First Canadian report of transmission of fluconazole-resistant Candida parapsilosis within two hospital networks confirmed by genomic analysis.

Candida parapsilosis is a common cause of non-albicans candidemia. It can be transmitted in healthcare settings resulting in serious healthcare-associated infections and can develop drug resistance to commonly used antifungal agents. Following a significant increase in the percentage of fluconazole (FLU)-nonsusceptible isolates from sterile site specimens of patients in two Ontario acute care hospital networks, we used whole genome sequence (WGS) analysis to retrospectively investigate the genetic relatedness of isolates and to assess potential in-hospital spread. Phylogenomic analysis was conducted on all 19 FLU-resistant and seven susceptible-dose dependent (SDD) isolates from the two hospital networks, as well as 13 FLU susceptible C. parapsilosis isolates from the same facilities and 20 isolates from patients not related to the investigation. Twenty-five of 26 FLU-nonsusceptible isolates (resistant or SDD) and two susceptible isolates from the two hospital networks formed a phylogenomic cluster that was highly similar genetically and distinct from other isolates. The results suggest the presence of a persistent strain of FLU-nonsusceptible C. parapsilosis causing infections over a 5.5-year period. Results from WGS were largely comparable to microsatellite typing. Twenty-seven of 28 cluster isolates had a K143R substitution in lanosterol 14-α-demethylase (ERG11) associated with azole resistance. As the first report of a healthcare-associated outbreak of FLU-nonsusceptible C. parapsilosis in Canada, this study underscores the importance of monitoring local antimicrobial resistance trends and demonstrates the value of WGS analysis to detect and characterize clusters and outbreaks. Timely access to genomic epidemiological information can inform targeted infection control measures.

Gut microbiome modified by bariatric surgery improves insulin sensitivity and correlates with increased brown fat activity and energy expenditure.

Alterations in the microbiome correlate with improved metabolism in patients following bariatric surgery. While fecal microbiota transplantation (FMT) from obese patients into germ-free (GF) mice has suggested a significant role of the gut microbiome in metabolic improvements following bariatric surgery, causality remains to be confirmed. Here, we perform paired FMT from the same obese patients (BMI > 40; four patients), pre- and 1 or 6 months post-Roux-en-Y gastric bypass (RYGB) surgery, into Western diet-fed GF mice. Mice colonized by FMT from patients' post-surgery stool exhibit significant changes in microbiota composition and metabolomic profiles and, most importantly, improved insulin sensitivity compared with pre-RYGB FMT mice. Mechanistically, mice harboring the post-RYGB microbiome show increased brown fat mass and activity and exhibit increased energy expenditure. Moreover, improvements in immune homeostasis within the white adipose tissue are also observed. Altogether, these findings point to a direct role for the gut microbiome in mediating improved metabolic health post-RYGB surgery.

First reported case of Robinsoniella peoriensis pyometra and bloodstream infection: A case report and review of the literature.

We report on a 47-year-old woman with jejunal adenocarcinoma and concurrent endometrial cancer, admitted with sepsis. Uterine fluid and blood cultures were positive for Robinsoniella peoriensis. This is the first case report of Robinsoniella peoriensis in Canada. We encourage clinicians to publish their experience treating gynecologic infections caused by Robinsoniella peoriensis. Failure to recognize this pathogen as causative for pyometra, may result in insufficient antimicrobial treatment, and death.

Canadian Society of Clinical Chemists (CSCC) consensus guidance for testing, selection and quality management of SARS-CoV-2 point-of-care tests.

OBJECTIVES: A consensus guidance is provided for testing, utility and verification of SARS-CoV-2 point-of-care test (POCT) performance and implementation of a quality management program, focusing on nucleic acid and antigen targeted technologies. DESIGN AND METHODS: The recommendations are based on current literature and expert opinion from the members of Canadian Society of Clinical Chemists (CSCC), and are intended for use inside or outside of healthcare settings that have varied levels of expertise and experience with POCT. RESULTS AND CONCLUSIONS: Here we discuss sampling requirements, biosafety, SARS-CoV-2 point-of-care testing methodologies (with focus on Health Canada approved tests), test performance and limitations, test selection, testing utility, development and implementation of quality management systems, quality improvement, and medical and scientific oversight.

Dissemination of Verona Integron-encoded Metallo-ß-lactamase among clinical and environmental Enterobacteriaceae isolates in Ontario, Canada.

Surveillance data from Southern Ontario show that a majority of Verona Integron-encoded Metallo-ß-lactamase (VIM)-producing Enterobacteriaceae are locally acquired. To better understand the local epidemiology, we analysed clinical and environmental blaVIM-positive Enterobacteriaceae from the area. Clinical samples were collected within the Toronto Invasive Bacterial Diseases Network (2010-2016); environmental water samples were collected in 2015. We gathered patient information on place of residence and hospital admissions prior to the diagnosis. Patients with and without plausible source of acquisition were compared regarding risk exposures. Microbiological isolates underwent whole-genome sequencing (WGS); blaVIM carrying plasmids were characterized. We identified 15 patients, thereof 11 with blaVIM-1-positive Enterobacter hormaechei within two genetic clusters based on WGS. Whereas no obvious epidemiologic link was identified among cluster I patients, those in cluster II were connected to a hospital outbreak. Except for patients with probable acquisition abroad, we did not identify any further risk exposures. Two blaVIM-1-positive E. hormaechei from environmental waters matched with the clinical clusters; plasmid sequencing suggested a common ancestor plasmid for the two clusters. These data show that both clonal spread and horizontal gene transfer are drivers of the dissemination of blaVIM-1-carrying Enterobacter hormaechei in hospitals and the aquatic environment in Southern Ontario, Canada.

Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide.

The COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), was declared on March 11, 2020 by the World Health Organization. As of the 31st of May, 2020, there have been more than 6 million COVID-19 cases diagnosed worldwide and over 370,000 deaths, according to Johns Hopkins. Thousands of SARS-CoV-2 strains have been sequenced to date, providing a valuable opportunity to investigate the evolution of the virus on a global scale. We performed a phylogenetic analysis of over 1,225 SARS-CoV-2 genomes spanning from late December 2019 to mid-March 2020. We identified a missense mutation, D614G, in the spike protein of SARS-CoV-2, which has emerged as a predominant clade in Europe (954 of 1,449 (66%) sequences) and is spreading worldwide (1,237 of 2,795 (44%) sequences). Molecular dating analysis estimated the emergence of this clade around mid-to-late January (10-25 January) 2020. We also applied structural bioinformatics to assess the potential impact of D614G on the virulence and epidemiology of SARS-CoV-2. In silico analyses on the spike protein structure suggests that the mutation is most likely neutral to protein function as it relates to its interaction with the human ACE2 receptor. The lack of clinical metadata available prevented our investigation of association between viral clade and disease severity phenotype. Future work that can leverage clinical outcome data with both viral and human genomic diversity is needed to monitor the pandemic.

Issues beyond resistance: inadequate antibiotic therapy and bacterial hypervirulence.

The administration of antibiotics while critical for treatment, can be accompanied by potentially severe complications. These include toxicities associated with the drugs themselves, the selection of resistant organisms and depletion of endogenous host microbiota. In addition, antibiotics may be associated with less well-recognized complications arising through changes in the pathogens themselves. Growing evidence suggests that organisms exposed to antibiotics can respond by altering the expression of toxins, invasins and adhesins, as well as biofilm, resistance and persistence factors. The clinical significance of these changes continues to be explored; however, it is possible that treatment with antibiotics may inadvertently precipitate a worsening of the clinical course of disease. Efforts are needed to adjust or augment antibiotic therapy to prevent the transition of pathogens to hypervirulent states. Better understanding the role of antibiotic-microbe interactions and how these can influence disease course is critical given the implications on prescription guidelines and antimicrobial stewardship policies.

Ethical implications of recruiting universal stool donors for faecal microbiota transplantation.

Faecal microbiota transplantation is an effective therapy for recurrent Clostridioides difficile infection, with potential therapeutic applications in other health conditions. As research uncovers potential associations between the intestinal microbiome and various disease states, stool donor screening has become increasingly stringent, leading to low donor acceptance. Many stool banks have opted to recruit universal stool donors, who are encouraged to donate frequently over a prolonged period and whose stool is used to treat multiple patients. However, various ethical concerns arise when recruiting universal stool donors, which need to be addressed to mitigate harm to donors. In this Personal View, we describe the major ethical issues with universal stool banks across six domains: informed consent, privacy, the imposing of restrictions on autonomy, stewardship of microbiome information, financial incentives, and preventing a sense of obligation. We also suggest several priorities for future research that should be pursued to address these crucial issues and develop more donor-centric stool banks.

Long-Term Effects of Phased Implementation of Antimicrobial Stewardship in Academic ICUs: 2007-2015.

OBJECTIVES: Antimicrobial stewardship is advocated to reduce antimicrobial resistance in ICUs by reducing unnecessary antimicrobial consumption. Evidence has been limited to short, single-center studies. We evaluated whether antimicrobial stewardship in ICUs could reduce antimicrobial consumption and costs. DESIGN: We conducted a phased, multisite cohort study of a quality improvement initiative. SETTING: Antimicrobial stewardship was implemented in four academic ICUs in Toronto, Canada beginning in February 2009 and ending in July 2012. PATIENTS: All patients admitted to each ICU from January 1, 2007, to December 31, 2015, were included. INTERVENTIONS: Antimicrobial stewardship was delivered using in-person coaching by pharmacists and physicians three to five times weekly, and supplemented with unit-based performance reports. Total monthly antimicrobial consumption (measured by defined daily doses/100 patient-days) and costs (Canadian dollars/100 patient-days) before and after antimicrobial stewardship implementation were measured. MEASUREMENTS AND MAIN RESULTS: A total of 239,123 patient-days (57,195 patients) were analyzed, with 148,832 patient-days following introduction of antimicrobial stewardship. Antibacterial use decreased from 120.90 to 110.50 defined daily dose/100 patient-days following introduction of antimicrobial stewardship (adjusted intervention effect -12.12 defined daily dose/100 patient-days; 95% CI, -16.75 to -7.49; p < 0.001) and total antifungal use decreased from 30.53 to 27.37 defined daily doses/100 patient-days (adjusted intervention effect -3.16 defined daily dose/100 patient-days; 95% CI, -8.33 to 0.04; p = 0.05). Monthly antimicrobial costs decreased from $3195.56 to $1998.59 (adjusted intervention effect -$642.35; 95% CI, -$905.85 to -$378.84; p < 0.001) and total antifungal costs were unchanged from $1771.86 to $2027.54 (adjusted intervention effect -$355.27; 95% CI, -$837.88 to $127.33; p = 0.15). Mortality remained unchanged, with no consistent effects on antimicrobial resistance and candidemia. CONCLUSIONS: Antimicrobial stewardship in ICUs with coaching plus audit and feedback is associated with sustained improvements in antimicrobial consumption and cost. ICUs with high antimicrobial consumption or expenditure should consider implementing antimicrobial stewardship programs.

Challenges establishing a multi-purpose fecal microbiota transplantation stool donor program in Toronto, Canada.

Background: The success of fecal microbiota transplantation (FMT) programs depends on maintaining suitable stool donors. We describe challenges recruiting and retaining universal donors in the first 2 years of an FMT clinical and research program in Toronto and identify opportunities for improvement. Methods: A four-stage screening process is used to identify suitable FMT donors in the Microbiota Therapeutics Outcomes Program. Donor screening follows Health Canada recommendations and excludes persons with history or risk for diseases associated with dysbiosis. Donors are rescreened microbiologically approximately every 1-3 months and answer ongoing health, exposure, and dietary questionnaires. Results: In the first 2 years of our program, 5 of 322 (1.6%) prospective stool donors passed initial screening, and only 2 (0.6%) were retained. Most prospective donors were excluded on telephone screening, at which point high BMI, medication use, and family history of relevant illness were common exclusions. No candidate was excluded because of a concerning physical examination. Microbiologic reasons for donor exclusion included carriage of Blastocystis hominis (n = 2), Helicobacter pylori (n = 2), extended spectrum beta-lactamase producing organisms (n = 1), Shiga-toxin producing Escherichia coli (n = 1), and sapovirus (n = 1). Universal donors were lost temporarily because of travel, antibiotic exposures, and transient carriage of antibiotic-resistant organisms. Conclusions: Recruiting and retaining suitable donors for FMT is challenging because of rigorous exclusions and labour-intensive screening processes. We present considerations for efficiency in donor screening, including targeting recruitment populations, expanded website self-screening, eliminating physical examinations, and streamlining post-travel risk assessment.

Historique: Le succès des programmes de transplantation de microbiote fécal (TMF) dépend de la rétention de donneurs fécaux appropriés. Les auteurs décrivent les difficultés à recruter et à conserver des donneurs universels dans les deux premières années d'un programme clinique et de recherche de TMF à Toronto ainsi qu'à déterminer les possibilités d'amélioration. Méthodologie: Un processus de sélection en quatre étapes permet de déterminer les donneurs de TMF appropriés au sein du programme de résultats thérapeutiques du microbiote. La sélection des donneurs suit les recommandations de Santé Canada et exclut les personnes ayant des antécédents ou un risque de maladies associés à la dysbiose. Les donneurs reprennent une sélection microbiologique environ tous les un à trois mois et répondent à des questionnaires sur la santé, l'exposition et le régime alimentaire. Résultats: Au cours de deux premières années du programme, cinq des 322 donneurs prospectifs de matière fécale (1,6 %) ont réussi la sélection initiale, et seulement deux (0,6 %) ont été retenus. La plupart des donneurs prospectifs ont été exclus à la sélection téléphonique; un IMC élevé, la prise de médicaments et des antécédents familiaux de maladie pertinente étaient des exclusions courantes. Aucun candidat n'a été exclu à cause d'un examen physique inquiétant. Les raisons microbiologiques d'exclure les donneurs incluaient le portage de Blastocystis hominis (n = 2), d'Helicobacter pylori (n = 2), d'organismes producteurs de bêta-lactamase à large spectre (n = 1), d'Escherichia coli producteur de la toxine de Shiga (n = 1) et du sapovirus (n = 1). Des donneurs temporaires étaient perdus temporairement à cause de voyages, d'exposition à des antibiotiques et de portage transitoire d'organismes antibiorésistants. Conclusions: Il est difficile de recruter et de retenir des donneurs appropriés de TMF en raison des exclusions rigoureuses et des processus de dépistage fastidieux. Les auteurs présentent des considérations d'efficacité pour le dépistage des donneurs, y compris le ciblage de populations à recruter, l'autodépistage élargi dans les sites Web, l'élimination des examens physiques et la rationalisation de l'évaluation du risque après le voyage.

Emerging antimicrobial resistance among Escherichia coli strains in bloodstream infections in Toronto, 2006-2016: a retrospective cohort study.

BACKGROUND: Enterobacteriaceae that produce extended-spectrum ß-lactamase (ESBL) have emerged as a serious threat, with variable rates depending on geographic region. We determined the prevalence of ESBL-producing Escherichia coli, Klebsiella pneumoniae, K. oxytoca and Proteus mirabilis in bloodstream infections in Toronto from 2006 through 2016. METHODS: All patients with E. coli, K. pneumoniae, K. oxytoca and P. mirabilis isolated from blood in a tertiary care microbiology laboratory in Toronto between 2006 and 2016 (1 isolate per species per patient per year) were included in this retrospective cohort study. Organisms were identified by conventional methods, and susceptibility testing was performed according to Clinical and Laboratory Standards Institute standards. Screening for ESBL and phenotypic confirmatory testing were done with a modified Clinical and Laboratory Standards Institute method. ST131 clonal type was determined by means of an established protocol. RESULTS: The proportion of ESBL-producing E. coli isolates increased significantly between 2006 and 2016, from 6.4% (19/296) to 17.3% (89/513) (p < 0.001). This trend was seen in both intensive care units and emergency departments. Concurrently, the proportion of ST131 among ESBL-producing E. coli also increased significantly, from 31.6% (6/19) in 2006 to 73.0% (65/89) in 2016 (p = 0.03). Among ESBL-producing E. coli, significant resistance was noted to multiple antimicrobial classes. Comparable increases in the proportion of ESBL-producing K. pneumoniae, K. oxytoca and P. mirabilis were not noted. INTERPRETATION: We observed a significant increase in the proportion of ESBL-producing E. coli in bloodstream infections in Toronto temporally correlated with an increase in the ST131 clonal type. Recognition of this dramatic rise is important to inform empiric antibiotic treatment.

Emergence of Carbapenemase-Producing Enterobacteriaceae, South-Central Ontario, Canada1.

We analyzed population-based surveillance data from the Toronto Invasive Bacterial Diseases Network to describe carbapenemase-producing Enterobacteriaceae (CPE) infections during 2007-2015 in south-central Ontario, Canada. We reviewed patients' medical records and travel histories, analyzed microbiologic and clinical characteristics of CPE infections, and calculated incidence. Among 291 cases identified, New Delhi metallo-ß-lactamase was the predominant carbapenemase (51%). The proportion of CPE-positive patients with prior admission to a hospital in Canada who had not received healthcare abroad or traveled to high-risk areas was 13% for patients with oxacillinase-48, 24% for patients with New Delhi metallo-ß-lactamase, 55% for patients with Klebsiella pneumoniae carbapenemase, and 67% for patients with Verona integron-encoded metallo-ß-lactamase. Incidence of CPE infection increased, reaching 0.33 cases/100,000 population in 2015. For a substantial proportion of patients, no healthcare abroad or high-risk travel could be established, suggesting CPE acquisition in Canada. Policy and practice changes are needed to mitigate nosocomial CPE transmission in hospitals in Canada.