Human-specific E. coli single nucleotide polymorphism (SNP) genotypes detected in a South-East Queensland waterway, Australia

The World Health Organization recommends that the majority of water monitoring laboratories in the world should test for E. coli daily since thermotolerant coliforms and E. coli are key indicators for risk assessment of recreational waters. Recently, we developed a new SNP method for typing E. coli strains, by which human-specific genotypes were identified. Here, we report the presence of these previously described specific SNP profiles in environmental water, sourced from the Coomera River, located on South East Queensland, Australia, over a period of two years. This study tested for the presence of human-specific E. coli to ascertain whether hydrologic and anthropogenic activity plays a key role in the pollution of the investigated watershed or whether the pollution is from other sources. We found six human-specific SNP profiles and one animal-specific SNP profile consistently across sampling sites and times. We have demonstrated that our SNP genotyping method is able to rapidly identify and characterise human- and animal-specific E. coli isolates in water sources.

SNP diversity of Enterococcus faecalis and Enterococcus faecium in a South East Queensland waterway, Australia, and associated antibiotic resistance gene profiles

BACKGROUND: Enterococcus faecalis and Enterococcus faecium are associated with faecal pollution of water, linked to swimmer-associated gastroenteritis and demonstrate a wide range of antibiotic resistance. The Coomera River is a main water source for the Pimpama-Coomera watershed and is located in South East Queensland, Australia, which is used intensively for agriculture and recreational purposes. This study investigated the diversity of E. faecalis and E. faecium using Single Nucleotide Polymorphisms (SNPs) and associated antibiotic resistance profiles. RESULTS: Total enterococcal counts (cfu/ml) for three/six sampling sites were above the United States Environmental Protection Agency (USEPA) recommended level during rainfall periods and fall into categories B and C of the Australian National Health and Medical Research Council (NHMRC) guidelines (with a 1-10% gastrointestinal illness risk). E. faecalis and E. faecium isolates were grouped into 29 and 23 SNP profiles (validated by MLST analysis) respectively. This study showed the high diversity of E. faecalis and E. faecium over a period of two years and both human-related and human-specific SNP profiles were identified. 81.8% of E. faecalis and 70.21% of E. faecium SNP profiles were associated with genotypic and phenotypic antibiotic resistance. Gentamicin resistance was higher in E. faecalis (47% resistant) and harboured the aac(6')-aph(2') gene. Ciprofloxacin resistance was more common in E. faecium (12.7% resistant) and gyrA gene mutations were detected in these isolates. Tetracycline resistance was less common in both species while tet(L) and tet(M) genes were more prevalent. Ampicillin resistance was only found in E. faecium isolates with mutations in the pbp5 gene. Vancomycin resistance was not detected in any of the isolates. We found that antibiotic resistance profiles further sub-divided the SNP profiles of both E. faecalis and E. faecium. CONCLUSIONS: The distribution of E. faecalis and E. faecium genotypes is highly diverse in the Coomera River. The SNP genotyping method is rapid and robust and can be applied to study the diversity of E. faecalis and E. faecium in waterways. It can also be used to test for human-related and human-specific enterococci in water. The resolving power can be increased by including antibiotic-resistant profiles which can be used as a possible source tracking tool. This warrants further investigation.

#qldfloods and @QPSMedia: Crisis Communication on Twitter in the 2011 South East Queensland Floods

Social media, including Facebook and Twitter, played an important role in crisis communication at the height of the 2011 South East Queensland floods crisis (10-16 January). This report examines the role of the short-messaging system Twitter in disseminating and sharing crisis information and updates from state and local authorities as well as everyday citizens. We assess the overall use of Twitter, as well as that of the most important emergency service account, the Queensland Police’s @QPSMedia account.

Social infrastructure planning and sustainable communities : Example from South East Queensland, Australia

From its early birth through to the twenty-first century, the planning for social infrastructure has been viewed as a crucial element in promoting the development of healthy communities. The existence of good social infrastructure in every level of human settlement (i.e. neighbourhoods, districts, regions etc.) is vital because it is considered to be an element that impacts positively and meaningfully on the quality of life for members of the targeted community. The increasing importance of the sustainable development agenda in human settlements has prompted concerns over the cost of the government’s failure to provide for adequate social infrastructure for their communities. Part of this failure is attributed to the inconsistent outcome from the use of traditional planning standards that are based on population-to-facility ratios. This paper explores the literature discussion on social infrastructure for sustainable communities. It examines how a participation-oriented, need-sensitive approach in the planning and provision of social infrastructure is used as an alternative to the traditional standards that are based on population-to-facility ratios. It does this by giving an overview of its application in the planning and provision of social infrastructure for Australia’s fastest growing region of South-East Queensland.

Models of South-East Asian organised crime drug operations in Queensland

In 2002, the United Nations Office on Drugs and Crime (UNODC) issued a report entitled Results of a pilot survey of forty selected organized criminal groups in sixteen countries which established five models of organised crime. This paper reviews these and other common organised crime models and drug trafficking models, and applies them to cases of South East Asian drug trafficking in the Australian state of Queensland. The study tests the following hypotheses: (1) South-East Asian drug trafficking groups in Queensland will operate within a criminal network or core group; (2) Wholesale drug distributors in Queensland will not fit consistently under any particular UN organised crime model; and (3) Street dealers will have no organisational structure. The study concluded that drug trafficking or importation closely resembles a criminal network or core group structure. Wholesale dealers did not fit consistently into any UN organised crime model. Street dealers had no organisational structure as an organisational structure is typically found in mid- to high-level drug trafficking.

Measuring urban form : a comparative analysis of South East Queensland and South Florida

At first glance the built environments of South Florida and South East Queensland appear very similar, particularly along the highly urbanized coast. However this apparent similarity belies some fundamental differences between the two regions in terms of context and the approach to regulating development. This paper describes some of these key differences, but focuses on two research questions: 1) do these differences affect the built environment; and 2) if so, how does the built form differ? There has been considerable research on how to best measure urban form, particularly as it relates to measuring urban sprawl (Schwarz 2010; Clifton et al. 2008). Some of the key questions identified by this research include: what are the best variables to use?; what scale should be used?; and what time period to use? We will assimilate this research in order to develop a methodology for measuring urban form and apply it to both case study regions. There are several potential outcomes from this research -- one is that the built form between the two regions is quite different; and the second is that it is similar. The first outcome is what might be expected given the differences in context and development regulation. However how might the second outcome be explained – major differences in context and development regulation resulting in minor differences in key measures of urban form? One explanation is that differences in the way development is regulated are not as important in determining the built form as are private market forces.

Do planning regulations matter? : a comparison of South East Queensland and South Florida

At one level the urban landscapes of South Florida and South East Queensland look quite similar. However at another level the context of planning and planning control and regulation is quite different. To understand the contextual differences between South Florida and South East Queensland, four themes will be used, some of which were based on Cullingworth and Booth. The four themes include: demography, governance, the law and regulatory philosophy. After having evaluated South Florida and South East Queensland across these four themes, we propose a framework for examining whether these differences have shaped planning outcomes and in particular, the built form.

An analysis of holding cost impact on housing affordability in relation to midsized Greenfield residential property developments in South East Queensland

The position of housing demand and supply is not consistent. The Australian situation counters the experience demonstrated in many other parts of the world in the aftermath of the Global Financial Crisis, with residential housing prices proving particularly resilient. A seemingly inexorable housing demand remains a critical issue affecting the socio-economic landscape. Underpinned by high levels of population growth fuelled by immigration, and further buoyed by sustained historically low interest rates, increasing income levels, and increased government assistance for first home buyers, this strong housing demand level ensures problems related to housing affordability continue almost unabated. A significant, but less visible factor impacting housing affordability relates to holding costs. Although only one contributor in the housing affordability matrix, the nature and extent of holding cost impact requires elucidation: for example, the computation and methodology behind the calculation of holding costs varies widely - and in some instances completely ignored. In addition, ambiguity exists in terms of the inclusion of various elements that comprise holding costs, thereby affecting the assessment of their relative contribution. Such anomalies may be explained by considering that assessment is conducted over time in an ever-changing environment. A strong relationship with opportunity cost - in turn dependant inter alia upon prevailing inflation and / or interest rates - adds further complexity. By extending research in the general area of housing affordability, this thesis seeks to provide a detailed investigation of those elements related to holding costs specifically in the context of midsized (i.e. between 15-200 lots) greenfield residential property developments in South East Queensland. With the dimensions of holding costs and their influence over housing affordability determined, the null hypothesis H0 that holding costs are not passed on can be addressed. Arriving at these conclusions involves the development of robust economic and econometric models which seek to clarify the componentry impacts of holding cost elements. An explanatory sequential design research methodology has been adopted, whereby the compilation and analysis of quantitative data and the development of an economic model is informed by the subsequent collection and analysis of primarily qualitative data derived from surveying development related organisations. Ultimately, there are significant policy implications in relation to the framework used in Australian jurisdictions that promote, retain, or otherwise maximise, the opportunities for affordable housing.

Viruses of banana in East Africa

Bananas are one of the world's most important food crops, providing sustenance and income for millions of people in developing countries and supporting large export industries. Viruses are considered major constraints to banana production, germplasm multiplication and exchange, and to genetic improvement of banana through traditional breeding. In Africa, the two most important virus diseases are bunchy top, caused by Banana bunchy top virus (BBTV), and banana streak disease, caused by Banana streak virus (BSV). BBTV is a serious production constraint in a number of countries within/bordering East Africa, such as Burundi, Democratic Republic of Congo, Malawi, Mozambique, Rwanda and Zambia, but is not present in Kenya, Tanzania and Uganda. Additionally, epidemics of banana streak disease are occurring in Kenya and Uganda. The rapidly growing tissue culture (TC) industry within East Africa, aiming to provide planting material to banana farmers, has stimulated discussion about the need for virus indexing to certify planting material as virus-free. Diagnostic methods for BBTV and BSV have been reported and, for BBTV, PCR-based assays are reliable and relatively straightforward. However for BSV, high levels of serological and genetic variability and the presence of endogenous virus sequences within the banana genome complicate diagnosis. Uganda has been shown to contain the greatest diversity in BSV isolates found anywhere in the world. A broad-spectrum diagnostic test for BSV detection, which can discriminate between endogenous and episomal BSV sequences, is a priority. This PhD project aimed to establish diagnostic methods for banana viruses, with a particular focus on the development of novel methods for BSV detection, and to use these diagnostic methods for the detection and characterisation of banana viruses in East Africa. A novel rolling-circle amplification (RCA) method was developed for the detection of BSV. Using samples of Banana streak MY virus (BSMYV) and Banana streak OL virus (BSOLV) from Australia, this method was shown to distinguish between endogenous and episomal BSV sequences in banana plants. The RCA assay was used to screen a collection of 56 banana samples from south-west Uganda for BSV. RCA detected at least five distinct BSV isolates in these samples, including BSOLV and Banana streak GF virus (BSGFV) as well as three BSV isolates (Banana streak Uganda-I, -L and -M virus) for which only partial sequences had been previously reported. These latter three BSV had only been detected using immuno-capture (IC)-PCR and thus were possible endogenous sequences. In addition to its ability to detect BSV, the RCA protocol was also demonstrated to detect other viruses within the family Caulimoviridae, including Sugar cane bacilliform virus, and Cauliflower mosaic virus. Using the novel RCA method, three distinct BSV isolates from both Kenya and Uganda were identified and characterised. The complete genome of these isolates was sequenced and annotated. All six isolates were shown to have a characteristic badnavirus genome organisation with three open reading frames (ORFs) and the large polyprotein encoded by ORF 3 was shown to contain conserved amino acid motifs for movement, aspartic protease, reverse transcriptase and ribonuclease H activities. As well, several sequences important for expression and replication of the virus genome were identified including the conserved tRNAmet primer binding site present in the intergenic region of all badnaviruses. Based on the International Committee on Taxonomy of Viruses (ICTV) guidelines for species demarcation in the genus Badnavirus, these six isolates were proposed as distinct species, and named Banana streak UA virus (BSUAV), Banana streak UI virus (BSUIV), Banana streak UL virus (BSULV), Banana streak UM virus (BSUMV), Banana streak CA virus (BSCAV) and Banana streak IM virus (BSIMV). Using PCR with species-specific primers designed to each isolate, a genotypically diverse collection of 12 virus-free banana cultivars were tested for the presence of endogenous sequences. For five of the BSV no amplification was observed in any cultivar tested, while for BSIMV, four positive samples were identified in cultivars with a B-genome component. During field visits to Kenya, Tanzania and Uganda, 143 samples were collected and assayed for BSV. PCR using nine sets of species-specific primers, and RCA, were compared for BSV detection. For five BSV species with no known endogenous counterpart (namely BSCAV, BSUAV, BSUIV, BSULV and BSUMV), PCR was used to detect 30 infections from the 143 samples. Using RCA, 96.4% of these samples were considered positive, with one additional sample detected using RCA which was not positive using PCR. For these five BSV, PCR and RCA were both useful for identifying infected samples, irrespective of the host cultivar genotype (Musa A- or B-genome components). For four additional BSV with known endogenous counterparts in the M. balbisiana genome (BSOLV, BSGFV, BSMYV and BSIMV), PCR was shown to detect 75 infections from the 143 samples. In 30 samples from cultivars with an A-only genome component there was 96.3% agreement between PCR positive samples and detection using RCA, again demonstrating either PCR or RCA are suitable methods for detection. However, in 45 samples from cultivars with some B-genome component, the level of agreement between PCR positive samples and RCA positive samples was 70.5%. This suggests that, in cultivars with some B-genome component, many infections were detected using PCR which were the result of amplification of endogenous sequences. In these latter cases, RCA or another method which discriminates between endogenous and episomal sequences, such as immuno-capture PCR, is needed to diagnose episomal BSV infection. Field visits were made to Malawi and Rwanda to collect local isolates of BBTV for validation of a PCR-based diagnostic assay. The presence of BBTV in samples of bananas with bunchy top disease was confirmed in 28 out of 39 samples from Malawi and all nine samples collected in Rwanda, using PCR and RCA. For three isolates, one from Malawi and two from Rwanda, the complete nucleotide sequences were determined and shown to have a similar genome organisation to previously published BBTV isolates. The two isolates from Rwanda had at least 98.1% nucleotide sequence identity between each of the six DNA components, while the similarity between isolates from Rwanda and Malawi was between 96.2% and 99.4% depending on the DNA component. At the amino acid level, similarities in the putative proteins encoded by DNA-R, -S, -M, - C and -N were found to range between 98.8% to 100%. In a phylogenetic analysis, the three East African isolates clustered together within the South Pacific subgroup of BBTV isolates. Nucleotide sequence comparison to isolates of BBTV from outside Africa identified India as the possible origin of East African isolates of BBTV.

Health status and use of health services among recently arrived men with refugee backgrounds: A comparative analysis of urban and regional settlement in South-east Queensland

Approximately one-third of refugee and humanitarian entrants to Australia are adult men. Many of these men and their families settle in regional areas. Little is known about the health status of refugee men and the use of health services, and whether or not there are differences between those living in urban and regional areas. This paper reports on the cross-sectional differences in health status and use of health services among a group of 233 recently arrived refugee men living in urban and regional areas of South-east Queensland. Overall, participants reported good levels of subjective health status, moderate to good levels of well-being, and low prevalence of mental illness. Men living in urban areas were more likely to have a longstanding illness and report poorer health status than those settled in regional areas. In contrast, men living in regional areas reported poorer levels of well-being in the environment domain and were more likely to visit hospital emergency departments. Targeted health promotion programs will ensure that refugee men remain healthy and develop their full potential as members of the Australian community. Programs that facilitate refugees’ access to primary health care in regional areas may promote more appropriate use of hospital emergency departments by these communities.

Education and training of medical physicists in south East Asia: Accomplishments and challenges

John Cameron has made significant contributions to the field of Medical Physics. His contributions encompassed research and development, technical developments and education. He had a particular interest in the education of medical physicists in developing countries. Structured clinical training is also an essential component of the professional development of a medical physicist. This paper considers aspects of the clinical training and education of medical physicists in South-East Asia and the challenges facing the profession in the region if it is to keep pace with the rapid increase in the amount and technical complexity of medical physics infrastructure in the region.

Sustainable urban infrastructure development in South East Asia : evidence from Hong Kong, Kuala Lumpur and Singapore

Many South East Asian cities have experienced substantial physical, economic and social transformations during the past several decades. The rapid pace of globalization and economic restructuring has resulted in these cities receiving the full impact of urbanization pressures. In an attempt to ease these pressures, cities such as Singapore, Hong Kong and Kuala Lumpur have advocated growth management approaches focusing especially on urban infrastructure sustainability. These approaches aim to achieve triple bottom line sustainability by balancing economic and social development, and environmental protection. This chapter evaluates three Asia-Pacific city cases, Singapore, Hong Kong and Kuala Lumpur, and assesses their experiences in managing their urban forms and infrastructure whilst promoting sustainable patterns of urban development.