Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Central Nervous System Infections: Advances and Challenges.

Central nervous system (CNS) infections carry a substantial burden of morbidity and mortality worldwide, and accurate and timely diagnosis is required to optimize management. Metagenomic next-generation sequencing (mNGS) has proven to be a valuable tool in detecting pathogens in patients with suspected CNS infection. By sequencing microbial nucleic acids present in a patient's cerebrospinal fluid, brain tissue, or samples collected outside of the CNS, such as plasma, mNGS can detect a wide range of pathogens, including rare, unexpected, and/or fastidious organisms.

De novo synthetic antimicrobial peptide design with a recurrent neural network.

Antibiotic resistance is recognized as an imminent and growing global health threat. New antimicrobial drugs are urgently needed due to the decreasing effectiveness of conventional small-molecule antibiotics. Antimicrobial peptides (AMPs), a class of host defense peptides, are emerging as promising candidates to address this need.

Receipt of Opioid Agonist Treatment in provincial correctional facilities in British Columbia is associated with a reduced hazard of nonfatal overdose in the month following release.

Background: In many jurisdictions, policies restrict access to Opioid Agonist Treatment (OAT) in correctional facilities. Receipt of OAT during incarceration is associated with reduced risk of fatal overdose after release but little is known about the effect on nonfatal overdose. This study aimed to examine the association between OAT use during incarceration and nonfatal overdose in the 30 days following release.

Impact of COVID-19 pandemic on hepatocellular carcinoma surveillance in British Columbia, Canada: An interrupted time series study.

We assessed the impact of the COVID-19 pandemic on hepatocellular carcinoma (HCC) surveillance among individuals with HCV diagnosed with cirrhosis in British Columbia (BC), Canada. We used data from the British Columbia Hepatitis Testers Cohort (BC-HTC), including all individuals in the province tested for or diagnosed with HCV from 1 January 1990 to 31 December 2015, to assess HCC surveillance. To analyse the impact of the pandemic on HCC surveillance, we used pre-policy (January 2018 to February 2020) and post-policy (March to December 2020) periods.

'Sometimes white doctors are not very friendly or inclusive': a Critical Race Theory analysis of racism within and beyond sexual health settings.

Many Two-Spirit, gay, bisexual, transgender, and other queer Black, Indigenous, people of colour in Canada encounter racism when testing for sexually transmitted and blood-borne infections. Our objective in this study was to understand how racism shapes testing experiences for these communities in Ontario, Canada. Four peer researchers conducted recruitment and data collection in consultation with a community advisory board.

Longitudinal evolution of the HIV effective reproduction number following sequential expansion of treatment as prevention and pre-exposure prophylaxis in British Columbia, Canada: a population-level programme evaluation.

Background: Treatment as prevention and pre-exposure prophylaxis (PrEP) are key strategies in the control of HIV/AIDS. We aimed to characterise the longitudinal effects of antiretroviral therapy (ART), followed by treatment as prevention and the addition of PrEP, on the HIV effective reproduction number (R) in British Columbia, Canada.

Methods: This population-level programme evaluation used data from the Drug Treatment Program of the British Columbia Centre for Excellence in HIV/AIDS (Vancouver, British Columbia, Canada).

Improving prevalence estimates of mental health and well-being indicators among sexual minority men: a propensity-weighting approach.

The prevalence and relative disparities of mental health outcomes and well-being indicators are often inconsistent across studies of sexual minority men (SMM) due to selection biases in community-based surveys (nonprobability sample), as well as misclassification biases in population-based surveys where some SMM often conceal their sexual orientation identities. The present study estimated the prevalence of mental health related outcomes (depressive symptoms, mental health service use, anxiety) and well-being indicators (loneliness and self-rated mental health) among SMM, broken down by sexual orientation using the adjusted logistic propensity score (ALP) weighting. We applied the ALP to correct for selection biases in the 2019 Sex Now data (a community-based survey of SMMs in Canada) by reweighting it to the 2015-2018 Canadian Community Health Survey (a population survey from Statistics Canada).

Invasive group A streptococcal disease surveillance in Canada, 2021-2022.

Background: Invasive group A streptococcal (iGAS, ) disease has been a nationally notifiable disease in Canada since 2000. This report summarizes the demographics, types, and antimicrobial resistance of iGAS isolates collected in Canada in 2021 and 2022.

Methods: The Public Health Agency of Canada's National Microbiology Laboratory collaborates with provincial and territorial public health laboratories to conduct national surveillance of invasive .

The BC Radon Data Repository (BCRDR) and BC Radon Map: Integrating disparate data sources for improved public health communication.

Setting: The potential for exposure to indoor radon varies dramatically across British Columbia (BC) due to varied geology. Individuals may struggle to understand their exposure risk and agencies may struggle to understand the value of population-level programs and policies to mitigate risk.

Intervention: The BC Centre for Disease Control (BCCDC) established the BC Radon Data Repository (BCRDR) to facilitate radon research, public awareness, and action in the province.

Correlates of Breakthrough SARS-CoV-2 Infections in People with HIV: Results from the CIHR CTN 328 Study.

COVID-19 breakthrough infection (BTI) can occur despite vaccination. Using a multi-centre, prospective, observational Canadian cohort of people with HIV (PWH) receiving ≥2 COVID-19 vaccines, we compared the SARS-CoV-2 spike (S) and receptor-binding domain (RBD)-specific IgG levels 3 and 6 months post second dose, as well as 1 month post third dose, in PWH with and without BTI. BTI was defined as positivity based on self-report measures (data up to last study visit) or IgG data (up to 1 month post dose 3).

Impact of the COVID-19 Pandemic on Hepatitis C Treatment Initiation in British Columbia, Canada: An Interrupted Time Series Study.

We investigated the impacts of the COVID-19 pandemic on hepatitis C (HCV) treatment initiation, including by birth cohort and injection drug use status, in British Columbia (BC), Canada. Using population data from the BC COVID-19 Cohort, we conducted interrupted time series analyses, estimating changes in HCV treatment initiation following the introduction of pandemic-related policies in March 2020. The study included a pre-policy period (April 2018 to March 2020) and three follow-up periods (April to December 2020, January to December 2021, and January to December 2022).

Acceptability of integrating mental health and substance use care within sexual health services among young sexual and gender minority men in Vancouver, Canada.

Background: Despite well-established evidence showing that young sexual and gender minority (SGM) men experience disproportionate mental health and substance use inequities, few sexual health services provide mental health and substance use care. This qualitative study examined the experiences and perspectives about integrated care models within sexual health services among young SGM men experiencing mental health and substance use challenges.

Methods: Semi-structured interviews were conducted with 50 SGM men aged 18-30 years who reported using substances with sex in Vancouver, Canada.

The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.

The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts.

Scoping review of exposure questionnaires and surveys in interstitial lung disease.

Background: Many interstitial lung diseases (ILDs) have clear causal relationships with environmental and occupational exposures. Exposure identification can assist with diagnosis, understanding disease pathogenesis, prognostication and prevention of disease progression and occurrence in others at risk. Despite the importance of exposure identification in ILD, there is no standardised assessment approach.

SARS-CoV-2 Surveillance of Wild Mice and Rats in North American Cities.

From July 2020 to June 2021, 248 wild house mice (Mus musculus), deer mice (Peromyscus maniculatus), brown rats (Rattus norvegicus), and black rats (Rattus rattus) from Texas and Washington, USA, and British Columbia, Canada, were tested for SARS-CoV-2 exposure and infection. Two brown rats and 11 house mice were positive for neutralizing antibodies using a surrogate virus neutralization test, but negative or indeterminate with the Multiplexed Fluorometric ImmunoAssay COVID-Plex, which targets full-length spike and nuclear proteins. Oro-nasopharyngeal swabs and fecal samples tested negative by RT-qPCR, with an indeterminate fecal sample in one house mouse.

Validation of an Automated, End-to-End Metagenomic Sequencing Assay for Agnostic Detection of Respiratory Viruses.

Background: Current molecular diagnostics are limited in the number and type of detectable pathogens. Metagenomic next-generation sequencing (mNGS) is an emerging, and increasingly feasible, pathogen-agnostic diagnostic approach. Translational barriers prohibit the widespread adoption of this technology in clinical laboratories.

Risk of Major Adverse Cardiovascular Events After SARS-CoV-2 Infection in British Columbia: A Population-Based Study.

Background: COVID-19 is associated with increased risk of post-acute cardiovascular outcomes. Population-based evidence for long periods of observation is still limited.

Methods: This population-based cohort study was conducted using data (2020-2021) from the British Columbia COVID-19 Cohort.

An Ensemble Framework for Projecting the Impact of Lymphatic Filariasis Interventions Across Sub-Saharan Africa at a Fine Spatial Scale.

Background: Lymphatic filariasis (LF) is a neglected tropical disease targeted for elimination as a public health problem by 2030. Although mass treatments have led to huge reductions in LF prevalence, some countries or regions may find it difficult to achieve elimination by 2030 owing to various factors, including local differences in transmission. Subnational projections of intervention impact are a useful tool in understanding these dynamics, but correctly characterizing their uncertainty is challenging.