Development of rapid and highly resolving combinatorial genotyping schemes for Campylobacter jejuni and Campylobacter coli

Campylobacter jejuni followed by Campylobacter coli contribute substantially to the economic and public health burden attributed to food-borne infections in Australia. Genotypic characterisation of isolates has provided new insights into the epidemiology and pathogenesis of C. jejuni and C. coli. However, currently available methods are not conducive to large scale epidemiological investigations that are necessary to elucidate the global epidemiology of these common food-borne pathogens. This research aims to develop high resolution C. jejuni and C. coli genotyping schemes that are convenient for high throughput applications. Real-time PCR and High Resolution Melt (HRM) analysis are fundamental to the genotyping schemes developed in this study and enable rapid, cost effective, interrogation of a range of different polymorphic sites within the Campylobacter genome. While the sources and routes of transmission of campylobacters are unclear, handling and consumption of poultry meat is frequently associated with human campylobacteriosis in Australia. Therefore, chicken derived C. jejuni and C. coli isolates were used to develop and verify the methods described in this study. The first aim of this study describes the application of MLST-SNP (Multi Locus Sequence Typing Single Nucleotide Polymorphisms) + binary typing to 87 chicken C. jejuni isolates using real-time PCR analysis. These typing schemes were developed previously by our research group using isolates from campylobacteriosis patients. This present study showed that SNP + binary typing alone or in combination are effective at detecting epidemiological linkage between chicken derived Campylobacter isolates and enable data comparisons with other MLST based investigations. SNP + binary types obtained from chicken isolates in this study were compared with a previously SNP + binary and MLST typed set of human isolates. Common genotypes between the two collections of isolates were identified and ST-524 represented a clone that could be worth monitoring in the chicken meat industry. In contrast, ST-48, mainly associated with bovine hosts, was abundant in the human isolates. This genotype was, however, absent in the chicken isolates, indicating the role of non-poultry sources in causing human Campylobacter infections. This demonstrates the potential application of SNP + binary typing for epidemiological investigations and source tracing. While MLST SNPs and binary genes comprise the more stable backbone of the Campylobacter genome and are indicative of long term epidemiological linkage of the isolates, the development of a High Resolution Melt (HRM) based curve analysis method to interrogate the hypervariable Campylobacter flagellin encoding gene (flaA) is described in Aim 2 of this study. The flaA gene product appears to be an important pathogenicity determinant of campylobacters and is therefore a popular target for genotyping, especially for short term epidemiological studies such as outbreak investigations. HRM curve analysis based flaA interrogation is a single-step closed-tube method that provides portable data that can be easily shared and accessed. Critical to the development of flaA HRM was the use of flaA specific primers that did not amplify the flaB gene. HRM curve analysis flaA interrogation was successful at discriminating the 47 sequence variants identified within the 87 C. jejuni and 15 C. coli isolates and correlated to the epidemiological background of the isolates. In the combinatorial format, the resolving power of flaA was additive to that of SNP + binary typing and CRISPR (Clustered regularly spaced short Palindromic repeats) HRM and fits the PHRANA (Progressive hierarchical resolving assays using nucleic acids) approach for genotyping. The use of statistical methods to analyse the HRM data enhanced sophistication of the method. Therefore, flaA HRM is a rapid and cost effective alternative to gel- or sequence-based flaA typing schemes. Aim 3 of this study describes the development of a novel bioinformatics driven method to interrogate Campylobacter MLST gene fragments using HRM, and is called ‘SNP Nucleated Minim MLST’ or ‘Minim typing’. The method involves HRM interrogation of MLST fragments that encompass highly informative “Nucleating SNPS” to ensure high resolution. Selection of fragments potentially suited to HRM analysis was conducted in silico using i) “Minimum SNPs” and ii) the new ’HRMtype’ software packages. Species specific sets of six “Nucleating SNPs” and six HRM fragments were identified for both C. jejuni and C. coli to ensure high typeability and resolution relevant to the MLST database. ‘Minim typing’ was tested empirically by typing 15 C. jejuni and five C. coli isolates. The association of clonal complexes (CC) to each isolate by ‘Minim typing’ and SNP + binary typing were used to compare the two MLST interrogation schemes. The CCs linked with each C. jejuni isolate were consistent for both methods. Thus, ‘Minim typing’ is an efficient and cost effective method to interrogate MLST genes. However, it is not expected to be independent, or meet the resolution of, sequence based MLST gene interrogation. ‘Minim typing’ in combination with flaA HRM is envisaged to comprise a highly resolving combinatorial typing scheme developed around the HRM platform and is amenable to automation and multiplexing. The genotyping techniques described in this thesis involve the combinatorial interrogation of differentially evolving genetic markers on the unified real-time PCR and HRM platform. They provide high resolution and are simple, cost effective and ideally suited to rapid and high throughput genotyping for these common food-borne pathogens.

A modified quality control method for manufacturing process in mask industry

Masks are widely used in different industries, for example, traditional metal industry, hospitals or semiconductor industry. Quality is a critical issue in mask industry as it is related to public health and safety. Traditional quality practices for manufacturing process have some limitations in implementing them in mask industries. This paper aims to investigate the suitability of Six Sigma quality control method for the manufacturing process in the mask industry to provide high quality products, enhancing the process capacity, reducing the defects and the returned goods arising in a selected mask manufacturing company. This paper suggests that modifications necessary in Six Sigma method for effective implementation in mask industry.

Safety impacts of alcohol and other drugs in the construction industry : a research methodology

Anecdotal evidence from the infrastructure and building sectors highlights issues of drugs and alcohol and its association with safety risk on construction sites. Operating machinery and mobile equipment, proximity to live traffic together with congested sites, electrical equipment and operating at heights conspire to accentuate the potential adverse impact of drugs and alcohol in the workplace. While most Australian jurisdictions have identified this as a critical safety issue, information is limited regarding the prevalence of alcohol and other drugs in the workplace and there is limited evidential guidance regarding how to effectively and efficiently address such an issue. No known study has scientifically evaluated the relationship between the use of drugs and alcohol and safety impacts in construction, and there has been only limited adoption of nationally coordinated strategies, supported by employers and employees to render it socially unacceptable to arrive at a construction workplace with impaired judgement from drugs and alcohol. A nationally consistent collaborative approach across the construction workforce - involving employers and employees; clients; unions; contractors and sub-contractors is required to engender a cultural change in the construction workforce – in a similar manner to the on-going initiative in securing a cultural change to drink-driving in our society where peer intervention and support is encouraged. This study has four key objectives. Firstly, using the standard World Health Organisation AUDIT, a national qualitative and quantitative assessment of the use of drugs and alcohol will be carried out. This will build upon similar studies carried out in the Australian energy and mining sectors. Secondly, the development of an appropriate industry policy will adopt a non-punitive and rehabilitative approach developed in consultation with employers and employees across the infrastructure and building sectors, with the aim it be adopted nationally for adoption at the construction workplace. Thirdly, an industry-specific cultural change management program will be developed through a nationally collaborative approach to reducing the risk of impaired performance on construction sites and increasing workers’ commitment to drugs and alcohol safety. Finally, an implementation plan will be developed from data gathered from both managers and construction employees. Such an approach stands to benefit not only occupational health and safety, through a greater understanding of the safety impacts of alcohol and other drugs at work, but also alcohol and drug use as a wider community health issue. This paper will provide an overview of the background and significance of the study as well as outlining the proposed methodology that will be used to evaluate the safety impacts of alcohol and other drugs in the construction industry.

Resilience in critical infrastructures : the case of the Queensland electricity industry

The reliability of Critical Infrastructure is considered to be a fundamental expectation of modern societies. These large-scale socio-technical systems have always, due to their complex nature, been faced with threats challenging their ongoing functioning. However, increasing uncertainty in addition to the trend of infrastructure fragmentation has made reliable service provision not only a key organisational goal, but a major continuity challenge: especially given the highly interdependent network conditions that exist both regionally and globally. The notion of resilience as an adaptive capacity supporting infrastructure reliability under conditions of uncertainty and change has emerged as a critical capacity for systems of infrastructure and the organisations responsible for their reliable management. This study explores infrastructure reliability through the lens of resilience from an organisation and system perspective using two recognised resilience-enhancing management practices, High Reliability Theory (HRT) and Business Continuity Management (BCM) to better understand how this phenomenon manifests within a partially fragmented (corporatised) critical infrastructure industry – The Queensland Electricity Industry. The methodological approach involved a single case study design (industry) with embedded sub-units of analysis (organisations), utilising in-depth interviews and document analysis to illicit findings. Derived from detailed assessment of BCM and Reliability-Enhancing characteristics, findings suggest that the industry as a whole exhibits resilient functioning, however this was found to manifest at different levels across the industry and in different combinations. Whilst there were distinct differences in respect to resilient capabilities at the organisational level, differences were less marked at a systems (industry) level, with many common understandings carried over from the pre-corporatised operating environment. These Heritage Factors were central to understanding the systems level cohesion noted in the work. The findings of this study are intended to contribute to a body of knowledge encompassing resilience and high reliability in critical infrastructure industries. The research also has value from a practical perspective, as it suggests a range of opportunities to enhance resilient functioning under increasingly interdependent, networked conditions.

Rural Poultry in the Developing world

In 2007 I travelled to Mozambique and Tanzania to photographically document the work undertaken by a group of Australians who are working to bring a self sufficient lifestyle back to the HIV Aids stricken communities of Africa. University of Queensland veterinary researchers have developed a vaccination that can eradicate disease from local rural poultry. The Kyeema Foundation is working in country to supply this vaccine to families battling HIV AIDS and to teach local residents how to successfully implement it. QUT, AusAID and the Kyeema Foundation funded the trip.

Safety impacts of alcohol and other drugs in the construction industry : Preliminary findings

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AIDS and pro-social television : industry, policy and Australian television drama

This thesis examines the intersection of popular cultural representations of HIV and AIDS and the discourses of public health campaigns. Part Two provides a comprehensive record of all HIV related storylines in Australian television drama from the first AIDS episode of The Flying Doctors in 1986 to the ongoing narrative of Pacific Drive, with its core HIV character, in 1996. Textual representations are examined alongside the agency of "cultural technicians" working within the television industry. The framework for this analysis is established in Part One of the thesis, which examines the discursive contexts for speaking about HIV and AIDS established through national health policy and the regulatory and industry framework for broadcasting in Australia. The thesis examines the dominant liberal democratic framework for representation of HIV I AIDS and adopts a Foucauldian understanding of the processes of governmentality to argue that during the period of the 1980s and 1990s a strand of social democratic discourse combined with practices of self management and the management of the Australian population. The actions of committed agents within both domains of popular culture and health education ensured that more challenging expressions of HIV found their way into public culture.