Invited Review: Improved control of Johne's disease in dairy cattle through advancements in diagnostics, testing and management of young stock.

Johne's disease (JD; paratuberculosis) control programs have been regionally implemented across the globe, but few have successfully eradicated the pathogen (Mycobacterium avium ssp. paratuberculosis (MAP)) causing this disease. The limited success may partly be attributed to excluding young stock (calves and replacement heifers or bulls) from testing strategies aimed at identifying MAP-infected cattle. Young stock can shed MAP in feces and can have detectable MAP-specific antibodies in blood, as confirmed in experimentally and naturally infected cattle. Furthermore, MAP transmission causes new infections in young stock. Calves and heifers are often included in JD management strategies on dairy farms but excluded from conventional diagnostic tests due to a presumed lag between infection and detection of MAP shedding and/or MAP-specific serum antibodies. We summarize evidence of MAP shedding early in the course of infection and discuss promising diagnostics, testing and management strategies to support inclusion of young stock in JD control programs. Improvements in fecal Polymerase Chain Reaction, interferon-gamma release assay (IGRA), and enzyme-linked immunosorbent assay (ELISA) enable earlier detection of MAP and specific early immune responses. Studies on IGRA and ELISA have focused on evaluation of new antigens and optimal age of testing. There are new diagnostics, including phage-based tests to detect viable MAP, and gene expression patterns and metabolomics to detect MAP-infected young stock. In addition, refinements in testing and management of calves and heifers may enable reductions in MAP prevalence. We provide recommendations for dairy farmers, researchers, veterinarians, and other stakeholders that may improve JD control programs with an objective to control and potentially eradicate JD. Additionally, we have identified the most pressing gaps in knowledge that currently hamper inclusion of young stock in JD prevention and control programs. In summary, transmission among young stock may cause new MAP infections, and appropriate use of new diagnostic tests, testing and management strategies for young stock may improve the efficacy of JD control programs.

Systematic review of bovine and zoonotic tuberculosis in the Western Pacific and the Southeast Asia regions of the World Health Organization.

Introduction: Tuberculosis (TB) remains a leading cause of mortality worldwide. We conducted this systematic review to understand the distribution of bovine and zoonotic tuberculosis in the World Health Organization (WHO)'s Southeast Asia Region (SEAR) and Western Pacific Region (WPR) to inform our understanding of the risk posed by this disease. Methods: A two-pronged strategy was used by evaluating data from peer-reviewed literature and official reports. A systematic search was conducted using a structured query in four databases (Web of Science, Scopus, Medline, and PubMed) to identify any reports of the occurrence of zoonotic TB. No language and time constraints were used during the search, but non-English language articles were later excluded. The official data were sourced from the World Organization for Animal Health's (WOAH) World Animal Health Information System (WAHIS) and WHO's global TB database. Results: The retrieved records from SEAR and WPR (n = 113) were screened for eligibility, and data about disease occurrence were extracted and tabulated. In SEAR, all of the five studies that conducted Mycobacterium speciation (5/6) in humans were from India, and the reported Mycobacterium species included M. tuberculosis, M. bovis, M. scrofulacium, M. kansasii, M. phlei, M. smegmatis and M. orygis. In WPR, Mycobacterium speciation investigations in humans were conducted in Australia (8), China (2), Japan (2), NewZealand (2) and Malaysia (1), and the reported Mycobacterium species included M. bovis, M. africanum and M. tuberculosis. Seven countries in WHO's SEAR have officially reported the occurrence of Mycobacterium bovis in their animals: Bangladesh, India, Indonesia, Myanmar, Nepal, Sri Lanka and Thailand. In WPR, the WAHIS information system includes reports of the identification of M. bovis from 11 countries - China, Fiji, Japan, Malaysia, Mongolia, New Zealand, the Philippines, the Republic of Korea, Singapore, Tonga and Viet Nam. In contrast, human zoonotic TB cases in the WHO database were only listed from Australia, Brunei Darussalam and Palau countries. Discussion: The available data suggests under-reporting of zoonotic TB in the regions. Efforts are required to strengthen zoonotic TB surveillance systems from both animal and human health sides to better understand the impact of zoonotic TB in order to take appropriate action to achieve the goal of ending the TB epidemic.

Host characteristics and their influence on zoonosis, disease emergence and multi-host pathogenicity.

The interplay between agent-host-environment characteristics is responsible for the emergence and zoonotic potential of infectious disease pathogens. Many studies have investigated key agent characteristics and environmental factors responsible for these phenomena. However, little is known about the role played by host characteristics in zoonoses, disease emergence and the ability of pathogens to infect multiple hosts. We compiled a dataset of 8114 vertebrate host-agent interactions from published literature. Multiple host characteristics and the pathogen's zoonotic, emergence and multi-host potential were then linked to the dataset. The associations between zoonotic, emerging human pathogen and multi-host pathogenicity and several host characteristics were explored using logistic regression models. The numbers of publications and sequences from the agent-host combinations were used to control for the research effort. Hosts in the class Aves (odds ratio [OR] 20.87, 95% CI 2.66-163.97) and Mammalia (OR 26.09, 95% CI 3.34-203.87) were more likely to host a zoonotic pathogen compared to the class Amphibia. Similarly, hosts having Bursa fabricii (i.e., birds) (OR 1.8, 95% CI 1.4-2.3) were more likely to host an emerging human pathogen. The odds of being a zoonotic pathogen were highest when the host female required a greater number of days for maturity, and the pathogen was able to affect a greater number of host species. In contrast, the hosts from which a higher number of pathogens were reported were less likely (OR 0.39, 95% CI 0.31-0.49) to be associated with an emerging human pathogen. The odds of an emerging human pathogen were highest when the host had a higher adult body mass, and the specific pathogen could affect more host species. The odds of a pathogen infecting multiple hosts were highest when a host had shorter female maturity days (>670-2830 days) and lower birth/hatching weight (>42.2-995 g) compared to longer female maturity days (>2830-6940 days) and greater birth/hatching weight (>3.31-1160 kg). We conclude that several host characteristics - such as mass, maturity, immune system and pathogen permissiveness- are linked with zoonoses, disease emergence or multi-host pathogenicity. These findings can contribute to preparedness for emerging infections and zoonotic diseases.

One Health activities to reinforce intersectoral coordination at local levels in India.

India's dense human and animal populations, agricultural economy, changing environment, and social dynamics support conditions for emergence/re-emergence of zoonotic diseases that necessitate a One Health (OH) approach for control. In addition to OH national level frameworks, effective OH driven strategies that promote local intersectoral coordination and collaboration are needed to truly address zoonotic diseases in India. We conducted a literature review to assess the landscape of OH activities at local levels in India that featured intersectoral coordination and collaboration and supplemented it with our own experience conducting OH related activities with local partners. We identified key themes and examples in local OH activities. Our landscape assessment demonstrated that intersectoral collaboration primarily occurs through specific research activities and during outbreaks, however, there is limited formal coordination among veterinary, medical, and environmental professionals on the day-to-day prevention and detection of zoonotic diseases at district/sub-district levels in India. Examples of local OH driven intersectoral coordination include the essential role of veterinarians in COVID-19 diagnostics, testing of human samples in veterinary labs for Brucella and leptospirosis in Punjab and Tamil Nadu, respectively, and implementation of OH education targeted to school children and farmers in rural communities. There is an opportunity to strengthen local intersectoral coordination between animal, human and environmental health sectors by building on these activities and formalizing the existing collaborative networks. As India moves forward with broad OH initiatives, OH networks and experience at the local level from previous or ongoing activities can support implementation from the ground up.

A randomised control trial to evaluate the effectiveness of a commercial vaccine for pinkeye in Australian beef cattle.

Pinkeye (a generic term to describe infectious bovine keratoconjunctivitis) is a significant disease of cattle worldwide, impacting productivity and animal welfare. One commercial pinkeye vaccine, a systematically administered Moraxella bovis bacterin, has been available in Australia since 2007. This is the first field trial of the effectiveness of this vaccine for the prevention of naturally occurring disease in Australia. Extensively run beef herds in southwest Queensland that regularly experienced pinkeye were enrolled in the trial and animals were randomly allocated to vaccinated and control groups in different proportions in each herd. The subsequent incidence of clinical pinkeye between the two groups was compared for animals less than one-year-old. Data were analysed from 649 cattle from five herds over two pinkeye seasons: three herds of 390 calves from 1st November 2019 to 20th January 2020 and two herds of 259 calves from 23rd September 2020 to 21st April 2021. Pinkeye was common with 24% of all calves (156/649) contracting the disease during the trial. Univariable and multivariable binary logistic mixed-effect models were fitted to account for clustered data and potential residual confounding due to sex, weight, breed, coat colour, and periocular pigmentation. The incidence of pinkeye was not significantly different between vaccinated and control groups, both alone (p = 0.67) and after adjusting for sex and weight differences (p = 0.69). The vaccine was not protective against naturally occurring pinkeye under the field conditions.

A survey to understand farmers' perceptions and risk factors for hoof diseases including footrot in sheep in New South Wales, Australia.

The aims of this study were to develop an understanding of farmers' perceptions and risk factors for footrot, including its less severe forms, and other hoof diseases in sheep in New South Wales (NSW). A questionnaire was developed and administered to sheep farmers in Local Land Services (LLS) regions across NSW. LLS staff selected sheep farmers who met the inclusion criteria which included farmers with a minimum of 100 sheep, a history of having had foot problems in their flock or having expressed an interest in improving sheep health and production. Farmers completed the questionnaire either by telephone or via the REDCap online survey platform. Descriptive analyses and multivariable logistic regression models were created. The survey was completed by 43 sheep farmers with a median farm size of 1,500 Ha and flock size of 2,300; footrot was present on 39% of farms while 75.6% had other hoof diseases. A flock of >3,000 sheep were more likely to have footrot than a smaller flock (OR = 11.99, 90% CI = 3.02-63.92, P-value = 0.005) and footrot was less likely to be present on farms when an Animal Health Statement was requested while purchasing sheep (OR = 0.10, 90% CI = 0.01-0.56, P-value = 0.04). Hoof conditions other than footrot were likely to be present in flocks when foot inspections were conducted at a time other than weekly inspections (OR = 0.13, 90% CI = 0.01-0.68, P-value = 0.04) and flocks kept on undulating ground were more likely to have diseases other than footrot compared to those kept on flat ground (OR = 3.72, 90% CI = 1.02-15.80, P-value = 0.09). Most farmers agreed that footrot including its less severe forms can cause production losses and negatively affect animal health and welfare. Limitations of the study were the sample size and dry environmental conditions prior to and during study period in many regions of NSW which limited the expression of footrot.

Perceptions of Australian cattle farmers regarding the impact of pinkeye on farm productivity and animal welfare.

Pinkeye (infectious bovine keratoconjunctivitis, IBK) is an important disease of cattle worldwide. It has a substantial negative impact on farm productivity and is a major cost burden, but specific data on losses are lacking. This study was conducted to understand farmers' perceptions of the impact of pinkeye on farm productivity and animal welfare, and factors influencing the money farmers estimated spending on pinkeye in 2018. Data were collected by the first Australia-wide online survey on pinkeye. There were 1035 suitable responses analysed for impact on farm productivity. From these 82% of respondents represented farms in southern Australia, 58% reported cattle breeding as their main enterprise, and 89% bred animals on farm. Farmers were more likely to rank the impact of pinkeye on farm productivity as high if they had younger cattle, treated cattle with pinkeye more frequently, and as their herd size increased. Fewer farmers chose pinkeye as an animal welfare concern than as an economic and farm management issue, but overall animal welfare was rated by the greatest number of farmers as a high severity concern (n = 691), followed by decreased sale value and farm profits (n = 561). This suggests a shift in the equipoise between the economics of food animal production and animal welfare expectations. The median amount reportedly spent on pinkeye in 2018 by Australian farmers (n = 779) was $250.00 per farm. Farmers reported spending more money on pinkeye as herd size and number of cattle affected by pinkeye increased, their perception of pinkeye impact on farm productivity and animal welfare increased, if they treated pinkeye more frequently, reported higher fly worry, if their herds contained Angus cattle, if they bred on farm, and if they were located in southern Australian regions. Study findings should be used to better understand pinkeye, target expenditure, and improve outcomes for cattle and farmers.

Stray Dogs and Public Health: Population Estimation in Punjab, India.

The overpopulation of stray dogs is a serious public health and animal welfare concern in India. Neglected zoonotic diseases such as rabies and echinococcosis are transmitted at the stray-dog human interface, particularly in low to middle-income countries. The current study was designed to estimate the stray dog populations in Punjab to enhance the implementation of animal birth and disease (for example, rabies vaccination) control programs. This is the first systematic estimation of the stray dog population using a recommended method (mark-re-sight) in Punjab, India. The study was conducted from August 2016 to November 2017 in selected villages or wards in Punjab. For the rural areas, 22 sub-districts in each district were randomly selected, then one village from each of the 22 selected sub-districts was selected (by convenience sampling). For urban areas, 3 towns (less than 100,000 human population) and 2 large cities (more than or equal to 100,000 human population) were randomly selected, followed by convenience selection of two wards from each of the 5 selected towns/cities. To estimate the dog population size, we used a modified mark-re-sight procedure and analysed counts using two methods; the Lincoln-Petersen formula with Chapman's correction, and an application of Good-Turing theory (SuperDuplicates method; estimated per km2 and per 1000 adult humans and were compared between localities (villages vs. towns), dog sex (male vs. female) and age group (young vs. adult) using linear mixed models with district as a random effect. The predicted mean (95% CI) count of the dogs per village or ward were extrapolated to estimate the number of stray dogs in Punjab based on (a) the number of villages and wards in the state; (b) the adult human population of the state and (c) the built-up area of the state. Median stray dog populations per village and per ward using the Lincoln-Petersen formula with Chapman's correction were estimated to be 33 and 65 dogs, respectively. Higher estimates of 61 per village and 112 per ward are reported using the SuperDuplicates method. The number of males was significantly higher than the number of females and the number of adult dogs was about three times the number of young dogs. Based on different methods, estimates of the mean stray dog population in the state of Punjab ranged from 519,000 to 1,569,000. The current study revealed that there are a substantial number of stray dogs and a high number reside in rural (versus urban) areas in Punjab. The estimated stray dog numbers pose a potential public health hazard in Punjab. This impact requires assessment. The estimated stray dog numbers will help develop a dog population and rabies control program in which information about the logistics required as well as costs of implementing such programmes in Punjab can be incorporated.

Novel Hendra Virus Variant Detected by Sentinel Surveillance of Horses in Australia.

We identified and isolated a novel Hendra virus (HeV) variant not detected by routine testing from a horse in Queensland, Australia, that died from acute illness with signs consistent with HeV infection. Using whole-genome sequencing and phylogenetic analysis, we determined the variant had ≈83% nt identity with prototypic HeV. In silico and in vitro comparisons of the receptor-binding protein with prototypic HeV support that the human monoclonal antibody m102.4 used for postexposure prophylaxis and current equine vaccine will be effective against this variant. An updated quantitative PCR developed for routine surveillance resulted in subsequent case detection. Genetic sequence consistency with virus detected in grey-headed flying foxes suggests the variant circulates at least among this species. Studies are needed to determine infection kinetics, pathogenicity, reservoir-species associations, viral-host coevolution, and spillover dynamics for this virus. Surveillance and biosecurity practices should be updated to acknowledge HeV spillover risk across all regions frequented by flying foxes.

Disability-adjusted life years (DALYs) due to the direct health impact of COVID-19 in India, 2020.

COVID-19 has affected all countries. Its containment represents a unique challenge for India due to a large population (> 1.38 billion) across a wide range of population densities. Assessment of the COVID-19 disease burden is required to put the disease impact into context and support future pandemic policy development. Here, we present the national-level burden of COVID-19 in India in 2020 that accounts for differences across urban and rural regions and across age groups. Input data were collected from official records or published literature. The proportion of excess COVID-19 deaths was estimated using the Institute for Health Metrics and Evaluation, Washington data. Disability-adjusted life years (DALY) due to COVID-19 were estimated in the Indian population in 2020, comprised of years of life lost (YLL) and years lived with disability (YLD). YLL was estimated by multiplying the number of deaths due to COVID-19 by the residual standard life expectancy at the age of death due to the disease. YLD was calculated as a product of the number of incident cases of COVID-19, disease duration and disability weight. Scenario analyses were conducted to account for excess deaths not recorded in the official data and for reported COVID-19 deaths. The direct impact of COVID-19 in 2020 in India was responsible for 14,100,422 (95% uncertainty interval [UI] 14,030,129-14,213,231) DALYs, consisting of 99.2% (95% UI 98.47-99.64%) YLLs and 0.80% (95% UI 0.36-1.53) YLDs. DALYs were higher in urban (56%; 95% UI 56-57%) than rural areas (44%; 95% UI 43.4-43.6) and in men (64%) than women (36%). In absolute terms, the highest DALYs occurred in the 51-60-year-old age group (28%) but the highest DALYs per 100,000 persons were estimated for the 71-80 years old age group (5481; 95% UI 5464-5500 years). There were 4,815,908 (95% UI 4,760,908-4,924,307) DALYs after considering reported COVID-19 deaths only. The DALY estimations have direct and immediate implications not only for public policy in India, but also internationally given that India represents one sixth of the world's population.

Brucellosis in India: Comparing exposure amongst veterinarians, para-veterinarians and animal handlers.

The exposure to Brucella species is an occupational hazard for veterinary personnel in India. In our previous study, paraveterinarians and animal handlers were found to be at higher risk of being seropositive. In the present study, we further investigate comparative exposure risk to brucellosis amongst the veterinary professionals, identify risk factors, and evaluate the perceptions and practices towards using adequate personal protective equipment (PPE) while attending high risk veterinary interventions. A cross-sectional study was conducted amongst veterinary personnel in the Punjab state of India. Logistic and negative binomial regression models were constructed to interpret the influence of categorical and numerical variables on prevalence of brucellosis and the adequacy of PPE use, respectively. Compared to veterinarians, animal handlers were less likely to consider veterinary practice in sheep and goats (odds ratio [OR] 0.3; 95% confidence interval [CI]: 0.2-0.7) or assisting in obstetric interventions (OR 0.3, 95% CI 0.1-0.8) as potential exposures. They were less aware of the signs and symptoms of the disease in humans (OR 0.05, 95% CI 0.02-0.14) and of the availability of vaccines for cattle (OR 0.07, 95% CI 0.01-0.3) than the veterinarians, and were least likely of the three groups to recommend vaccination of cattle against brucellosis to animal owners (OR 0.1, 95% CI 0.02-0.3). Compared to veterinarians, they were also less likely to consider zoonotic risk (OR 0.4, 95% CI 0.2-0.8) or better efficiency (OR 0.1, 95% CI 0.05-0.4) as enablers of PPE use during veterinary procedures. Of the three occupational groups, animal handlers were also less likely to use adequate PPE during high-risk veterinary exposures, although they were found to have handled the highest number of cases of abortion. The average use of adequate PPE during high-risk interventions in one month preceding this study was lowest for animal handlers. Veterinary personnel with a higher rate of PPE use during high-risk veterinary interventions were likely to obtain information on brucellosis from government sources (p = 0.06) and felt that PPE use enhanced their professional efficiency (Incidence rate ratio [IRR] 3.3, 95% CI 1.5-8.1) compared to those who were less likely to use adequate PPE. We recommend concerted efforts to increase awareness amongst veterinary personnel, particularly amongst animal handlers, regarding brucellosis and the importance of biosecurity measures in veterinary practice. Designing training courses on the importance of PPE use along with formulation of biosecurity guidelines at local levels could help reduce the prevalence of the disease in veterinary personnel.

Geodemography, environment and societal characteristics drive the global diversity of emerging, zoonotic and human pathogens.

Understanding human disease, zoonoses and emergence is a global priority. A deep understanding of pathogen ecology and the complex inherent relationships at the agent-environment interface are essential to inform disease control and mitigation and to predict the next zoonotic pandemic. Here, we present the first analysis of social and environmental factors associated with human, zoonotic and emerging pathogen diversity at a global scale, controlling for research effort. Predictor-response associations were captured by generalized additive models. We used national level data to aid in policy development to inform control and mitigation. We show that human population density, land area, temperature and the human development index at the country level are associated with human, emerging and zoonotic pathogen diversity. Multiple models demonstrating society-agent-environment interactions demonstrate that social, environmental and geographical factors predict global pathogen diversity. The analyses demonstrate that weather variables (temperature and rainfall) have the potential to influence pathogen diversity.

Inherent virus characteristics and host range drive the zoonotic and emerging potential of viruses.

Understanding the zoonotic and emerging potential of viruses is critical to prevent and control spread that can cause disease epidemics or pandemics. We developed a database using the most up-to-date information from the International Committee on Taxonomy of Viruses (4958 virus species) and identified 1479 vertebrate virus species and their host ranges. Viral traits and host ranges were then used as predictors in generalized linear mixed models for three host-associated outcomes - confirmed zoonotic, potential zoonotic and disease emergence. We identified significant interactions between host range and viral characteristics, not previously reported, that influence the zoonotic and emergence potential of viruses. Bat- and livestock-adapted viruses posed high risk, and the risk increased substantially if these viruses were also present in other vertebrates or were not reported from invertebrates. Our model predicted 39 viruses of interest that have never been reported to have zoonotic potential (27) or to potentially become emerging human viruses (12). We conclude that nucleic acid type is important in identifying the zoonotic and emerging potential of viruses. We recommend enhanced surveillance and monitoring of these virus species identified with a zoonotic and emerging potential to mitigate disease outbreaks and future epidemics.

The epidemic volatility index, a novel early warning tool for identifying new waves in an epidemic.

Early warning tools are crucial for the timely application of intervention strategies and the mitigation of the adverse health, social and economic effects associated with outbreaks of epidemic potential such as COVID-19. This paper introduces, the Epidemic Volatility Index (EVI), a new, conceptually simple, early warning tool for oncoming epidemic waves. EVI is based on the volatility of newly reported cases per unit of time, ideally per day, and issues an early warning when the volatility change rate exceeds a threshold. Data on the daily confirmed cases of COVID-19 are used to demonstrate the use of EVI. Results from the COVID-19 epidemic in Italy and New York State are presented here, based on the number of confirmed cases of COVID-19, from January 22, 2020, until April 13, 2021. Live daily updated predictions for all world countries and each of the United States of America are publicly available online. For Italy, the overall sensitivity for EVI was 0.82 (95% Confidence Intervals: 0.75; 0.89) and the specificity was 0.91 (0.88; 0.94). For New York, the corresponding values were 0.55 (0.47; 0.64) and 0.88 (0.84; 0.91). Consecutive issuance of early warnings is a strong indicator of main epidemic waves in any country or state. EVI's application to data from the current COVID-19 pandemic revealed a consistent and stable performance in terms of detecting new waves. The application of EVI to other epidemics and syndromic surveillance tasks in combination with existing early warning systems will enhance our ability to act swiftly and thereby enhance containment of outbreaks.

Perceptions and practices of Australian cattle farmers for the treatment of pinkeye (infectious bovine keratoconjunctivitis).

Pinkeye or infectious bovine keratoconjunctivitis is a globally significant disease and occurs in every state of Australia. Economic loss due to pinkeye can be considerable and it is a major welfare concern, but not all cattle with the disease are treated by farmers. This study was conducted to understand the perceptions and practices of Australian farmers regarding the treatment of pinkeye: factors influencing when farmers treat pinkeye, treatments used and considered effective, and reasons for not treating. Data were gathered using a custom designed online questionnaire. Farmer responses suitable for assessment (n = 985) were analysed using descriptive analyses along with univariable and multivariable ordinal logistic regression models to evaluate the association of 15 explanatory variables with the outcome "when do you treat pinkeye?". Results revealed three variables, farm size, times yarded and ranking of the pain caused by pinkeye, were significantly associated with the frequency of pinkeye treatment. Specifically, farmers with smaller farm sizes were more likely to treat their cattle for pinkeye more frequently. So too were those who yarded their cattle more, and those that rated pinkeye as highly painful. The most used treatments for pinkeye in Australia were pinkeye ointments (n = 861), followed by eye patches (n = 637), pinkeye spray (n = 623), fly control (n = 507), and pinkeye powder (n = 408). Over half of those who had used subconjunctival injection, pinkeye ointments, eye patches, injectable antibiotics and veterinarians rated them as highly effective treatments. Kerosene is still used by some farmers (n = 106). The most common reason for not treating pinkeye was that it was 'too difficult to treat individuals'. These findings provide insight into the attitudes of Australian farmers to the treatment of pinkeye and should be used to improve pinkeye outcomes in cattle.

Comparison of the current abattoir surveillance system for detection of paratuberculosis in Australian sheep with quantitative PCR tissue strategies using simulation modelling.

Abattoir surveillance for Johne's disease monitoring in Australia has provided valuable feedback to producers about their flock's disease status since its commencement in 1999. The current surveillance system relies on the identification of gross lesions in sheep carcases at an abattoir, followed by sampling and histopathology testing. This manual inspection system has not been adapted to meet the changing disease situation, as infection prevalence levels have declined over time due to vaccination. This simulation study compares the current system with two alternative approaches utilising a validated quantitative (q)PCR method for the detection of Mycobacterium avium subsp. paratuberculosis in tissues, with random systematic sampling either alone or in conjunction with sampling of a single carcass presenting gross lesions. Consigned sheep were randomly simulated as either infected or uninfected according to defined prevalence levels of infection, with varying histopathological lesion severity and the presence or absence of gross lesions. These sheep were then allocated into multiple 'lines' (group of sheep slaughtered together) within each consignment, with each line subjected to testing with the three sampling strategies for the estimation of line and flock (consignment) sensitivity. The line sensitivity described the proportion of infected lines that tested positive, whereas the flock sensitivity was the proportion of consignments from the simulated infected flocks that had one or more lines test positive for paratuberculosis infection. The tissue qPCR strategy with gross lesion detection achieved marginally higher line sensitivity than the current abattoir surveillance strategy. The simulation of unvaccinated infected flocks with low to moderate prevalence levels demonstrated similar flock sensitivity for all three sampling models. However, the current strategy had very low line sensitivity for the simulated vaccinated infected flocks when the infection prevalence level was <2%. There were substantial differences in flock sensitivity between the two tissue qPCR approaches and the current abattoir surveillance strategy for vaccinated infected flocks, whereas, only marginal differences in flock sensitivity were evident between the two tissue qPCR models. Our results demonstrate that the current strategy is not effective at identifying infected animals at very low infection prevalence levels. The tissue qPCR approach investigated in this study is better as it removes the reliance on meat inspectors to identify gross lesions and can also assist in identifying flocks that have subclinical infected sheep not displaying gross lesions. Therefore, the sheep industry may benefit from incorporating tissue qPCR for Johne's disease surveillance, however the logistics and costs of conducting this type of testing would need to be considered prior to implementing any changes.

Risk factors associated with pinkeye in Australian cattle.

Pinkeye is the most important bovine ocular disease worldwide and a major welfare and economic concern to the Australian cattle industry. Pinkeye can occur in epidemic proportions, but severity and susceptibility vary within and between herds, indicating that the disease is multifactorial. This study was conducted to identify the on-farm risk factors associated with pinkeye disease in Australian cattle. Data were gathered from cattle farmers using a custom designed online questionnaire. Farmer responses suitable for assessment (n = 999) were analysed with descriptive, univariable and multivariable logistic regression to evaluate the association of 26 explanatory variables with pinkeye within-herd prevalence. Results revealed that farm location, farm grazing area, farmer-reported dust levels, fly levels, rain levels, animal zebu content and cattle age were significantly associated with pinkeye prevalence. More specifically, having a farm located in southern Australia, of smaller grazing area with cattle ≤ 2 years of age, was associated with a higher pinkeye prevalence. Pinkeye prevalence was also greater if respondents ranked their farms as having high fly levels compared to moderate and low fly levels, respectively and on farms ranked low for rainfall compared to moderate and high rainfall, respectively. Those that ranked their farms as having high dust levels had more pinkeye compared to moderate and low dust levels, but moderate dust levels were protective compared to low dust levels. The results confirm that pinkeye disease is multifactorial and is associated with a range of host and environmental factors. These findings should be used to assist in the control of the disease and improve pinkeye outcomes in Australian cattle.

Factors influencing the effectiveness of the Gudair vaccine for controlling Johne's disease in sheep flocks in Australia.

Ovine Johne's disease is a chronic debilitating disease of sheep caused by Mycobacterium avium subsp. paratuberculosis (Mptb) which results in diarrhoea, emaciation and mortalities in infected animals. Vaccination with Gudair® has been a key strategy for controlling the disease in Australia since its approval in 2002. Previous research conducted in Australia has demonstrated that the vaccine is quite effective in reducing sheep mortalities. While some farms have also been successful in reducing the prevalence of the disease in their flocks to undetectable levels, sheep in other flocks continue to shed Mptb in faeces even after an ongoing vaccination program . This study was conducted to investigate management, husbandry and biosecurity factors associated with paratuberculosis infection in Gudair® vaccinated sheep flocks in Australia. We enrolled 64 sheep farmers and interviewed them to obtain information about their management and biosecurity practices. Pooled faecal samples were collected from sheep at each farm and cultured to create two outcome variables: Mptb positive (yes/no) and disease prevalence level (nil, < 1 %, ≥ 1 %). Binary and ordinal logistic regression analyses were conducted to evaluate the association of management, husbandry and biosecurity factors with these outcome variables. Farms were more likely to have Mptb positive sheep and a higher disease prevalence in their flocks if they: (a) provided supplementary feed on the ground (instead of in a trough); (b) had a greater number of neighbours with sheep; and (c) had introduced rams from a greater number of sources. The results suggest the effectiveness of Gudair® vaccination to control OJD can be improved if sheep producers maintain other risk management strategies and biosecurity practices. Extension agencies should advise farmers not to relax their biosecurity practices and to purchase rams from only low-risk sources, even if they are continuing to vaccinate their flocks.

Simulation modelling to estimate the herd-sensitivity of various pool sizes to test beef herds for Johne's disease in Australia.

Johne's disease is a chronic intestinal disease affecting livestock. It leads to the shedding of Mycobacterium avium subspecies paratuberculosis (MAP) in the faeces, wasting and eventually death, with animal welfare, economic, and trade implications. The Johne's Beef Assurance Scheme, used in Australia to determine the risk of Johne's disease on beef properties and facilitate trade, is based on testing a subset of the herd with pooled faecal quantitative PCR. This study aimed to model the herd-sensitivity of pooled faecal testing under different Australian farming scenarios. Animals from simulated herds were randomly sampled and allocated into their respective pools. Each tested pool was provided a test outcome, with herd-sensitivity estimated as the probability of detecting a truly infected herd. The models simulated the test performance for the 'Sample' and 'Check' tests used in the assurance schemes (recommended sample sizes of 300 and 50, respectively) for a range of herd sizes, infection prevalence and MAP faecal shedding levels for the pool sizes of 5, 10, 15 and 20. Sensitivity and specificity input values of each pool size were obtained from a previous laboratory investigation. The herd-sensitivity estimate increased with herd size and infection prevalence levels, regardless of the pool size. Higher herd-sensitivity was also achieved for testing scenarios involving larger sample sizes. A pool size of 10 achieved similar herd-sensitivity to that of the current pool size for the majority of the Sample test and Check test scenarios. This was particularly evident when pool-specificity was assumed to be perfect. The overall herd-sensitivity of the Check test was very low for all infection prevalence levels and pool sizes, but it more than doubled, when the sample size increased from 50 to 100 animals (11% versus 26% for a herd size of 500 cattle with a 2% infection prevalence). The results show that the majority of beef producers participating in the assurance scheme can benefit from using a larger pool size for the pooled faecal quantitative PCR testing of their herd, in comparison to the pool size currently used.