About the project
The COVID-19 pandemic has demonstrated the importance of the role of genomic characterisation of pathogens for pandemic management, infection prevention and control, and individual patient care. Genomic surveillance provides insights into the biology, evolution and transmission of infectious pathogens and improves awareness of transmissions, transmission chains, clusters and outbreaks; it contributes to the prevention of nosocomial infections, i.e. infections acquired in the context of medical treatment. Multidrug-resistant pathogens are of great clinical importance due to the limited treatment options for infected patients, with Carbapenemase-producing Enterobacterales (CPE) being the most feared. As there can be a long period of time between infection and illness with CPE, the global spread of these pathogens has also been referred to as a "silent pandemic".
The GenSurv+ project aims at an extension of the ongoing GenSurv project to enable the characterisation of whole genome sequencing data of bacterial pathogens, in particular multidrug-resistant bacteria, to combat this hidden pandemic. The specific objectives are i.) whole genome sequencing of CPE as a model organism at the different NUM sites and ii.) uploading these datasets together with relevant epidemiological metadata to the GenSurv Data Hub, which iii.) will be modified and extended within this project to ensure the subsequent analysis of these datasets.
GenSurv+ faces the challenge of containing the spread of the "silent pandemic" of multi-drug resistant pathogens with the help of genomic surveillance. The integration and analysis of sequencing data requires coordination between NUM sites, the public health service and laboratories as well as strong data protection compliance and integration with existing infrastructures. In particular, the involvement of local health authorities requires clear recommendations, technological interfaces and guidelines for the effective use of genetic data. In addition, the sequencing of bacterial genomes is more difficult due to the higher complexity compared to viruses.
The project aims to overcome these hurdles and establish genomic surveillance as a key tool in infection control in Germany.
The GenSurv+ project implements a sophisticated project setup to expand the genomic surveillance of multi-resistant pathogens. The implementation includes the sequencing of multi-resistant bacteria, data upload to the GenSurv Data Hub and analysis using various methods. This is carried out in close cooperation between the participating NUM sites, the Robert Koch-Institute, the National Reference Centre for Gram-negative Hospital Pathogens and participating state offices and health authorities.
GenSurv+ consists of a total of five work packages (WP). WP1 lays the groundwork by formulating the strategy for the selection of strains to be sequenced and conducting a needs assessment with health authorities to clarify the need for successful integration of whole genome sequencing-based surveillance into public health measures. WP2 focuses on the identification of sequencing datasets from CPE in the participating laboratories (based on the strategy agreed in WP1) and the subsequent upload of the data to the Data Hub. In order to achieve uniform typing quality, it is planned to carry out a round robin test. WP3 involves the development of analysis pipelines within the GenSurv Data Hub infrastructure for bacterial pathogens. This consists of a module for determining genetic distances between bacterial genomes, a function for automatically recognising clusters and a module for determining resistance and virulence genes. WP4 is responsible for analysing/interpreting the data and compiling the results in comprehensive reports. This work package also facilitates communication and information exchange with the health authorities in the event of a possible cluster. WP5 serves as a central coordination centre that consistently monitors and supports the progress of the other work packages. Coordination is supported by various committees that have been set up as part of the governance structure. This combined infrastructure is designed to be fundamentally scalable and internationally compatible. Our infrastructure is based on cross-institutional, cross-sector, cross-professional and supra-regional cooperation in a spirit of trust. We co-operate with other infrastructures and initiatives within and outside the NUM. The principles of openness, collaboration, quality assurance and efficiency in accordance with the FAIR principles form the basis of our work.
People in the NUM
