GENSAM - Joint national management of clinical microbial sequencing data

Important results from the project

Controlling infectious diseases and antibiotic resistance in a globalized world is a challenge for public health. Whole genome sequencing of pathogens facilitates through identification, survey and monitoring a more efficient management of infectious diseases and spread of antibiotic resistance. However, new demands arise regarding quality control, standardization, sharing of data and harmonized interpretation. During stage-1, a detailed project plan was conceptualized including profound analyses of demands, risks, legal and technical aspects.

Expected long term effects

To make use of the growing amount of NGS-data, capable analysis tools are needed which however depend on accessible, structured and quality-checked data. GENSAM provides a web-based platform for access, management, and analyses of microbial NGS-data as well as accompanying metadata. Clinical microbiological laboratories can upload NGS-data and analyze sequencing data of microbial pathogens in near real-time. Computation of for example relatedness to sequences in the database aids epidemiological analyses and investigations of outbreaks.

Approach and implementation

During stage-1 the primary users (clinical microbial laboratories) as well as hygienic care units and units for infectious diseases took part in analyzing the demand and requirements through workshops and surveys. The need of specific functionalities and processes was gathered for implementation and tests in subsequent project phases. Legal and technical analyses provide the basis for developing GENSAM in line with both GDPR and the user’s demands. During stage-1 an early prototype has been developed to communicate the projects objective and to bring it in line with the demand.