Clinical evaluation of the APAS® Independence: Automated imaging and interpretation of urine cultures using artificial intelligence with composite reference standard discrepant resolution.

Background: This study reports the outcome of the first evaluation of the APAS® Independence for automated reading and preliminary interpretation of urine cultures in the routine clinical microbiology laboratory. In a 2-stage evaluation involving 3000 urine samples, two objectives were assessed; 1) the sensitivity and specificity of the APAS® Independence compared to microbiologists using colony enumeration as the primary determinant, and 2) the variability between microbiologists in enumerating bacterial cultures using traditional culture reading techniques, performed independently to APAS® Independence interpretation.

Methods: Routine urine samples received into the laboratory were processed and culture plates were interpreted by standard methodology and with the APAS® Independence.

Multicenter Evaluation of an Image Analysis Device (APAS): Comparison Between Digital Image and Traditional Plate Reading Using Urine Cultures.

Background: The application of image analysis technologies for the interpretation of microbiological cultures is evolving rapidly. The primary aim of this study was to establish whether the image analysis system named Automated Plate Assessment System (APAS; LBT Innovations Ltd., Australia) could be applied to screen urine cultures.

Biochemistry and genetics of taste- and odor-producing cyanobacteria.

Cyanobacteria are one of the principal sources of volatile organic compounds (VOCs) which cause offensive taste and odor (T&O) in drinking and recreational water, fish, shellfish and other seafood. Although non-toxic to humans, these T&O compounds severely undermine public trust in these commodities, resulting in substantial costs in treatment, and lost revenue to drinking water, aquaculture, food and beverage and tourist/hospitality industries. Mitigation and control have been hindered by the complexity of the communities and processes which produce and modify T&O events, making it difficult to source-track the major producer(s) and the factors governing VOC production and fate.

Evaluation of an Image Analysis Device (APAS) for Screening Urine Cultures.

While advancements have been made in some areas of pathology with diagnostic materials being screened using image analysis technologies, the reporting of cultures from agar plates remains a manual process. We compared the results for 2,163 urine cultures read by a reference panel of microbiologists, by the routine laboratory process, and by an automated plate reading system, APAS (LBT Innovations Ltd., South Australia).

Surveillance for antimicrobial resistance in Australian isolates of Clostridium difficile, 2013-14.

Objectives: The objective of this study was to determine the activity of fidaxomicin and comparator antimicrobials against Clostridium difficile isolated from patients with C. difficile infection (CDI) in Australian hospitals and in the community.

Methods: One private and one public laboratory from five states in Australia submitted a total of 474 isolates/PCR-positive stool samples during three collection periods in August-September 2013 (n = 175), February-March 2014 (n = 134) and August-September 2014 (n = 165).

Opportunistic Pathogens Mycobacterium Avium Complex (MAC) and Legionella spp. Colonise Model Shower.

Legionella spp. and Mycobacterium avium complex (MAC) are opportunistic pathogens of public health concern. Hot water systems, including showers, have been identified as a potential source of infection.

The role of environmental reservoirs in human campylobacteriosis.

Campylobacteriosis is infection caused by the bacteria Campylobacter spp. and is considered a major public health concern. Campylobacter spp.

Monitoring of geosmin producing Anabaena circinalis using quantitative PCR.

Geosmin is one of the most commonly detected off-flavor chemicals present in reservoirs and drinking water systems. Quantitative real-time PCR (qPCR) is useful for quantifying geosmin-producers by focusing on the gene encoding geosmin synthase, which is responsible for geosmin synthesis. In this study, several primers and probes were designed and evaluated to detect the geosmin synthase gene in cyanobacteria.

Establishment of quantitative PCR methods for the quantification of geosmin-producing potential and Anabaena sp. in freshwater systems.

Geosmin has often been associated with off-flavor problems in drinking water with Anabaena sp. as the major producer. Rapid on-site detection of geosmin-producers as well as geosmin is important for a timely management response to potential off-flavor events.

EXPRESSION OF THE GEOSMIN SYNTHASE GENE IN THE CYANOBACTERIUM ANABAENA CIRCINALIS AWQC318(1).

The occurrence of taste and odor episodes attributed to geosmin continues to trouble water utilities worldwide, and only recently have advances been made in our fundamental understanding of the biochemical and genetic mechanisms responsible for the production of geosmin in microorganisms. For the first time, we have examined the expression of the geosmin synthase gene and corresponding geosmin production by Anabaena circinalis Rabenh. ex Bornet et Flahault AWQC318 under conditions of continuous light illumination and the removal of light as a stimulus and demonstrate that the expression of geosmin synthase appears to be constitutive under these conditions.

Exploring the relationship between viscous bulking and ammonia-oxidiser abundance in activated sludge: A comparison of conventional and IFAS systems.

This study investigated the nature of viscous sludge bulking within a molasses-fed integrated fixed-film activated sludge (IFAS) and conventional activated sludge (AS) plant by routinely measuring the total carbohydrate and protein fractions of the mixed liquor (ML). The impacts of sludge settleability and plant performance on the relative abundance of ammonia-oxidising bacteria (AOB) (Nitrosomonas oligotropha-cluster) were also investigated using quantitative polymerase chain reaction (qPCR). Results showed that sludge volume index (SVI) correlated positively with the amount of ML total carbohydrate in both the IFAS and traditional AS plants, highlighting the influential role that ML polysaccharide concentration plays on sludge settleability in these reactors.

Isolation and characterization of the gene associated with geosmin production in cyanobacteria.

Geosmin is a secondary metabolite responsible for earthy tastes and odors in potable water supplies. Geosmin continues to be a challenge to water utility management regimes and remains one of the most common causes of consumer complaints, as the taste of "dirty" water may suggest a failed disinfection regime and that the water may be unsafe to drink. Although cyanobacteria have been reported to be largely responsible for these taste and odor events, the answer as to how or why geosmin is produced has eluded researchers.

Legionella confirmation using real-time PCR and SYTO9 is an alternative to current methodology.

The currently accepted culture techniques for the detection of Legionella spp. in water samples (AS/NZS 3896:1998 and ISO 11731 standard methods) are slow and laborious, requiring from 7 to 14 days for a result. We describe a fully validated rapid confirmation technique that uses real-time PCR incorporating the intercalating dye SYTO9 for the direct identification of primary cultures, significantly decreasing turnaround time and allowing faster remedial action to be taken by the industry.

Nucleic acid amplification-based techniques for pathogen detection and identification.

Nucleic acid amplification techniques have revolutionised diagnostic and research industries. Current technologies that allow the detection of amplification in real-time are fast becoming industry standards, particularly in a diagnostic context. In this review, we describe and explore the application of numerous real-time detection chemistries and amplification techniques for pathogen detection and identification, including the polymerase chain reaction, nucleic acid sequence-based amplification, strand displacement amplification and the ligase chain reaction.

Emerging technologies for the detection and genetic characterization of protozoan parasites.

The development and adaptation of new technologies for the genetic characterization and identification of parasites continue to accelerate, providing an increasing number of research and analytical tools. We review emerging technologies that have applications in this area, including real-time PCR and microarrays, and discuss the fundamental principles of some of these technologies and how they are applied to characterize parasites. We give special consideration to the application of genetic data to biological questions, where selection of the most appropriate technique depends on the biological question posed by the investigator.

Comparison of SYTO9 and SYBR Green I for real-time polymerase chain reaction and investigation of the effect of dye concentration on amplification and DNA melting curve analysis.

Following the initial report of the use of SYBR Green I for real-time polymerase chain reaction (PCR) in 1997, little attention has been given to the development of alternative intercalating dyes for this application. This is surprising considering the reported limitations of SYBR Green I, which include limited dye stability, dye-dependent PCR inhibition, and selective detection of amplicons during DNA melting curve analysis of multiplex PCRs. We have tested an alternative to SYBR Green I and report the first detailed evaluation of the intercalating dye SYTO9.

Demonstration of preferential binding of SYBR Green I to specific DNA fragments in real-time multiplex PCR.

SYBR Green I (SG) is widely used in real-time PCR applications as an intercalating dye and is included in many commercially available kits at undisclosed concentrations. Binding of SG to double-stranded DNA is non-specific and additional testing, such as DNA melting curve analysis, is required to confirm the generation of a specific amplicon. The use of melt curve analysis eliminates the necessity for agarose gel electrophoresis because the melting temperature (T(m)) of the specific amplicon is analogous to the detection of an electrophoretic band.