Development of an integrated genomic surveillance (IGS) of public health relevant pathogens in Germany

Integrated genomic surveillance (IGS) is an effective public health strategy for the surveillance of infectious pathogens, which is becoming increasingly important worldwide. IGS combines the results of DNA sequencing and bioinformatics genome analyses of pathogen isolates from patient samples with epidemiological information from the reporting system and further data.

The main objective of IGS is to rapidly detect spread of infectious agents and to identify links, even between agents detected at different times and locations. The combination of genomic pathogen sequence data with selected epidemiological information on infected individuals allows outbreaks and transmission chains to be identified quickly and targeted interventions to contain the outbreak to be initiated at an early stage. In addition, the IGS offers the possibility of continuous detection and surveillance of pathogen variants with changing characteristics (e.g. transmissibility, virulence, AMR). The IGS also makes an important contribution to the decision-making process of public health authorities.

Two projects funded by the Federal Ministry of Health are currently underway with the aim to establish an IGS at the RKI in cooperation with the National Reference Centres (NRZ) and the Consiliary Laboratories (KL) as well as other stakeholders such as the health authorities of the federal states and the Network University Medicine (NUM). The necessary processes and an efficient infrastructure will be developed and established for the long-term implementation of the IGS according to §13 of the Infection Protection Act.

The necessary framework conditions for the systematic sequencing of infectious pathogens in the corresponding NRZ/KL have been created. The expansion of the German Electronic Reporting and Information system (DEMIS) for the transmission of genomic data is underway, as is the establishment of a high-performance IT infrastructure for the genome analysis, linking with epidemiological data, visualisation and provision of the information to stakeholders.

The so far established IGS nucleus should be stringently developed into a comprehensive sustainable Public Health Instrument in Germany.