Canadian Public Health Laboratory Network Research Articles

Comparison of PCV10, PCV13, PCV15, PCV20 and PPSV23 vaccine coverage of invasive Streptococcus pneumoniae isolate serotypes in Canada: the SAVE study, 2011-20.

As pneumococci evolve under vaccine, antimicrobial and other selective pressures, it is important to track isolates covered by established (PCV10, PCV13 and PPSV23) and new (PCV15 and PCV20) vaccine formulations. To compare invasive pneumococcal disease (IPD) isolates from serotypes covered by PCV10, PCV13, PCV15, PCV20 and PPSV23, collected in Canada from 2011 to 2020, by demographic category and antimicrobial resistance phenotype. IPD isolates from the SAVE study were initially collected by members of the Canadian Public Health Laboratory Network (CPHLN) as part of a collaboration between the Canadian Antimicrobial Resistance Alliance (CARA) and the Public Health Agency of Canada (PHAC). Serotypes were determined by quellung reaction, and antimicrobial susceptibility testing was performed using the CLSI broth microdilution method. A total of 14 138 invasive isolates were collected from 2011 to 2020, with 30.7% of isolates covered by the PCV13 vaccine, 43.6% of isolates covered by the PCV15 vaccine (including 12.9% non-PCV13 serotypes 22F and 33F), and 62.6% of isolates covered by the PCV20 vaccine (including 19.0% non-PCV15 serotypes 8, 10A, 11A, 12F and 15B/C). Non-PCV20 serotypes 2, 9N, 17F and 20, but not 6A (present in PPSV23) represented 8.8% of all IPD isolates. Higher-valency vaccine formulations covered significantly more isolates by age, sex, region and resistance phenotype including MDR isolates. Coverage of XDR isolates did not significantly differ between vaccine formulations. When compared with PCV13 and PCV15, PCV20 covered significantly more IPD isolates stratified by patient age, region, sex, individual antimicrobial resistance phenotypes and MDR phenotype.

Canadian Public Health Laboratory Network guidelines for the use of point-of-care tests for Treponema pallidum in Canada.

Over the past few years, the increase in infectious syphilis outbreaks in major urban centres and remote or rural locations in Canada, often affecting hard-to-reach patient populations, has renewed an interest and urgency in studying the use of point-of-care tests (POCTs) that can provide test results at the time and place of primary health care delivery, obviating the repeat visit necessary with traditional syphilis serology or molecular diagnostic tests. In 2015, the Canadian Public Health Laboratory Network released its first laboratory guideline for the use of POCTs in the diagnosis of syphilis in Canada. Although Canada has no licensed POCT, two POCTs (Syphilis Health Check and the DPP® HIV Syphilis System) have received US Food and Drug Administration (FDA) approval under premarket approval applications. Most syphilis POCTs detect antibodies to treponemal antigens, so their results cannot be used to differentiate between active and past infection. The only POCT that detects antibodies to both treponemal and non-treponemal antigens does not yet have Health Canada or FDA approval. In this updated guideline, the current landscape of POCTs for syphilis, with an emphasis on data from low-prevalence countries, is described. Individual operators should consider the questions of where, when, how, and why a POCT is used before its actual implementation. Training in the operation and interpretation, quality control, proficiency program, safety, and careful documentation of the process and results are especially important for the successful implementation of POCTs.

Canadian Public Health Laboratory Network Statement on Point-of-Care Serology Testing in COVID-19.

Canadian Public Health Laboratory Network Statement on Point-of-Care Serology Testing in COVID-19.

Canadian Public Health Laboratory Network Statement on Point-of-Care Serology Testing in COVID-19

Canadian Public Health Laboratory Network Statement on Point-of-Care Serology Testing in COVID-19

Estimating the population health burden of Lyme disease in Ontario, Canada: a microsimulation modelling approach.

Background:If untreated, Lyme disease can lead to long-term sequelae and post-treatment Lyme disease syndrome (PTLDS), resulting in reduced health-related quality of life. The objective of this study was to develop a microsimulation model to estimate the population-level health burden of Lyme disease in Ontario, Canada.Methods:We developed a Lyme disease history model using microsimulation, simulating 100 000 people (mean age 37.6 yr, 51% female) from 2017 in Ontario over a lifetime risk of infection and time horizon. We extracted the sensitivity and specificity of the 2-tier testing recommended by the Canadian Public Health Laboratory Network, probabilities and health state utility values from the published literature and health administrative data. Our reported outcomes from our stochastic analysis include diagnosed cases of Lyme disease (stratified by stage), undiagnosed infections, sequelae, individuals with PTLDS and quality-adjusted life-years (QALYs) lost.Results:Our model estimated 333 (95% confidence interval [CI] 329–337) infections over the lifetime of 100 000 simulated people (mean age 37.6 yr, 51% female), with 92% (95% CI 91%–93%) of infections diagnosed. Of those 308 people with Lyme Disease diagnoses, 67 (95% CI 65–69) developed sequelae (e.g., arthritic, cardiac, neurologic sequelae), and 34 (95% CI 33–35) developed PTLDS. Lyme disease resulted in a loss of 84.5 QALYs (95% CI 82.9–86.2) over the lifetime of the simulated cohort. Sensitivity and scenario analysis showed that increasing incidence rates of Lyme disease, potential underreporting, duration of PTLDS and quality of life (health state utility) associated with PTLDS had the greatest impact on health burden.Interpretation:Lyme disease contributes considerable health burden in terms of QALYs lost. Our analysis provides evidence to understand the disease burden and lays the foundation to assess the cost-effectiveness of pharmaceutical and nonpharmaceutical interventions.

Evaluation of commercial SARS-CoV-2 serological assays in Canadian public health laboratories

The COVID-19 pandemic has led to the influx of immunoassays for the detection of antibodies towards severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into the global market. The Canadian Public Health Laboratory Network Serology Task Force undertook a nationwide evaluation of twelve laboratory and 6 point-of-care based commercial serological assays for the detection of SARS-CoV-2 antibodies. We determined that there was considerable variability in the performance of individual tests and that an orthogonal testing algorithm should be prioritized to maximize the accuracy and comparability of results across the country. The manual enzyme immunoassays and point-of-care tests evaluated had lower specificity and increased coefficients of variation compared to automated enzyme immunoassays platforms putting into question their utility for large-scale sero-surveillance. Overall, the data presented here provide a comprehensive approach for applying accurate serological assays for longitudinal sero-surveillance and vaccine trials while informing Canadian public health policy.

Laboratory response checklist for infectious disease outbreaks-preparedness and response considerations for emerging threats.

The purpose of the Laboratory Response Checklist for Infectious Disease Outbreaks (the Checklist) is to provide public health laboratories and laboratory networks operating at multiple jurisdictional levels with a useful, adaptable tool to help rapidly identify important outbreak response considerations, particularly when investigating a previously unknown infectious disease threat. The Checklist was developed by the National Microbiology Laboratory of Canada in collaboration with provincial/territorial, national and international laboratory experts, including the Canadian Public Health Laboratory Network, and the Global Health Security Action Group Laboratory Network. While the Checklist was initially designed to reflect lessons learned through National Microbiology Laboratory participation in extended national and international outbreak responses (e.g. Zika virus epidemic [2015-2016], Ebola virus epidemic, West Africa [2014-2016]), the importance of optimizing laboratory response coordination has only been underscored by the ongoing challenges presented by the coronavirus disease 2019 (COVID-19) pandemic response requirements. The Checklist identifies five highly interdependent laboratory response themes, each of which encompasses multiple considerations that may be critical to a coordinated, strategic outbreak response. As such, the comprehensive review of Checklist considerations by responding laboratory organizations may provide a valuable opportunity to quickly detect key response considerations and interdependencies, and mitigate risks with the potential to impact public health action.

Canadian Public Health Laboratory Network: Prioritized support for northern, remote and isolated communities in Canada

Canadian Public Health Laboratory Network: Prioritized support for northern, remote and isolated communities in Canada

Canadian Public Health Laboratory Network: Prioritized support for northern, remote and isolated communities in Canada

Canadian Public Health Laboratory Network: Prioritized support for northern, remote and isolated communities in Canada

The Canadian Public Health Laboratory Network protocol for microbiological investigations of emerging respiratory pathogens, including severe acute respiratory infections

The Canadian Public Health Laboratory Network protocol for microbiological investigations of emerging respiratory pathogens, including severe acute respiratory infections

The Canadian Pu0062lic Health Laboratory Network protocol for microbiological investigations of emerging respiratory pathogens, including severe acute respiratory infections.

The Canadian Pu0062lic Health Laboratory Network protocol for microbiological investigations of emerging respiratory pathogens, including severe acute respiratory infections.

Canadian Public Health Laboratory Network Best Practices for COVID-19.

The ability to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is a foundational component of Canada's containment and mitigation strategies. Laboratory confirmation of COVID-19 cases allows the appropriate clinical management and public health interventions. Whether the local goal is containment or mitigation will depend on local epidemiology of the pandemic. The Respiratory Virus Infections Working Group of the Canadian Public Health Laboratory Network has developed comprehensive Best Practice Guidelines for detection of SARS-CoV-2. Best practices for specimen collection, transportation, testing and biosafety are addressed from the perspective of Canadian public health laboratories to ensure a consistent approach across the country: Population-based testing for COVID-19 should initially be carried out for surveillanceNasopharyngeal swab is the specimen of choice for routine testingNucleic acid amplification tests (such as real-time reverse transcription polymerase chain reaction) are the method of choice for routine testing of SARS-CoV-2The decentralization of nucleic acid amplification testing for COVID-19 to hospital or other high complexity medical laboratories should be promoted to increase test capacity and meet increased demandsIn the early stages of the pandemic, positive (approximately 10-20) and negative (approximately 50) tests by a provincial laboratory require confirmation at the National Microbiology LaboratoryCo-circulation of other viral agents associated with influenza-like Illnesses (e.g. influenza A and B and respiratory syncytial virus) should be monitored as capacity permits, as part of ongoing surveillanceOnce validated, serological testing may be utilized for assessing the presence/absence of immune response to the SARS-CoV-2 at either the population or individual level for select indications, but is likely to be of limited utility in diagnosis of acute COVID-19 illness These recommendations will be updated as new information becomes available.

Canadian Public Health Laboratory Network Statement on Point-of-Care Serology Testing in COVID-19

Canadian Public Health Laboratory Network Statement on Point-of-Care Serology Testing in COVID-19

Canadian Public Health Laboratory Network Statement on Point-of-Care Serology Testing in COVID-19.

Canadian Public Health Laboratory Network Statement on Point-of-Care Serology Testing in COVID-19.

Canadian Public Health Laboratory Network Best Practices for COVID-19

Canadian Public Health Laboratory Network Best Practices for COVID-19

CPHLN recommendations for the laboratory detection of Shiga toxin-producing Escherichia coli (O157 and non-O157).

Shiga toxin-producing Escherichia coli (STEC) are important enteric pathogens responsible for sporadic cases and outbreaks of gastroenteritis. E.coli O157:H7/NM (STEC O157) are the most commonly known STEC serotypes but it is now increasingly apparent that non-O157 STEC serotypes have been underreported in the past because they were not part of routine screening in many front-line laboratories. The Canadian Public Health Laboratory Network (CPHLN) has identified the need for improved detection and surveillance of non-O157 STEC and has developed the following recommendations to assist in the decision-making process for clinical and reference microbiology laboratories. These recommendations should be followed to the best of a laboratory's abilities based on the availability of technology and resources. The CPHLN recommends that when screening for the agents of bacterial gastroenteritis from a stool sample, front-line laboratories use either a chromogenic agar culture or a culture-independent diagnostic test (CIDT). CIDT options include nucleic acid amplification tests (NAATs) to detect Shiga toxin genes or enzyme immunoassays (EIAs) to detect Shiga toxins. If either CIDT method is positive for possible STEC, laboratories must have a mechanism to culture and isolate STEC in order to support both provincial and national surveillance as well as outbreak investigations and response. These CPHLN recommendations should result in improved detection of STEC in patients presenting with diarrhea, especially when due to the non-O157 serotypes. These measures should enhance the overall quality of healthcare and food safety, and provide better protection of the public via improved surveillance and outbreak detection and response.

Canadian recommendations for laboratory interpretation of multiple or extensive drug resistance in clinical isolates of Enterobacteriaceae, Acinetobacter species and Pseudomonas aeruginosa

The goal of this document was to provide Canadian laboratories with a framework for consistent reporting and monitoring of multidrug resistant organisms (MDRO) and extensively drug resistant organisms (XDRO) for common gram-negative pathogens. This is the final edition of the interim recommendations, which were modified after one year of broad consultative review. This edition represents a consensus of peer-reviewed information and was co-authored by the Canadian Public Health Laboratory Network and the Canadian Association of Clinical Microbiology and Infectious Diseases. There are two main recommendations. The first recommendation provides standardized definitions for MDRO and XDRO for gram-negative organisms in clinical specimens. These definitions were limited to antibiotics that are commonly tested clinically and, to reduce ambiguity, resistance (rather than non-susceptibility) was used to calculate drug resistance status. The second recommendation identifies the use of standardized laboratory reporting of organisms identified as MDRO or XDRO. Through the broad consultation, which included public health and infection prevention and control colleagues, these definitions are ready to be applied for policy development. Both authoring organizations intend to review these recommendations regularly as antibiotic resistance testing evolves in Canada.

Canadian Public Health Laboratory Network position statement: Non-culture based diagnostics for gastroenteritis and implications for public health investigations.

As clinical laboratories transition to using culture-independent detection test (CIDT) panels for cases of acute gastroenteritis, culture of clinical specimens is becoming less common. The reduction in bacterial cultures available for public health activities is expected to hinder surveillance and outbreak response by public health laboratories at the local, provincial, national and international levels. These recommendations are intended to serve as guidelines for the implementation of CIDT panels in frontline laboratories in Canada. The United States of America has already seen a significant reduction in culture of stool specimens despite the Association of Public Health Laboratories recommendation to perform reflex culture on positive CIDT specimens. Priority public health organisms addressed in these Canadian guidelines include Shiga toxin-producing Escherichia coli, Shigella and Salmonella and, under regional circumstances, other organisms such as Campylobacter jejuni/coli and Yersinia enterocolitica. These recommendations suggest active engagement between primary diagnostic laboratories and provincial public health laboratories to determine the workflow and protocols for reflex or parallel culture. Consequently, notifiable disease definitions will also need modification, with consultation of all stakeholders. Stakeholders need to work together to enhance recovery of bacterial isolates with best practices used for stool transport and storage.

Canadian Public Health Laboratory Network position statement: Nonculture based diagnostics for gastroenteritis and implications for public health investigations

Canadian Public Health Laboratory Network position statement: Nonculture based diagnostics for gastroenteritis and implications for public health investigations

Canadian Public Health Laboratory Network laboratory guidelines for the diagnosis of neurosyphilis in Canada.

Neurosyphilis refers to infection of the central nervous system by Treponema pallidum, which may occur at any stage. Neurosyphilis has been categorized in many ways including early and late, asymptomatic versus symptomatic and infectious versus non-infectious. Late neurosyphilis primarily affects the central nervous system parenchyma, and occurs beyond early latent syphilis, years to decades after the initial infection. Associated clinical syndromes include general paresis, tabes dorsalis, vision loss, hearing loss and psychiatric manifestations. Unique algorithms are recommended for HIV-infected and HIV-uninfected patients, as immunocompromised patients may present with serologic and cerebrospinal fluid findings that are different from immunocompetent hosts. Antibody assays include a VDRL assay and the FTA-Abs, while polymerase chain reaction for T. pallidum can be used as direct detection assays for some specimens. This chapter reviews guidelines for specimen types and sample collection, and identifies two possible algorithms for use with immunocompromised and immunocompetent hosts using currently available tests in Canada, along with a review of treatment response and laboratory testing follow-up.