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Pandemic Preparedness Capabilities

Integrative Outbreak Simulation: A One Health Approach for Enhanced Pandemic Preparedness


PI(s)/Head responsible for the resource:

René Kaden

Host organisation(s):

Uppsala University Hospital/Akademiska Sjukhuset Clinical Microbiology, Dept. of Medical Sciences, Uppsala University

Resource description:

This collaborative project, including 6 PLP partners and the National Veterinary Institute (SVA) (see the full list of participants below), is designed to simulate an outbreak scenario by dispatching clinical samples that are spiked with unusual microorganisms to the contributing clinical microbiology laboratories. These samples are delivered in a manner that facilitates enrichment and mimick authentic patient and wastewater samples. The scenarios may encompass complex, potentially zoonotic outbreaks, thus embracing the One Health concept by engaging partners from both human and animal health.

All project phases will be meticulously documented, and progress updates on the outbreak scenario will be shared via the Swedish Pathogens Portal. This approach ensures real-time project monitoring and public accessibility to information.

The primary objectives include assessing response times and the laboratory’s capacity to detect and identify the pathogen, developing diagnostic methods, treatment recommendations, but also scaling up sequencing, bioinformatics, and investigate storage capacities at the National Pandemic Center (NPC). The project leverages the synergistic effects of collaborations between laboratories. Participating laboratories will receive samples in a time series, emulating a natural pathogen distribution.

The project serves to evaluate pandemic preparedness effectiveness and identify areas for potential enhancement. Through these concerted efforts, this initiative aims to strengthen our collective capacity to respond swiftly and effectively to emerging infectious threats.

List of participants:

In total, there are 10 participants in 11 institutes:

  • Akademiska Sjukhus Uppsala
  • Clinical Genomics Stockholm (SciLifeLab infrastructure unit)
  • Clinical Genomics Umeå (SciLifeLab infrastructure unit)
  • Clinical Genomics Örebro (SciLifeLab infrastructure unit)
  • Karolinska Institute (P3 facility)
  • KTH Royal Institute of Technology
  • Linköping University Hospital
  • National Pandemic Centre (NPC)
  • National Veterinary Institute (SVA)
  • Swedish Pathogens Portal
  • The Swedish University of Agricultural Sciences (SLU)
Outcomes
Summary of the sequence of events
  • Weeks 33–38: Samples for the project were prepared.
  • Week 39 (Sept 23–29): Samples were sent out and held by the delivery company until October 2nd (13:00), and were delivered to labs with case information.
  • Weeks 39–41 (Oct 2–21): Labs tested the first set of samples, logging activities chronologically. The testing deadline was October 21 (8:00).
  • 23rd Oct 2024:  Stage 1 Discussion Meeting. Analysis methods and procedures were discussed and compared.
  • Week 41 (Oct 21–27): Second set of samples, sent out on October 23 (13:00).
  • Weeks 42–44 (Oct 23–Nov 4): Labs tested the second set of samples, logging their activities chronologically. The deadline was November 4 (8:00).
  • Week 47 (26th Nov): Stage 2 Discussion Meeting. Analysis methods and procedures were discussed and compared.

The labs recorded their procedures chronologically in a pre-prepared log template. The granularity of data which labs could share was limited by data governance regulation. All the labs received different samples and their analysis methods remained unique to address the sample. During the first phase of the outbreak simulation the labs we were given an unidentified sample for pathogen identification, the analysis time varied from 6 days to 26 days with an average of 14 days. The second phase included testing a larger sample size of unidentified sample to deduce and group them based on results, the analysis time was between 12 days to 26 days with an average of 12 days.

The different analysis methods used during the course of pathogen identification were reported as:

  • Incubation/Cultivation
  • RNA and DNA Extractions
  • Nanopore Squencing, Amplicon sequencing, RNA Immunoprecipitation Sequencing (RIP-seq), Sequencing
  • Metagenomics
  • Matrix-assisted laser desorption/ionization
  • Risk Assessment
  • Technical and Medical Assessment

The pathogens identified during the outbreak simulation was reported to be Christensenella Hongkongensis by Lab 2 and Catabacter Hongkongensis by Lab 3.

Lab activities visualisations: Phase 1

Code used to produce plot: Script to produce plot.

Lab activities visualisations: Phase 2

Code used to produce plot: Script to produce plot.

Contact information:

René Kaden
Uppsala University Hospital/Akademiska Sjukhuset Clinical Microbiology, Dept of Medical Sciences, Uppsala University
Email: rene.kaden@medsci.uu.se or rene.kaden@akademiska.se