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Review article: Biomedical intelligence

Vol. 148 No. 4950 (2018)

Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform

  • Adrian Egli
  • Dominique S. Blanc
  • Gilbert Greub
  • Peter M. Keller
  • Vladimir Lazarevic
  • Aitana Lebrand
  • Stephen Leib
  • Richard A. Neher
  • Vincent Perreten
  • Alban Ramette
  • Jacques Schrenzel
  • Roger Stephan
  • Karoline Wagner
  • Daniel Wüthrich
  • Ioannis Xenarios
Cite this as:
Swiss Med Wkly. 2018;148:w14693


Facing multidrug resistant (MDR) bacterial pathogens is one of the most important challenges for our society. The spread of highly virulent and resistant pathogens can be described using molecular typing technologies; in particular, whole genome sequencing (WGS) data can be used for molecular typing purposes with high resolution. WGS data analysis can explain the spatiotemporal patterns of pathogen transmission. However, the transmission between compartments (human, animal, food, environment) is very complex. Interoperable and curated metadata are a key requirement for fully understanding this complexity. In addition, high quality sequence data are a key element between centres using WGS data for diagnostic and epidemiological applications. We aim to describe steps to improve WGS data analysis and to implement a molecular surveillance platform allowing integration of high resolution WGS typing data and epidemiological data.


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