Are the Australian poultry industries vulnerable to large outbreaks of highly pathogenic avian influenza?

An overview of avian influenza in the context of the Australian commercial poultry industry

From 1976 Australia has experienced seven highly pathogenic avian influenza (HPAI) outbreaks in poultry farms and there have been a total of 16 confirmed low pathogenic avian influenza (LPAI) cases in poultry in Australia at the time of writing. This paper describes all past LPAI and HPAI detections in Australian poultry and reviews avian influenza risk in the Australian commercial chicken industry. The factors that influence this risk are also discussed; notably the nomadic nature of Australian waterfowl, the increasing demand of free range poultry egg and meat production in Australia, and biosecurity practices implemented across farms including farm separations.

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Australia has experienced seven highly pathogenic avian influenza (HPAI) outbreaks in poultry farms

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There have been 16 confirmed low pathogenic avian influenza (LPAI) cases in poultry in Australia at the time of writing

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Australian waterfowl are nomadic in nature

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There is increasing demand of free range poultry production in Australia

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Mathematical models for avian influenza risk in Australia have been reviewed

Knowledge and remaining gaps on the role of animal and human movements in the poultry production and trade networks in the global spread of avian influenza viruses - A scoping review

Poultry production has significantly increased worldwide, along with the number of avian influenza (AI) outbreaks and the potential threat for human pandemic emergence. The role of wild bird movements in this global spread has been extensively studied while the role of animal, human and fomite movement within commercial poultry production and trade networks remains poorly understood. The aim of this work is to better understand these roles in relation to the different routes of AI spread. A scoping literature review was conducted according to the PRISMA guidelines (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) using a search algorithm combining twelve domains linked to AI spread and animal/human movements within poultry production and trade networks. Only 28 out of 3,978 articles retrieved dealt especially with the role of animal, human and fomite movements in AI spread within the international trade network (4 articles), the national trade network (8 articles) and the production network (16 articles). While the role of animal movements in AI spread within national trade networks has been largely identified, human and fomite movements have been considered more at risk for AI spread within national production networks. However, the role of these movements has never been demonstrated with field data, and production networks have only been partially studied and never at international level. The complexity of poultry production networks and the limited access to production and trade data are important barriers to this knowledge. There is a need to study the role of animal and human movements within poultry production and trade networks in the global spread of AI in partnership with both public and private actors to fill this gap.

Modelling the impact of biosecurity practices on the risk of high pathogenic avian influenza outbreaks in Australian commercial chicken farms

As of 2018, Australia has experienced seven outbreaks of highly pathogenic avian influenza (HPAI) in poultry since 1976, all of which involved chickens. There is concern that increases in free-range farming could heighten HPAI outbreak risk due to the potential for greater contact between chickens and wild birds that are known to carry low pathogenic avian influenza (LPAI). We use mathematical models to assess the effect of a shift to free-range farming on the risk of HPAI outbreaks of H5 or H7 in the Australian commercial chicken industry, and the potential for intervention strategies to reduce this risk. We find that a shift of 25% of conventional indoor farms to free-range farming practices would result in a 6-7% increase in the risk of a HPAI outbreak. Current practices to treat water are highly effective, reducing the risk of outbreaks by 25-28% compared to no water treatment. Halving wild bird presence in feed storage areas could reduce risk by 16-19% while halving wild bird access of potential bridge-species to sheds could reduce outbreak risk by 23-25%, and relatively small improvements in biosecurity measures could entirely compensate for increased risks due to the increasing proportion of free-range farms in the industry. The short production cycle and cleaning practices for chicken meat sheds considerably reduce the risk that an introduced low pathogenic avian influenza virus is maintained in the flock until it is detected as HPAI through increased mortality of chickens. These findings help explain HPAI outbreak history in Australia and suggest practical changes in biosecurity practices that could reduce the risk of future outbreaks.

Low- and High-Pathogenic Avian Influenza H5 and H7 Spread Risk Assessment Within and Between Australian Commercial Chicken Farms

This study quantified and compared the probability of avian influenza (AI) spread within and between Australian commercial chicken farms via specified spread pathways using scenario tree mathematical modeling. Input values for the models were sourced from scientific literature, expert opinion, and a farm survey conducted during 2015 and 2016 on Australian commercial chicken farms located in New South Wales (NSW) and Queensland. Outputs from the models indicate that the probability of no establishment of infection in a shed is the most likely end-point after exposure and infection of low-pathogenic avian influenza (LPAI) in one chicken for all farm types (non-free range meat chicken, free range meat chicken, cage layer, barn layer, and free range layer farms). If LPAI infection is established in a shed, LPAI is more likely to spread to other sheds and beyond the index farm due to a relatively low probability of detection and reporting during LPAI infection compared to high-pathogenic avian influenza (HPAI) infection. Among farm types, the median probability for HPAI spread between sheds and between farms is higher for layer farms (0.0019, 0.0016, and 0.0031 for cage, barn, and free range layer, respectively) than meat chicken farms (0.00025 and 0.00043 for barn and free range meat chicken, respectively) due to a higher probability of mutation in layer birds, which relates to their longer production cycle. The pathway of LPAI spread between sheds with the highest average median probability was spread via equipment (0.015; 5-95%, 0.0058-0.036) and for HPAI spread between farms, the pathway with the highest average median probability was spread via egg trays (3.70 × 10^-5; 5-95%, 1.47 × 10^-6-0.00034). As the spread model did not explicitly consider volume and frequency of the spread pathways, these results provide a comparison of spread probabilities per pathway. These findings highlight the importance of performing biosecurity practices to limit spread of the AI virus. The models can be updated as new information on the mechanisms of the AI virus and on the volume and frequency of movements shed-to-shed and of movements between commercial chicken farms becomes available.

Assessing the probability of introduction and spread of avian influenza (AI) virus in commercial Australian poultry operations using an expert opinion elicitation

The objective of this study was to elicit experts’ opinions and gather estimates on the perceived probability of introduction and spread of avian influenza (AI) virus in the Australian broiler and layer industry. Using a modified Delphi method and a 4-step elicitation process, 11 experts were asked to give initial individual estimates for the various pathways and practices in the presented scenarios using a questionnaire. Following this, a workshop was conducted to present group averages of estimates and discussion was facilitated to obtain final individual estimates. For each question, estimates for all experts were combined using a discrete distribution, with weights allocated representing the level of expertise. Indirect contact with wild birds either via a contaminated water source or fomites was considered the most likely pathway of introduction of low pathogenic avian influenza (LPAI) on poultry farms. Presence of a water body near the poultry farm was considered a potential pathway for introduction only when the operation type was free range and the water body was within 500m distance from the shed. The probability that LPAI will mutate to highly pathogenic avian influenza (HPAI) was considered to be higher in layer farms. Shared personnel, equipment and aerosol dispersion were the most likely pathways of shed to shed spread of the virus. For LPAI and HPAI spread from farm to farm, shared pick-up trucks for broiler and shared egg trays and egg pallets for layer farms were considered the most likely pathways. Findings from this study provide an insight on most influential practices on the introduction and spread of AI virus among commercial poultry farms in Australia, as elicited from opinions of experts. These findings will be used to support parameterization of a modelling study assessing the risk of AI introduction and spread among commercial poultry farms in Australia.

Demographics and practices of semi-intensive free-range farming systems in Australia with an outdoor stocking density of ≤1500 hens/hectare

Baseline information on demographics and practices on semi-intensive free-range egg farms with an outdoor stocking density of ≤1500 hens/hectare in Australia is presented. Free-range egg production is changing the structure of the egg industry in Australia and a broad variety and tiers of free-range systems have emerged due to lack of concrete legislative standards on outdoor stocking densities in the past. Information was extracted from a pre-existing online free-range poultry survey dataset, consisting of a total of 79 questions related to nutrition, pasture management, welfare and health, animal housing, environmental impact and economics. Forty-one free-range egg farms, with an outdoor stocking density of ≤1500 hens/hectare, were identified in the dataset from all major Australian states. Two types of semi-intensive free-range housing systems were documented: mobile (modified caravan/trailer) housing (56%), and fixed sheds (44%). Seventy-two percent of respondents reported >75% of the hens in the flock used the outdoor range. All respondents reported ingestion of range components by hens in the form of vegetation, insects, stones and grit. Up to 10% mortality was reported by 40% respondents with predation (34%), cannibalism (29%), heat stress (24%) and grass impaction (19.5%) as major causes. Biosecurity on farms was sub-optimal with 8 of the 10 actions implemented by <50% respondents. Customer demand, consumer sentiment and welfare were the major factors for farmers moving into free-range egg production. This study resulted in identification of current practices and key challenges on semi-intensive free-range egg farms. Applied research and communication of results to farmers is highly recommended to ensure optimum health and welfare of free-range laying hens and sustained egg production.

Prospective study of avian influenza H9 infection in commercial poultry farms of Punjab Province and Islamabad Capital Territory, Pakistan

A prospective study was conducted from November 2013 to February 2014 to estimate the spatial clustering; cumulative incidence and risk factors associated with avian influenza (AI) subtype H9 infection on commercial poultry farms of Pakistan. A total of 400 farms were enrolled and followed during the study period. Among these, 109 farms submitted samples suspected for AI to the laboratory, and only 47 farms were confirmed positive by hemagglutinin inhibition (HI) test. Data was collected from these 109 farms about their demography, management, and biosecurity practices. The cumulative incidence of H9N2 was 11.75 % (95 % confidence interval (CI) 8.76–15.23). The highest number of cases (40.42 %) was reported in January. One most likely cluster (p = 0.009, radius = 4.61 km) occurred in the Kasur district. Multivariable logistic regression analyses showed that the presence of wild birds on the farms (odds ratio (OR) = 16.18; 95 % CI 3.94–66.45) was independently associated with H9N2 infection. Cleaning of cages before delivery on farm (OR = 0.16; 95 % CI = 0.06–0.47), presence of a footbath at the entrance of farm (OR = 0.24; 95 % CI 0.08–0.79), and changing of gloves (OR = 0.33; 95 % CI 0.11–0.99) were protective factors against H9N2 infection. Reducing the exposure to risk factors and adapting biosecurity measures may reduce the risk of AI H9N2 infection on commercial poultry farms in Pakistan.

Evaluating the risk of avian influenza introduction and spread among poultry exhibition flocks in Australia

Some practices undertaken by poultry exhibitors, such as allowing wild birds to contact domestic birds, the high frequency of bird movements and the lack of appropriate isolation for incoming birds, pose a risk for disease introduction and spread. The aim of the current study was to quantitatively assess the probability of introduction of low pathogenic avian influenza (LPAI) viruses from wild waterfowl into poultry exhibition flocks and the subsequent spread to other poultry flocks. Exposure and consequence assessments, using scenario trees and Monte Carlo stochastic simulation modelling, were conducted to identify potential pathways of introduction and spread and calculate the probabilities of these pathways occurring. Input parameters were estimated from two recently conducted cross-sectional studies among poultry exhibitors in Australia (Dusan et al., 2010; Hernández-Jover et al., 2013) and other scientific literature. According to reported practices of poultry exhibitors and the LPAI prevalence in wild birds in Australia, this assessment estimates a median (5-95%) probability of exposure of a bird kept by a poultry exhibitor of 0.004 (0.003-0.005). Due to the higher susceptibility of infection of turkeys and waterfowl, this probability is higher in flocks keeping these bird species than in those keeping chickens or pigeons only. Similarly, once exposure has occurred, establishment of infection and subsequent spread are more likely in those flocks keeping waterfowl and turkeys than in those keeping chicken and pigeons only. Spread through movement of birds is the most likely pathway of spread, followed by contaminated fomites, wild birds and airborne spread. The median probability of LPAI spread through movement of birds in flocks keeping waterfowl and turkeys was estimated to be 0.280 (0.123-0.541) and 0.230 (0.104-0.421), respectively. A lower probability was estimated for chicken (0.087; 0.027-0.202) and pigeon (0.0003; 3.0×10(-5)-0.0008) flocks. The sensitivity analysis indicates that the prevalence of LPAI in wild waterfowl and the probability of contact of domestic birds with wild waterfowl are the most influential parameters on the probability of exposure; while the probability of spread is mostly influenced by the probability of movement of birds and the probability of the exhibitor detecting and reporting LPAI. To minimize the potential risk of AI introduction and spread, poultry exhibitors should prevent contact of domestic birds with wild birds, and implement appropriate biosecurity practices. In addition, adequate extension services are required to improve exhibitors' abilities to recognize diseases and reporting behaviour.

Risk-based surveillance of avian influenza in Australia's wild birds

Context. The epidemiology of avian influenza and the ecology of wild birds are inextricably linked. An understanding of both is essential in assessing and managing the risks of highly pathogenic avian influenza (HPAI). Aims. This project investigates the abundance, movements and breeding ecology of Australia’s Anseriformes in relation to the prevalence of low-pathogenicity avian influenza (LPAI) and provides risk profiles to improve the efficiency and relevance of wild-bird surveillance. Methods. Generalised linear models and analysis of variance were used to examine the determinants of Anseriformes abundance and movements in Australia, and the observed prevalence of LPAI in Australia (n = 33 139) and overseas (n = 93 344). Risk profiles were developed using poultry density, estimated LPAI prevalence, the abundance of Anseriformes, and the probability of Anseriformes moving from areas of HPAI epizootics. Key results. Analysis of Australian wild-bird surveillance data strongly supports other studies that have found the prevalence of LPAI in wild birds to be much lower (1%) in Australia than that in other countries (4.7%). LPAI prevalence was highly variable among sampling periods and locations and significantly higher in dabbling ducks than in other functional groups. Trends in Anseriformes movements, abundance and breeding are also variable, and correlated with rainfall, which could explain low prevalence and the failure to detect seasonal differences in LPAI in wild birds. Virus prevalence of faecal samples was significantly lower, whereas collecting faecal samples was 3–5 times less expensive and logistically simpler, than that of cloacal samples. Overall priority areas for on-going surveillance are provided for Australia. Conclusions. Previous surveillance has occurred in high-priority areas, with the exception of Mareeba (North Queensland), Brisbane and Darwin, and has provided valuable information on the role of wild birds in maintaining avian influenza viruses. However, several practical considerations need to be addressed for future surveillance. Implications. Long-term surveillance studies in wild birds in priority areas are required, which incorporate information on bird abundance, age, behaviour, breeding and movements, particularly for dabbling ducks. This is important to validate trends of LPAI prevalence, in understanding the main determinants for virus spread and persistence, and in predicting and managing future epizootics of HPAI in Australia.