Investigating the population structure of Queensland invasive Streptococcus pneumoniae isolates in children: Using a modified multi-locus variable number of tandem repeat analysis and a novel minimum SNPs capsular typing method

This research investigated the use of DNA fingerprinting to characterise the bacteria Streptococcus pneumoniae or pneumococcus, and hence gain insight into the development of new vaccines or antibiotics. Different bacterial DNA fingerprinting methods were studied, and a novel method was developed and validated, which characterises different cell coatings that pneumococci produce. This method was used to study the epidemiology of pneumococci in Queensland before and after the introduction of the current pneumococcal vaccine. This study demonstrated that pneumococcal disease is highly prevalent in children under four years, that the bacteria can `switch' its cell coating to evade the vaccine, and that some DNA fingerprinting methods are more discriminatory than others. This has an impact on understanding which strains are more prone to cause invasive disease. Evidence of the excellent research findings have been published in high impact internationally refereed journals.

Hot spot detection and spatio-temporal dynamics of dengue in Queensland, Australia

Dengue has been a major public health concern in Australia since it re-emerged in Queensland in 1992-1993. This study explored spatio-temporal distribution and clustering of locally-acquired dengue cases in Queensland State, Australia and identified target areas for effective interventions. A computerised locally-acquired dengue case dataset was collected from Queensland Health for Queensland from 1993 to 2012. Descriptive spatial and temporal analyses were conducted using geographic information system tools and geostatistical techniques. Dengue hot spots were detected using SatScan method. Descriptive spatial analysis showed that a total of 2,398 locally-acquired dengue cases were recorded in central and northern regions of tropical Queensland. A seasonal pattern was observed with most of the cases occurring in autumn. Spatial and temporal variation of dengue cases was observed in the geographic areas affected by dengue over time. Tropical areas are potential high-risk areas for mosquito-borne diseases such as dengue. This study demonstrated that the locally-acquired dengue cases have exhibited a spatial and temporal variation over the past twenty years in tropical Queensland, Australia. There is a clear evidence for the existence of statistically significant clusters of dengue and these clusters varied over time. These findings enabled us to detect and target dengue clusters suggesting that the use of geospatial information can assist the health authority in planning dengue control activities and it would allow for better design and implementation of dengue management programs.

Monitoring illicit drug use through wastewater analysis in south east Queensland, Australia

Introduction and Aims: Wastewater analysis has become a useful technique for monitoring illicit drug use in communities. Findings have been reported from different countries in Europe and North America. We applied this technique to gauge the illicit drug consumption in an urban catchment from South East Queensland, Australia. Design and Methods: The sampling campaigns were conducted in 2009 (21st November – 2nd December) and 2010 (19th – 25th November). We collected daily composite wastewater samples from the inlet of the sewage treatment plant using continuous flow-proportional sampling. Ten illicit drug residues (parent compounds and key metabolites) in the samples were measured using liquid chromatography coupled to tandem mass spectrometer. Results: Seven compounds were quantified in all the samples. Our data indicated higher drug consumption on weekends. Cannabis was the highest used drug in both sampling periods. Compared to the first sampling campaign which indicated that cocaine and methamphetamine use exceeded ecstasy usage, the second sampling campaign suggested the use of methamphetamine exceeded that of ecstasy which in turn exceeded cocaine use. Discussion and Conclusions: The observed weekly trend of drug use in our study is in agreement with findings in other studies. The variation between two sampling periods in the prevalence of drug use may relate to the availability and prices of the drugs on markets. The cocaine use we estimated in 2009 was much greater than estimations obtained through the national household survey [1], implying under- reporting of cocaine use in surveys. Future work is underway to tackle methodological challenges for more accurate estimation.

Measuring drug use patterns in Queensland through wastewater analysis

Estimating the use of illicit drugs in the general community is an important task with ramifications for law enforcement agencies, as well as health portfolios. Australia has four ongoing drug monitoring systems, including the AIC’s DUMA program, the National Drug Strategy Household Survey, the Illicit Drug Reporting System and the Ecstasy and Related Drug Reporting System. The systems vary in methods, but broadly they are reliant upon self-report data and may be subject to selection biases. The present study employed a completely different method. By chemically analysing sewerage water, the study produced daily estimates of consumption of methamphetamine, MDMA and cocaine. Samples were collected in November 2009 and November 2010 from a municipality in Queensland, with an population of over 150,000 people. Estimates were made of the average daily dose and average daily street value per 1,000 people. On the basis of estimated dose and price, the methamphetamine market appeared considerably stronger than either MDMA or cocaine. This paper explains the strengths and weaknesses of wastewater analysis. It considers the potential value of wastewater analysis in measuring net consumption of illicit drugs and the effectiveness of law enforcement agency strategies.

Drink driving among Indigenous people in Far North Queensland and northern New South Wales: A summary of the qualitative findings

Purpose In response to the threat that drink drivers pose to themselves and others, drink driving programs form an important part of a suite of countermeasures used in Australia and internationally. Unlike New Zealand/Aotearoa, United States and Canada that have programs catering for their First Peoples, all Australian programs are designed for the general driver population. The aim of this study was to identify the factors that contribute to Indigenous drink driving in order to inform appropriate recommendations related to developing a community-based program for Indigenous communities. Broader drivers licensing policy recommendations are also discussed. Methods A sample of 73 Indigenous people from Queensland and in New South Wales with one or more drink driving convictions completed a semi-structured interview in respect of the to their drink driving behaviour. Participants were asked to disclose information regarding their drink driving history, and alcohol and drug use. If participants self-reported no longer drink driving, they were probed about what factors had assisted them to avoid further offending. Results Key themes which emerged to maintain drink driving include motivations to drink and drive, and belief in the ability to manage the associated risks. Factors that appeared to support others from avoiding further offending include re-connecting with culture and family support. Conclusions and Implications A range of recommendations regarding delivery and content of a program for regional and remote communities as well as other policy implications are discussed.

Rank regression analysis of correlated water quality data from South East Queensland

With growing population and fast urbanization in Australia, it is a challenging task to maintain our water quality. It is essential to develop an appropriate statistical methodology in analyzing water quality data in order to draw valid conclusions and hence provide useful advices in water management. This paper is to develop robust rank-based procedures for analyzing nonnormally distributed data collected over time at different sites. To take account of temporal correlations of the observations within sites, we consider the optimally combined estimating functions proposed by Wang and Zhu (Biometrika, 93:459-464, 2006) which leads to more efficient parameter estimation. Furthermore, we apply the induced smoothing method to reduce the computational burden. Smoothing leads to easy calculation of the parameter estimates and their variance-covariance matrix. Analysis of water quality data from Total Iron and Total Cyanophytes shows the differences between the traditional generalized linear mixed models and rank regression models. Our analysis also demonstrates the advantages of the rank regression models for analyzing nonnormal data.

Cane Weevil Borer, Rhabdoscelus obscurus (Coleoptera: Curculionidae), a pest of palms in Northern Queensland, Australia

In recent years the cultivation of ornamental palms (Arecaceae) has increased markedly in northern Queensland. Consequently, several insects have become important pests, particularly Rhabdoscelus obscurus (Boisduval), the cane weevil borer. The larvae of this beetle feed on various species of palms, making the plants unsaleable. Death or lodging of the trees may also result. This paper documents its pest status, derived from information in the literature and from consultation with local growers.

Low-density koala (Phascolarctos cinereus) populations in the mulgalands of south-west Queensland. II. Distribution and diet

This study used faecal pellets to investigate the broadscale distribution and diet of koalas in the mulgalands biogeographic region of south-west Queensland. Koala distribution was determined by conducting faecal pellet searches within a 30-cm radius of the base of eucalypts on 149 belt transects, located using a multi-scaled stratified sampling design. Cuticular analysis of pellets collected ffom 22 of these sites was conducted to identify the dietary composition of koalas within the region. Our data suggest that koala distribution is concentrated in the northern and more easterly regions of the study area, and appears to be strongly linked with annual rainfall. Over 50% of our koala records were obtained from non-riverine communities, indicating that koalas in the study area are not primarily restricted to riverine communities, as bas frequently been suggested. Cuticular analysis indicates that more than 90% of koala diet within the region consists of five eucalypt species. Our data highlights the importance of residual Tertiary landforms to koala conservation in the region.

Candidatus Phytoplasma australiense is associated with pumpkin yellow leaf curl disease in Queensland, Western Australia and the Northern Territory

Pumpkin plants (Cucurbita maxima and C. moschata) with pumpkin yellow leaf curl (PYLC) disease were observed at production fields in Queensland, Western Australia and the Northern Territory. Diseased samples were positive for a phytoplasma indistinguishable from Candidatus Phytoplasma australiense, the phytoplasma associated with papaya dieback and strawberry lethal yellows. This is the first time Candidatus Phytoplasma australiense has been detected in pumpkin.

Resistance of Brassicaceae plants to root-knot nematode (Meloidogyne spp.) in northern Australia

Brassicaceae plants have the potential as part of an integrated approach to replace fumigant nematicides, providing the biofumigation response following their incorporation is not offset by reproduction of plant-parasitic nematodes on their roots. Forty-three Brassicaceae cultivars were screened in a pot trial for their ability to reduce reproduction of three root-knot nematode isolates from north Queensland, Australia: M. arenaria (NQ1), M. javanica (NQ2) and M. arenaria race 2 (NQ5/7). No cultivar was found to consistently reduce nematode reproduction relative to forage sorghum, the current industry standard, although a commercial fodder radish (Raphanus sativus) and a white mustard (Sinapis alba) line were consistently as resistant to the formation of galls as forage sorghum. A second pot trial screened five commercially available Brassicaceae cultivars, selected for their biofumigation potential, for resistance to two nematode species, M. javanica (NQ2) and M. arenaria (NQ5/7). The fodder radish cv. Weedcheck, was found to be as resistant as forage sorghum to nematode reproduction. A multivariate cluster analysis using the resistance measurements, gall index, nematode number per g of root and multiplication for two nematode species (NQ2 and NQ5/7) confirmed the similarity in resistance between the radish cultivar and forage sorghum. A field trial confirmed the resistance of the fodder radish cv. Weedcheck, with a similar reduction in the number of Meloidogyne spp. juveniles recovered from the roots 8 weeks after planting. The use of fodder radish cultivars as biofumigation crops to manage root-knot nematodes in tropical vegetable production systems deserves further investigation.

Fishery biology and management of Protonibea diacanthus (Sciaenidae) aggregations in far Northern Cape York Peninsula waters

The sciaenid Protonibea diacanthus is a large, long-lived predatory fish of inshore northern Australian waters, which forms annual aggregations that are fished extensively by traditional (subsistence) and recreational fishers. There are now widespread concerns that the resource is being overexploited. Indigenous fishers of the Cape York Northern Peninsula Area (NPA) relate that large adult fish (up to 1500 mm total length (TL)) made up the bulk of the catch from the sciaenid aggregations until about 1994. In contrast, sexually mature P. diacanthus comprised only a small component (12 fish out of 270=4.4%) examined in a 1999–2000 sampling programme that was biased towards the largest individuals available. At 790 mm TL, the minimum size at first maturity for female P. diacanthus in this study is much smaller than the 920 mm TL reported previously in Queensland waters. Developing ovaries were observed in specimens sampled from sciaenid aggregations which formed in NPA waters between May and September 2000. However, no fish with ripe or spent gonads were found in the study, so the current timing and location of the spawning season for P. diacanthus in the region remain unknown. Food items observed in the analysis of the diet of P. diacanthus from the NPA included a variety of teleosts and invertebrates. The range of animal taxa represented in the prey items support the description of an ‘opportunistic predator’ attributed to the species. In our sampling, the stomach contents of fish caught during the time of the aggregation events did not differ from those observed at other times of the year. A total of 114 P. diacanthus were tagged and released at aggregation sites during the study period, and 3 fish (2.6%) were subsequently recaptured. The low rate of tag returns from the wild stock tagging programme, both in this study (2.6%) and from recreational fisher tag/release programmes for the sciaenid elsewhere in Queensland (6.5%), were not explained by tag loss nor mortality, given the high retention rate of tags and the zero mortality seen in tank trials. In response to the biological findings from this study, indigenous community councils of the NPA imposed a 2-year fishing moratorium for P. diacanthus. Surveys at aggregation sites in 2002 and 2003 established that much larger fish (mean size 103.5 cm TL) were again present on the grounds, albeit in very low numbers. These recent preliminary results highlight the critical need for continued monitoring and management of the P. diacanthus fishery in the NPA, if prospects for resource recovery are to be realised. The NPA initiative has provided a rare opportunity to negotiate a co-management strategy, based on scientific data and traditional knowledge, for the recovery of a cultural and economically significant fished resource.

A contemporary assessment of land condition in the Northern Gulf region of Queensland

A framework using assessments of soil condition, pasture composition and woodland density was applied to describe 14 grazing land types as being in A (100% of original carrying capacity), B (75%), C (45%) or D (20%) condition. We assessed the condition of 260 sites, principally along public and some station roads, to provide a benchmark for current land condition. Land types were also assigned relative grazing values between 10 (best) and 0, reflecting soil fertility and potential biomass production. The method identifies particular, 'at-risk' land types for priority investment of resources, while the rationale behind assessments might point to management interventions to improve the condition of those land types. Across all land types, 47% of sites were in A condition, 34% in B condition, 17% in C condition and only 2% in D condition. Seventy-five percent of land types with grazing values >5 were in A or B condition, compared with 88% for those with grazing values ?5. For Georgetown granites, only 27% of sites were in A or B condition, with values for other land types being: alluvials 59%, black soils 64% and red duplex soils 57%, suggesting that improving management of these land types is a priority issue. On land types with high grazing value, the major discounting factor was pasture composition (72% of sites discounted), while increasing woodland density was the main discount (73% of sites discounted) on low grazing value land types.

Two new species and a new Australian record of Bactrocera Macquart (Diptera : Tephritidae : Dacinae) from Northern Queensland, Torres Strait and Papua New Guinea

Bactrocera (Bactrocera) speewahensis Fay & Hancock sp. n. is described from northern Queensland and B. (B.) torresiae Huxham & Hancock sp. n. is described from Boigu, Saibai and Dauan islands in Torres Strait and southern Papua New Guinea. Bactrocera (B.) nigrovittata Drew is newly recorded from Australia. All records are of male flies responding to chemical lures.

Incidence and pathogenicity of Phytophthora palmivora and Pythium vexans associated with durian decline in far northern Queensland

In recent years, dieback of durian has become a major problem in mature orchards in the northern Queensland wet tropics region. A survey of 13 durian orchards was conducted during the dry season (July-September 2001) and following wet season (February-April 2002), with roots and soil from the root zone of affected trees being sampled. Phytophthora palmivora was recovered from the roots of affected trees on 12 of the 13 farms in the dry season, and all farms in the wet season. Pythium vexans was recovered from all 13 farms in both seasons. P. palmivora and P. vexans were recovered from diseased roots of 3-month-old durian seedlings cv. Monthong artificially inoculated with these organisms.

Screening selected myrtaceous tree species for production of essential oils in northern Queensland

Trials to identify alternative cropping options to Melaleuca alternifolia for northern Queensland essential oil growers were established at Dimbulah and Innot Hot Springs in 2001. Seed sources of Asteromyrtus symphyocarpa (1,8-cineole form), Eucalyptus staigeriana (citral), Melaleuca cajuputi subsp. cajuputi (trans-nerolidol), M. ericifolia (d-linalool), M. quinquenervia (trans-nerolidol and viridiflorol forms) and M. viridiflora (methyl cinnamate) with potential to produce commercial foliar oils were evaluated. Information was gathered on their adaptability, growth and oil yields over 49 months and 52 months (two harvests) from planting at Dimbulah and Innot Hot Springs, respectively. Of the species and chemotypes evaluated, M. quinquenervia showed potential for commercial production of trans-nerolidol, a compound used in perfumery. It had a very high survival rate (96%) and yields could be expected to improve dramatically from the average 100 kg/ha per harvest achieved in these trials with further research into selection of seed source, control of insect damage and breeding for genetic improvement. M. cajuputi subsp. cajuputi gave a similar performance to M. quinquenervia. The rarity of the trans-nerolidol form of this species and remoteness of its natural occurrence are impediments to further planting and research. E. staigeriana, with second harvest yields of ~600 kg/ha, performed exceptionally well on both sites but potential for development is limited by the ready availability of competitively priced E. staigeriana oil produced in South America. Survival of M. ericifolia ranged from 62% to 82% at 32 months (second harvest) at Innot Hot Springs and was deemed a failure at Dimbulah with poor growth and low survival, raising a major question about the suitability of this species for cultivation in the seasonally dry tropics. Planting of this species on a wider scale in northern Queensland cannot be recommended until more is known about factors affecting its survival. A. symphyocarpa and M. viridiflora were too slow-growing to warrant further consideration as potential oil-producing species at this time.