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Evaluation of emergency plant pathogen surveillance and surveillance methods for demonstrating pest freedom in Western Australia

Hammond, Nichole (2010) Evaluation of emergency plant pathogen surveillance and surveillance methods for demonstrating pest freedom in Western Australia. PhD thesis, Murdoch University.

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The focus of this study was to explore current methodology for evaluating plant health surveillance systems for their ability to provide confidence towards demonstrating pest freedom using surveillance for Tilletia indica, an exotic fungal pathogen of wheat, in Western Australia as a model. Tilletia indica causes a disease commonly known as Karnal bunt and is an important pathogen in international trade, with many countries having phytosanitary restrictions. If T. indica were to become established in Australia it would cause considerable damage to the country’s economy through loss of domestic and international markets. Maintaining pest free status for T. indica is important to maintain Australia’s grain export markets.

Integral to effective surveillance for T. indica are methods involved in the collection of grain samples and the sensitivity of the laboratory tests used in the surveillance systems. These surveillance ‘tools’ have been investigated and the current techniques have been shown to be effective. Grain sampling occurring at delivery during harvest provides an efficient way to collect samples representative of export quality grain. Stochastic modelling of the sampling process shows that test samples obtained using the current protocol will contain teliospores at detectable levels. In samples from delivery parcels there is a high probability (> 95%) that test samples will contain 5 or more teliospores where the prevalence is at least 1 infected grain in 100 kg. For test samples collected from general siding samples there is a greater than 75% probability that teliospores will be present in the samples where the prevalence is at least 0.5% of delivery parcels and 10 infected grains per kg within parcels. Investigations also indicated that clustering of teliospores within infected grains did not influence the probability of test samples being infected.

Evaluation of the diagnostic protocols currently used in the surveillance programs for T. indica using traditional ‘gold-standard’ methods and a Bayesian statistical framework indicates that the sieve-wash protocol with microscopic observation has a high diagnostic sensitivity (> 84.8%) and specificity (> 96.0%) for detection of teliospores of T. indica, and similar results were obtained for related Tilletia species. The molecular protocol, proposed as the new ‘enhanced’ surveillance tool for detection of T. indica in grain samples, did not perform as well, with a sensitivity and specificity of 48.0% and 48.4% respectively. The estimates were comparable between the two evaluation methods, suggesting that the current protocol, sieve-wash test with microscopic examination, is still the most suitable protocol for grain surveillance for Tilletia species.

The expectation, under the SPS Agreement, that claims of pest freedom be supported by scientific evidence means that there is an increasing need for methods to evaluate the information collected during surveillance activities to provide a quantitative level of confidence upon which claims of freedom can be based. Ten years of historical grain surveillance, utilising samples collected at delivery and the sieve-wash test with microscopic examination, were evaluated using scenario tree methodology and have been shown to provide a high probability of freedom (>95%) from T. indica for Western Australia. The active surveillance systems were evaluated at a range of prevalence levels and were shown to provide a high probability of freedom for design prevalences above one in five regions infected, with 0.25% delivery parcels infected at a rate of 1 infected grain in 100 kg after evaluation of the ten years of surveillance.

Passive surveillance systems can also provide evidence to support claims of pest freedom. The reporting mechanisms in Western Australia for grains pests were investigated, along with attitudes and behaviours relating to the likelihood that members of the grains industry would report a suspect pest or disease. The information gathered was used to inform an evaluation of two passive surveillance system components operating in Western Australia, grower reporting and routine seed testing. Grower reporting was found to provide a high probability of freedom (> 95%) at a design prevalence level of one in five regions infected with 0.25% delivery parcels infected at a rate of 10 infected grains in 1 kg. The Seed Testing surveillance system component was found to provide little contribution to confidence in freedom, due to the low number of wheat samples tested annually. This study demonstrates that passive surveillance provides significant confidence in freedom for T. indica, but that the active surveillance programs provide additional confidence that Western Australia is free from T. indica at lower prevalence levels. Finally, recommendations are provided for future surveillance activities to maintain Western Australia’s confidence in from T. indica.

Publication Type: Thesis (PhD)
Murdoch Affiliation: School of Veterinary and Biomedical Sciences
Supervisor: Robertson, Ian and Reid, Simon
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