Enhancing clinical microbiological whole-genome sequencing capacity as well as analysis, management and sharing of respective sequencing data in Sweden

The project aims to enhance the national capacity of whole genome sequencing within clinical microbiology by extending the clinical microbiological labs'Äô ability to sequence more pathogens and enhancing the national processing of the data downstream at the Public Health Agency of Sweden (PHAS) for data and results dissemination. The transition from conventional methods for the characterisation of pathogens to whole genome sequencing is further to be promoted by supplying an advanced IT infrastructure for analysis, management and sharing of respective sequencing data and results at the national level, as well as enabling cross-border information sharing to other public health agencies in EU. The IT platform, currently being developed at the PHAS, has a modular approach enabling the implementation of additional pipelines for automated analysis of many pathogens. Sequencing data will be stored and managed using on-premise cloud infrastructure, and APIs facilitate sharing of specific data to relevant parties through an open data approach (open as possible, closed as necessary). Recently established IT hardware and infrastructure at the PHAS, laboratory instrumentation and workflows at the regional labs, and ongoing development of the bioinformatics and data management platform at the PHAS represent the foundation upon which this project will build. Focused on SARS-CoV-2 during the last two and a half years, WGS is now to be implemented at a larger scale for additional pathogens from the lab and data perspective. Ultimately, the goal is to strengthen the implementation of WGS in clinical microbiology to elevate this technique into a routine application and ensure preparedness for future health threats. For this, the use of established networks, collaboration and communication efforts is how the project's impact is ensured.