About the project
The COVID-19 pandemic has demonstrated the important role of genomic characterisation of pathogens for pandemic management, infection prevention and control and individual patient care. It provides insights into the biology, evolution and transmission of infectious pathogens and improves the perception 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.
In contrast to the Netherlands and the UK, for example, the use of genomic pathogen surveillance in Germany is still in its infancy. Within GenSurv, an infrastructure for genomic pathogen surveillance is therefore to be established in Germany in cooperation with the RKI. A major limitation of genomic pathogen surveillance in Germany is the insufficient involvement of local health authorities and the public health service. This is where MolTraX comes in and addresses these limitations by expanding the GenSurv infrastructure.
Our vision
We harness the genomic data of infectious pathogens and ensure the protection of the population through rapid and improved detection of transmission events. Through close cooperation with national, regional and local health authorities, we support the public health service and political decision-makers significantly in the development and adaptation of focussed, in some cases regional and comprehensible measures (e.g. for pandemic management) and thus increase acceptance among all parties involved. The interdisciplinary and sector-linking infrastructure initiated in this way also provides an important basis for action and prevention for other current pathogens or future pathogen-based crisis situations.
A major limitation of genomic pathogen surveillance in Germany is the insufficient involvement of local health authorities and the public health service. It is at this interface in particular that genomic pathogen surveillance can contribute most directly to pandemic management, e.g. through improved detection of outbreaks - complementary to outreach epidemiology - and improved contact tracing. The reasons for these limitations are (i) the lack of clear recommendations on when and how local health authorities should participate in genomic surveillance; (ii) the lack of technologies and interfaces for the integrated analysis of genetic data at the public health service; (iii) a widespread lack of knowledge and expertise in handling genomic data; and (iv) the lack of clear recommendations for the interpretation and use of genomic surveillance data for downstream local decision-making in the healthcare system.
MolTraX focuses on supporting and expanding the expertise of local health authorities in the field of genomic pathogen surveillance. This includes the connection to the GenSurv genomic pathogen surveillance system (https://cogdat.de/) and support in the interpretation of complex genetic pathogen data. In close co-operation with the public health sector, we identify when and how participation in GES makes sense and how the findings can be used (recommendations for action). In doing so, we rely on a mutual exchange of knowledge and expertise and also take into account possible requirements and hurdles.
During the MolTraX project to date, cooperation with the public health service has been established and strengthened at national level (Robert Koch-Institute), regional level (e.g. Lower Saxony State Health Office, North Rhine-Westphalia State Health Centre) and local level. Together, areas of application and challenges in the use of genomic pathogen surveillance were identified.
For the effective analysis of SARS-CoV-2 sequencing data by the public health service, the availability of easy-to-use tools for data analysis plays an important role, as does the possibility of linking existing data with genomic data. A dashboard-based solution is available at gensurv-ph.bi.denbi.de, which enables local health authorities to analyse SARS-CoV-2 sequencing data. An interface to the similarity search for viral genomes provided in GenSurv has also been established. This can be equated to "Google for Corona", i.e. it provides the possibility to search specifically for similar viral isolates in the existing data for Germany, e.g. to search for possible chains of infection.
A total of around 200 viral genomes were sequenced within various outbreak scenarios. The results are now available for use case tests in which the health authorities can try out the tools developed.
All of the findings will be incorporated into a letter of recommendation for the use of genomic pathogen surveillance in the public health service and into the organisation of capacity building workshops.
People in the NUM
Highlights
Successful application of genomic pathogen surveillance in Düsseldorf to track SARS-CoV-2 transmission chains in the population
As part of GenSurv and MolTrax, the successful application of integrated genomic surveillance in Düsseldorf to track SARS-CoV-2 transmission chains in the population and to detect and investigate travel-associated SARS-CoV-2 infection clusters was demonstrated. An article on this was published in the journal Eurosurveillance at the end of October 2022.
"Where do people actually get infected?" Düsseldorf researchers active in the Network University Medicine (NUM) have been trying to answer this question since the beginning of the coronavirus pandemic using modern methods of genomic epidemiology. In a recent publication, the scientists now show that the Düsseldorf system of "integrated genomic surveillance" developed by them actually makes it possible to trace infection chains in the population - and thus allows conclusions to be drawn about the role of travellers returning to the country in the infection process, for example. Reliable data on the spread of pathogens in the population is not only of scientific interest, but also highly relevant for infection prevention - i.e. the prevention of infections, e.g. through targeted countermeasures.
In the Düsseldorf system, modern genomic methods are combined with classic epidemiology and contact tracing data from the Düsseldorf Health Department in order to better understand infection chains.
Perspective paper on the establishment of genomic pathogen surveillance in Germany published in the journal Infection
On 2 May 2023, an article based on the position paper on establishing a network for genomic pathogen surveillance (GES) was published in the English-language journal Infection. An appeal for strengthening genomic pathogen surveillance to improve pandemic preparedness and infection prevention: the German perspective is the result of collaboration between experts from GenSurv, the Robert Koch-Institute (RKI) and other institutions and organisations in bioinformatics, genomics, microbiology, virology, infectiology, hygiene and infection prevention, epidemiology and the public health service, including heads of reference and consiliary laboratories. The paper focusses on best practices and lessons learned from the UK and the Netherlands and transfers these to Germany.
Position paper on the establishment of genomic pathogen surveillance in Germany published in the Bundesgesundheitsblatt A position paper on the establishment of genomic pathogen surveillance (GES) was published in the Bundesgesundheitsblatt on 22 February 2023
On 22 February 2023, a position paper on the establishment of genomic pathogen surveillance (GES) was published in the Bundesgesundheitsblatt. It is the result of a collaboration between experts from GenSurv, the Robert Koch-Institute (RKI) and other institutions and organisations from the fields of bioinformatics, genomics, microbiology, virology, infectiology, hygiene and infection prevention, epidemiology and the public health service, including heads of reference and consiliary laboratories.
The aim of this paper is to emphasise the urgency and outline proposals for establishing an efficient, adaptable and responsive GES network, taking into account external framework conditions and internal standards. The proposals developed are based on global and country-specific best practices and strategy papers. The concrete next steps for realising an integrated GES include enabling the linking of epidemiological data with genome data of the pathogens, the joint and coordinated use of existing resources, the utilisation of the resulting surveillance data for relevant decision-makers, the public health service and the scientific community as well as the involvement of all stakeholders. The establishment of a GES network is essential for the continuous, stable, active surveillance of infection events in Germany, both during and outside of pandemic phases.
Expert workshop on the future of genomic pathogen surveillance in Germany
On 6 July and 7 July 2022, a joint workshop of GenSurv and the Robert Koch-Institute (RKI) took place in Berlin. Participants were experts from GenSurv and the RKI as well as from other institutions and organisations in bioinformatics, genomics, microbiology, virology, infectiology, hygiene and infection prevention, epidemiology and the public health service, including heads of reference and consiliary laboratories. During the two days, the basis for a joint strategy for genomic pathogen surveillance in Germany was laid. A white paper was jointly drafted and submitted to the Federal Ministry of Health (BMG) and the Federal Ministry of Education and Research (BMBF).