Networking of Public Health Microbiology Laboratories Bolsters Europe's Defenses against Infectious Diseases

Reference, calibration and referral laboratories - a look at current European provisions and beyond

European Union (EU) regulations on in vitro diagnostics (IVD) and on serious cross-border threats to health provide for the establishment of European Reference Laboratories (EURLs) and their harmonization and cooperation with National Reference Laboratories (NRLs). While the EURLs under the IVD Regulation will be operational by 1 October 2024, the EURLs under the Regulation on serious cross-border threats to health will be operational by January 2025. Although NRLs may have been operating for a long time on the basis of national legislation, they should now cooperate with each other and with EURLs in a network of centers of excellence for the authorization and post-market surveillance of IVDs and for the epidemiological surveillance and control of communicable diseases. The term "reference laboratory" has long been used colloquially to refer to many kinds of laboratories, regardless of their tasks, competencies, responsibilities and designation. A literature search and analysis confirmed this by showing that a considerable proportion of scientific publications in 2024 use the term "reference laboratory" inappropriately. In order to clarify the roles and functioning of EURLs and NRLs, we have evaluated the relevant current EU provisions and compared the findings with those of reference laboratories designated by other organizations, calibration (reference) laboratories and referral laboratories, which are simply referred to as "reference laboratories". With the forthcoming implementation of the EU regulations, at least the goals of providing safe and high-quality IVDs and adequate public health surveillance for communicable diseases appear to be achievable.

Operationalising Regional Cooperation for Infectious Disease Control: A Scoping Review of Regional Disease Control Bodies and Networks

BACKGROUND

The rapid spread of the coronavirus disease 2019 (COVID-19) pandemic demonstrates the value of regional cooperation in infectious disease prevention and control. We explored the literature on regional infectious disease control bodies, to identify lessons, barriers and enablers to inform operationalisation of a regional infectious disease control body or network in southeast Asia.

METHODS

We conducted a scoping review to examine existing literature on regional infectious disease control bodies and networks, and to identify lessons that can be learned that will be useful for operationalisation of a regional infectious disease control body such as the Association of Southeast Asian Nations (ASEAN) Center for Public Health Emergency and Emerging Diseases.

RESULTS

Of the 57 articles included, 53 (93%) were in English, with two (3%) in Spanish and one (2%) each in Dutch and French. Most were commentaries or review articles describing programme initiatives. Sixteen (28%) publications focused on organisations in the Asian continent, with 14 (25%) focused on Africa, and 14 (25%) primarily focused on the European region. Key lessons focused on organisational factors, diagnosis and detection, human resources, communication, accreditation, funding, and sustainability. Enablers and constraints were consistent across regions/ organisations. A clear understanding of the regional context, budgets, cultural or language issues, staffing capacity and governmental priorities, is pivotal. An initial workshop inclusive of the various bodies involved in the design, implementation, monitoring or evaluation of programmes is essential. Clear governance structure, with individual responsibilities clear from the beginning, will reduce friction. Secure, long-term funding is also a key aspect of the success of any programme.

CONCLUSION

Operationalisation of regional infectious disease bodies and networks is complicated, but with extensive groundwork, and focus on organisational factors, diagnosis and detection, human resources, communication, accreditation, funding, and sustainability, it is achievable. Ways to promote success are to include as many stakeholders as possible from the beginning, to ensure that context-specific factors are considered, and to encourage employees through capacity building and mentoring, to ensure they feel valued and reduce staff turnover.

Leveraging of SARS-CoV-2 PCR Cycle Thresholds Values to Forecast COVID-19 Trends

Introduction: We assessed the usefulness of SARS-CoV-2 RT-PCR cycle thresholds (Ct) values trends produced by the LHUB-ULB (a consolidated microbiology laboratory located in Brussels, Belgium) for monitoring the epidemic's dynamics at local and national levels and for improving forecasting models.

Methods: SARS-CoV-2 RT-PCR Ct values produced from April 1, 2020, to May 15, 2021, were compared with national COVID-19 confirmed cases notifications according to their geographical and time distribution. These Ct values were evaluated against both a phase diagram predicting the number of COVID-19 patients requiring intensive care and an age-structured model estimating COVID-19 prevalence in Belgium.

Results: Over 155,811 RT-PCR performed, 12,799 were positive and 7,910 Ct values were available for analysis. The 14-day median Ct values were negatively correlated with the 14-day mean daily positive tests with a lag of 17 days. In addition, the 14-day mean daily positive tests in LHUB-ULB were strongly correlated with the 14-day mean confirmed cases in the Brussels-Capital and in Belgium with coinciding start, peak, and end of the different waves of the epidemic. Ct values decreased concurrently with the forecasted phase-shifts of the diagram. Similarly, the evolution of 14-day median Ct values was negatively correlated with daily estimated prevalence for all age-classes.

Conclusion: We provide preliminary evidence that trends of Ct values can help to both follow and predict the epidemic's trajectory at local and national levels, underlining that consolidated microbiology laboratories can act as epidemic sensors as they gather data that are representative of the geographical area they serve.

42936 pathogens from Canadian hospitals: 10 years of results (2007-16) from the CANWARD surveillance study

OBJECTIVES

The CANWARD surveillance study was established in 2007 to annually assess the in vitro susceptibilities of a variety of antimicrobial agents against bacterial pathogens isolated from patients receiving care in Canadian hospitals.

METHODS

42 936 pathogens were received and CLSI broth microdilution testing was performed on 37 355 bacterial isolates. Limited patient demographic data submitted with each isolate were collated and analysed.

RESULTS

Of the isolates tested, 43.5%, 33.1%, 13.2% and 10.2% were from blood, respiratory, urine and wound specimens, respectively; 29.9%, 24.8%, 19.0%, 18.1% and 8.2% of isolates were from patients in medical wards, emergency rooms, ICUs, hospital clinics and surgical wards. Patient demographics associated with the isolates were: 54.6% male/45.4% female; 13.1% patients aged ≤17 years, 44.3% 18-64 years and 42.7% ≥65 years. The three most common pathogens were Staphylococcus aureus (21.2%, both methicillin-susceptible and MRSA), Escherichia coli (19.6%) and Pseudomonas aeruginosa (9.0%). E. coli were most susceptible to meropenem and tigecycline (99.9%), ertapenem and colistin (99.8%), amikacin (99.7%) and ceftolozane/tazobactam and plazomicin (99.6%). Twenty-three percent of S. aureus were MRSA. MRSA were most susceptible to ceftobiprole, linezolid and telavancin (100%), daptomycin (99.9%), vancomycin (99.8%) and tigecycline (99.2%). P. aeruginosa were most susceptible to ceftolozane/tazobactam (98.3%) and colistin (95.0%).

CONCLUSIONS

The CANWARD surveillance study has provided 10 years of reference antimicrobial susceptibility testing data on pathogens commonly causing infections in patients attending Canadian hospitals.

Ontology-Based Graphs of Research Communities: A Tool for Understanding Threat Reduction Networks

Scientific research communities can be represented as heterogeneous or multidimensional networks encompassing multiple types of entities and relationships. These networks might include researchers, institutions, meetings, and publications, connected by relationships like authorship, employment, and attendance. We describe a method for efficiently and flexibly capturing, storing, and extracting information from multidimensional scientific networks using a graph database. The database structure is based on an ontology that captures allowable types of entities and relationships. This allows us to construct a variety of projections of the underlying multidimensional graph through database queries to answer specific research questions. We demonstrate this process through a study of the U.S. Biological Threat Reduction Program (BTRP), which seeks to develop Threat Reduction Networks to build and strengthen a sustainable international community of biosecurity, biosafety, and biosurveillance experts to address shared biological threat reduction challenges. Networks like these create connectional intelligence among researchers and institutions around the world, and are central to the concept of cooperative threat reduction. Our analysis focuses on a series of seven BTRP genome sequencing training workshops, showing how they created a growing network of participants and countries over time, which is also reflected in coauthorship relationships among attendees. By capturing concept and relationship hierarchies, our ontology-based approach allows us to pose general or specific questions about networks within the same framework. This approach can be applied to other research communities or multidimensional social networks to capture, analyze, and visualize different types of interactions and how they change over time.

Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies

Clinical microbiology is experiencing revolutionary advances in the deployment of molecular, genome sequencing-based, and mass spectrometry-driven detection, identification, and characterization assays. Laboratory automation and the linkage of information systems for big(ger) data management, including artificial intelligence (AI) approaches, also are being introduced. The initial optimism associated with these developments has now entered a more reality-driven phase of reflection on the significant challenges, complexities, and health care benefits posed by these innovations. With this in mind, the ongoing process of clinical laboratory consolidation, covering large geographical regions, represents an opportunity for the efficient and cost-effective introduction of new laboratory technologies and improvements in translational research and development. This will further define and generate the mandatory infrastructure used in validation and implementation of newer high-throughput diagnostic approaches. Effective, structured access to large numbers of well-documented biobanked biological materials from networked laboratories will release countless opportunities for clinical and scientific infectious disease research and will generate positive health care impacts. We describe why consolidation of clinical microbiology laboratories will generate quality benefits for many, if not most, aspects of the services separate institutions already provided individually. We also define the important role of innovative and large-scale diagnostic platforms. Such platforms lend themselves particularly well to computational (AI)-driven genomics and bioinformatics applications. These and other diagnostic innovations will allow for better infectious disease detection, surveillance, and prevention with novel translational research and optimized (diagnostic) product and service development opportunities as key results.

A systematic review on integration mechanisms in human and animal health surveillance systems with a view to addressing global health security threats

BACKGROUND

Health surveillance is an important element of disease prevention, control, and management. During the past two decades, there have been several initiatives to integrate health surveillance systems using various mechanisms ranging from the integration of data sources to changing organizational structures and responses. The need for integration is caused by an increasing demand for joint data collection, use and preparedness for emerging infectious diseases.

OBJECTIVE

To review the integration mechanisms in human and animal health surveillance systems and identify their contributions in strengthening surveillance systems attributes.

METHOD

The review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols (PRISMA-P) 2015 checklist. Peer-reviewed articles were searched from PubMed, HINARI, Web of Science, Science Direct and advanced Google search engines. The review included articles published in English from 1900 to 2018. The study selection considered all articles that used quantitative, qualitative or mixed research methods. Eligible articles were assessed independently for quality by two authors using the QualSyst Tool and relevant information including year of publication, field, continent, addressed attributes and integration mechanism were extracted.

RESULTS

A total of 102 publications were identified and categorized into four pre-set integration mechanisms: interoperability (35), convergent integration (27), semantic consistency (21) and interconnectivity (19). Most integration mechanisms focused on sensitivity (44.1%), timeliness (41.2%), data quality (23.5%) and acceptability (17.6%) of the surveillance systems. Generally, the majority of the surveillance system integrations were centered on addressing infectious diseases and all hazards. The sensitivity of the integrated systems reported in these studies ranged from 63.9 to 100% (median = 79.6%, n = 16) and the rate of data quality improvement ranged from 73 to 95.4% (median = 87%, n = 4). The integrated systems were also shown improve timeliness where the recorded changes were reported to be ranging from 10 to 91% (median = 67.3%, n = 8).

CONCLUSION

Interoperability and semantic consistency are the common integration mechanisms in human and animal health surveillance systems. Surveillance system integration is a relatively new concept but has already been shown to enhance surveillance performance. More studies are needed to gain information on further surveillance attributes.

Systemic resilience to cross-border infectious disease threat events in Europe

Recurrent health emergencies threaten global health security. International Health Regulations (IHR) aim to prevent, detect and respond to such threats, through increase in national public health core capacities, but whether IHR core capacity implementation is necessary and sufficient has been contested. With a longitudinal study we relate changes in national IHR core capacities to changes in cross-border infectious disease threat events (IDTE) between 2010 and 2016, collected through epidemic intelligence at the European Centre for Disease Prevention and Control (ECDC). By combining all IHR core capacities into one composite measure we found that a 10% increase in the mean of this composite IHR core capacity to be associated with a 19% decrease (p = 0.017) in the incidence of cross-border IDTE in the EU. With respect to specific IHR core capacities, an individual increase in national legislation, policy & financing; coordination and communication with relevant sectors; surveillance; response; preparedness; risk communication; human resource capacity; or laboratory capacity was associated with a significant decrease in cross-border IDTE incidence. In contrast, our analysis showed that IHR core capacities relating to point-of-entry, zoonotic events or food safety were not associated with IDTE in the EU. Due to high internal correlations between core capacities, we conducted a principal component analysis which confirmed a 20% decrease in risk of IDTE for every 10% increase in the core capacity score (95% CI: 0.73, 0.88). Globally (EU excluded), a 10% increase in the mean of all IHR core capacities combined was associated with a 14% decrease (p = 0.077) in cross-border IDTE incidence. We provide quantitative evidence that improvements in IHR core capacities at country-level are associated with fewer cross-border IDTE in the EU, which may also hold true for other parts of the world.

Whole genome sequence of Vibrio cholerae directly from dried spotted filter paper

BACKGROUND

Global estimates for cholera annually approximate 4 million cases worldwide with 95,000 deaths. Recent outbreaks, including Haiti and Yemen, are reminders that cholera is still a global health concern. Cholera outbreaks can rapidly induce high death tolls by overwhelming the capacity of health facilities, especially in remote areas or areas of civil unrest. Recent studies demonstrated that stool specimens preserved on filter paper facilitate molecular analysis of Vibrio cholerae in resource limited settings. Specimens preserved in a rapid, low-cost, safe and sustainable manner for sequencing provides previously unavailable data about circulating cholera strains. This may ultimately contribute new information to shape public policy response on cholera control and elimination.

METHODOLOGY/PRINCIPAL FINDINGS

Whole genome sequencing (WGS) recovered close to a complete sequence of the V. cholerae O1 genome with satisfactory genome coverage from stool specimens enriched in alkaline peptone water (APW) and V. cholerae culture isolates, both spotted on filter paper. The minimum concentration of V. cholerae DNA sufficient to produce quality genomic information was 0.02 ng/μL. The genomic data confirmed the presence or absence of genes of epidemiological interest, including cholera toxin and pilus loci. WGS identified a variety of diarrheal pathogens from APW-enriched specimen spotted filter paper, highlighting the potential for this technique to explore the gut microbiome, potentially identifying co-infections, which may impact the severity of disease. WGS demonstrated that these specimens fit within the current global cholera phylogenetic tree, identifying the strains as the 7th pandemic El Tor.

CONCLUSIONS

WGS results allowed for mapping of short reads from APW-enriched specimen and culture isolate spotted filter papers. This provided valuable molecular epidemiological sequence information on V. cholerae strains from remote, low-resource settings. These results identified the presence of co-infecting pathogens while providing rare insight into the specific V. cholerae strains causing outbreaks in cholera-endemic areas.