Physician perspectives of Helicobacter pylori diagnostic and treatment practices in Canada: results of a Canadian survey.

Background: Helicobacter pylori infection is prevalent worldwide and can lead to peptic ulcer disease (PUD) and gastric cancer. Effective diagnosis and treatment of H. pylori infection by gastroenterologists and family physicians is crucial.

Urine Biopsy as Dynamic Biomarker to Enhance Clinical Staging of Bladder Cancer in Radical Cystectomy Candidates.

Purpose: There is significant interest in identifying complete responders to neoadjuvant chemotherapy (NAC) before radical cystectomy (RC) to potentially avoid removal of a pathologically benign bladder. However, clinical restaging after NAC is highly inaccurate. The objective of this study was to develop a next-generation sequencing-based molecular assay using urine to enhance clinical staging of patients with bladder cancer.

Levitation and dynamics of bodies in supersaturated fluids.

A body immersed in a supersaturated fluid like carbonated water can accumulate a dynamic field of bubbles upon its surface. If the body is mobile, the attached bubbles can lift it upward against gravity, but a fluid-air interface can clean the surface of these lifting agents and the body may plummet. The process then begins anew, and continues for as long as the concentration of gas in the fluid supports it.

Impact of the COVID-19 Pandemic on the Reported Incidence of Select Bacterial Enteric Diseases in Canada, 2020.

The aim of this study was to describe the impact of the COVID-19 pandemic on reported cases and clusters of select enteric diseases in Canada, for the period of March 2020 to December 2020. Weekly counts of laboratory confirmed cases of , , Shiga toxin-producing (STEC), and were obtained from laboratory surveillance data. These data were supplemented with epidemiological information on the suspected source of illness, collected for cases identified within whole genome sequencing clusters.

Functional Penile Length After Penile Plication: "Empha-sizing" What Matters.

Objective: To reassess penile length changes after penile plication (PP), we defined a novel measurement of functional penile length (FPL) and compared preoperative and postoperative measurements. PP reduces penile curvature in Peyronie's Disease (PD) patients, but is traditionally thought to reduce overall penile length. However, the literature on PD lacks a standardization for penile length measurement techniques, leading to high inter-study variability.

Quantifying Glans Width Changes in Response to Preoperative Androgen Stimulation in Patients Undergoing Hypospadias Repair.

Purpose: Testosterone (T) administration prior to hypospadias surgery to increase glans size remains controversial. Understanding T's effect on glans width (GW) is essential to understanding its potential impact on surgical outcomes. We hypothesized that preoperative T in prepubertal boys significantly increases GW at the time of hypospadias surgery.

ECTyper: serotype and species prediction from raw and assembled whole-genome sequence data.

is a priority foodborne pathogen of public health concern and phenotypic serotyping provides critical information for surveillance and outbreak detection activities. Public health and food safety laboratories are increasingly adopting whole-genome sequencing (WGS) for characterizing pathogens, but it is imperative to maintain serotype designations in order to minimize disruptions to existing public health workflows. Multiple tools have been developed for predicting serotypes from WGS data, including SRST2, SerotypeFinder and EToKi EBEis, but these tools were not designed with the specific requirements of diagnostic laboratories, which include: speciation, input data flexibility (fasta/fastq), quality control information and easily interpretable results.

Comparison of Molecular and In Silico Serotyping for Surveillance.

surveillance and outbreak management is a key function of public health. Laboratories are shifting from antigenic serotype determination to molecular methods including microarray or whole genome sequencing technologies. The objective of this study was to compare the Check&Trace Salmonella™ DNA microarray (CTS), a commercially available assay with the in silico typing resource (SISTR), which uses whole genome sequencing technology for serotyping clinical strains in Alberta, Canada, collected over an 18-month period.

Multidisciplinary management of adult cloacal exstrophy complications: A challenging case of nephrolithiasis and abdominal wall extrusion of a catheterizable ileal pouch.

Cloacal exstrophy is a rare congenital syndrome which comprises multiple genitourinary, gastrointestinal and musculoskeletal anomalies. The long-term effects following childhood cloacal exstrophy management is poorly characterized in living adults. In this report, a 42-year-old female born with cloacal exstrophy presented after numerous prior surgical reconstructions with abdominal extrusion of a catheterizable ileal pouch and bilateral staghorn calculi.

A Multi-institutional Assessment of Multimodal Analgesia in Penile Implant Recipients Demonstrates Dramatic Reduction in Pain Scores and Narcotic Usage.

Introduction: Despite the pain associated with inflatable penile prosthesis (IPP) implantation, there has been a lack of standardized, nonopioid pain control regimens described to date.

Aim: To assess the effectiveness of a multimodal analgesic regimen in patients undergoing implantation of an IPP compared with patients treated with an opioid-only regimen.

Methods: A large, multicenter patient cohort undergoing IPP implantation whose pain was managed using a multimodal analgesia (MMA) protocol (preoperative and postoperative acetaminophen, meloxicam orcelecoxib, and gabapentin and intraoperative dorsal and pudendal nerve blocks) was compared with a matched cohort of patients managed via an opioid-only protocol.

CPHLN recommendations for the laboratory detection of Shiga toxin-producing (O157 and non-O157).

Shiga toxin-producing (STEC) are important enteric pathogens responsible for sporadic cases and outbreaks of gastroenteritis. O157:H7/NM (STEC O157) are the most commonly known STEC serotypes but it is now increasingly apparent that non-O157 STEC serotypes have been underreported in the past because they were not part of routine screening in many front-line laboratories. The Canadian Public Health Laboratory Network (CPHLN) has identified the need for improved detection and surveillance of non-O157 STEC and has developed the following recommendations to assist in the decision-making process for clinical and reference microbiology laboratories.

Tuberculosis transmission in the Indigenous peoples of the Canadian prairies.

Setting: The prairie provinces of Canada.

Objective: To characterize tuberculosis (TB) transmission among the Indigenous and non-Indigenous Canadian-born peoples of the prairie provinces of Canada.

Design: A prospective epidemiologic study of consecutively diagnosed adult (age ≥ 14 years) Canadian-born culture-positive pulmonary TB cases on the prairies, hereafter termed "potential transmitters," and the transmission events generated by them.

Application of whole genome sequence analysis to the study of Mycobacterium tuberculosis in Nunavut, Canada.

Canada has one of the lowest rates of tuberculosis (TB) in the world, however, among certain sub-populations, disease incidence rates approach those observed in sub-Saharan Africa, and other high incidence regions. In this study, we applied mycobacterial interspersed repetitive unit (MIRU) variable number of tandem repeat (VNTR) and whole genome sequencing (WGS) to the analysis of Mycobacterium tuberculosis isolates obtained from Northern communities in the territory of Nunavut. WGS was carried out using the Illumina MiSeq, with identified variants used to infer phylogenetic relationships and annotated to infer functional implications.

The Validation and Implications of Using Whole Genome Sequencing as a Replacement for Traditional Serotyping for a National Reference Laboratory.

serotyping remains the gold-standard tool for the classification of isolates and forms the basis of Canada's national surveillance program for this priority foodborne pathogen. Public health officials have been increasingly looking toward whole genome sequencing (WGS) to provide a large set of data from which all the relevant information about an isolate can be mined. However, rigorous validation and careful consideration of potential implications in the replacement of traditional surveillance methodologies with WGS data analysis tools is needed.

Time-to-Detection of Inducible Macrolide Resistance in Mycobacterium abscessus Subspecies and Its Association with the Erm(41) Sequevar.

Mutations in the erm(41) gene of M.abscessus group organisms are associated with differences in inducible macrolide resistance, with current recommendations being to hold rapidly growing isolates for up to 14 days in order to ensure that resistance which develops more slowly can be detected. This study aimed to determine the ideal incubation time for accurate identification of inducible macrolide resistance as well as to determine if there was an association between the time taken to detect inducible resistance in M.

Oma1 Links Mitochondrial Protein Quality Control and TOR Signaling To Modulate Physiological Plasticity and Cellular Stress Responses.

A network of conserved proteases known as the intramitochondrial quality control (IMQC) system is central to mitochondrial protein homeostasis and cellular health. IMQC proteases also appear to participate in establishment of signaling cues for mitochondrion-to-nucleus communication. However, little is known about this process.

Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis.

The advent and widespread application of next-generation sequencing (NGS) technologies to the study of microbial genomes has led to a substantial increase in the number of studies in which whole genome sequencing (WGS) is applied to the analysis of microbial genomic epidemiology. However, microorganisms such as Mycobacterium tuberculosis (MTB) present unique problems for sequencing and downstream analysis based on their unique physiology and the composition of their genomes. In this study, we compare the quality of sequence data generated using the Nextera and TruSeq isolate preparation kits for library construction prior to Illumina sequencing-by-synthesis.

Re-evaluation of the critical concentration for ethambutol antimicrobial sensitivity testing on the MGIT 960.

The critical concentration (CC) for ethambutol testing on the Bactec MGIT 960 M. tuberculosis susceptibility testing has been questioned in recent publications. In this study, we correlate susceptibility results from the Bactec 460, MGIT 960 and embB gene sequencing to determine if the Bactec MGIT 960 adequately detects ethambutol resistance.

Haldane's rule is linked to extraordinary sex ratios and sperm length in stalk-eyed flies.

We use three allopatric populations of the stalk-eyed fly Teleopsis dalmanni from Southeast Asia to test two predictions made by the sex chromosome drive hypothesis for Haldane's rule. The first is that modifiers that suppress or enhance drive should evolve rapidly and independently in isolated populations. The second is that drive loci or modifiers should also cause sterility in hybrid males.

Stress-triggered activation of the metalloprotease Oma1 involves its C-terminal region and is important for mitochondrial stress protection in yeast.

Functional integrity of mitochondria is critical for optimal cellular physiology. A suite of conserved mitochondrial proteases known as intramitochondrial quality control represents one of the mechanisms assuring normal mitochondrial function. We previously demonstrated that ATP-independent metalloprotease Oma1 mediates degradation of hypohemylated Cox1 subunit of cytochrome c oxidase and is active in cytochrome c oxidase-deficient mitochondria.

Rapid molecular detection of macrolide resistance in the Mycobacterium avium complex: are we there yet?

Macrolides are an important tool in the treatment of Mycobacterium avium complex infections. Here, we evaluate the use of 23S rRNA gene sequencing for the rapid detection of macrolide resistance. Routine sequencing of the 23S rRNA gene is highly specific for macrolide resistance but lacks in sensitivity.