Perception of urinary biomarker tests among patients referred with suspected urological malignancy.

Objective: To determine the acceptability of a non-invasive urinary biomarker test in place of conventional flexible cystoscopy for the diagnosis of bladder cancer in patients referred to a Rapid Access Haematuria Clinic (RAHC) with suspected urological malignancy. Patients and methods: Patients attending a RAHC were recruited to a prospective observational study evaluating a novel urinary biomarker (URO17™) for the detection of bladder cancer and invited to complete a two-part structured questionnaire. Questions related to demographics, attitudes towards conventional cystoscopy and the minimal acceptable sensitivity (MAS) at which a urinary biomarker would be considered an alternative to flexible cystoscopy both before and after undergoing the procedure. Results: A total of 250 patients completed the survey; the majority of whom were referred with visible haematuria (75.2%). One hundred seventy-one (68.4%) would be willing to accept a urinary biomarker in place of cystoscopy, with 59 (23.6%) expressing preference for the biomarker with a MAS as low as 85%. Conversely, 74 patients (29.6%) would not be willing to accept a urinary biomarker, regardless of its sensitivity. A significant number of patients reported a change in MAS after undergoing cystoscopy, with 80 (32.0%) and 16 (6.4%) increasing and decreasing the required value respectively (P = 0.001). The greatest increase was seen in the proportion of patients unwilling to accept a urinary biomarker regardless of its sensitivity, rising from 29.6% to 38.4%. Conclusions: Although many patients attending a RAHC would be willing to accept a urinary biomarker test in place of conventional flexible cystoscopy for the detection of bladder cancer, effective patient, public and clinician engagement will be necessary at all stages of implementation if it is to become an established component of the diagnostic pathway.

Development of a high-throughput SARS-CoV-2 antibody testing pathway using dried blood spot specimens.

BACKGROUND: Serological assays for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have roles in seroepidemiology, convalescent plasma-testing, antibody durability and vaccine studies. Currently, SARS-CoV-2 serology is performed using serum/plasma collected by venepuncture. Dried blood spot (DBS) testing offers significant advantages as it is minimally invasive, avoids venepuncture with specimens being mailed to the laboratory. METHODS: A pathway utilizing a newborn screening laboratory infrastructure was developed using an enzyme-linked immunosorbent assay to detect IgG antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein in DBS specimens. Paired plasma and DBS specimens from SARS-CoV-2 antibody-positive and -negative subjects and polymerase chain reaction positive subjects were tested. DBS specimen stability, effect of blood volume and punch location were also evaluated. RESULTS: DBS specimens from antibody-negative (n = 85) and -positive (n = 35) subjects and polymerase chain reaction positive subjects (n = 11) had a mean (SD; range) optical density (OD) of 0.14 (0.046; 0.03-0.27), 0.98 (0.41; 0.31-1.64) and 1.12 (0.37; 0.49-1.54), respectively. An action value OD >0.28 correctly assigned all cases. The weighted Deming regression for comparison of the DBS and the plasma assay yielded: y = 0.004041 + 1.005x, r = 0.991, Sy/x 0.171, n = 82. Extraction efficiency of antibodies from DBS specimens was >99%. DBS specimens were stable for at least 28 days at ambient room temperature and humidity. CONCLUSIONS: SARS-CoV-2 IgG receptor-binding domain antibodies can be reliably detected in DBS specimens. DBS serological testing offers lower costs than either point of care or serum/plasma assays that require patient travel, phlebotomy and hospital/clinic resources; the development of a DBS assay may be particularly important for resource poor settings.

Identification of clinical and urine biomarkers for uncomplicated urinary tract infection using machine learning algorithms.

Women with uncomplicated urinary tract infection (UTI) symptoms are commonly treated with empirical antibiotics, resulting in overuse of antibiotics, which promotes antimicrobial resistance. Available diagnostic tools are either not cost-effective or diagnostically sub-optimal. Here, we identified clinical and urinary immunological predictors for UTI diagnosis. We explored 17 clinical and 42 immunological potential predictors for bacterial culture among women with uncomplicated UTI symptoms using random forest or support vector machine coupled with recursive feature elimination. Urine cloudiness was the best performing clinical predictor to rule out (negative likelihood ratio [LR-] = 0.4) and rule in (LR+ = 2.6) UTI. Using a more discriminatory scale to assess cloudiness (turbidity) increased the accuracy of UTI prediction further (LR+ = 4.4). Urinary levels of MMP9, NGAL, CXCL8 and IL-1ß together had a higher LR+ (6.1) and similar LR- (0.4), compared to cloudiness. Varying the bacterial count thresholds for urine culture positivity did not alter best clinical predictor selection, but did affect the number of immunological predictors required for reaching an optimal prediction. We conclude that urine cloudiness is particularly helpful in ruling out negative UTI cases. The identified urinary biomarkers could be used to develop a point of care test for UTI but require further validation.

An improved cell-permeable fluorogenic substrate as the basis for a highly sensitive test for NAD(P)H quinone oxidoreductase 1 (NQO1) in living cells.

NAD(P)H:quinone oxidoreductase 1 (NQO1) is a flavoenzyme upregulated in response to oxidative stress and in some cancers. Its upregulation by compounds has been used as an indicator of their potential anti-cancer properties. In this study we have designed, produced and tested a fluorogenic coumarin conjugate which selectively releases highly fluorescent 4-methylumbelliferone (4-MU) in the presence of NQO1. It was found that measuring 4-MU release rapidly and specifically quantitated NQO1 levels in vitro and in live cells. Both the substrate and its products freely perfused through cell membranes and were non-toxic. The substrate was very specific with low background, and the assay itself could be done in less than 10minutes. This is the first assay to allow the quantitation of NQO1 in live cells which can then be retained for further experiments.

Machine-learning algorithms define pathogen-specific local immune fingerprints in peritoneal dialysis patients with bacterial infections.

The immune system has evolved to sense invading pathogens, control infection, and restore tissue integrity. Despite symptomatic variability in patients, unequivocal evidence that an individual's immune system distinguishes between different organisms and mounts an appropriate response is lacking. We here used a systematic approach to characterize responses to microbiologically well-defined infection in a total of 83 peritoneal dialysis patients on the day of presentation with acute peritonitis. A broad range of cellular and soluble parameters was determined in peritoneal effluents, covering the majority of local immune cells, inflammatory and regulatory cytokines and chemokines as well as tissue damage-related factors. Our analyses, utilizing machine-learning algorithms, demonstrate that different groups of bacteria induce qualitatively distinct local immune fingerprints, with specific biomarker signatures associated with Gram-negative and Gram-positive organisms, and with culture-negative episodes of unclear etiology. Even more, within the Gram-positive group, unique immune biomarker combinations identified streptococcal and non-streptococcal species including coagulase-negative Staphylococcus spp. These findings have diagnostic and prognostic implications by informing patient management and treatment choice at the point of care. Thus, our data establish the power of non-linear mathematical models to analyze complex biomedical datasets and highlight key pathways involved in pathogen-specific immune responses.

Characterization of a Blood Spot Creatine Kinase Skeletal Muscle Isoform Immunoassay for High-Throughput Newborn Screening of Duchenne Muscular Dystrophy.

BACKGROUND: Duchenne muscular dystrophy (DMD) is a progressive, lethal X-linked neuromuscular disorder with an average worldwide incidence of 1:5000. Blood spot creatine kinase (CK) enzyme assays previously used in newborn screening programs for DMD are nonspecific because measured CK enzyme activity is attributable to 3 isoenzyme forms of CK (CK-MM, CK-MB, and CK-BB) and it is the CK-MM isoform that is found predominantly in skeletal muscle. CK-MM is increased in boys with DMD owing to muscle damage. We describe a sensitive and specific automated immunoassay for CK-MM to screen for DMD in blood spots. METHODS: The prototype assay was developed on the PerkinElmer GSP® analyzer to enable high-throughput screening. CK-MM was assayed using a solid phase, 2-site immunofluorometric system. Purified human CK-MM was used to create calibrators and controls. RESULTS: The limit of blank (LOB), detection (LOD), and quantification (LOQ) values were <1, 3, and 8 ng/mL, respectively. The analytical measurement range was 4-8840 ng/mL. Interassay (n = 40) imprecision was <7% across the analytical range. Cross-reactivity was <5% for CK-MB and 0% for CK-BB. The mean recovery of CK-MM was 101% (range 87%-111%). Blood spots from newborn infants (n = 277) had a mean CK-MM concentration of 155 ng/mL and a 99th centile of 563 ng/mL. The mean blood spot CK-MM concentration from 10 cases of DMD was 5458 ng/mL (range 1217-9917 ng/mL). CONCLUSIONS: CK-MM can be reliably quantified in blood spots. The development of this CK-MM assay on a commercial immunoassay analyzer would enable standardized and high-throughput newborn blood spot screening of DMD.

Quantitative analysis of gene expression changes in response to genotoxic compounds.

Techniques that quantify molecular endpoints sufficiently sensitive to identify and classify potentially toxic compounds have wide potential for high-throughput in vitro screening. Expression of three genes, RAD51C, TP53 and cystatin A (CSTA), in HEPG2 cells was measured by Q-PCR amplification. In parallel, we developed alternative assays for the same 3 gene signature based on an acridinium-ester chemiluminescent reporter molecule. HEPG2 cells were challenged with eighteen different compounds (n=18) chosen to represent compounds that are genotoxic (n=8), non-genotoxic non-carcinogenic (n=2) or have a less well defined mechanism of action with respect to genotoxicity (n=8). At least one of the three genes displayed dysregulated expression in the majority of compounds tested by Q-PCR and ten compounds changed the CSTA expression significantly. Acridinium-ester labelled probes for the three genes were synthesised and tested. Analytical sensitivity was characterised and suggested a limit of detection generally better than 0.1fmol but often 10-50 attomol. A linear amplification step was optimised and this quantitative method detected statistically significant increases in RAD51C and CSTA expression in agreement with the Q-PCR results, demonstrating the potential of this technology. The broad agreement of the amplified chemiluminescent method and Q-PCR in measuring gene expression suggests wider potential application for this chemiluminescent technology.

Spectrally resolved chemiluminescent probes for sensitive multiplex molecular quantification.

Luminophores are frequently utilized probe labels for detecting biological analytes. Multiple fluorescent luminophores, or fluorophores, can be readily distinguished from one another based on different energy excitation and emission wavelengths and lifetimes. However, suitable methods and reagents for distinguishing multiples of the much more sensitive chemically initiated luminophores have been limited. Herein we describe a new class of hybrid luminophore probes that emit light of distinct wavelength ranges and intensities upon energy transfer (ET) from an in-common, acridinium ester chemiluminophore to a covalently conjugated fluorophore. This format supports rapid, rational design of spectrally resolvable, chemically initiated probes. Time-resolved spectrographic and luminescence characterizations indicate that ET is not dependent on overlap in the emission spectrum of the luminophore and the absorption spectra of acceptors, suggesting a non-Förster resonance ET mechanism. Analysis of a combination of the chemiluminophore and new chemiluminophore-acceptor conjugate probes demonstrates the benefits of their use in sensitive, multiplex quantification of nucleic acid sequences indicative of environmentally relevant microbes without prior enzymatic amplification.

Simultaneous quantification of multiple nucleic acid targets using chemiluminescent probes.

A novel method is described for simultaneous detection and quantification of attomoles or a few femtomoles of two (or potentially more) nucleic acid targets, without need for amplification. The technique depends on spectral-temporal resolution of chemiluminescence emitted from independent hybridization-induced chemiluminescent signal probes. The probes are internally quenched except in the presence of their specific targets, thereby allowing detection limits up to 10,000 times lower than with fluorescent probes. This is sufficient to obviate the need for amplification in many cases. The utility of the technique has been demonstrated by use of resolvable N-linked acridinium and 2,7-dimethoxyacridinium ester labeled probes in a homogeneous assay for sensitive and simultaneous independent quantification of pan-bacterial and pan-fungal target sequences in seawater.

Development and application of a novel acridinium ester for use as a chemiluminescent emitter in nucleic acid hybridisation assays using chemiluminescence quenching.

Chemiluminescent acridinium esters (AEs) permit the development of high sensitivity ligand binding assays due to a combination of high intensity light emission and very low backgrounds. Here these advantages are exploited for use in homogeneous nucleic acid hybridisation assays using quenched chemiluminescence. AE chemiluminescence is conventionally initiated at highly alkaline pH. Novel "active" AEs were designed that permit initiation under conditions compatible with maintenance of nucleic acid hybrids (i.e. pH less than 9). Methyl red was found to be a dark quencher species capable of functioning at this pH. Practical application of the chemiluminescence quenching assay system has been demonstrated using two model nucleic acid hybridisation assays based on intra- and intermolecular emitter/quencher pairs.

Investigation of transcription-mediated amplification as a rapid test method for Enterococci in recreational water.

Growth-based methods for detecting faecal contamination of recreational water require at least 24 hours to yield results, which can delay detection, action and remediation, if required. Such delays can put human health at risk while closing beaches inappropriately can cause unnecessary economic losses. There is a requirement for more rapid methods to facilitate the management of pollution events. In this study, undertaken in our respective laboratories, a molecular assay based on transcription-mediated amplification (TMA) technology was compared with established growth-based methods. The assays were used to quantitate enterococcal faecal indicator bacteria (relative to the legislative threshold of 104 colony forming units/100 mL) in 138 water samples collected from 41 different locations, representative of different recreational water types routinely sampled in Southern California. The results demonstrate the efficacy of the TMA assay for the detection of Enterococcus species in recreational water as a rapid alternative to traditional methods.

Comparison of transcription-mediated amplification and growth-based methods for the quantitation of Enterococcus bacteria in environmental waters.

An assay based on transcription-mediated amplification (TMA) technology was used to quantitate Enterococcus fecal indicator bacteria in environmental water samples. The results generated by this and two growth-based methods relative to the 104 most-probable-number or CFU-per-100-ml threshold show that the three methods are in good qualitative agreement when tested against a range of water samples taken from different locations. The results demonstrate sensitive and rapid detection (approximately 4 h from sample collection to result) and quantitation of Enterococcus bacteria compared to the results with the growth-based methods.

Rapid tests for detection and quantitation of Enterococcus contamination in recreational waters.

Presently, growth-based tests are used for the detection and quantitation of microbiological contaminants in the environment. These tests take a minimum of 24 h to generate a result, which compromises the ability to take the most appropriate action. This report describes a rapid test for Enterococcus in recreational water as an indicator of faecal contamination. This method involves (1) isolation and lysis of the target organism, (2) purification of ribosomal RNA (rRNA) from the lysate and (3) amplification and detection of the purified rRNA. rRNA is used as the target since, in contrast to DNA, there are hundreds to thousands of copies in the cell. The rRNA is purified from the lysate by target capture onto magnetic microspheres, which removes interfering substances present in the sample. The rRNA is then quantitated using transcription-mediated amplification (TMA) with real-time homogeneous detection of amplicon using a fluorescent oligonucleotide probe. Compared to polymerase chain reaction (PCR) amplification, TMA is isothermal, more rapid, and ideally suited to RNA detection. The test described here demonstrates sensitive detection and quantitation of enterococci over a wide dynamic range with a high level of analytical specificity. The latter is particularly important for accurate and relevant monitoring both for protecting public health and for source tracking. Many conventional microbiological tests are time-consuming, exhibit limited dynamic range and are known to lack specificity. This assay demonstrates the advantages achievable by the application of TMA of rRNA targets to current environmental testing challenges.

Risk factors for increased BTEX exposure in four Australian cities.

Benzene, toluene, ethylbenzene and xylenes (BTEX) are common volatile organic compounds (VOCs) found in urban airsheds. Elevated levels of VOCs have been reported in many airsheds at many locations, particularly those associated with industrial activity, wood heater use and heavy traffic. Exposure to some VOCs has been associated with health risks. There have been limited investigations into community exposures to BTEX using personal monitoring to elucidate the concentrations to which members of the community may be exposed and the main contributors to that exposure. In this cross sectional study we investigated BTEX exposure of 204 non-smoking, non-occupationally exposed people from four Australian cities. Each participant wore a passive BTEX sampler over 24h on five consecutive days in both winter and summer and completed an exposure source questionnaire for each season and a diary for each day of monitoring. The geometric mean (GM) and range of daily BTEX concentrations recorded for the study population were benzene 0.80 (0.04-23.8 ppb); toluene 2.83 (0.03-2120 ppb); ethylbenzene 0.49 (0.03-119 ppb); and xylenes 2.36 (0.04-697 ppb). A generalised linear model was used to investigate significant risk factors for increased BTEX exposure. Activities and locations found to increase personal exposure included vehicle repair and machinery use, refuelling of motor vehicles, being in an enclosed car park and time spent undertaking arts and crafts. A highly significant difference was found between the mean exposures in each of the four cities, which may be explained by differences in fuel composition, differences in the mix and density of industry, density of motor vehicles and air pollution meteorology.

Quantitative measurement of fathead minnow vitellogenin mRNA using hybridization protection assays.

We have developed a novel test system for the quantitative assessment of gene transcription. The procedure involves the use of chemiluminescent-labeled oligonucleotide probes in a hybridization protection assay (HPA) format. We have used this technology to measure changes in vitellogenin mRNA to demonstrate the impact of estrogen exposure in the juvenile fathead minnow (Pimephales promelas). Marked changes in mRNA expression were observed in response to intraperitoneal injection of 17beta-estradiol demonstrating the utility of this technique for the identification and monitoring of toxic responses to xenobiotics.