Clinical epidemiology and impact of Haemophilus influenzae airway infections in adults with cystic fibrosis.

Background: Haemophilus influenzae is prevalent within the airways of persons with cystic fibrosis (pwCF). H. influenzae is often associated with pulmonary exacerbations (PEx) in pediatric cohorts, but in adults, studies have yielded conflicting reports around the impact(s) on clinical outcomes such as lung function decline.

Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.

Modern sequencing instruments bring unprecedented opportunity to study within-host viral evolution in conjunction with viral transmissions between hosts. However, no computational simulators are available to assist the characterization of within-host dynamics. This limits our ability to interpret epidemiological predictions incorporating within-host evolution and to validate computational inference tools.

Population-based genomic surveillance of Pseudomonas aeruginosa causing bloodstream infections in a large Canadian health region.

Purpose: Population-based surveillance was undertaken to determine clinical factors, susceptibility patterns, and incidence rates (IR) of Pseudomonas aeruginosa causing bloodstream infections (BSIs) in a Canadian region (2010-2018).

Methods: We combined clinical data with genomics to characterize P. aeruginosa (BSIs) (n = 167) in a well-defined Canadian (Calgary) human population over a 9-year period (2010-2018).

natural history and evolution in the airways of adults with cystic fibrosis.

Introduction: is an opportunistic pathogen infecting persons with cystic fibrosis (pwCF) and portends a worse prognosis. Studies of infection dynamics have been limited by cohort size and follow-up. We investigated the natural history, transmission potential, and evolution of in a large Canadian cohort of 321 pwCF over a 37-year period.

Hepatosplenic mucormycosis due to identified by panfungal PCR/sequencing of ribosomal ITS2 and LSU regions in a patient with acute myelogenous leukemia: A case report.

Background: Angioinvasive infection with dissemination to the liver and spleen is exceedingly uncommon, representing less than 1% of reported cases of mucormycosis.

Methods: Diagnosis of mucormycosis is often difficult using conventional methods that rely on broad-based non-septate hyphae present on histologic examination and morphological identification of the cultured organism. Our laboratory also uses an in-house panfungal molecular assay to rapidly diagnose invasive fungal infection when conventional methods do not provide definitive results.

Incidence, susceptibility and outcomes of candidemia in adults living in Calgary, Alberta, Canada (2010-2018).

Background: Candidemia is increasing in frequency and is associated with high mortality. We sought to determine the burden of illness, the population it affects and its resistance profile in our region.

Methods: The Calgary Zone (CZ) provides all care for residents of Calgary and surrounding communities (~ 1.

Microbiological Characterization of Actinotignum schaalii Strains Causing Invasive Infections during a Multiyear Period in a Large Canadian Health Care Region.

Actinotignum schaalii is an underrecognized Gram-positive bacillus that is associated with urinary tract infections and cutaneous abscesses. The role of A. schaalii in invasive infections continues to be unappreciated because the bacteria can be isolated from a diverse spectrum of clinical specimens, ranging from being a single pathogen in urine and blood cultures to being deemed a colonizer in polymicrobial anaerobic cultures of sterile fluids and tissues.

A pragmatic randomized controlled trial of rapid on-site influenza and respiratory syncytial virus PCR testing in paediatric and adult populations.

Background: Rapid/point-of-care respiratory virus nucleic acid tests (NAT) may improve oseltamivir, antibiotic, diagnostic test, and hospital bed utilization. Previous randomized controlled trials (RCT) on this topic have not used standard procedures of an accredited healthcare and laboratory system.

Methods: We conducted a parallel RCT at two hospitals [paediatric = Alberta Children's Hospital (ACH); primarily adult = Peter Lougheed Centre (PLC)].

Genomic analysis of group A isolated during a correctional facility outbreak of MRSA in 2004.

Background: In 2004-2005, an outbreak of impetigo occurred at a correctional facility during a sentinel outbreak of methicillin- resistant (MRSA) in Alberta, Canada. Next-generation sequencing (NGS) was used to characterize the group A (GAS) isolates and evaluate whether genomic biomarkers could distinguish between those recovered alone and those co-isolated with .

Methods: Superficial wound swabs collected from all adults with impetigo during this outbreak were cultured using standard methods.

Characterizing infections in a large Canadian healthcare region.

We characterize the epidemiology of within a large Canadian region after implementation of improved identification methods. Positive cultures for from a centralized microbiology laboratory in Canada were analyzed. Clinical data were retrieved through administrative databases and chart reviews.

The natural history and genetic diversity of Haemophilus influenzae infecting the airways of adults with cystic fibrosis.

Haemophilus influenzae is a Gram-negative pathobiont, frequently recovered from the airways of persons with cystic fibrosis (pwCF). Previous studies of H. influenzae infection dynamics and transmission in CF predominantly used molecular methods, lacking resolution.

Risk Factors and Outcomes of Bloodstream Infections Among People With Human Immunodeficiency Virus: A Longitudinal Cohort Study From 2000 to 2017.

Background: Bloodstream infections (BSIs) among people with human immunodeficiency virus (PWH) remain a poorly studied source of morbidity and mortality. We characterize the epidemiology, microbiology, and clinical outcomes including reinfection, hospitalization, and mortality rates of both community-acquired and hospital-acquired BSI in PWH.

Methods: We identified all BSI, between January 1, 2000 and December 31, 2017 in PWH in care at Southern Alberta Clinic, by linking data from laboratory and clinical databases.

Genomic Characterization of From Beef Cattle Feedlots and Associated Environmental Continuum.

Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum.

Using a systematic approach to strategic innovation in laboratory medicine to bring about change.

There is a growing mismatch with regard to demand, supply, and affordability in healthcare systems in developed countries. Innovation is required to address this, but roadmaps for innovation in laboratory medicine are largely lacking. Advances in process and instrument digitization are driving a revolution in medical laboratory practice but changes are not strategically focused on improved patient care.

A case of multisystem inflammatory syndrome in adults following natural infection and subsequent immunization.

Multisystem inflammatory syndrome in adults is a rare and life-threatening complication that follows natural COVID-19 infection and primarily affects young unvaccinated adults. This complication is seldom described following vaccination, which would have important implications for the vaccination timing and platform in this population. COVID-19 vaccines are extremely effective; however, the risk of rare adverse events needs to be balanced with the vaccination benefits.

A longitudinal population-based study of predictors of mortality from bloodstream infections in Calgary, Alberta, Canada.

To study the predictors of mortality from nine major pathogens causing approximately 70% of cases over a 7-year period. A population-based surveillance cohort of all adult and pediatric patients in the Calgary Zone with an initial episode of bloodstream infections (BSI). The 1-year mortality was 29.

Age and sex-specific incidence rates of group A streptococcal pharyngitis between 2010 and 2018: a population-based study.

Group A streptococcus (GAS) pharyngitis is a common clinical infection with significant morbidity but remains understudied. We sought to assess the rates of testing and incidence of GAS pharyngitis in Calgary, Alberta based on age and sex. A total of 1,074,154 tests were analyzed (58.

Longitudinal evaluation of risk factors and outcomes of blood stream infections due to s species in persons with HIV: An observational cohort study.

Background: Staphylococcal blood stream infections (SBSI) are a significant cause of morbidity and mortality, however there is little data on such infections in persons with HIV (PWH) in the combination antiretroviral therapy era, particularly when divided by species; methicillin-sensitive (MSSA) and methicillin-resistant (MRSA) and coagulase-negative (CoNS).

Methods: Using linked longitudinal clinical and microbiologic databases, all cases of SBSI in PWH accessing care at Southern Alberta Clinic were identified and demographic features and outcomes characterized. We compared participants with SBSI to those with no SBSI and determined the 1-year all-cause mortality following SBSI and longitudinally over the study period.

Comparison of Accelerate PhenoTest BC Kit and MALDI-TOF MS/VITEK 2 System for the rapid identification and antimicrobial susceptibility testing of gram-negative bacilli causing bloodstream infections.

Background: Our laboratory uses matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI) and the VITEK 2 system (DV2) directly from positive blood cultures (BC) for organism identification (ID) and antimicrobial susceptibility testing (AST). Our objective was to compare direct MALDI-DV2 with a commercial BC ID-AST platform, the Accelerate Pheno system (AXDX), in the ID-AST of clinical and seeded BC positive for gram-negative bacilli (GNB).

Methods: BC positive for GNB were collected over a 3-mo period and tested using AXDX and direct MALDI-DV2 and compared with conventional methods.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory.

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences.

Rapid detection of carbapenemase-producing organisms directly from blood cultures positive for Gram-negative bacilli.

Introduction: The rapid detection of carbapenemase-producing organisms (CPOs) directly from blood cultures (BCs) positive for Gram-negative bacilli (GNB) may accelerate the appropriate treatment of at-risk patients.

Objective: To evaluate the performance of two commercial assays in the rapid detection of CPOs directly from BC positive for GNB.

Methods: BC positive for GNB were tested for the presence of CPOs with β CARBA® and NG-Test® CARBA 5.

Author Correction: Surveillance of Enterococcus spp. reveals distinct species and antimicrobial resistance diversity across a One-Health continuum.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A One Health Comparative Assessment of Antimicrobial Resistance in Generic and Extended-Spectrum Cephalosporin-Resistant from Beef Production, Sewage and Clinical Settings.

This study aimed to compare antimicrobial resistance (AMR) in extended-spectrum cephalosporin-resistant and generic from a One Health continuum of the beef production system in Alberta, Canada. A total of 705 extended-spectrum cephalosporin-resistant (ESC) were obtained from: cattle feces (CFeces, = 382), catch basins (CBasins, = 137), surrounding streams (SStreams, = 59), beef processing plants (BProcessing, = 4), municipal sewage (MSewage; = 98) and human clinical specimens (CHumans, = 25). Generic isolates (663) included: CFeces ( = 142), CBasins ( = 185), SStreams ( = 81), BProcessing ( = 159) and MSewage ( = 96).