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Pandemic Preparedness Capabilities

CRITICAL MICROBES – Comprehensive Research on InfecTIons Complications Across the Lifespan – MICROBiology Epidemiology in Sweden


PI(s)/Head responsible for the resource:

Anne-Marie Fors Connolly

Host organisation(s):

Umeå University

Resource description:

CRITICAL MICROBES will develop and deploy a national research infrastructure that links clinical microbiology test results (positive and negative) from Swedish Clinical Microbiology Laboratories (from all 21 of Sweden´s Regions) to population registries and intensive care/mortality data. The unmet clinical and technological need is the current fragmentation of clinical microbiology laboratory outputs, which delays threat detection and prevents comparable, cross-pathogen severity grading and risk stratification at the start of outbreaks.

We will harmonise heterogeneous laboratory formats into a unified data model; implement secure, pseudonymised extract–transform–load (ETL) pipelines with continuous updates; adapt and validate a registry-based disease severity framework for respiratory infections to enable standardised severity grading across pathogens, and build user-facing dashboards and documentation to accelerate analyses. The work is performed with SciLifeLab infrastructure (NBIS, SIT) for data standards, reproducible pipelines and long-term sustainability, fully aligned with PLP priorities.

Deliverables include a production-ready codebase, validated severity tiers anchored in Swedish registries, and a governance model for safe access. The resource generalises beyond pandemics to precision medicine and broader infectious health crises. The project leverages an existing nationwide research dataset situation in the Fors-Connolly research team at Umeå University, with addition of positive and negative test results for all pathogens diagnosed in Sweden and an approved ethical framework, ensuring feasibility and immediate impact.

Contact information:

Anne-Marie Fors Connolly
Department of Clinical Microbiology, Umeå University
Email: Anne-marie.fors.connolly@umu.se