing professional visits. Similarly, the variables representing the effectiveness of disinfecting vehicles, using a disinfectant footbath, changing into clean clothes on arrival at the premises and washing hands before contact with managed horses were clustered together. In contrast, horse managers believing in the effectiveness of disinfecting vehicles (hygiene measure) were less likely to believe in the effectiveness of controlling who has access to managed horses (access control). The findings of this analysis provide new insights into the relationships between perceptions of effectiveness of different biosecurity measures. Different extension education strategies might be required for horse managers believing more strongly in the effectiveness of access control or hygiene measures.

Understanding the associations between on-farm biosecurity practice and equine influenza infection during the 2007 outbreak in Australia.

In a previous premises-level case-control study of the 2007 equine influenza outbreak in Australia, the protective effect of several variables representing on-farm biosecurity practices was identified. However, using logistic regression it was not possible to definitively identify individual effects and associations between each of the personal biosecurity measures implemented by horse premises owners and managers in the face of the outbreak. In this study we apply Bayesian network modelling to identify the complex web of associations between these variables, horse premises infection status and other premises-level covariates. We focussed this analysis primarily on the inter-relationship between the nine variables representing on-farm personal biosecurity measures (of people residing on the premises and those visiting), and all other variables from the final logistic regression model of our previous analysis. Exact structure discovery was used to identify the globally optimal model from across the landscape of all directed acyclic graphs possible for our dataset. Bootstrapping was used to adjust the model for over-fitting. Our final Bayesian graphic network model included 18 variables linked by 23 arcs, each arc analogous to a single multivariable generalised linear model, combined in a probabilistically coherent way. Amongst the personal biosecurity measures, having a footbath in place, certain practices of visitors (hand-washing, changing clothes and shoes) in contact with the horses, and the regularity of horse handling were statistically associated with premises infection status. The results of this in-depth analysis provide new insight into the complex web of direct and indirect associations between risk factors and horse premises infection status during the first 7 weeks of the 2007 equine influenza outbreak in Australia. In future outbreaks, unnecessary contact and handling of horses should be avoided, especially by those coming from off the premises. Prior to any such contact, persons handling horses should use a footbath (if present), change their clothes and shoes, and wash their hands.