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). RESULTS: The annual population IR per 100,000 patient years increased from 3.4/100,000 in 2010 to 5.9/100,000 in 2018, with the highest IRs in elderly males from the hospital setting. Over a quarter of patients presented with febrile neutropenia, followed by urinary tract infections and pneumonia. Antimicrobial resistance (AMR) rates and determinants were rare. The P. aeruginosa population was polyclonal consisting of three dominant sequence types (STs), namely ST244, ST111, and ST17. Antimicrobial-susceptible ST244 was the most common clone and belonged to three clades (A, B, C). The ST244 IR/100,000 increased over time due to the expansion of clade C. Multidrug-resistant ST111 was the second most common clone and IR/100,000 decreased over time. ST111 belonged to three clades (A, B, C) with clade C containing blaVIM-2. Different serotypes were linked to various STs. The IR/100,000 of P. aeruginosa that belonged to serotypes O6 increased significantly over time. CONCLUSION: An effective multivalent vaccine consisting of five serotypes (O1, O3, O5, O6, O11) would confer protection to > 70% of Calgary residents with P. aeruginosa BSIs. This study has provided a unique perspective of the population dynamics over time of P. aeruginosa STs, clades, and serotypes responsible for BSIs.

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

Introduction: Stenotrophomonas maltophilia is an opportunistic pathogen infecting persons with cystic fibrosis (pwCF) and portends a worse prognosis. Studies of S. maltophilia infection dynamics have been limited by cohort size and follow-up. We investigated the natural history, transmission potential, and evolution of S. maltophilia in a large Canadian cohort of 321 pwCF over a 37-year period. Methods: One-hundred sixty-two isolates from 74 pwCF (23%) were typed by pulsed-field gel electrophoresis, and shared pulsotypes underwent whole-genome sequencing. Results: S. maltophilia was recovered at least once in 82 pwCF (25.5%). Sixty-four pwCF were infected by unique pulsotypes, but shared pulsotypes were observed between 10 pwCF. In chronic carriage, longer time periods between positive sputum cultures increased the likelihood that subsequent isolates were unrelated. Isolates from individual pwCF were largely clonal, with differences in gene content being the primary source of genetic diversity objectified by gene content differences. Disproportionate progression of CF lung disease was not observed amongst those infected with multiple strains over time (versus a single) or amongst those with shared clones (versus strains only infecting one patient). We did not observe evidence of patient-to-patient transmission despite relatedness between isolates. Twenty-four genes with ≥ 2 mutations accumulated over time were identified across 42 sequenced isolates from all 11 pwCF with ≥ 2 sequenced isolates, suggesting a potential role for these genes in adaptation of S. maltophilia to the CF lung. Discussion: Genomic analyses suggested common, indirect sources as the origins of S. maltophilia infections in the clinic population. The information derived from a genomics-based understanding of the natural history of S. maltophilia infection within CF provides unique insight into its potential for in-host evolution.

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

Background: Angioinvasive Rhizomucor pusillus 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. Results: Herein we present a case of disseminated mucormycosis with hepatosplenic involvement in a 49-year-old female with acute myelogenous leukemia following induction chemotherapy. But in this case repeated tissue biopsy cultures were negative. R. pusillus infection was diagnosed using an in-house panfungal PCR/sequencing assay based on dual priming oligonucleotide primers. Conclusions: New molecular assays facilitate prompt diagnosis of invasive fungal infections.

Historique: L'infection à Rhizomucor pusillus angio-invasive avec dissémination au foie et à la rate est très peu courante, puisqu'elle représente 1% des cas de mucormycose déclarés. Méthodologie: Le diagnostic de mucormycose est souvent difficile à poser au moyen des méthodes habituelles, qui reposent sur la présence d'hyphes non cloisonnées généralisées à l'examen histologique et sur l'identification morphologique de l'organisme mis en culture. Le laboratoire recourt également à un dosage moléculaire panfongique maison pour diagnostiquer rapidement l'infection fongique invasive lorsque les méthodes habituelles ne fournissent pas de résultats définitifs. Résultats: Les chercheurs présentent un cas de mucormycose disséminée avec atteinte hépatosplénique chez une femme de 49 ans atteinte de leucémie myélogène aiguë après une chimiothérapie d'induction. Dans ce cas, les résultats des biopsies tissulaires répétées étaient négatifs. L'infection à R. pusillus a été diagnostiquée au moyen d'un dosage maison par séquençage ou PRC panfongique d'après des amorces oligonucléotidiques à double usage. Conclusions: Les nouveaux dosages moléculaires facilitent un diagnostic rapide d'infection fongique invasive.

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 (~ 1.69 million) via five tertiary hospitals each served by a common single laboratory for acute care microbiology. All adult patients in the CZ with at least one Candida spp.-positive blood culture between January 1, 2010, and December 31, 2018, were identified using microbiological data from Calgary Lab Services, the laboratory that processes > 95% of all blood culture samples in the CZ, were reviewed for the study. RESULTS: The overall annual incidence of candidemia among individuals living in the CZ was 3.8 per 100,000 persons (Median age 61 years (IQR 48-72) and 221/455 (47.4%) were female). C. albicans was the most common species (50.6%), followed by C. glabrata, (24.0%). No other species accounted for more than 7% of cases. Overall mortality at 30, 90, and 365 days was 32.2, 40.1, and 48.1% respectively. Mortality rate did not differ by Candida species. Of individuals who developed candidemia, more than 50% died within the next year. No new resistance pattern has emerged in the most common Candida species in Calgary, Alberta. CONCLUSIONS: In Calgary, Alberta, the incidence of candidemia has not increased in the last decade. C. albicans was the most common species and it remains susceptible to fluconazole.

Genomic analysis of group A Streptococcus 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 Staphylococcus aureus (MRSA) in Alberta, Canada. Next-generation sequencing (NGS) was used to characterize the group A Streptococcus (GAS) isolates and evaluate whether genomic biomarkers could distinguish between those recovered alone and those co-isolated with S. aureus. METHODS: Superficial wound swabs collected from all adults with impetigo during this outbreak were cultured using standard methods. NGS was used to characterize and compare all of the GAS and S. aureus genomes. RESULTS: Fifty-three adults were culture positive for GAS, with a subset of specimens also positive for MRSA (n = 5) or methicillin-sensitive S. aureus (n = 3). Seventeen additional MRSA isolates from this facility from the same time frame (no GAS co-isolates) were also included. All 78 bacterial genomes were analyzed for the presence of known virulence factors, plasmids, and antimicrobial resistance (AMR) genes. Among the GAS isolates were 12 emm types, the most common being 41.2 (n = 27; 51%). GAS genomes were phylogenetically compared with local and public datasets of invasive and non-invasive isolates. GAS genomes had diverse profiles for virulence factors, plasmids, and AMR genes. Pangenome analysis did not identify horizontally transferred genes in the co-infection versus single infections. CONCLUSIONS: GAS recovered from invasive and non-invasive sources were not genetically distinguishable. Virulence factors, plasmids, and AMR profiles grouped by emm type, and no genetic changes were identified that predict co-infection or horizontal gene transfer between GAS and S. aureus.

HISTORIQUE: En 2004­2005, une éclosion d'impétigo s'est manifestée dans un établissement correctionnel pendant une éclosion sentinelle de Staphylococcus aureus résistante à la méthicilline (SRAM) en Alberta, au Canada. Le séquençage de prochaine génération (SPG) a été utilisé pour caractériser les isolats du streptocoque du groupe (SGA) et évaluer si les biomarqueurs génomiques peuvent distinguer ceux qui se rétablissent seuls de ceux qui ont co-isolé le S. aureus. MÉTHODOLOGIE: Les chercheurs ont mis en culture des écouvillons de plaies cutanées superficielles prélevés chez tous les adultes atteints d'impétigo pendant cette éclosion. Ils ont utilisé le SNG pour caractériser et comparer tous les génomes du SPG et du S. aureus récupérés. RÉSULTATS: Cinquante-trois adultes étaient positifs au SGA, un sous-groupe d'échantillons était également positif au SRAM (n = 5) ou au S. aureus (n = 3) sensible à la méthicilline. Dix-sept autres isolats de SRAM provenant de cet établissement pendant la même période (pas de co-isolats du SGA) ont été inclus. Ils ont analysé l'ensemble des 78 génomes bactériens pour déceler la présence de facteurs de virulence connus, de plasmides et de gènes de résistance antimicrobienne (RAM). Parmi les isolats du SGA se trouvaient 12 types d'emm, les plus courants étant 41,2 (n = 27, 51 %). Les génomes du SGA ont été comparés sur le plan phylogénétique aux données locales et publiques sur les isolats invasifs et non invasifs. Les génomes du SGA présentaient divers profils de facteurs de virulence, de plasmides et de gènes de RAM. L'analyse du pangénome n'a pas permis de repérer les gènes transférés dans les génomes de co-infection ou les adaptations génétiques associées à une co-infection plutôt par rapport aux infections uniques. CONCLUSIONS: Le SGA prélevé de sources invasives ou non invasives n'était pas reconnaissable sur le plan génétique. Les facteurs de virulence, les plasmides et les profils de résistance antimicrobienne regroupés par type d'emm ne présentaient pas de changements génétiques prédicteurs d'une co- infection ou d'un transfert génétique horizontal entre le SGA et le S. aureus.

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. We conducted a microbiological analysis of clinical isolates obtained from 2012 through 2019. A total of 86 isolates were analyzed; 37 (43%) were from blood cultures, 35 (41%) were from deep wounds and abscesses, 6 (7%) were from urine samples, and the rest were recovered from peritoneal, kidney, and scrotal fluid samples. Urinary tract infections were clinically identified as the source of most cases of bacteremia, although no simultaneous urine cultures yielded positive results. The 16S rRNA gene sequences were available for 32 isolates (37%). Phylogenetic analysis revealed that AS.1/AS.2 strains caused a larger proportion of bloodstream infections (BSIs) (100% versus 52% [P = 0.01]) and trended toward a higher rate of hospitalization (91% versus 76% [P = 0.18]) but had a lower clindamycin MIC90 (0.12 versus >256 µg/mL). Our study emphasizes the emergence of A. schaalii as a pathogen in human urine samples, BSIs, and skin and soft tissue infections. It highlights the pitfalls of current laboratory methods in recovering and identifying this organism from clinical specimens, particularly urine samples. Phylogenetic analysis showed unique genotypic sequences for A. schaalii AS.1/AS.2 strains causing urosepsis, which requires further study to identify potential virulence factors. IMPORTANCE Actinotignum schaalii is an underrecognized Gram-positive bacillus due to its special growth requirements and prior phenotypic identification methods, and it is often mistaken as a contaminant. It has been associated with various clinical syndromes, from urinary tract infections to cutaneous infections. The widespread use of molecular diagnostic methods allowed for improved detection. However, its role in invasive infections remains underappreciated. We conducted a detailed microbiological analysis to improve our understanding of this organism's genotypic and phenotypic characteristics. Our results highlight the pitfalls of clinical laboratory recovery, particularly from urine cultures. Although most BSIs were caused by urinary tract infections, no simultaneous urine cultures identified A. schaalii, largely due to the failure of phenotypic methods to reliably isolate and identify this organism. Additionally, this is the first study demonstrating A. schaalii strains with differences in clinical and microbiological characteristics, raising the possibility of potential bacterial virulence factors contributing to invasive infections.

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)]. Patients with a respiratory viral testing order were randomized to testing at either a central accredited laboratory (standard arm) or with a rapid polymerase chain reaction test at an on-site accredited laboratory followed by standard testing [rapid on-site test (ROST) arm] based on day of specimen receipt at the laboratory. Patients and clinicians were blinded to assignment. The primary outcome for ACH was inpatient length of stay (LOS) and for PLC was the proportion of inpatients prescribed oseltamivir. RESULTS: 706 patient encounters were included at ACH; 322 assigned to ROST (181 inpatients) and 384 to the standard arm (194 inpatients). 422 patient encounters were included at PLC; 200 assigned to ROST (157 inpatients) and 222 to the standard arm (175 inpatients). The rate of oseltamivir prescription and number of doses given was reduced in PLC inpatients negative for influenza in the ROST arm compared to standard arm [mean 14.9% (95% CI 9.87-21.9) vs. 27.5% (21.0-35.2), p = 0.0135; mean 2.85 doses (SEM 2.39-3.32) vs. 4.17 doses (3.85-4.49) p = 0.022, respectively]. ROST also significantly reduced oseltamivir use at ACH, reduced chest radiographs (ACH), and laboratory test ordering (PLC), but not antibiotic prescriptions. ROST also reduced the median turnaround time by > 24 h (ACH and PLC). The LOS at ACH was not significantly different between the ROST and standard arms [median 4.05 days (SEM 1.79-18.2) vs 4.89 days (2.07-22.9), p = 0.062, respectively]. No adverse events were reported. CONCLUSIONS: In a RCT representing implementation of ROST in an accredited laboratory system, we found that a ROST improved oseltamivir utilization and is the first RCT to show reduced ancillary testing in both paediatric and adult populations. A larger study is required to assess reduction in paediatric LOS as ACH was underpowered. These findings help justify the implementation of rapid on-site respiratory virus testing for inpatients. Trial registration ISRCTN, number 10110119, Retrospectively Registered, 01/12/2021.

Characterizing Actinotignum schaalii infections in a large Canadian healthcare region.

Aims: We characterize the epidemiology of Actinotignum schaalii within a large Canadian region after implementation of improved identification methods. Patients & methods: Positive cultures for A. schaalii from a centralized microbiology laboratory in Canada were analyzed. Clinical data were retrieved through administrative databases and chart reviews. Primary outcome was incidence of A. schaalii infections; secondary outcomes included mortality, hospital admission and length of stay. Results & conclusions: 86 unique isolates were studied, 37 bloodstream infections (BSI) and 49 non-BSIs. Patients with BSIs were older with more comorbidities, with urinary tract infections implicated as the most frequent source; skin abscesses caused the most non-BSIs. Hospitalization and 90-day mortality was higher in the BSI group. A. schaalii is an important community-acquired pathogen with the potential to cause invasive infections.

Actinotignum schaalii bacteria require special conditions and substances for their growth. Normally, A. schaalii reside in the urogenital tract without causing harm; however, they can be associated with urinary tract infections. Severe infections are increasingly identified with improved identification methods. This retrospective study included all positive cultures for A. schaalii from a centralized microbiology laboratory in Canada from 2012 to 2019. Eighty-six unique isolates were studied, including 37 bloodstream infections (BSIs) and 49 non-BSIs. The mean incidence rate of infections increased during the study. BSIs were seen in older men with other medical comorbidities and were associated with high hospitalization and mortality. Skin and soft-tissue infections comprised the majority of non-BSIs, occurring in younger patients and who had better clinical outcomes. Our population-based study of A. schaalii infections highlights the potential of this pathogen to cause severe infections.

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. In this retrospective cohort study, representative yearly H. influenzae isolates from all pwCF attending the Calgary Adult CF Clinic with H. influenzae positive sputum cultures between 2002 and 2016 were typed by pulsed-field gel electrophoresis. Isolates with shared pulsotypes common to ≥ 2 pwCF were sequenced by Illumina MiSeq. Phylogenetic and pangenomic analyses were used to assess genetic relatedness within shared pulsotypes, and epidemiological investigations were performed to assess potential for healthcare associated transmission. H. influenzae infection was observed to be common (33% of patients followed) and dynamic in pwCF. Most infected pwCF exhibited serial infections with new pulsotypes (75% of pwCF with ≥ 2 positive cultures), with up to four distinct pulsotypes identified from individual patients. Prolonged infection by a single pulsotype was only rarely observed. Intra-patient genetic diversity was observed at the single-nucleotide polymorphism and gene content levels. Seven shared pulsotypes encompassing 39% of pwCF with H. influenzae infection were identified, but there was no evidence, within our sampling scheme, of direct patient-to-patient infection transmission.

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. Crude incidence rates per 1000 person-years for BSI and death were calculated. Cox proportional hazards models estimated crude and adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) to conduct a risk factor analysis of BSI in PWH. Logistic regression models with generalized estimating equations estimated crude and adjusted odds ratios (aORs) to identify characteristics associated with 1-year mortality after BSI. Results: Among 2895 PWH, 396 BSI episodes occurred in 228 (8%) PWH. There were 278 (72%) Gram-positive and 109 (28%) Gram-negative BSI. People with human immunodeficiency virus with lower CD4 nadirs, higher Charlson comorbidity indices, and hepatitis C virus were at highest risk for BSI. Long-term all-cause mortality was greater in those experiencing BSI (HR, 5.25; 95% CI, 4.21-6.55). CD4 count <200 cells/mm3 measured closest to the time of BSI was associated with 1-year mortality after BSI (aOR, 3.88; 95% CI, 1.78-8.46). Repeat episodes (42%) and polymicrobial BSI (19%) were common. Conclusions: Bloodstream infections continue to occur at an elevated rate among PWH with high reoccurrence rates and associated morbidity and mortality. To risk stratify and develop targeted interventions, we identified PWH at greatest risk for BSI. People with human immunodeficiency virus with low immunity at the time of BSI are at highest risk of poor outcomes.

Genomic Characterization of Enterococcus hirae 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. This study focused on Enterococcus hirae isolates (n = 4,601) predominantly isolated from beef production systems including bovine feces (n = 4,117, 89.5%), catch-basin water (n = 306, 66.5%), stockpiled bovine manure (n = 24, 0.5%), and natural water sources near feedlots (n = 145, 32%), and a few isolates from urban wastewater (n = 9, 0.2%) denoted as human-associated environmental samples. Antimicrobial susceptibility profiling of a subset (n = 1,319) of E. hirae isolates originating from beef production systems (n = 1,308) showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multi-drug resistance, whereas urban wastewater isolates (n = 9) were resistant to nitrofurantoin (44.5%) and tigecycline (44.5%) followed by linezolid (33.3%). Genes for tetracycline (tetL, M, S/M, and O/32/O) and macrolide resistance erm(B) were frequently found in beef production isolates. Antimicrobial resistance profiles of E. hirae isolates recovered from different environmental settings appeared to reflect the kind of antimicrobial usage in beef and human sectors. Comparative genomic analysis of E. hirae isolates showed an open pan-genome that consisted of 1,427 core genes, 358 soft core genes, 1701 shell genes, and 7,969 cloud genes. Across species comparative genomic analysis conducted on E. hirae, Enterococcus faecalis and Enterococcus faecium genomes revealed that E. hirae had unique genes associated with vitamin production, cellulose, and pectin degradation, traits which may support its adaptation to the bovine digestive tract. E. faecium and E. faecalis more frequently harbored virulence genes associated with biofilm formation, iron transport, and cell adhesion, suggesting niche specificity within these species.

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. Laboratory services therefore largely remain transactional so that customer access and experience are suboptimal, especially for vulnerable populations. Laboratory medicine must be integrated back into clinical care pathways, thereby transforming services to be more responsive to end-user needs. Healthcare trends show that patients, physicians, and allied healthcare professionals will increasingly dictate what and how services are provided. Laboratories will be pressed to restructure to address these healthcare trends. Since the primary goal of ambulatory practice is to prevent expensive hospital admissions for patients with complex chronic diseases, specific services (e.g. ambulatory clinics, surgeries, deliveries, procedures) that could be safely provided in the community are moving out of acute care hospitals. This review addresses the existing barriers to innovation faced by medical/scientific and managerial services as well as outlines a systematic approach used by other industries to bring about transformative change. Enabling disruptive innovation that improves the clinical and economic effectiveness of laboratory practice is critical to sustain clinically relevant services as an essential cornerstone of patient care within the healthcare systems of developed countries.

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

Aim: To study the predictors of mortality from nine major pathogens causing approximately 70% of cases over a 7-year period. Materials & methods: A population-based surveillance cohort of all adult and pediatric patients in the Calgary Zone with an initial episode of bloodstream infections (BSI). Results: The 1-year mortality was 29.2% among 9524 patients (5164 males [54%]). Incidence rates for BSI increased annually to 119.7/100,000 persons by 2016. Distinct survival curves were found for each specific pathogen. Age, comorbidity burden and infecting organism were significantly associated with increased hazard of death. No relationship occurred between the time to positivity for blood cultures and overall mortality. Conclusion: BSI has a high mortality, but overall survival depends on underlying host health and the type of pathogen acquired.

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.

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

Aim: Group A streptococcus (GAS) pharyngitis is a common clinical infection with significant morbidity but remains understudied. Materials & methods: We sought to assess the rates of testing and incidence of GAS pharyngitis in Calgary, Alberta based on age and sex. Results: A total of 1,074,154 tests were analyzed (58.8% female, mean age 24.8 years) of which 16.6% were positive. Age-standardized testing and positivity was greatest in the 5-14 years age group and lowest in persons over 75 years. Females had greater rates of testing and positivity throughout. Testing rates (incidence rate ratios: 1.40, 95% CI: 1.39-1.41) and case rates (incidence rate ratios: 1.36, 95% CI: 1.33-1.39) increased over time. Conclusion: Future studies should focus on evaluating disparities in testing and treatment outcomes to optimize the approach to this infection.

Longitudinal evaluation of risk factors and outcomes of blood stream infections due to Staphylococcus 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 Staphylococcus aureus (MRSA) and coagulase-negative Staphylococcus (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. FINDINGS: From 2000 to 2018, 130 SBSI occurred in 95 PWH over 21,526 patient-years follow-up. MSSA caused 38.4%, MRSA 26.1% and CoNS 35.3% of SBSI. Highest risks for SSBI were in Hepatitis C coinfection, low CD4 nadir, Indigenous/Metis ethnicity and in persons who use injection drugs (PWID). During follow-up, 423 deaths occurred in all PWH. Mortality rates for PWH with SBSI was 74.9/1000 patient-years (95% CI 59.2-94.9) compared with no SBSI 16.0/1000 patient-years (95% CI 14.4-17.7). The mortality Hazard Ratio was 2.61(95% CI 1.95-3.49, P= <0.001) for SBSI compared to no SBSI, following adjusting for confounding. Seventy deaths occurred in persons with SBSI with 40% in the first year. Higher 1-year mortality rates occurred in hospital-acquired infections. INTERPRETATION: Incidence rates of SBSI are high in PWH, with identified characteristics that further increase this risk. PWH who experience SBSI have a significant mortality risk within the first year of follow-up, however they also have greater long-term all-cause mortality compared to those with no SBSI. Further investigation is needed in PWH evaluating host, environment and pathogen differences that lead to differing rates of SBSI and mortality seen here. FUNDING: No funding was received for this work.

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 ß CARBA® and NG-Test® CARBA 5. A subset of sterile BC samples was seeded with multidrug-resistant (MDR) GNB. Positive BCs from clinical and seeded samples were tested directly with ß CARBA and CARBA 5 from BC pellets. RESULTS: Sixty-five samples were tested (30 clinical, 35 seeded). ß CARBA had a sensitivity, specificity, NPV, and PPV of 100%, 65.7%, 100%, and 71.4%, respectively. CARBA 5 had a sensitivity, specificity, NPV, and PPV of 90.0%, 100%, 92.1%, and 100%. False negatives for CARBA 5 occurred with 1 GES, 1 VIM-1, and 1 IMP-14. CONCLUSIONS: This study demonstrates that the detection of CPOs directly from positive BC can be accurately achieved. ß CARBA had excellent sensitivity but suffered from poor specificity. CARBA 5 had good sensitivity and specificity but is unable to detect certain CPOs.

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. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.