Use of spatio-temporal habitat suitability modelling to prioritise areas for common carp biocontrol in Australia using the virus CyHV-3.

Common carp (Cyprinus carpio) are an invasive species of the rivers and waterways of south-eastern Australia, implicated in the serious decline of many native fish species. Over the past 50 years a variety of control options have been explored, all of which to date have proved either ineffective or cost prohibitive. Most recently the use of cyprinid herpesvirus 3 (CyHV-3) has been proposed as a biocontrol agent, but to assess the risks and benefits of this, as well as to develop a strategy for the release of the virus, a knowledge of the fundamental processes driving carp distribution and abundance is required. To this end, we developed a novel process-based modelling framework that integrates expert opinion with spatio-temporal datasets via the construction of a Bayesian Network. The resulting weekly networks thus enabled an estimate of the habitat suitability for carp across a range of hydrological habitats in south-eastern Australia, covering five diverse catchment areas encompassing in total a drainage area of 132,129 km2 over a period of 17-27 years. This showed that while suitability for adult and subadult carp was medium-high across most habitats throughout the period, nevertheless the majority of habitats were poorly suited for the recruitment of larvae and young-of-year (YOY). Instead, high population abundance was confirmed to depend on a small number of recruitment hotspots which occur in years of favourable inundation. Quantification of the underlying ecological drivers of carp abundance thus makes possible detailed planning by focusing on critical weaknesses in the population biology of carp. More specifically, it permits the rational planning for population reduction using the biocontrol agent, CyHV-3, targeting areas where the total population density is above a "damage threshold" of approximately 100 kg/ha.

Social network analysis of the movement of poultry to and from live bird markets in Bali and Lombok, Indonesia.

Highly pathogenic avian influenza H5N1 has resulted in large losses to the Indonesian poultry sector. Evidence suggests that live bird markets (LBMs) play an important role in the epidemiology of the disease. Knowledge of the frequency and type of contact between the various poultry market players should allow animal health authorities to develop a better understanding of factors influencing virus transmission between Indonesian villages. A questionnaire-based cross-sectional survey was conducted in 17 LBMs on the neighbouring Indonesian islands of Bali and Lombok to investigate the movement patterns of poultry to and from markets. Using social network analyses, a network of contacts was created for each island from a total of 413 live poultry traders and 134 customers. Individual nodes with high degree and/or betweenness were identified in each network. The Lombok network was more dense and connected than the Bali network indicating that disease transmission would be more efficient in the Lombok network. Our findings indicate that whilst live poultry are typically transported over relatively short distances of approximately 10 km, it is not uncommon for traders and customers to travel in excess of 100 km to buy or sell poultry, which may facilitate the spread of disease over a large geographical area. This study highlights the different roles markets play in poultry movement networks and their potential for disease dissemination. The identification of highly influential market nodes allows authorities to target HPAI surveillance activities to locations where disease is more likely to be present, which is crucial in low-resource settings.

Turnover of Village Chickens Undermines Vaccine Coverage to Control HPAI H5N1.

Highly pathogenic avian influenza (HPAI) subtype H5N1 remains an enzootic disease of village chickens in Indonesia, posing ongoing risk at the animal-human interface. Previous modelling showed that the fast natural turnover of chicken populations might undermine herd immunity after vaccination, although actual details of how this effect applies to Indonesia's village chicken population have not been determined. We explored the turnover effect in Indonesia's scavenging and mixed populations of village chickens using an extended Leslie matrix model parameterized with data collected from village chicken flocks in Java region, Indonesia. Population dynamics were simulated for 208 weeks; the turnover effect was simulated for 16 weeks after vaccination in two 'best case' scenarios, where the whole population (scenario 1), or birds aged over 14 days (scenario 2), were vaccinated. We found that the scavenging and mixed populations have different productive traits. When steady-state dynamics are reached, both populations are dominated by females (54.5%), and 'growers' and 'chicks' represent the most abundant age stages with 39% and 38% in the scavenging, and 60% and 25% in the mixed population, respectively. Simulations showed that the population turnover might reduce the herd immunity below the critical threshold that prevents the re-emergence of HPAI H5N1 4-8 weeks (scavenging) and 6-9 weeks (mixed population) after vaccination in scenario 1, and 2-6 weeks (scavenging) and 4-7 weeks (mixed population) after vaccination in scenario 2. In conclusion, we found that Indonesia's village chicken population does not have a unique underlying population dynamic and therefore, different turnover effects on herd immunity may be expected after vaccination; nonetheless, our simulations carried out in best case scenarios highlight the limitations of current vaccine technologies to control HPAI H5N1. This suggests that the improvements and complementary strategies are necessary and must be explored.

Responses to diagnostic tests for bovine tuberculosis in dairy and non-dairy cattle naturally exposed to Mycobacterium bovis in Great Britain.

Field surveillance of British cattle using the single intradermal comparative cervical tuberculin (SICCT) test shows a higher incidence rate of bovine tuberculosis (bTB) in dairy compared to beef herds, but a lower probability of post-mortem examination confirmed (PMC) Mycobacterium bovis infection in dairy herds. A cross-sectional study was conducted to compare animal level differences in bTB detection between dairy and non-dairy cattle in Great Britain. During the period from 2002 to 2005, 200 (41% dairy) reactors in the SICCT test (standard interpretation) were randomly selected, and 200 in-contact cattle (43% dairy) were purposively selected from bTB-infected herds. Interferon (IFN)-γ responses in blood to bovine and avian purified protein derivative (PPD), and early secretory antigen target 6 kDa and culture filtrate protein 10 (ESAT-6/CFP10), were measured. The post-mortem examination included gross pathological examination, mycobacterial culture and histopathology. The proportions of cattle positive to ESAT6/CFP10 were 26% (95% confidence interval, CI, 15-39%) in dairy reactors and 62% (95% CI 51-72%) in non-dairy reactors (P <0.001). PMC risk was 34% (95% CI 24-45%) in dairy reactors and 69% (95% CI 60-78%) in non-dairy reactors (P <0.001). The odds ratio for PMC risk in dairy reactors compared to non-dairy reactors, after controlling for bTB prevalence, herd size and SICCT test response, was 0.27 (95% CI 0.14-0.53; P <0.001). In surveillance data, adjusted animal level PMC risks were lower for dairy reactors than for beef reactors aged >2 years (P <0.001).

Hendra Virus Infection Dynamics in the Grey-Headed Flying Fox (Pteropus poliocephalus) at the Southern-Most Extent of Its Range: Further Evidence This Species Does Not Readily Transmit the Virus to Horses.

Hendra virus (HeV) is an important emergent virus in Australia known to infect horses and humans in certain regions of the east coast. Whilst pteropid bats ("flying foxes") are considered the natural reservoir of HeV, which of the four mainland species is the principal reservoir has been a source of ongoing debate, particularly as shared roosting is common. To help resolve this, we sampled a colony consisting of just one of these species, the grey-headed flying fox, (Pteropus poliocephalus), at the southernmost extent of its range. Using the pooled urine sampling technique at approximately weekly intervals over a two year period, we determined the prevalence of HeV and related paramyxoviruses using a novel multiplex (Luminex) platform. Whilst all the pooled urine samples were negative for HeV nucleic acid, we successfully identified four other paramyxoviruses, including Cedar virus; a henipavirus closely related to HeV. Collection of serum from individually caught bats from the colony showed that antibodies to HeV, as estimated by a serological Luminex assay, were present in between 14.6% and 44.5% of animals. The wide range of the estimate reflects uncertainties in interpreting intermediate results. Interpreting the study in the context of HeV studies from states to the north, we add support for an arising consensus that it is the black flying fox and not the grey-headed flying fox that is the principal source of HeV in spillover events to horses.

Modelling spatio-temporal patterns of long-distance Culicoides dispersal into northern Australia.

Novel arboviruses, including new serotypes of bluetongue virus, are isolated intermittently from cattle and insects in northern Australia. These viruses are thought to be introduced via windborne dispersal of Culicoides from neighbouring land masses to the north. We used the HYSPLIT particle dispersal model to simulate the spatio-temporal patterns of Culicoides dispersal into northern Australia from nine putative source sites across Indonesia, Timor-Leste and Papua New Guinea. Simulated dispersal was found to be possible from each site, with the islands of Timor and Sumba highlighted as the likely principal sources and February the predominant month of dispersal. The results of this study define the likely spatial extent of the source and arrival regions, the relative frequency of dispersal from the putative sources and the temporal nature of seasonal winds from source sites into arrival regions. Importantly, the methodology and results may be applicable to other insect and pathogen incursions into northern Australia.

Bayesian hierarchical modelling to enhance the epidemiological value of abattoir surveys for bovine fasciolosis.

Four classes of Bayesian hierarchical models were evaluated using an historical dataset from an abattoir survey for fasciolosis conducted in Victoria, Australia. The purpose of this analysis was to identify areas of high prevalence and to explain these in terms of environmental covariates. The simplest of the Bayesian models, with a single random effect, validated the use of smoothed maps for cartographic display when the sample sizes vary. The model was then extended to partition the random effect into spatially structured and unstructured components, thus allowing for spatial autocorrelation. Rainfall, irrigation, temperature-adjusted rainfall and a remotely sensed surrogate for rainfall, the normalised difference vegetation index (NDVI), were then introduced into the models as explanatory variables. The variable that best explained the observed distribution was irrigation. Associations between prevalence and both rainfall and NDVI that were significant in fixed effects models were shown to be due to spatial confounding. Nevertheless, provided they are used cautiously, confounded variables may be valid predictors for the prevalence of disease.

Use of web-enabled databases for complex animal health investigations.

Web-enabled databases developed in the late 1990s to help organise large web sites and allow data capture via browser-based forms. By enabling users outside a closed network access to a central database, they permit greater flexibility than traditional 'client-server' systems. Accordingly, web-enabled databases introduce a new tool for epidemiologists, permitting direct data capture at source and thus avoiding many of the delays and errors arising from paper forms and manual data entry. In addition, real-time data collection permits sophisticated decision support and reporting, and thus improved project co-ordination and participation. Nevertheless, the technology is complex and the development of a web-application requires an attention to information technology project management equal to that of the scientific trial or investigation. The potential and problems of web database applications are illustrated by a bespoke system ('PathMan') developed by the Veterinary Laboratories Agency of the United Kingdom Department for Environment, Food and Rural Affairs to manage a large multi-site study investigating the pathogenesis of bovine tuberculosis in England and Wales.

How best to geo-reference farms? A case study from Cornwall, England.

The commonest way of geo-referencing farms as single points is using the location of the farmhouse as either read off a map or approximated by its postcode. While these two methods may be adequate for small farms, they are unlikely to be satisfactory for large ones, or alternatively when they are comprised of several discrete units or holdings. In order to investigate the best representation of the total farm polygon(s) by a single point, we undertook a study using nearly 500 actual farm boundaries in the county of Cornwall, England. For each farm, the farm boundaries were digitised, and its area and centroid determined using ArcView 3.2. A variety of point geo-referencing systems were tested to find the best single point location for a farm, as judged by the proportion of farm area captured. Whilst the centroid was found to capture the largest area, the main farm building was judged to be the best geo-referencing method for practical purposes. In contrast, the various systems of geo-coding using the farm postal address performed relatively poorly. Where there are separate parcels of land managed together in a single parish, they may be identified as a single unit, but if there are separate parcels in different parishes they should be identified as separate units.The implications of these results for Great Britain's national animal health information system (VETNET) are discussed.

Molecular epidemiology of bovine tuberculosis. II. Applications of genotyping.

The applications of genotyping of Mycobacterium bovis are reviewed. Published research to date has been conducted predominantly within the context of validating typing methods, and few studies have been specifically epidemiological. This is contrasted with the situation in human tuberculosis, where the application of restriction fragment length polymorphism typing using insertion sequence IS6110 has successfully led to insights into the epidemiology and molecular evolution of the pathogen. Based upon the medical experience, the adoption of an integrated approach which combines epidemiology and molecular biology is recommended for future studies. Accordingly, clear identification and explanation of type clustering should be possible, which should facilitate decisions related to disease control.

Molecular epidemiology of bovine tuberculosis. I. Mycobacterium bovis genotyping.

The lack of a typing system for Mycobacterium bovis has, until recently, been an impediment to undertaking sophisticated epidemiological studies to assist in the control and eradication of tuberculosis in domestic animals. Molecular biology techniques for mycobacteria have been in development since the mid-1980s, leading to the availability of a number of genetic typing systems for M. bovis. The authors summarise the available techniques, identify those which are most useful at present and those which might prove useful in the future. The present recommendation is to use spoligotyping analysis for rapid, large scale screening of M. bovis isolates, and to use restriction fragment length polymorphism analysis using the polymorphic guanine and cytosine-rich repeat sequences probe where greater differentiation of isolates is required. In the future, systematic analysis of the genome sequence of M. bovis will allow the development of improved techniques that combine good discrimination with ease of use.