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Seventy four SNP genotypes and 54 E. coli genomes from kangaroo, Tasmanian devil, reptile, cattle, dog, horse, duck, bird, fish, rodent, human and environmental water sources were screened for the presence of the CRISPR 2.1 loci flanked by cas2 and iap genes. CRISPR 2.1 regions were found in 49% of the strains analysed. The majority of human E. coli isolates lacked the CRISPR 2.1 locus. We described 76 CRISPR 2.1 positive isolates originating from Australian animals and humans, which contained a total of 764 spacer sequences. CRISPR arrays demonstrated a long history of phage attacks especially in isolates from birds (up to 40 spacers). The most prevalent spacer (1.6%) was an ancient spacer found mainly in human, horse, duck, rodent, reptile and environmental water sources. The sequence of this spacer matched the intestinal P7 phage and the pO111 plasmid of E. coli. [ABSTRACT FROM AUTHOR]

Animal faecal contamination of surface waters poses a human health risk, as they may contain pathogenic bacteria or viruses. Of the numerous animal species residing along surface waterways in Australia, macropod species are a top contributor to wild animals' faecal pollution load. We characterised the gut microbiota of 30 native Australian Eastern Grey Kangaroos from six geographical regions (five kangaroos from each region) within South East Queensland in order to establish their bacterial diversity and identify potential novel species-specific bacteria for the rapid detection of faecal contamination of surface waters by these animals. Using three hypervariable regions (HVRs) of the 16S rRNA gene (i.e., V1–V3, V3–V4, and V5–V6), for their effectiveness in delineating the gut microbial diversity, faecal samples from each region were pooled and microbial genomic DNA was extracted, sequenced, and analysed. Results indicated that V1-V3 yielded a higher taxa richness due to its larger target region (~480 bp); however, higher levels of unassigned taxa were observed using the V1-V3 region. In contrast, the V3–V4 HVR (~569 bp) attained a higher likelihood of a taxonomic hit identity to the bacterial species level, with a 5-fold decrease in unassigned taxa. There were distinct dissimilarities in beta diversity between the regions, with the V1-V3 region displaying the highest number of unique taxa (n = 42), followed by V3–V4 (n = 11) and V5–V6 (n = 8). Variations in the gut microbial diversity profiles of kangaroos from different regions were also observed, which indicates that environmental factors may impact the microbial development and, thus, the composition of the gut microbiome of these animals. [ABSTRACT FROM AUTHOR]

The theory of reasoned action proposes that turnover intentions are a function of an individual's attitudes toward performing a behavior coupled with the perceived attitude of important others toward the performance of the behavior. Intentions to search for an alternative position should be predicted by attitudes and subjective norms concerning the behavior of searching. Likewise, intentions to resign should be predicted by attitudes and subjective norms toward the behavior of resigning a current position. Research scientists at a government research laboratory completed a survey designed to measure attitudes and subjective norms toward searching for an alternative position and resigning from the current position. The model of reasoned action was tested for its effectiveness in predicting turnover intentions. Data comparisons between government and contractor researchers found no significant difference in attitude and subjective norms between the two groups however statistically significant results for the intention to search for an alternative job and resign the current job were found. Research findings and the effectiveness of the reasoned action model as applied to scientific researchers are discussed. [ABSTRACT FROM AUTHOR]

Multiplex polymerase chain reaction (PCR) is an effective tool for simultaneous detection of target genes. Nevertheless, their use has been restricted due to the intrinsic interference between primer pairs. Performing several single PCRs in an array format instead of a multiplex PCR is a simple way to overcome this obstacle. However, there are still major technical challenges in designing a new generation of single PCR microreactors with a small sample volume, rapid thermal cycling, and no evaporation during amplification. We report a simple and robust core-shell bead array for a series of single amplifications. Four core-shell beads with a polymer coating and PCR mixture were synthesized using liquid marble formation and subsequent photo polymerization. Each bead can detect one target gene. We constructed a customised system for thermal cycling of these core-shell beads. Phylogrouping of the E. coli strains was carried out based on the fluorescent signal of the core-shell beads. This platform can be a promising alternative for multiplex nucleic acid analyses due to its simplicity and high throughput. The platform reported here also reduces the cycling time and avoids evaporation as well as contamination of the sample during the amplification process. [ABSTRACT FROM AUTHOR]

Over the last three decades, the protocols and procedures of the DNA amplification technique, polymerase chain reaction (PCR), have been optimized and well developed. However, there have been no significant innovations in processes for sample dispersion for PCR that have reduced the amount of single-use or unrecyclable plastic waste produced. To address the issue of plastic waste, this paper reports the synthesis and successful use of a core-shell bead microreactor using photopolymerization of a composite liquid marble as a dispersion process. This platform uses the core-shell bead as a simple and effective sample dispersion medium that significantly reduces plastic waste generated compared to conventional PCR processes. Other improvements over conventional PCR processes of the novel dispersion platform include increasing the throughput capability, enhancing the performance and portability of the thermal cycler, and allowing for the contamination-free storage of samples after thermal cycling. [ABSTRACT FROM AUTHOR]

The polymerase chain reaction (PCR) is a robust technique used to make multiple copies of a segment of DNA. However, the available PCR platforms require elaborate and time-consuming operations or costly instruments, hindering their application. Herein, we introduce a sandwiched glass–polydimethylsiloxane (PDMS)–glass microchip containing an array of reactors for the real-time PCR-based detection of multiple waterborne bacteria. The PCR solution was loaded into the array of reactors in a single step utilising capillary filling, eliminating the need for pumps, valves, and liquid handling instruments. Issues of generating and trapping bubbles during the loading chip step were addressed by creating smooth internal reactor surfaces. Triton X-100 was used to enhance PCR compatibility in the chip by minimising the nonspecific adsorption of enzymes. A custom-made real-time PCR instrument was also fabricated to provide thermal cycling to the array chip. The microfluidic device was successfully demonstrated for microbial faecal source tracking (MST) in water. [ABSTRACT FROM AUTHOR]

Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process. [ABSTRACT FROM AUTHOR]

Waste stabilisation ponds (WSP) are designed to treat wastewater through natural microbiological, photosynthetic, biochemical, physico-chemical and hydrodynamic processes. They are used throughout the world for wastewater treatment due to their minimal technical requirements, low cost and minimal energy consumption. It is well recognised that WSP hydrodynamics plays a crucial role influencing WSP treatment efficiency. In this study, published WSP literature is reviewed with a focus on the importance of environmental forces, pond configurations and pond loadings on WSP hydrodynamics and pond treatment efficiency. The findings are used to propose future WSP design and modelling requirements. It has been found that the interrelated effects of multiple factors such as pond length-to-width ratio, inlet/outlet configuration, temperature, solar radiation and wind on WSP treatment performance are not investigated sufficiently at present. It is suggested that a system based on numerical pond modelling and field measuring analyses be formulated to address the interacting influences of these factors on WSPs. Consequently, field studies on full-scale WSPs are required to obtain a complete dataset for validation purposes. In this regard, a combination of three-dimensional pond water temperature survey and tracer concentration mapping is suggested. Details of specific modelling components, such as sludge accumulation, turbulence mechanisms and the assumption of constant influent conditions, require further attention. As a result of this review process, a strategic evaluation framework together with the required dataset for the modelling and field work activities are proposed. This paves the way for subsequent studies on WSP hydrodynamics and treatment efficiency, thus benefitting pond design and operation processes. [ABSTRACT FROM AUTHOR]

There is a widespread need for the use of quantitative microbial risk assessment (QMRA) to determine reclaimed water quality for specific uses, however neither faecal indicator levels nor pathogen concentrations alone are adequate for assessing exposure health risk. The aim of this study was to build a conceptual model representing factors contributing to the microbiological health risks of reusing water treated in maturation ponds. This paper describes the development of an unparameterised model that provides a visual representation of theoretical constructs and variables of interest. Information was collected from the peer-reviewed literature and through consultation with experts from regulatory authorities and academic disciplines. In this paper we explore how, considering microbial risk as a modular system, following the QMRA framework enables incorporation of the many factors influencing human exposure and dose response, to better characterise likely human health impacts. By using and expanding upon the QMRA framework we deliver new insights into this important field of environmental exposures. We present a conceptual model of health risk of microbial exposure which can be used for maturation ponds and, more importantly, as a generic tool to assess health risk in diverse wastewater reuse scenarios. [ABSTRACT FROM AUTHOR]

Background Quantitative microbial risk assessment (QMRA) is the current method of choice for determining the risk to human health from exposure to microorganisms of concern. However, current approaches are often constrained by the availability of required data, and may not be able to incorporate the many varied factors that influence this risk. Systems models, based on Bayesian networks (BNs), are emerging as an effective complementary approach that overcomes these limitations. Objectives This article aims to provide a comparative evaluation of the capabilities and challenges of current QMRA methods and BN models, and a scoping review of recent published articles that adopt the latter for microbial risk assessment. Pros and cons of systems approaches in this context are distilled and discussed. Methods A search of the peer-reviewed literature revealed 15 articles describing BNs used in the context of QMRAs for foodborne and waterborne pathogens. These studies were analysed in terms of their application, uses and benefits in QMRA. Discussion The applications were notable in their diversity. BNs were used to make predictions, for scenario assessment, risk minimisation, to reduce uncertainty and to separate uncertainty and variability. Most studies focused on a segment of the exposure pathway, indicating the broad potential for the method in other QMRA steps. BNs offer a number of useful features to enhance QMRA, including transparency, and the ability to deal with poor quality data and support causal reasoning. Conclusion The method has significant untapped potential to describe the complex relationships between microbial environmental exposures and health. [ABSTRACT FROM AUTHOR]

Animal wastes are a major contributor of nutrients and enteric microorganisms to surface water and ground water. Polyacrylamide (PAM) mixtures are an effective flocculent, and we hypothesized that they would reduce transport of microorganisms in flowing water. After waste water running at 60.0 1 min(-1) flowed over PAM + Al2(SO4)3, or PAM + CaO in furrows, total coliform bacteria (TC) and fecal coliform bacteria (FC) were reduced by 30-50% at 1 and 50 m downstream of the treatments compared to the control. In a column study, PAM + Al2(SO4)3, and PAM + CaO applied to sandy, sandy loam, loam, and clay soils reduced NH4+ and ortho-P concentrations in leachate compared to the source waste water and the control. PAM + Al2(SO4)3 and PAM + CaO applied to sandy, sandy loam and loam soils reduced both total and ortho-P, concentrations in leachate compared to he source wastewater and control treatment. In a field study, PAM + Al2(SO4)3, or PAM + CaO treatments did not consistently reduce NH4+, NO3-, ortho-P, and total P concentrations in wastewater flowing over any soil compared to inflow wastewater or the control treatment. With proper application PAM + Al2(SO4)3 and PAM + CaO may be able to reduce the numbers of enteric bacteria in slowly flowing wastewater running off animal confinement areas, reducing the amount of pollutants entering surface water and groundwater.