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Abstract

The Swiss Pathogen Surveillance Platform (SPSP) is a shared secure surveillance platform between human and veterinary medicine, to also include environmental and foodborne isolates. It enables rapid and detailed transmission monitoring and outbreak surveillance of pathogens using whole genome sequencing data and associated metadata. It features controlled data access, complex dynamic queries, dedicated dashboards and automated data sharing with international repositories, providing actionable results for public health and the vision to improve societal well-being and health.

Funding
This study was supported by the:
  • Institut für Medizinische Mikrobiologie, Universität Zürich
    • Principle Award Recipient: AdrianEgli
  • ELIXIR CONVERGE
    • Principle Award Recipient: AitanaNeves
  • State Secretariat for Education, Research and Innovation
    • Principle Award Recipient: AitanaNeves
  • swissuniversities
    • Principle Award Recipient: AdrianEgli
  • Gottfried und Julia Bangerter-Rhyner-Stiftung
    • Principle Award Recipient: AdrianEgli
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Award 407240_177504)
    • Principle Award Recipient: AdrianEgli
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Award 310030_192515)
    • Principle Award Recipient: AdrianEgli
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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/content/journal/mgen/10.1099/mgen.0.001001
2023-05-12
2024-04-28
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References

  1. Kwong JC, McCallum N, Sintchenko V, Howden BP. Whole genome sequencing in clinical and public health microbiology. Pathology 2015; 47:199–210 [View Article] [PubMed]
    [Google Scholar]
  2. Moustafa AM, Lal A, Planet PJ. Comparative genomics in infectious disease. Curr Opin Microbiol 2020; 53:61–70 [View Article] [PubMed]
    [Google Scholar]
  3. Simar SR, Hanson BM, Arias CA. Techniques in bacterial strain typing: past, present, and future. Curr Opin Infect Dis 2021; 34:339–345 [View Article] [PubMed]
    [Google Scholar]
  4. Gona F, Comandatore F, Battaglia S, Piazza A, Trovato A et al. Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis. Microb Genom 2020; 6:e000347 [View Article] [PubMed]
    [Google Scholar]
  5. Lytsy B, Engstrand L, Gustafsson Å, Kaden R. Time to review the gold standard for genotyping vancomycin-resistant enterococci in epidemiology: comparing whole-genome sequencing with PFGE and MLST in three suspected outbreaks in Sweden during 2013-2015. Infect Genet Evol 2017; 54:74–80 [View Article] [PubMed]
    [Google Scholar]
  6. Atlas RM. One Health: its origins and future. Curr Top Microbiol Immunol 2013; 365:1–13 [View Article] [PubMed]
    [Google Scholar]
  7. Purushothaman S, Meola M, Egli A. Combination of whole genome sequencing and metagenomics for microbiological diagnostics. Int J Mol Sci 2022; 23:9834 [View Article] [PubMed]
    [Google Scholar]
  8. Oude Munnink BB, Worp N, Nieuwenhuijse DF, Sikkema RS, Haagmans B et al. The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology. Nat Med 2021; 27:1518–1524 [View Article] [PubMed]
    [Google Scholar]
  9. Harrison PW, Lopez R, Rahman N, Allen SG, Aslam R et al. The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. Nucleic Acids Res 2021; 49:W619–W623 [View Article] [PubMed]
    [Google Scholar]
  10. Khare S, Gurry C, Freitas L, Schultz MB, Bach G et al. GISAID’s role in pandemic response. China CDC Wkly 2021; 3:1049–1051 [View Article] [PubMed]
    [Google Scholar]
  11. Hadfield J, Megill C, Bell SM, Huddleston J, Potter B et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018; 34:4121–4123 [View Article] [PubMed]
    [Google Scholar]
  12. Rossen JWA, Friedrich AW, Moran-Gilad J. ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD) Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology. Clin Microbiol Infect 2018; 24:355–360 [View Article] [PubMed]
    [Google Scholar]
  13. Egli A, Blanc DS, Greub G, Keller PM, Lazarevic V et al. Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform. Swiss Med Wkly 2018; 148:w14693 [View Article] [PubMed]
    [Google Scholar]
  14. Wilkinson MD, Dumontier M, Aalbersberg IJJ, Appleton G, Axton M et al. The FAIR guiding principles for scientific data management and stewardship. Sci Data 2016; 3:160018 [View Article] [PubMed]
    [Google Scholar]
  15. Lawrence AK, Selter L, Frey U. SPHN - The Swiss Personalized Health Network initiative. Stud Health Technol Inform 2020; 270:1156–1160 [View Article] [PubMed]
    [Google Scholar]
  16. Coman Schmid D, Crameri K, Oesterle S, Rinn B, Sengstag T et al. SPHN - The BioMedIT network: a secure IT platform for research with sensitive human data. Stud Health Technol Inform 2020; 270:1170–1174 [View Article] [PubMed]
    [Google Scholar]
  17. Bhattacharyya SB. Introduction to SNOMED CT Singapore: Springer; 2018
    [Google Scholar]
  18. Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database 2020; 2020:baaa062 [View Article] [PubMed]
    [Google Scholar]
  19. Macdonald K, Potvin K. Interprovincial variation in access to publicly funded pharmaceuticals: a review based on the WHO anatomical therapeutic chemical classification system. Can Pharm J 2004; 137:29–34
    [Google Scholar]
  20. O’Toole Á, Scher E, Underwood A, Jackson B, Hill V et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol 2021; 7:veab064 [View Article] [PubMed]
    [Google Scholar]
  21. Aksamentov I, Roemer C, Hodcroft E, Neher R. Nextclade: clade assignment, mutation calling and quality control for viral genomes. JOSS 2021; 6:3773 [View Article]
    [Google Scholar]
  22. Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E et al. Nextflow enables reproducible computational workflows. Nat Biotechnol 2017; 35:316–319 [View Article] [PubMed]
    [Google Scholar]
  23. Gaudet-Blavignac C, Raisaro JL, Touré V, Österle S, Crameri K et al. A national, semantic-driven, three-pillar strategy to enable health data secondary usage interoperability for research within the swiss personalized health network: methodological study. JMIR Med Inform 2021; 9:e27591 [View Article] [PubMed]
    [Google Scholar]
  24. Chen Z, Azman AS, Chen X, Zou J, Tian Y et al. Global landscape of SARS-CoV-2 genomic surveillance and data sharing. Nat Genet 2022; 54:499–507 [View Article] [PubMed]
    [Google Scholar]
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