A Bayesian Approach to Estimate OJD Prevalence From Pooled Fecal Samples of Variable Pool Size

This paper describes a Bayesian approach to prevalence estimation based on pooled samples that accommodates variation in pool size and adjusts for test imperfection. A logistic model was developed for pooled fecal culture (PFC) sensitivity as a function of pool size and a logistic mixed model for ovine Johne’s disease (OJD) prevalence as a function of covariates that were found significant in a recent OJD risk factor study conducted in Australia. Available data on these factors and prior information about prevalence and sensitivity were incorporated into a Bayesian model to estimate OJD prevalence from PFC data. Overall, posterior cohort OJD prevalence was estimated to be 0.16 (range of prevalences across cohorts 0.002 to 0.72). The average prevalence was higher in wethers than ewes. PFC sensitivities for pool sizes 10, 30 and 50 were estimated to be 0.91 (95% probability intervals 0.80, 0.96), 0.85 (0.80, 0.90) and 0.77 (0.65, 0.88), respectively. Posterior specificity of PFC was almost perfect though based primarily on the prior. Results suggest the Bayesian model successfully estimated the animal-level prevalence after accounting for variable pool size and imperfect test parameters. The method can be easily adapted for other conditions and diseases where pooled samples are collected. WinBugs code for the article is available online. Key Words: Diagnostic test Mycobacterium Ovine Johne’s disease Paratuberculosis Prevalence Sensitivit

Horse owners' biosecurity practices following the first equine influenza outbreak in Australia

A cross-sectional study was conducted involving 759 Australian horse owners to determine their biosecurity practices and perceptions one year after the 2007 equine influenza outbreak and to investigate the factors influencing these perceptions and practices. A web link to an online questionnaire was sent to 1224 horse owners as a follow-up to a previous study to obtain information about biosecurity perceptions and practices, impacts of the 2007 EI outbreak, demographic information and information about horse industry involvement. Ordinal logistic regression analyses were conducted to determine factors associated with poor biosecurity practices. Biosecurity compliance (low, medium, high), as determined by horse owners’ responses to a 16-item question on the frequency of various biosecurity measures, was used as the outcome variable in ordinal logistic regression analyses. Variables with a univariable p-value ≤0.2 were eligible for inclusion in multivariable models built using a manual stepwise approach. Variables with a p-value <0.05 in multivariable models were retained in the final model. Two potential confounders - age and gender of participants- were included in the final model irrespective of their p-values. Thirty percent of the respondents had low biosecurity compliance and were performing biosecurity practices ‘not very often’ or ‘never’. Younger people, people with two or more children, those who were not involved with horses commercially and those who had no long-term business impacts resulting from the 2007 EI outbreak were more likely to have lower biosecurity compliance. People who were not fearful of a future outbreak of equine influenza in Australia and those who thought their current hygiene and access control practices were not very effective in protecting their horses also had poor biosecurity practices. In this observational study we identified factors associated with a group of horse owners with low levels of biosecurity compliance. As this cross-sectional study only assesses associations, the identified factors should be further investigated in order to be considered in the design of extension activities to increase horse owners’ biosecurity compliance. Keywords: Biosecurity; Equine; Owner perceptions; Ordinal logistic regression

Survey of Australian equine veterinarians evaluating their biosecurity training and perceptions and opinions about the management of the 2007 equine influenza outbreak

Objectives To evaluate the level of biosecurity training among Australian equine veterinarians, to assess their biosecurity and infectious disease perceptions and their opinions about the 2007 equine influenza outbreak management. Design Cross sectional study. Procedure A survey was conducted among equine veterinarians attending the 2010 annual conference of the Equine Veterinarian Association (EVA) in Australia. Data were collected using a selfcompleted questionnaire and analysed using Fisher’s exact tests to assess veterinarians’ level of biosecurity training, infectious disease perceptions and views regarding the 2007 equine influenza outbreak management. Results A total of 46 out of the 196 attending veterinarians (23.5%) completed the questionnaire. Significantly greater proportions of recently graduated veterinarians received theoretical and practical biosecurity training at veterinary schools than their counterparts The majority considered their likelihood of spreading infectious diseases from one client’s horse to another to be low (84%). More than half (58%) of the veterinarians considered that hand-washing/ wearing gloves was very effective in preventing disease spread. However, around a quarter (27%) reported a degree of reservation about the practicality of performing general biosecurity practices in everyday working life. Overall veterinarians were satisfied with the equine influenza outbreak response but had mixed opinions about the control measures used and communications. Conclusion Levels of biosecurity training and the frequency of biosecurity advice provided by veterinarians have increased over time, although practicality of biosecurity practices is a concern for some of the veterinarians. Further investigations of the barriers for the use of various biosecurity practices are required in order to inform training programs. Keywords: equine, veterinarians, biosecurity, perceptions, equine influenza, training.financial support of the Rural Industries, Research and Development Corporation (RIRDC

Estimation of sensitivity and flock-sensitivity of pooled faecal culture for Mycobacterium avium subsp. paratuberculosis in sheep

Pooled faecal culture (PFC) is a widely used test in ovine Johne’s disease (OJD) control programmes in Australia but information about its characteristics is limited. We conducted this study to estimate sensitivity and flock-sensitivity of PFC in sheep with different OJD histopathological lesions in simulated flocks with a range of infection prevalence levels. Initially, a known quantity of faeces from sheep with pauci- or multi-bacillary lesions was pooled with uncontaminated faeces from confirmed non-infected sheep and cultured using PFC technique. PFC sensitivity, calculated as a proportion of the pools of a particular size that tested positive, was determined to be 90% in sheep with the multibacillary form of the disease but varied with pool size in sheep with the paucibacillary form of OJD. Subsequently, probabilistic models were developed to estimate overall pool-sensitivity achieved in a flock (Sek) and flock-sensitivity of PFC (FSe) in various simulated scenarios. In flocks with a given ratio of multi- to pauci-bacillary sheep and with low to moderate infection prevalence level, Sek decreased with increase in pool size, but increased with pool size in flocks with ≥ 10 % prevalence. FSe, in contrast, increased with pool size in all the tested scenarios. Both Sek and FSe increased with infection prevalence, ratio of multi- to pauci-bacillary sheep and the number of pools sourced from flocks. Sensitivity analyses indicated that the estimates and trends were robust to moderate changes in input parameters. The results suggest that the current testing of seven pools of size 50 is adequate for most scenarios, however, for very low prevalence flocks, a gain in FSe can be made by increasing the number of pools tested and a higher Sek can be achieved by reducing pool sizes. Keywords: pooling, paratuberculosis, ovine Johne’s disease, Australia, Mycobacterium, epidemiology.Meat and livestock australi

Controlling Equine Influenza: Policy Networks and Decision-Making During the 2007 Australian Equine Influenza Outbreak.

Rapid, evidence-based decision-making is critical during a disease outbreak response however compliance by stakeholders is necessary to ensure that such decisions are effective – especially if the response depends on voluntary action. This mixed method study evaluated technical policy decision-making processes during the 2007 outbreak of equine influenza in Australia by identifying and analysing the stakeholder network involved and the factors driving policy decision-making. The study started with a review of the outbreak literature and published policy documents. This identified six policy issues regarding policy modifications or differing interpretations by different state agencies. Data on factors influencing the decision-making process for these six issues and on stakeholder interaction were collected using a pre-tested, semi-structured questionnaire. Face-to-face interviews were conducted with 24 individuals representing 12 industry and government organisations. Quantitative data were analysed using social network analysis. Qualitative data were coded and patterns matched to test a pre-determined general theory using a method called theory-oriented process-tracing. Results revealed that technical policy decisions were framed by social, political, financial, strategic and operational considerations. Industry stakeholders had influence through formal pre-existing channels, yet specific gaps in stakeholder interaction were overcome by reactive alliances formed during the outbreak response but outside the established system. Overall, the crisis management system and response was seen as positive and 75100% of individuals interviewed were supportive of, had interest in and considered the outcome as good for the majority of policy decisions, yet only 4675% of those interviewed considered that they had influence on these decisions. Training to increase awareness and knowledge of emergency animal diseases and response systems will improve stakeholder participation in emergency disease management and preparedness for future emergency animal disease incursions. Key words: emergency animal disease outbreak, policy decision-making, equine influenza, risk management, preparednessfinancial support of the Rural Industries Research and Development Corporation (RIRDC

Demographics and husbandry of pet cats living in Sydney, Australia: results of cross-sectional survey of pet ownership

Our aim was to collect baseline data on the age, gender, breed, reproductive status and husbandry (housing, diet, vaccination, veterinary attention) of pet cats living in Sydney. Accordingly, a cross-sectional survey of 2768 households was conducted using a postal questionnaire. The 2006 Sydney residential phone book was used as the sampling frame. Non-responders were re-mailed the questionnaire on two further occasions, two and four weeks after the first postings. Completed questionnaires were received from 884 households. No pets were kept by 387 (43.8%) respondents. Dogs and cats were owned by 295 (33.4%) and 198 (22.5%) of households, respectively, with 7.8% of households having both cat(s) and dog(s). Fish and birds were the next most popular pets. Of the 198 cat-owning households, 54.0% kept only cat(s), while 46.5% kept cats with other pets. The distribution of cat ownership across Sydney was non-uniform. Each cat-owning household kept 1.3 cats on average, with the majority keeping one (75.8% households) or two (18.7%). For the 260 cats, the mean age was 7.1 years, the median 6 years, with a range of 3 months to 22 years. There were significantly more female (143; 55%) than male cats (117; 45%). Only 7 cats (2.7%) were sexually entire, and these were all ≤ 6-years. Crossbred cats outnumbered pedigree cats by a ratio of 3.3:1. The Burmese was the most common breed, followed by the Persian. The median age of pedigree cats (5.5 years) was significantly lower than for domestic crossbred cats (7.0 years). Most cats were housed both indoors and outdoors (72.6%), with 19.7% being restricted to indoors and/or “pet park enclosures”. Pedigree cats were significantly more likely than crossbreds to be housed indoors. Most cat owners fed their cats a combination of commercial dry and canned food (38.1%), although fresh meat was popular also and either fed alone (1.6%) or in combination with dry food (14.4%), tinned food (1.6%) or canned and dry food (25.8%). A diet consisting of dry food alone was fed to cats in 13.4% of households. Ninety percent of cats had been vaccinated at least once, while 72.2% received a vaccination in the last three years. Older cats were less likely to have been vaccinated recently than younger cats. Only 5.8% of cats had never visited a veterinarian. For the 243 cats that had received veterinary attention, the average number of years since the last visit was 1.5. Keywords: cat, age, breed, gender, population, cross-sectional study, survey, Australiafunded by the Valentine Charlton Bequest of the Post Graduate Foundation (PGF) of Veterinary Science of the University of Sydne

One health in our backyard: Design and evaluation of an experiential learning experience for veterinary medical students

Background: New educational approaches are needed to improve student understanding of the wider sociological and ecological determinants of health as well as professional responsibilities in related areas. Field trips allow students to observe interaction between plant, animal and human communities, making them an ideal tool for teaching One Health concepts. Methods: Veterinary medical students participated in a field trip to a local parklands area, frequented by humans, dogs, horses, and wildlife. Students rotated through 5 learning activities (‘stations’) that focused on: (1) response to exotic animal disease incursion (equine influenza); (2) impact of cultures and belief systems on professional practice; (3) management of dangerous dogs; (4) land use change, biodiversity and emerging infectious disease; and (5) management of environmentally-acquired zoonoses (botulism). Intended learning outcomes were for students to: evaluate the various roles and responsibilities of veterinarians in society; compare the benefits and risks associated with human-animal and animal-animal interactions; and evaluate the contributions made by various professionals in safeguarding the health and welfare of animals, humans and the environment. Following the field trip, students participated in a debrief exercise and completed an online survey on their experiences. Results: Feedback from students collected in 2016/2017 (n = 211) was overwhelmingly positive. The learning experience at each station was rated as 4 (‘Good’) or 5 (‘Very Good’) out of 5 by 82–96% of students. Responses to closed- and open-ended questions − as well as outputs generated in the debrief session − indicated that students achieved the learning outcomes. Overall, 94% of students agreed or strongly agreed that they had a better understanding of One Health because of the field trip. Conclusions: Field trips to local parklands are effective in promoting learning about One Health and can be incorporated into the core curriculum to maximize student exposure at relatively low cost. Keywords: One health, Field trip, Experiential learning, Veterinary education, Cultural competence, Zoonoses, Animal behavio

Retrospective investigation of the 2019 African swine fever epidemic within smallholder pig farms in Oudomxay province, Lao PDR

The 2019 African swine fever (ASF) outbreak in the Lao People’s Democratic Republic (Lao PDR or Laos) represented a major epidemiologic event where a transitioning lower-middle income nation (LMIC) experienced a viral epidemic in a naïve pig population. The diversity of pig management styles creates challenges for local and regional policymakers when formulating recommendations to control an ASF outbreak. The aim of this study were to investigate the management of pigs in villages of Oudomxay province that were affected by ASF in 2019, as a case study in a smallholder pig-rasing system in northern Laos. The frequencies of well known risk factors were measured in the affected villages and the timelines and household level stock losses due to the outbreak were investigated. These findings were compared to data available from a similar outbreak in the southern province of Savannakhet. Disease control implications of these findings are discussed. Mean losses were 3.0–23.3 pigs per household, with a mean lost herd value of USD 349, 95% CI (294–415). These pig losses reflect those estimated in Savannakhet (6.7 pigs per household). However, the financial loss estimated per household was higher, USD 349 versus USD 215, possibly due to higher pig values and a higher input/output management approach in Oudomxay. The investigation revealed the presence of numerous ASF risk factors, such as swill-feeding and free-ranging. In addition, poor biosecurity practices – such as inappropriate garbage disposal and slaughtering – that could contaminate the environment were present. ASF cases occurred across all villages between June and December 2019, with outbreak periods ranging from 22–103 days. These values are consistent with the outbreak in Savannakhet; however, notable differences in management styles were observed. These findings demonstrate the need for more disease control resources from the village to the Governmental level. Villages need support in enacting context appropriate biosecurity measures, whilst the ongoing surveillance and investigation of ASF require investment in logistical and veterinary resources at the Governmental level

The Influence of Meteorology on the Spread of Influenza: Survival Analysis of an Equine Influenza (A/H3N8) Outbreak

The influences of relative humidity and ambient temperature on the transmission of influenza A viruses have recently been established under controlled laboratory conditions. The interplay of meteorological factors during an actual influenza epidemic is less clear, and research into the contribution of wind to epidemic spread is scarce. By applying geostatistics and survival analysis to data from a large outbreak of equine influenza (A/H3N8), we quantified the association between hazard of infection and air temperature, relative humidity, rainfall, and wind velocity, whilst controlling for premises-level covariates. The pattern of disease spread in space and time was described using extraction mapping and instantaneous hazard curves. Meteorological conditions at each premises location were estimated by kriging daily meteorological data and analysed as time-lagged time-varying predictors using generalised Cox regression. Meteorological covariates time-lagged by three days were strongly associated with hazard of influenza infection, corresponding closely with the incubation period of equine influenza. Hazard of equine influenza infection was higher when relative humidity was <60% and lowest on days when daily maximum air temperature was 20–25°C. Wind speeds >30 km hour−1 from the direction of nearby infected premises were associated with increased hazard of infection. Through combining detailed influenza outbreak and meteorological data, we provide empirical evidence for the underlying environmental mechanisms that influenced the local spread of an outbreak of influenza A. Our analysis supports, and extends, the findings of studies into influenza A transmission conducted under laboratory conditions. The relationships described are of direct importance for managing disease risk during influenza outbreaks in horses, and more generally, advance our understanding of the transmission of influenza A viruses under field conditions

Adsorption of Mycobacterium avium subsp. paratuberculosis to Soil Particles ▿

Attachment of Mycobacterium avium subsp. paratuberculosis to soil particles could increase their availability to farm animals, as well as influence the transportation of M. avium subsp. paratuberculosis to water sources. To investigate the possibility of such attachment, we passed a known quantity of M. avium subsp. paratuberculosis through chromatography columns packed with clay soil, sandy soil, pure silica, clay-silica mixture, or clay-silica complexes and measured the organisms recovered in the eluent using culture or quantitative PCR. Experiments were repeated using buffer at a range of pH levels with pure silica to investigate the effect of pH on M. avium subsp. paratuberculosis attachment. Linear mixed-model analyses were conducted to compare the proportional recovery of M. avium subsp. paratuberculosis in the eluent between different substrates and pH levels. Of the organisms added to the columns, 83 to 100% were estimated to be retained in the columns after adjustment for those retained in empty control columns. The proportions recovered were significantly different across different substrates, with the retention being significantly greater (P < 0.05) in pure substrates (silica and clay-silica complexes) than in soil substrates (clay soil and sandy soil). However, there were no significant differences in the retention of M. avium subsp. paratuberculosis between silica and clay-silica complexes or between clay soil and sandy soil. The proportion retained decreased with increasing pH in one of the experiments, indicating greater adsorption of M. avium subsp. paratuberculosis to soil particles at an acidic pH (P < 0.05). The results suggest that under experimental conditions M. avium subsp. paratuberculosis adsorbs to a range of soil particles, and this attachment is influenced by soil pH