Public Health Laboratory Network Research Articles

Navigating the network: a narrative overview of AMR surveillance and data flow in the United States.

The antimicrobial resistance (AMR) surveillance landscape in the United States consists of a data flow that starts in the clinical setting and is maintained by a network of national and state public health laboratories. These organizations are well established, with robust methodologies to test and confirm antimicrobial susceptibility. Still, the bridge that guides the flow of data is often one directional and caught in a constant state of rush hour that can only be refined with improvements to infrastructure and automation in the data flow. Moreover, there is an absence of information in the literature explaining the processes clinical laboratories use to coalesce and share susceptibility test data for AMR surveillance, further complicated by variability in testing procedures. This knowledge gap limits our understanding of what is needed to improve and streamline data sharing from clinical to public health laboratories. Successful models of AMR surveillance display attributes like 2-way communication between clinical and public health laboratories, centralized databases, standardized data, and the use of electronic health records or data systems, highlighting areas of opportunity and improvement. This article explores the roles and processes of the organizations involved in AMR surveillance in the United States and identifies current knowledge gaps and opportunities to improve communication between them through standardization, communication, and modernization of data flow.

Development of a national proficiency test for SARS-CoV-2 detection by PCR in Colombia.

Proficiency testing (PT) is a tool for ensuring the validity of results of testing laboratories and is essential when laboratories are working with assays authorised for emergency use or implementing novel techniques for detecting emerging pathogens. In collaboration with the National Health Institute of Colombia and with international support, we developed a qualitative PT for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse transcription polymerase chain reaction (RT-PCR). A proficiency test item (PTI) based on reference material (research grade) produced by the National Institute of Standards and Technologies (NIST) was prepared and characterised using three positive samples with varying concentrations of SARS-CoV-2 ribonucleic acid (RNA) and two negative (control) samples. Tests were distributed to 121 laboratories across the national network of public health laboratories in Colombia. Positive samples had varying concentrations of SARS-CoV-2 RNA and were quantified by digital PCR (RT-ddPCR) assays for the E gene of SARS-CoV-2. We tested the ability of laboratories to detect low and high levels of viral RNA using samples with SARS-CoV-2 RNA concentrations of 1417 ± 216, 146 ± 28, and 14 ± 10 copies /uL (expanded uncertainty, k = 2, 95% confidence level) We also performed a semiquantitative analysis of instrumental responses (Ct values) reported by participating laboratories and homogeneity, stability, and characterisation studies of the produced materials to determine the adequacy of these materials and methods for use in the qualitative PT scheme. The PT evaluated reports for individual target genes from each laboratory; 98.3% of laboratories had satisfactory performance and the remaining 1.7% of laboratories had unsatisfactory performance for the detection of at least one of the reported genes. This PT scheme identified the potential metrological weaknesses of laboratories in the detection of SARS-CoV-2 by RT-PCR and may facilitate improvements in the quality of measurements from the perspective of public health surveillance.

An assessment of the public health surveillance strategy based on molecular testing during three major pandemic waves of COVID-19 in Brazil.

A national laboratory-based surveillance system was adapted to monitor the situation of SARS-CoV-2 in Brazil. The objective of the study was to compare the challenges in implementing COVID-19 surveillance strategies based on the Ministry of Health's (MoH) distribution of RT-PCR tests to different types of laboratories. This retrospective study analyzed the MoH's testing policies and distribution of RT-PCR tests to laboratories during the first, second, and third waves. Recipient laboratories were divided into groups: public health laboratories that belonged to the national network of public health laboratories (Group 1); public laboratories granted authorization during the pandemic (Group 2); and High-Capacity Testing Centers (Group 3). We analyzed the timing and duration of COVID-19 testing policies and the allocation of tests to laboratories by group and wave. Using t-tests, we analyzed the difference in the weekly average of tests distributed to labs by group and using Pearson's correlation coefficient, analyzed the test distribution according to infection and death rates. Between epiweek 9, 2020, and epiweek 22, 2022, the MoH distributed an average of 263,004 RT-PCR tests per week. The weekly average of tests distributed was highest in the second wave (310,327 tests), followed by the first (218,005 tests) and third waves (201,226 tests). There was a significant increase in the mean weekly tests distributed in the second wave compared to the first and third waves (p = 0.047; IC 8.29-1110.71). We found a significant difference between the weekly average of tests distributed in the first and second wave (p < 0.001; IC -209.83-76.20) to Group 2. Group 3 received the second-highest number of tests from the MoH overall, with a reduction during the third wave to first-wave levels. The distribution of RT-PCR tests was not correlated with the case and death incidence.

Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil

The emergence and reemergence of mosquito-borne diseases in Brazil such as yellow fever, zika, chikungunya, and dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus across the country since its first detection in 2014 in Northeast Brazil. In this work, we carried out on-site training activities in genomic surveillance in partnership with the National Network of Public Health Laboratories that have led to the generation of 422 chikungunya virus genomes from 12 Brazilian states over the past two years (2021–2022), a period that has seen more than 312 thousand chikungunya fever cases reported in the country. These genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersal dynamics of the chikungunya virus East-Central-South-African lineage in Brazil. Tree branching patterns revealed the emergence and expansion of two distinct subclades. Phylogeographic analysis indicated that the northeast region has been the leading hub of virus spread towards other regions. Increased frequency of C > T transitions among the new genomes suggested that host restriction factors from the immune system such as ADAR and AID/APOBEC deaminases might be driving the genetic diversity of the chikungunya virus in Brazil.

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.

From ISET to InDRE. IV. Institute of Epidemiological Diagnosis and Reference: new orientation, 1990-2012.

From 1990 to 2012, the Sanitary and Tropical Diseases Institute experienced the most important changes. In 1989, its name and orientation were modified to become the National Institute of Epidemiological Diagnosis and Reference. Shortly before, it had been formalized as the apex of the National Network of Public Health Laboratories and had incorporated laboratories for preventive programs such as exfoliative cytology and rabies, malaria and tuberculosis diagnosis; subsequently, it would incorporate other networks that emerged as part of the response to major epidemic outbreaks and to the new epidemiological outlook. In this period, 27 priority diagnostic algorithms were defined, organized in 18 networks, some of which began to collaborate with global networks. In 2001, the Institute started working with pathogens related to bioterrorism. By then, space restrictions of the headquarter's building were evident; in 2008, starting the construction of new facilities was decided. The Institute and its diagnostic networks constitute a milestone in Latin American public health of the 21st century.

Diagnostic algorithm for the confirmation of cases of measles and rubella in Mexico.

Due to the successful implementation of measles and rubella elimination strategies, Mexico announced the interruption of endemic transmission of measles in 1996 and that of rubella in 2008. After a verification process, the region of the Americas was declared free of rubella and congenital rubella syndrome in 2015 and of measles in 2016. In order to maintain the elimination status in Mexico, it is essential to continue laboratory surveillance within the framework of the Global Measles and Rubella Laboratory Network. The Institute of Epidemiological Diagnosis and Reference, through the National Network of Public Health Laboratories, guarantees timely and reliable results in view of the possible reintroduction of these and other emerging pathogens.

Decentralised point-of-care testing for acute, chronic and infectious disease – benefits and challenges

The COVID-19 pandemic has reinforced Australia’s need for diagnostic testing frameworks that are well-prepared, well-resourced, responsive, appropriately governed, scalable, interdisciplinary and collaborative.1 Point-of-care (POC) technologies offer diagnostic solutions capable of delivering individual, community and public health benefits in settings where: a) laboratory testing is not available, b) rapid turn-around time is needed, c) high loss to follow-up occurs in high-risk populations with standard of care cascades and/or d) disease transmission rates exceed laboratory response capacity. Key translational research derived from collaborative point-of-care testing networks for a) diabetes management (238 remote health services; 3,233 operators; 172,069 HbA1c and 51,379 urine albumin:creatinine ratio tests), b) acute care (106 remote health services; 2,279 operators; 32,950 blood gas, 32,689 cardiac troponin, 46,418 urea/electrolytes, 48,193 international normalised ratio tests), c) hepatitis C virus (HCV) (41 sites; 110 operators; 5,733 HCV tests; 4,978 RNA, 755 antibody), d) syphilis screening (156 sites; 1,412 operators), e) chlamydia, gonorrhea or trichomonas (51 sites; 795 operators; >50,000 tests) or f) COVID-19 (101 remote health services, 733 operators, 72,624 tests) will be used to highlight operational, clinical, public health, and economic benefits of POC testing. Challenges associated with scale-up and accreditation pathways for decentralised POC testing will be discussed. Reference 1. Revised Testing Framework for COVID-19 in Australia, March 2022 Version 2.1. Communicable Disease Network Australia and Public Health Laboratory Network.

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.

Simultaneous Circulation of DENV, CHIKV, ZIKV and SARS-CoV-2 in Brazil: an Inconvenient Truth

The emergence of SARS-CoV-2 has prompted the mobilization of a network of public health laboratories to diagnose COVID-19 patients, trace contacts and identify hot-spot areas for active community transmission at the expense of arbovirus diagnosis and control practices. In this article, we discuss the unprecedented challenges faced by the Brazilian public health system in dealing with the incursion of SARS-CoV-2 in the midst of ongoing triple arboviral epidemics caused by dengue, chikungunya, and Zika virus. Finally, we highlight the importance of the introduction of one health approach as an effective inter-disciplinary response and management to mitigate the catastrophic effect caused by these pathogens.

Meningococcal Surveillance Australia Reporting period 1 April to 30 June 2020.

The reference laboratories of the National Neisseria Network, Australia report laboratory data on invasive meningococcal disease (IMD) cases confirmed by laboratory testing using culture- and non-culture-based techniques for the Australian Meningococcal Surveillance Programme. Culture-positive cases, where Neisseria meningitidis is grown from a normally sterile site or skin lesions, and non-culture-based diagnoses (nucleic acid amplification testing), are defined as IMD by the Public Health Laboratory Network definitions. Data contained in quarterly reports are restricted to a description of the numbers of cases by jurisdiction and serogroup, where known. Some minor corrections to data in Table 1 may be made in subsequent reports if additional data are received. A full analysis of laboratory-confirmed cases of IMD in each calendar year is contained in the AMSP annual report published in Communicable Diseases Intelligence.

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

Developing a National Public Health Laboratories Policy and Strategy

Abstract With the support of the European Union, the National Laboratory for Public Health and partners did an analysis of the primary healthcare and hospital laboratories in health facilities and identified strengths and weaknesses of the national network of public health laboratories. With that knowledge the LNSP developed in a participatory way a new national Laboratory Policy and thereafter a Strategic Plan 2019 - 2024 that guides the country in strengthening the labs at all levels. This is very much needed as Haiti still suffers of high levels of malaria, tuberculosis, HIV and other infectious diseases. The policy fits in the international Health Security Agenda. Most important lesson learned: by a systematic step by step process of analysis, policy formation and action planning, a research institute can - with support of stakeholders - make an impact on policies and practices.

Meningococcal Surveillance Australia Reporting period 1 January to 31 March 2020.

The reference laboratories of the National Neisseria Network, Australia, report laboratory data on invasive meningococcal disease (IMD) cases confirmed by laboratory testing using culture- and non-culture-based techniques for the Australian Meningococcal Surveillance Programme. Culture-positive cases, where Neisseria meningitidis is grown from a normally sterile site or from skin lesions, and non-culture-based diagnoses (nucleic acid amplification testing), are defined as IMD by the Public Health Laboratory Network definitions. Data contained in quarterly reports are restricted to a description of the numbers of cases by jurisdiction and serogroup, where known. Some minor corrections to data in Table 1 may be made in subsequent reports if additional data are received. A full analysis of laboratory-confirmed cases of IMD in each calendar year is contained in the AMSP annual report published in Communicable Diseases Intelligence.