High-Throughput COVID-19 Testing of Naso-Oropharyngeal Swabs Using a Sensitive Extraction-Free Sample Preparation Method.

High-throughput diagnostic assays are required for large-scale population testing for severe acute respiratory coronavirus 2 (SARS-CoV-2). The gold standard technique for SARS-CoV-2 detection in nasopharyngeal swab specimens is nucleic acid extraction followed by real-time reverse transcription-PCR. Two high-throughput commercial extraction and detection systems are used routinely in our laboratory: the Roche cobas SARS-CoV-2 assay (cobas) and the Roche MagNA Pure 96 system combined with the SpeeDx PlexPCR SARS-CoV-2 assay (Plex).

Qualitative and quantitative effects of thermal treatment of naso-oropharyngeal samples before cobas SARS-CoV-2 testing.

To improve laboratory safety we thermally treated naso-oropharyngeal samples before testing with the cobas SARS-CoV-2 assay. This study aimed to determine if thermal treatment significantly affects the qualitative detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the quantitative measurement of cobas SARS-CoV-2 ORF1a and E-gene target copy number using an in-house quantitative method. A collection of positive (n = 238) and negative samples (n = 196) was tested in parallel comparing thermal treatment (75 °C for 15 minutes) to room-temperature.

Bacteriology and clinical outcomes of patients with culture-positive pleural infection in Western Australia: A 6-year analysis.

Background And Objective: Pleural infection is a clinical challenge; its microbiology can be complex. Epidemiological and outcome data of pleural infection in adult Australians are lacking. We describe the bacteriology and clinical outcomes of Australian adults with culture-positive pleural infection (CPPI) over a 6-year period.

Streptococcus pneumoniae potently induces cell death in mesothelial cells.

Pleural infection/empyema is common and its incidence continues to rise. Streptococcus pneumoniae is the commonest bacterial cause of empyema in children and among the commonest in adults. The mesothelium represents the first line of defense against invading microorganisms, but mesothelial cell responses to common empyema pathogens, including S.

Human pleural fluid is a potent growth medium for Streptococcus pneumoniae.

Empyema is defined by the presence of bacteria and/or pus in pleural effusions. However, the biology of bacteria within human pleural fluid has not been studied. Streptococcus pneumoniae is the most common cause of pediatric and frequent cause of adult empyema.

Implanted brachytherapy seed movement reflecting transrectal ultrasound probe-induced prostate deformation.

Purpose: Compression of the prostate during transrectal ultrasound-guided permanent prostate brachytherapy is not accounted for during treatment planning. Dosimetry effects are expected to be small but have not been reported. The study aims to characterize the seed movement and prostate deformation due to probe pressure and to estimate the effects on dosimetry.

Pleural empyema caused by Klebsiella oxytoca: a case series.

We report on 19 patients from Western Australia of pleural empyema with Klebsiella oxytoca, an organism never before reported in association with this condition. Median age was 65 years, 14/17 (83%) had been in hospital within 30 days prior to diagnosis, 12/18 (67%) had active cancer, 9/17 (53%) had been in intensive care and 7/17 (41%) had prior surgery. Nine patients died at the time of censure, five within 90 days of infection.

Low vancomycin MICs and fecal densities reduce the sensitivity of screening methods for vancomycin resistance in Enterococci.

Active surveillance is part of a multifaceted approach used to prevent the spread of vancomycin-resistant enterococci (VRE). The impact of fecal density, the vancomycin MIC of the isolate, and the vancomycin concentration in liquid medium on test performance are uncertain. Using fecal specimens spiked with a collection of 18 VRE (predominantly vanB) with a wide vancomycin MIC range, we compared the performances of commercial chromogenic agars (CHROMagar VRE, chromID VRE, Brilliance VRE, and VRE Select) and 1 liquid medium (Enterococcosel enrichment broth) for VRE detection.

A comparison of phase, amplitude, and velocity binning for cone-beam computed tomographic projection-based motion reconstruction.

Purpose: We previously developed a motion estimation technique based on direct cone-beam projection analysis. It is able to reconstruct the complete motion trajectory of a radio-opaque marker, including cycle-to-cycle variability, using respiratory binning of the projection images. This paper investigates the use of phase, amplitude, and amplitude-velocity binning in the context of projection-based cone-beam motion estimation (CBME).

Quantitative rt-PCR holds promise as a screening tool for patients with severe sepsis.

Objective: The aim of the present study was to determine if the quantification of bacterial 16S rDNA could be clinically useful in predicting patients at increased risk of developing septic shock.

Methods: A retrospective study of patients with positive blood cultures taken on arrival to the ED. An EDTA sample was collected simultaneously with blood cultures and assayed by polymerase chain reaction to quantitate the bacterial 16S rDNA load.

Severity of pneumococcal pneumonia associated with genomic bacterial load.

Background: There is a clinical need for more objective methods of identifying patients at risk for septic shock and poorer outcomes among those with community-acquired pneumonia (CAP). As viral load is useful in viral infections, we hypothesized that bacterial load may be associated with outcomes in patients with pneumococcal pneumonia.

Methods: Quantification of Streptococcus pneumoniae DNA level by real-time polymerase chain reaction (rt-PCR) was prospectively conducted on whole-blood samples from a cohort of 353 patients who were displaying CAP symptoms upon their admission to the ED.

Brachytherapy for carcinoma of the cervix: a Canadian survey of practice patterns in a changing era.

Background And Purpose: This survey aimed to document practices of Canadian radiation oncologists performing gynecologic brachytherapy for carcinoma of the cervix and to determine what the effect of the phasing-out of LDR after-loading systems from the commercial market is having on practice.

Materials And Methods: A 26-item questionnaire was developed to survey various aspects of brachytherapy practice to include: number of patients treated, prescription points/volume, dose and fractionation, timing, critical structure delineation, expected changes due to the phasing-out of support for low dose rate systems, and support for the development of national guidelines. A link to a web-based survey collection instrument was emailed to each radiation oncologist in Canada practicing gynecologic brachytherapy.

Evaluation of linear accelerator performance standards using an outcome oriented approach.

Radiation therapy, along with other branches of medicine, is moving towards a firmer basis in evidence to optimally utilize resources. As new treatment technology and strategies place greater demands on quality assurance resources, the need to objectively evaluate equipment and process performance standards from the perspective of predicted clinical impact becomes more urgent. This study evaluates the appropriateness of recommended quality control tolerance and action levels for linear accelerators based on the calculated dosimetric impact of suboptimal equipment performance.

Verifying monitor unit calculations for tangential whole breast fields in 3-dimensional planning.

An essential component of quality assurance in radiation therapy is verifying the accuracy of monitor unit calculations. For tangential breast fields, monitor unit differences between primary calculations and second checks are usually larger than considered acceptable at other anatomical sites. A simple model to reconcile the differences between sophisticated and simple algorithms is presented, based on estimating the the volume irradiated by the field, replacing the breast contour with a rectangular block having an equal volume but a new field width which provides almost equivalent scatter to the prescription point.

Variability in patterns of BK viral load after renal transplantation.

BK virus (BKV) may cause nephropathy in renal transplant patients, resulting in graft dysfunction and possible graft loss. We used a sensitive quantitative BKV assay to monitor plasma BK viral loads in 11 renal transplant patients for periods ranging from 37 to 189 weeks posttransplant. Five patients remained negative for BKV, and 6 developed viremia, including 1 patient with a transient viremia.

Feasibility of real-time polymerase chain reaction in whole blood to identify Streptococcus pneumoniae in patients with community-acquired pneumonia.

We assessed a real-time quantitative polymerase chain reaction (PCR) assay targeting the lytA and ply gene of Streptococcus pneumoniae. Both assays were applied to whole blood samples from 28 adult patients with community-acquired pneumonia. Our findings suggest the lytA PCR is more sensitive, and the quantitative aspect of the assay shows promise as an aid to clinical judgment.

Enhanced efficiency and ergonomics of an intraoperative automated prostate brachytherapy delivery technique.

Introduction: In 2003, the Tom Baker Cancer Centre started a prostate brachytherapy program using Iodine-125 seeds, intraoperative treatment planning, and an automated remote afterloader, the seedSelectron. Over a 3-month period in 2004-2005, technologic changes were implemented with the intent of reducing the time spent in the operating room and improving ergonomics for the radiation oncologist/surgeon. New commercial software including inverse planning was installed, concurrent needle insertion and seed train building was implemented, and additional hardware (a slave monitor) was connected to the system.

Verifying monitor unit calculations for tangential breast fields.

An essential component of quality assurance in radiation therapy is verifying the accuracy of monitor unit calculations. Differences between between sophisticated algorithms using 2.5D or 3D calculations and simpler Monitor unit check algorithms assuming a flat water phantom must be expected.

A comparison of techniques for simulating set-up error and uncertainty in head and neck IMRT.

We have compared four computational methods for quantifying the effect of set-up error and uncertainty on delivered doses to targets and organs at risk in the intensity modulated radiation therapy treatment of head and neck cancer. These four methods were direct simulation, simple convolution, plus two modified convolution approaches. Discrepancies of up to 20% in the equivalent uniform dose (EUD) between direct simulation and simple convolution were estimated for the relatively superficial parotid gland at a systematic set-up error of 6 mm standard deviation and a random uncertainty of 2 mm standard deviation.

Bypassing the learning curve in permanent seed implants using state-of-the-art technology.

Purpose: The aim of this study was to demonstrate, based on clinical postplan dose distributions, that technology can be used efficiently to eliminate the learning curve associated with permanent seed implant planning and delivery.

Methods And Materials: Dose distributions evaluated 30 days after the implant of the initial 22 consecutive patients treated with permanent seed implants at two institutions were studied. Institution 1 (I1) consisted of a new team, whereas institution 2 (I2) had performed more than 740 preplanned implantations over a 9-year period before the study.

A technical evaluation of the Nucletron FIRST system: conformance of a remote afterloading brachytherapy seed implantation system to manufacturer specifications and AAPM Task Group report recommendations.

The Fully Integrated Real-time Seed Treatment (FIRST) system by Nucletron has been available in Europe since November 2001 and is being used more and more in Canada and the United States. Like the conventional transrectal ultrasound implant procedure, the FIRST system utilizes an ultrasound probe, needles, and brachytherapy seeds. However, this system is unique in that it (1) utilizes a low-dose-rate brachytherapy seed remote afterloader (the seedSelectron), (2) utilizes 3D image reconstruction acquired from electromechanically controlled, nonstepping rotation of the ultrasound probe, (3) integrates the control of a remote afterloader with electromechanical control of the ultrasound probe for integrating the clinical procedure into a single system, and (4) automates the transfer of planning information and seed delivery to improve quality assurance and radiation safety.