From Fragmented Data to Preparedness: Why Sweden Needs a Stronger Research Infrastructure for Infection Data
How do infections affect public health in Sweden? How many people are tested for different pathogens, how many tests are positive, and what happens after an infection is diagnosed? Who requires hospitalisation or intensive care, and what is the wider burden on healthcare and society?
Despite the extensive health data generated in Sweden, answering these seemingly basic questions at a national level can be surprisingly difficult. The problem is not necessarily a lack of data. Clinical microbiology laboratories, hospitals and health registries generate valuable information every day. The challenge is that these data are distributed across systems developed for different purposes and cannot easily be brought together to provide a comprehensive picture of infections and their consequences.
Why is it difficult to see the national picture?
Sweden’s healthcare system spans 21 regions, with clinical microbiology data distributed across separate infrastructures. Building a national picture can therefore require researchers to obtain and harmonise data from multiple sources. Access is only one challenge. This is complicated by changes in pathogen names, diagnostic technologies, laboratory methods, formats and terminology over time. Laboratory results must also be linked with information from other registries to understand outcomes such as hospitalisation and intensive care. While Sweden’s Communicable Disease Act ensures national reporting of positive results for notifiable infections, research often requires additional information, including how many people were tested and negative results, that may remain within clinical laboratories. Consequently, Sweden generates extensive infection-related information, but connecting these data remains challenging. A more harmonised research infrastructure could bring microbiological findings and patient outcomes together, making it easier to study infection burden across the population and over time and support more comprehensive national research on infectious diseases.
When gaps in data become gaps in knowledge
These limitations matter because research conclusions depend on the quality and completeness of available data. For example, Rosendal et al. (2025) reviewed procedure codes in the Swedish Intensive Care Registry. They found that inpatient procedure codes identified fewer than half of patients who had received intensive care, potentially resulting in an underestimation of disease severity. This highlights the importance of sustainable quality registries and professional data management for reliable research and public-health evidence. The need is increasingly important with an aging population and growing antimicrobial resistance. Infections also impose wider societal costs through sick leave, the care of ill children, and transmission to vulnerable groups, making comprehensive data essential for targeting effective interventions.
Can microbiology data speak the same language?
Ongoing national efforts are already improving standardisation in Swedish clinical microbiology, including NPU codes for consistent nomenclature of procedures and units (refer newsletter-3, available only in Swedish). However, historical data remain challenging because diagnostic methods, terminology, and data structures have changed over time, complicating comparisons across laboratories and periods. Better data can also support faster distinction between bacterial and viral infections, enabling more appropriate treatment and reducing unnecessary antibiotic use in line with antimicrobial resistance (AMR) objectives. Ultimately, more standardised and harmonised microbiology data can strengthen research, improve interventions, and provide better evidence for public-health planning and resource allocation.
Where do CRITICAL MICROBES fit in?
CRITICAL MICROBES (Comprehensive Research on InfecTIons Complications Across the Lifespan – MICROBiology Epidemiology in Sweden) aims to address the research gap created by Sweden’s fragmented microbiology data landscape. Led by Anne-Marie Fors Connolly at Umeå University, the project is part of SciLifeLab’s Pandemic Laboratory Preparedness program, contributing to efforts to strengthen Sweden’s capacity for infectious-disease research and future pandemic preparedness.
CRITICAL MICROBES aims to develop a national research infrastructure that brings together clinical microbiology results and links them with patient characteristics and health outcomes. It is not intended to replace statutory surveillance or function as a real-time national infection database. Instead, it addresses a complementary challenge: making microbiology data generated across Sweden more accessible, comparable and useful for research.
Currently, nationwide studies can require researchers to request data separately from Sweden’s 21 regions and subsequently reconcile differences in terminology, formats and diagnostic practices. CRITICAL MICROBES aims to reduce this burden by developing systematic approaches to harmonisation, including computational and AI-supported methods for heterogeneous historical data. The initiative can also build on national standardisation efforts, such as NPU codes.
The project combines research coordination, clinical expertise, and practical experience through contributors including Sara Kalucza, Tianyan Song, and Helena Nyström, whose pilot work involved requesting data from all 21 regions.
By connecting microbiological findings with patient outcomes, CRITICAL MICROBES can help transform routinely generated data into research-ready evidence—supporting better understanding of infection burden today while strengthening the knowledge foundation needed for future outbreak preparedness.
What can Sweden learn from Denmark?
Denmark provides an important example of what becomes possible when laboratory data can be systematically collected, harmonised and linked for research and public-health purposes.
The Danish Microbiology Database (MiBa) is a nationwide, automatically updated database containing microbiological test results from across Denmark. Established in 2010, MiBa supports clinical diagnostics, infection control, national surveillance, and research, providing healthcare professionals with access to microbiological results regardless of where in the country a sample was analysed.
Alongside MiBa, Denmark has a long history of using structured clinical laboratory information for research. The LABKA research database (Grann et al., 2011), based on the LABKA clinical laboratory information system, contains millions of laboratory test results from patients in Northern and Central Denmark. These data can be linked at the individual level with other Danish health registries, enabling researchers to investigate biomarkers, disease severity, prognosis and treatment outcomes.
Together, MiBa and LABKA illustrate different but complementary aspects of the Danish laboratory-data landscape: MiBa demonstrates the value of coordinated nationwide microbiological information for clinical care, surveillance and research, while LABKA demonstrates how systematically collected laboratory data can be linked with other health information to support large-scale epidemiological research.
For Sweden, the lesson is not that either system can simply be replicated. The organisational, legal, and historical contexts differ. Rather, the Danish experience demonstrates a broader principle; when laboratory information is structured, harmonised, and accessible for appropriate secondary use, data generated through routine healthcare can become a powerful resource for both research and preparedness.
This experience is directly relevant to CRITICAL MICROBES through collaboration with experts at Statens Serum Institut (SSI), including Marianne Voldstedlund, Head of Department for Data Integration and Analysis, Senior Consultant in Clinical Microbiology and founder of MiBa, and Tyra Grove Krause, Vice-Executive President and Senior Consultant in Public Health Medicine.
Data infrastructure is therefore not only a research resource, it is also an important component of public-health preparedness.
Building infrastructure through collaboration
A challenge involving laboratories, healthcare regions, registries, standards, governance and public-health organizations cannot be addressed by one research group alone. This was evident at a CRITICAL MICROBES workshop hosted by Statens Serum Institut (SSI) on 26–27 May 2025, which brought together Swedish and Danish expertise spanning clinical microbiology, infectious diseases, public health, research, data analysis, IT architecture, law and pandemic preparedness. Participants included expertise associated with SSI, the Public Health Agency of Sweden, the Swedish Research Council, Umeå University, the Swedish clinical microbiology community, and the Virus and Pandemic Foundation. This reflects the nature of the problem; harmonisation is not solely a technical exercise. It requires clinical interpretation, sustainable infrastructure, standards, governance and collaboration across institutions.
Connecting the data before the next outbreak
CRITICAL MICROBES cannot address every challenge in Sweden’s infection-data landscape or replace existing surveillance systems, registries and standardisation initiatives. Instead, it can help bridge these resources by linking microbiological results with patient characteristics and outcomes, harmonising historical data, and building on national standards and international experience. This could strengthen research and inform decisions on infection burden, diagnostics, antimicrobial resistance, resource allocation and preparedness.
Preparedness does not begin when the next outbreak arrives. It begins with sustainable registries, common standards, high-quality data and the ability to learn from the infections we are already seeing.
Sweden already generates much of the information required. The next challenge is to connect it. CRITICAL MICROBES offers one practical step toward doing so, strengthening research today while building the methods, evidence and collaborations needed for a more informed and prepared public-health system tomorrow.
