Presence and incidence of food-borne pathogens in Australian chicken litter.

1. Litter samples were collected at the end of the production cycle from spread litter in a single shed from each of 28 farms distributed across the three Eastern seaboard States of Australia. 2. The geometric mean for Salmonella was 44 Most Probable Number (MPN)/g for the 20 positive samples. Five samples were between 100 and 1000 MPN/g and one at 105 MPN/g, indicating a range of factors are contributing to these varying loads of this organism in litter. 3. The geometric mean for Campylobacter was 30 MPN/g for the 10 positive samples, with 7 of these samples being 100 MPN/g. The low prevalence and incidence of Campylobacter were possibly due to the rapid die-off of this organism. 4. E. coli values were markedly higher than the two key pathogens (geometric mean 20 x 105 colony forming units (cfu)/g) with overall values being more or less within the same range across all samples in the trial, suggesting a uniform contribution pattern of these organisms in litter. 5. Listeria monocytogenes was absent in all samples and this organism appears not to be an issue in litter. 6. The dominant (70% of the isolates) Salmonella serovar was S. Sofia (a common serovar isolated from chickens in Australia) and was isolated across all regions. Other major serovars were S. Virchow and S. Chester (at 10%) and S. Bovismorbificans and S. Infantis (at 8%) with these serovars demonstrating a spatial distribution across the major regions tested. 7. There is potential to re-use litter in the environment depending on end use and the support of relevant application practices and guidelines.

Raw data for project "Development of a DNA based aging technique for use in fisheries assessments" Fisheries and Development Corporation project 2007/033

The primary aim of this study was to determine the relationship between telomere length and age in a range of marine invertebrates including abalone (Haliotis spp) oysters (Saccostrea glomerata), spiny lobsters (Sagmariasus verreauxi formerly Jasus verreauxi and Jasus edwardsii) and school prawns (Metapenaeus macleayi). Additionally, this relationship was studied in a vertebrate organism using the freshwater fish Silver perch (Bidyanus bidyanus). Telomere length differences between tissues were also examined in some species such as Saccostrea glomerata, Sagmariasus verreauxi and Bidyanus bidyanus. In some cases cultured specimens of known age were used and this is quoted in the spreadsheets. For other wild-caught specimens where age was not known, size was used as a proxy for age. This may be a broad size class, or be determined by shell size or carapace length depending on the organism. Each spreadsheet contains raw data of telomere length estimates from Terminal Restriction Fragment Assays (TRF) for various individuals of each species including appropriate details such as age or size and tissue. Telomere length estimates are given in base pairs (bp). In most cases replicate experiments were conducted on groups of samples three times but on a small number of occasions only two replicate experiments were conducted. Further description of the samples can be found in final report of FRDC 2007/033. The arithmetic average for each individual (sample ID) across the two or three replicate experiments is also given. Bidyanus bidyanus (SilverPerch) Two sheets are contained within. a) Comparison of telomere length between different tissues (heart, liver and muscle) within the three year old age class - two replicate experiments were conducted. b) Comparison of telomere length between fish of different but known ages (0.25, 1, 2, and 3 years old) in each of three tissues, heart, liver and muscle – three replicate experiments were conducted per tissue. Haliotis spp (Abalone species) Three species were tested. H. asinina Telomere length was compared in two age classes-11 month and 18 month old abalone using muscle tissue from the foot. Within gel-variation was also estimated using a single sample run three times on one gel (replicate experiment). H. laevigata x H. rubra hybrids Telomere length was compared in three known age classes – two, three and four years old using muscle tissue from the foot. H. rubra Telomere length was compared in a range of different sized abalone using muscle tissue from the foot. Shell size is also given for each abalone Saccostrea glomerata Three sheets are contained within the file. a) Samples came from Moreton Bay Queensland in 2007. Telomere length was compared in two tissues (gill and mantle) of oysters in three age groups (1, 3 and 4 years) b) Samples came from Moreton Bay Queensland in 2009. Telomere length was compared in three age classes using DNA from gill tissue only c) Samples came from Wallis Lake, New South Wales. Telomere length was estimated from whole body minus the shell from 1 year old oysters, gill tissue of 3 age classes (1.5 years, 3 and 4 years), mantle tissue of two age classes (3 and 4 years). Sagmariasus verreauxi (formerly Jasus verreauxi) Telomere length was estimated from abdomen tissue of puerulus, gill and muscle tissue of 3 year old, large and very large size classes of lobsters. Jasus edwardsii Telomere length was measured in two size classes of lobsters- adults of varying sizes using muscle tissue and puerulus using tissues from the abdomen minus the exoskeleton. Metapenaeus macleayi Telomere length was measured in three size classes of school prawns adults. Muscle tissue was used, minus the exoskeleton.

Teratosphaeria pseudoeucalypti, new cryptic species responsible for leaf blight of Eucalyptus in subtropical and tropical Australia

Sub-tropical and tropical plantations of Eucalyptus grandis hybrids in eastern Australia have been severely affected by anamorphs of Teratosphaeria (formerly Kirramyces) causing a serious leaf blight disease. Initially the causal organism in Queensland, Australia, was identified as Teratosphaeria eucalypti, a known leaf parasite of endemic Eucalyptus spp. However, some inconsistencies in symptoms, damage and host range suggested that the pathogen in Queensland may be a new species. Isolates of T. eucalypti from throughout its known endemic range, including Queensland and New Zealand, where it is an exotic pathogen, were compared using multiple gene phylogenies. Phylogenetic studies revealed that the species responsible for leaf blight in Queensland represents a new taxon, described here as Teratosphaeria pseudoeucalypti. While the DNA sequence of T. pseudoeucalypti was more similar to T. eucalypti, the symptoms and cultural characteristics resembled that of T. destructans. The impact of this disease in central Queensland has increased annually and is the major threat to the eucalypt plantation industry in the region.

Salmonella Virchow and Salmonella Weltevreden in a Random Survey of the Asian House Gecko, Hemidactylus frenatus, in Houses in Northern Australia.

Background: Salmonella enterica serotype Virchow is the most common cause of invasive nontyphoid salmonellosis in North Queensland, particularly in infants, but the zoonotic source is unknown. This study aimed at determining (i) the prevalence of the introduced Asian house gecko, Hemidactylus frenatus, in houses in North Queensland and (ii) whether they were a potential source of Salmonella Virchow. Methods: Asian house geckos were collected in a random survey of houses in Townsville, North Queensland. Gut contents underwent microbiological analysis within 2 h of removal using both direct plating and enrichment broth methods. Any organism found to be a presumptive Salmonella spp. was then sent to a reference lab for confirmation of genus/species, serotyping, and phage typing if indicated. Results: One hundred Asian house geckos were collected from 57 houses. Geckos were present in 100% of houses surveyed, and prevalence of Salmonella in large intestinal contents was 7% (95% confidence interval 2, 12%). Three serotypes were found: Virchow (phage type 8), Weltevreden, and an untypable subspecies 1 serotype 11:-:1,7. Conclusion: Since Salmonella Virchow (phage type 8) is associated with invasive disease, the introduced Asian house gecko may play a significant role in the epidemiology of sporadic salmonellosis in places invaded by these peridomestic reptiles. These results justify more detailed epidemiological studies on the role of the Asian house gecko in sporadic salmonellosis and development of evidence-based strategies to decrease this potential zoonotic hazard.

The spatiotemporal dynamics of Tribolium castaneum (Herbst): adult flight and gene flow.

Tribolium castaneum (Herbst) has been used as a model organism to develop and test important ecological and evolutionary concepts and is also a major pest of grain and grain products globally. This beetle species is assumed to be a good colonizer of grain storages through anthropogenic movement of grain, and active dispersal by flight is considered unlikely. Studies using T. castaneum have therefore used confined or walking insects. We combine an ecological study of dispersal with an analysis of gene flow using microsatellites to investigate the spatiotemporal dynamics and adult flight of T. castaneum in an ecological landscape in eastern Australia. Flying beetles were caught in traps at grain storages and in fields at least 1 km from the nearest stored grain at regular intervals for an entire year. Significantly more beetles were trapped at storages than in fields, and almost no beetles were caught in native vegetation reserves many kilometres from the nearest stored grain. Genetic differentiation between beetles caught at storages and in fields was low, indicating that although T. castaneum is predominantly aggregated around grain storages, active dispersal takes place to the extent that significant gene flow occurs between them, mitigating founder effects and genetic drift. By combining ecological and molecular techniques, we reveal much higher levels of active dispersal through adult flight in T. castaneum than previously thought. We conclude that the implications of adult flight to previous and future studies on this model organism warrant consideration.

Phosphine Resistance in the Rust Red Flour Beetle, Tribolium castaneum (Coleoptera: Tenebrionidae): Inheritance, Gene Interactions and Fitness Costs

The recent emergence of heritable high level resistance to phosphine in stored grain pests is a serious concern among major grain growing countries around the world. Here we describe the genetics of phosphine resistance in the rust red flour beetle Tribolium castaneum (Herbst), a pest of stored grain as well as a genetic model organism. We investigated three field collected strains of T. castaneum viz., susceptible (QTC4), weakly resistant (QTC1012) and strongly resistant (QTC931) to phosphine. The dose-mortality responses of their test- and inter-cross progeny revealed that most resistance was conferred by a single major resistance gene in the weakly (3.2x) resistant strain. This gene was also found in the strongly resistant (431x) strain, together with a second major resistance gene and additional minor factors. The second major gene by itself confers only 12-206x resistance, suggesting that a strong synergistic epistatic interaction between the genes is responsible for the high level of resistance (431x) observed in the strongly resistant strain. Phosphine resistance is not sex linked and is inherited as an incompletely recessive, autosomal trait. The analysis of the phenotypic fitness response of a population derived from a single pair inter-strain cross between the susceptible and strongly resistant strains indicated the changes in the level of response in the strong resistance phenotype; however this effect was not consistent and apparently masked by the genetic background of the weakly resistant strain. The results from this work will inform phosphine resistance management strategies and provide a basis for the identification of the resistance genes.

Biodegradation of 1080: Testing soils in south-eastern Australia for sodium fluoroacetate-degrading micro-organisms

Sodium fluoroacetate (1080) is a vertebrate poison commonly used for the control of vertebrate pests in Australia. Long-term environmental persistence of 1080 from baiting operations has likely nontarget species and environmental impacts and is a matter of public concern. Defluorinating micro-organisms have been detected in soils of Western and central Australia, and Queensland, but not in south-eastern Australia. The presence or absence of defluorinating micro-organisms in soils from south-eastern Australia will assist in determining whether long-term environmental persistence of 1080 is or is not occurring. Soils from the Central West Slopes and Plains and Central Tablelands of New South Wales were sampled to investigate the presence and capability of 1080 defluorinating soil micro-organisms. Thirty-one species of micro-organisms were isolated from soils from each site after 10 days incubation in a 20 mM 1080 solution. Of these, 13 isolates showed measurable defluorinating ability when grown in a 1080 and sterile soil suspension. Two species, the bacteria Micromonospora, and the actinomycete Streptosporangium, have not been previously reported for their defluorinating ability. These results indicate that defluorinating micro-organisms are present in soils in south-eastern Australia, which adds weight to other studies that found that 1080 is subject to microbiological degradative processes following removal from the bait substrate. Soil micro-organism defluorination, in combination with physical breakdown and uptake by plants, indicates that fluoroacetate in soils and natural water ways is unlikely to persist. This has implications for the better informed use of 1080 in pest animal management programmes in south-eastern Australia.

First report of Pythiogeton ramosum (Pythiales) in Australia

In 2012, a project was initiated to assess if the soft rot disease of ginger in Australian fields was associated with pathogens other than Pythium myriotylum. Together with nine Pythium spp., ten isolates of a Pythium-like organism were also recovered from ginger with soft rot symptoms. These Pythium-like isolates were identified as Pythiogeton (Py.) ramosum based on its morphology and ITS sequences. In-vitro pathogenicity tests allowed confirmation of pathogenicity of Py. ramosum on excised carrot (Daucus carota), sweet potato (Ipomoea batatas) and potato (Solanum tubersum) tubers, although it was not pathogenic on excised ginger (Zingiber officinale) and radish (Raphanus sativus) rhizome/roots. In addition it was found to be pathogenic on bean (Phaseolus vulgaris), capsicum (Capsicum annuum) and cauliflower (Brassica oleracea var. botrytis) seedlings. This is the first record of Py. ramosum and its pathogenicity in Australia.

Quantitative effects of in-line operations on Campylobacter and Escherichia coli through two Australian broiler processing plants

Campylobacter is an important food borne pathogen, mainly associated with poultry. A lack of through-chain quantitative Campylobacter data has been highlighted within quantitative risk assessments. The aim of this study was to quantitatively and qualitatively measure Campylobacter and Escherichia coli concentration on chicken carcasses through poultry slaughter. Chickens (n = 240) were sampled from each of four flocks along the processing chain, before scald, after scald, before chill, after chill, after packaging and from individual caeca. The overall prevalence of Campylobacter after packaging was 83% with a median concentration of 0.8 log10 CFU/mL. The processing points of scalding and chilling had significant mean reductions of both Campylobacter (1.8 and 2.9 log10 CFU/carcase) and E. coli (1.3 and 2.5 log10 CFU/carcase). The concentration of E. coli and Campylobacter was significantly correlated throughout processing indicating that E. coli may be a useful indicator organism for reductions in Campylobacter concentration. The carriage of species varied between flocks, with two flocks dominated by Campylobacter coli and two flocks dominated by Campylobacter jejuni. Current processing practices can lead to significant reductions in the concentration of Campylobacter on carcasses. Further understanding of the variable effect of processing on Campylobacter and the survival of specific genotypes may enable more targeted interventions to reduce the concentration of this poultry associated pathogen.

Biodiversity, biosecurity and integrated pest management

Breaches of biosecurity, leading to incursions by invasive species, have the potential to cause substantial economic, social and environmental losses, including drastic reduction in biodiversity. It is argued that improving biosecurity reduces risk to biodiversity, while maintaining stable ecosystems through biodiversity can be a safeguard against biosecurity breaches. The global costs of invasive alien species (IAS) have been estimated at around US$350 billion, while alien invertebrate and vertebrate pests and weeds are estimated to cost Australia at least $7 billion a year. A striking, current, example is the incursion by Myrtle Rust (Puccinia psidii) an organism which can infect all members of the Myrtaceae, the most important family in the Australian flora. Myrtle rust was first detected on a property on the central coast of New South Wales in late April 2010. Two years later the disease has been detected in numerous locations in Queensland and New South Wales ranging from commercial plant nurseries and public amenities to large areas of bushland. This particular breach of biosecurity will, inevitably, diminish biodiversity of flora and fauna over large areas of the continent. Integrated pest management (IPM), an enrichment of diversity in managing invasive and other pest species, offers the best opportunity to address problems such as these. Australia's response to increasing biosecurity risk is comprehensive and includes national networking of scientists engaged in a complex program of biosecurity research and development, including studies of IPM. This network is being enhanced by the development of international linkages.

Molecular Breeding for Complex Adaptive Traits: How Integrating Crop Ecophysiology and Modelling Can Enhance Efficiency

Progress in crop improvement is limited by the ability to identify favourable combinations of genotypes (G) and management practices (M) in relevant target environments (E) given the resources available to search among the myriad of possible combinations. To underpin yield advance we require prediction of phenotype based on genotype. In plant breeding, traditional phenotypic selection methods have involved measuring phenotypic performance of large segregating populations in multi-environment trials and applying rigorous statistical procedures based on quantitative genetic theory to identify superior individuals. Recent developments in the ability to inexpensively and densely map/sequence genomes have facilitated a shift from the level of the individual (genotype) to the level of the genomic region. Molecular breeding strategies using genome wide prediction and genomic selection approaches have developed rapidly. However, their applicability to complex traits remains constrained by gene-gene and gene-environment interactions, which restrict the predictive power of associations of genomic regions with phenotypic responses. Here it is argued that crop ecophysiology and functional whole plant modelling can provide an effective link between molecular and organism scales and enhance molecular breeding by adding value to genetic prediction approaches. A physiological framework that facilitates dissection and modelling of complex traits can inform phenotyping methods for marker/gene detection and underpin prediction of likely phenotypic consequences of trait and genetic variation in target environments. This approach holds considerable promise for more effectively linking genotype to phenotype for complex adaptive traits. Specific examples focused on drought adaptation are presented to highlight the concepts.