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The COVID-19 pandemic has demonstrated the need for real-time, open-access epidemiological information to inform public health decision-making and outbreak control efforts. In Canada, authority for healthcare delivery primarily lies at the provincial and territorial level; however, at the outset of the pandemic no definitive pan-Canadian COVID-19 datasets were available. The COVID-19 Canada Open Data Working Group was created to fill this crucial data gap. As a team of volunteer contributors, we collect daily COVID-19 data from a variety of governmental and non-governmental sources and curate a line-list of cases and mortality for all provinces and territories of Canada, including information on location, age, sex, travel history, and exposure, where available. We also curate time series of COVID-19 recoveries, testing, and vaccine doses administered and distributed. Data are recorded systematically at a fine sub-national scale, which can be used to support robust understanding of COVID-19 hotspots. We continue to maintain this dataset, and an accompanying online dashboard, to provide a reliable pan-Canadian COVID-19 resource to researchers, journalists, and the general public., Measurement(s) COVID-19 Cases • COVID-19 Mortalities • COVID-19 vaccination Technology Type(s) digital curation Sample Characteristic - Organism Homo sapiens Sample Characteristic - Location Canada Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.14331311

BACKGROUND: Nonpharmaceutical interventions remain the primary means of controlling severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) until vaccination coverage is sufficient to achieve herd immunity. We used anonymized smartphone mobility measures to quantify the mobility level needed to control SARS-CoV-2 (i.e., mobility threshold), and the difference relative to the observed mobility level (i.e., mobility gap). METHODS: We conducted a time-series study of the weekly incidence of SARS-CoV-2 in Canada from Mar. 15, 2020, to Mar. 6, 2021. The outcome was weekly growth rate, defined as the ratio of cases in a given week versus the previous week. We evaluated the effects of average time spent outside the home in the previous 3 weeks using a log-normal regression model, accounting for province, week and mean temperature. We calculated the SARS-CoV-2 mobility threshold and gap. RESULTS: Across the 51-week study period, a total of 888 751 people were infected with SARS-CoV-2. Each 10% increase in the mobility gap was associated with a 25% increase in the SARS-CoV-2 weekly case growth rate (ratio 1.25, 95% confidence interval 1.20–1.29). Compared to the prepandemic baseline mobility of 100%, the mobility threshold was highest in the summer (69%; interquartile range [IQR] 67%–70%), and dropped to 54% in winter 2021 (IQR 52%–55%); a mobility gap was present in Canada from July 2020 until the last week of December 2020. INTERPRETATION: Mobility strongly and consistently predicts weekly case growth, and low levels of mobility are needed to control SARS-CoV-2 through spring 2021. Mobility measures from anonymized smartphone data can be used to guide provincial and regional loosening and tightening of physical distancing measures.

Background The proportion of patients infected with SARS-CoV-2 that are prescribed antibiotics is uncertain, and may contribute to patient harm and global antibiotic resistance. Objective The aim was to estimate the prevalence and associated factors of antibiotic prescribing in patients with COVID-19. Data Sources We searched MEDLINE, OVID Epub and EMBASE for published literature on human subjects in English up to June 9 2020. Study Eligibility Criteria We included randomized controlled trials; cohort studies; case series with ≥10 patients; and experimental or observational design that evaluated antibiotic prescribing. Participants The study participants were patients with laboratory-confirmed SARS-CoV-2 infection, across all healthcare settings (hospital and community) and age groups (paediatric and adult). Methods The main outcome of interest was proportion of COVID-19 patients prescribed an antibiotic, stratified by geographical region, severity of illness and age. We pooled proportion data using random effects meta-analysis. Results We screened 7469 studies, from which 154 were included in the final analysis. Antibiotic data were available from 30 623 patients. The prevalence of antibiotic prescribing was 74.6% (95% CI 68.3–80.0%). On univariable meta-regression, antibiotic prescribing was lower in children (prescribing prevalence odds ratio (OR) 0.10, 95% CI 0.03–0.33) compared with adults. Antibiotic prescribing was higher with increasing patient age (OR 1.45 per 10 year increase, 95% CI 1.18–1.77) and higher with increasing proportion of patients requiring mechanical ventilation (OR 1.33 per 10% increase, 95% CI 1.15–1.54). Estimated bacterial co-infection was 8.6% (95% CI 4.7–15.2%) from 31 studies. Conclusions Three-quarters of patients with COVID-19 receive antibiotics, prescribing is significantly higher than the estimated prevalence of bacterial co-infection. Unnecessary antibiotic use is likely to be high in patients with COVID-19.

Background Bacterial co-pathogens are commonly identified in viral respiratory infections and are important causes of morbidity and mortality. The prevalence of bacterial infection in patients infected with SARS-CoV-2 is not well understood. Aims To determine the prevalence of bacterial co-infection (at presentation) and secondary infection (after presentation) in patients with COVID-19. Sources We performed a systematic search of MEDLINE, OVID Epub and EMBASE databases for English language literature from 2019 to April 16, 2020. Studies were included if they (a) evaluated patients with confirmed COVID-19 and (b) reported the prevalence of acute bacterial infection. Content Data were extracted by a single reviewer and cross-checked by a second reviewer. The main outcome was the proportion of COVID-19 patients with an acute bacterial infection. Any bacteria detected from non-respiratory-tract or non-bloodstream sources were excluded. Of 1308 studies screened, 24 were eligible and included in the rapid review representing 3338 patients with COVID-19 evaluated for acute bacterial infection. In the meta-analysis, bacterial co-infection (estimated on presentation) was identified in 3.5% of patients (95%CI 0.4–6.7%) and secondary bacterial infection in 14.3% of patients (95%CI 9.6–18.9%). The overall proportion of COVID-19 patients with bacterial infection was 6.9% (95%CI 4.3–9.5%). Bacterial infection was more common in critically ill patients (8.1%, 95%CI 2.3–13.8%). The majority of patients with COVID-19 received antibiotics (71.9%, 95%CI 56.1 to 87.7%). Implications Bacterial co-infection is relatively infrequent in hospitalized patients with COVID-19. The majority of these patients may not require empirical antibacterial treatment., Graphical abstract Image 1

This cohort study examines whether the implementation of differentially timed restrictions in a highly interconnected metropolitan area was associated with increased interregional travel.

Urinary tract infections caused by the bacterium Escherichia coli are among the most frequently encountered infections and are a common reason for antimicrobial prescriptions. Resistance to fluoroquinolone antimicrobial agents, particularly ciprofloxacin, has increased in recent decades. It is intuitive that variation in fluoroquinolone resistance is driven by changes in antimicrobial use, but careful study of this association requires the use of time-series methods. Between April 2010 and December 2014, we studied seasonal variation in resistance to ciprofloxacin, trimethoprim-sulfamethoxazole, and ampicillin in community-acquired urinary E. coli isolates in Montreal, Quebec, Canada. Using dynamic linear models, we investigated whether seasonal variation in resistance could be explained by seasonal variation in community antimicrobial use. We found a positive association between total fluoroquinolone use lagged by 1 and 2 months and the proportion of isolates resistant to ciprofloxacin. Our results suggest that resistance to ciprofloxacin is responsive to short-term variation in antimicrobial use. Thus, antimicrobial stewardship campaigns to reduce fluoroquinolone use, particularly in the winter when use is highest, are likely to be a valuable tool in the struggle against antimicrobial resistance.

IntroductionAntimicrobial resistance undermines our ability to treat bacterial infections, leading to longer hospital stays, increased morbidity and mortality, and a mounting burden to the healthcare system. Antimicrobial stewardship is increasingly important to safeguard the efficacy of existing drugs, as few new drugs are in the developmental pipeline. While significant progress has been made with respect to stewardship in hospitals, relatively little progress has been made in the primary care setting, where the majority of antimicrobials are prescribed. OPEN Stewardship is an international collaboration to develop an automated feedback platform to improve responsible antimicrobial prescribing among primary care physicians and capable of being deployed across heterogeneous healthcare settings. We describe the protocol for an evaluation of this automated feedback intervention with two main objectives: assessing changes in antimicrobial prescribing among participating physicians and determining the usability and usefulness of the reports.Methods and analysisA non-randomised evaluation of the automated feedback intervention (OPEN Stewardship) will be conducted among approximately 150 primary care physicians recruited from Ontario, Canada and Southern Israel, based on a series of targeted stewardship messages sent using the platform. Using a controlled interrupted time-series analysis and multilevel negative binomial modelling, we will compare the antimicrobial prescribing rates of participants before and after the intervention, and also to the prescribing rates of non-participants (from the same healthcare network) during the same period. We will examine outcomes targeted by the stewardship messages, including prescribing for antimicrobials with duration longer than 7 days and prescribing for indications where antimicrobials are typically unnecessary. Participants will also complete a series of surveys to determine the usability and usefulness of the stewardship reports.Ethics and disseminationAll sites have obtained ethics committee approval to recruit providers and access anonymised prescribing data. Dissemination will occur through open-access publication, stakeholder networks and national/international meetings.

IntroductionAntimicrobial resistance (AMR) impacts the health and well-being of animals, affects animal owners both socially and economically, and contributes to AMR at the human and environmental interface. The overuse and/or inappropriate use of antibiotics in animals has been identified as one of the most important drivers of the development of AMR in animals. Effective antibiotic stewardship interventions such as feedback can be adopted in veterinary practices to improve antibiotic prescribing. However, the provision of dedicated financial and technical resources to implement such systems are challenging. The newly developed web-based Online Platform for Expanding Antibiotic Stewardship (OPEN Stewardship) platform aims to automate the generation of feedback reports and facilitate wider adoption of antibiotic stewardship. This paper describes a protocol to evaluate the usability and usefulness of a feedback intervention among veterinarians and assess its impact on individual antibiotic prescribing.Methods and analysisApproximately 80 veterinarians from Ontario, Canada and 60 veterinarians from Israel will be voluntarily enrolled in a controlled interrupted time-series study and their monthly antibiotic prescribing data accessed. The study intervention consists of targeted feedback reports generated using the OPEN Stewardship platform. After a 3-month preintervention period, a cohort of veterinarians (treatment cohort, n=120) will receive three feedback reports over the course of 6 months while the remainder of the veterinarians (n=20) will be the control cohort. A survey will be administered among the treatment cohort after each feedback cycle to assess the usability and usefulness of various elements of the feedback report. A multilevel negative-binomial regression analysis of the preintervention and postintervention antibiotic prescribing of the treatment cohort will be performed to evaluate the impact of the intervention.Ethics and disseminationResearch ethics board approval was obtained at each participating site prior to the recruitment of the veterinarians. The study findings will be disseminated through open-access scientific publications, stakeholder networks and national/international meetings.

Background Suicide is among the top 10 leading causes of premature morality in the United States and its rates continue to increase. Thus, its prevention has become a salient public health responsibility. Risk factors of suicide transcend the individual and societal level as risk can increase based on climatic variables. The purpose of the present study is to evaluate the association between average temperature and suicide rates in the five most populous counties in California using mortality data from 1999 to 2019. Methods Monthly counts of death by suicide for the five counties of interest were obtained from CDC WONDER. Monthly average, maximum, and minimum temperature were obtained from nCLIMDIV for the same time period. We modelled the association of each temperature variable with suicide rate using negative binomial generalized additive models accounting for the county-specific annual trend and monthly seasonality. Results There were over 38,000 deaths by suicide in California’s five most populous counties between 1999 and 2019. An increase in average temperature of 1 °C corresponded to a 0.82% increase in suicide rate (IRR = 1.0082 per °C; 95% CI = 1.0025–1.0140). Estimated coefficients for maximum temperature (IRR = 1.0069 per °C; 95% CI = 1.0021–1.0117) and minimum temperature (IRR = 1.0088 per °C; 95% CI = 1.0023–1.0153) were similar. Conclusion This study adds to a growing body of evidence supporting a causal effect of elevated temperature on suicide. Further investigation into environmental causes of suicide, as well as the biological and societal contexts mediating these relationships, is critical for the development and implementation of new public health interventions to reduce the incidence of suicide, particularly in the face increasing temperatures due to climate change.

Empirical treatment of urinary tract infections should be based on susceptibility profiles specific to the locale and patient population. Additionally, these susceptibility profiles should account for correlations between resistance to different types of antimicrobials., Empirical treatment of urinary tract infections should be based on susceptibility profiles specific to the locale and patient population. Additionally, these susceptibility profiles should account for correlations between resistance to different types of antimicrobials. We used hierarchical logistic regression models to investigate geographic, temporal, and demographic trends in resistance to six antimicrobials in community-acquired and nosocomial urinary E. coli isolates from three communities in the province of Quebec, Canada, procured between April 2010 and December 2017. A total of 74,986 community-acquired (patient age, ≥18 years) and 4,384 nosocomial isolates (patient age, ≥65 years) were analyzed. In both community-acquired and nosocomial isolates, we found geographic variation in the prevalence of resistance. Male sex (community-acquired hierarchical mean odds ratio [OR], 1.24; 95% credible interval [CI], 1.02 to 1.50; nosocomial hierarchical mean OR, 1.16, 95% CI, 0.92 to 1.41) and recent hospitalization (community-acquired hierarchical mean OR, 1.49; 95% CI, 1.33 to 1.66; nosocomial hierarchical mean OR, 1.31; 95% CI, 0.99 to 1.78) were associated with a higher risk of resistance to most types of antimicrobials. We found distinct seasonal trends in both community-acquired and nosocomial isolates, but only community-acquired isolates showed a consistent annual pattern. Ciprofloxacin resistance increased sharply with patient age. We found clinically relevant differences in antimicrobial resistance in urinary E. coli isolates between locales and patient populations in the province of Quebec. These results could help inform empirical treatment decisions for urinary tract infections. In the future, similar models integrating local, provincial, and national resistance data could be incorporated into decision support systems for clinicians.