SSI-Seq

Since 2013 whole genome sequencing (WGS) of microorganisms has been of high importance in Danish infection surveillance and preparedness. Although surveillance of microbial pathogens in Denmark is already of high quality, some aspects can be further improved. The COVID-19 pandemic has demonstrated the importance of standardised lab procedures and of a well-structured IT-system to handle WGS data. To effectively transform the generated WGS surveillance data into actionable insights, it's crucial to integrate WGS data, other laboratory findings, and epidemiological data into the supporting IT infrastructure. At the beginning of this project, this was done for some areas of microbial surveillance but not for others. In addition, SSI is committed to disseminate relevant information to national collaborators, ECDC and public repositories in a timely manner.

With financial support from the EU4Health programme , the SSI-Seq project SSIwill develop MicrobeSeq Denmark, a center dedicated to data sharing, communication and standardisation of microbial WGS data in Denmark.

Our three overall aims are:

1. Optimise and further develop surveillance related pipelines and workflows to ensure that WGS data for surveillance is of high and comparable quality.
2. Develop IT infrastructures and bioinformatics tools that allow for sharing WGS data and analysis results as real-time as possible.
3. Develop common protocols for producing, analysing and sharing of WGS data.

SSI-Seq is supported by co-funding from the European Union’s EU4Health programme under Grant Agreement Nr 101111879. Views and opinions expressed do not necessarily reflect those of the European Union or HaDEA. Neither the European Union nor the granting authority can be held responsible for them.

Read more about MicrobeSeq