Integrated genome based surveillance of salmonellae (GenoSalmSurv)

Salmonellosis is a disease caused by enterobacteria of the genus Salmonella. After campylobacteriosis, it is the second most frequently reported bacterial diarrheal disease in humans in Germany, but the hospitalization rate for salmonellosis is significantly higher than for campylobacter enteritis. It is also of particular health policy and socio-economic importance that this zoonotic pathogen causes many food-borne disease outbreaks. In the project, a model for an integrated genome-based surveillance of Salmonella was set up and evaluated, which is based on the use of modern high-resolution genome sequencing methods. Through the WGS and subsequent harmonized genome data analysis and data exchange processes, cluster detection, pathogen monitoring and infection source analysis can be carried out quickly across sectors (One Health concept). The Salmonella reference laboratories of human medicine (National Reference Center (NRZ) Salmonella at the Robert Koch Institute (RKI)) and food monitoring (National Reference Laboratory (NRL) Salmonella at the Federal Institute for Risk Assessment (BfRshort forGerman Federal Institute for Risk Assessment)) of the Federal Government worked together in cooperation with institutions of the public health service or the authorities for food safety and animal health of the federal states (Bavarian State Office for Health and Food Safety (LGL)) together. In the project, 1) typing methods including genome sequence analysis methods for Salmonella were collected, harmonized and bottlenecks identified, 2) license-free (open-source) sequence analysis programs for cluster identification and typing of Salmonella were evaluated and submitted to the supervisory authorities across sectors, 3) prospective genome sequencing was carried out and the sequence data results were combined and 4) the supervisory authorities of the federal states presented the concept.

The initial situation at the beginning of the funded GenoSalmSurv project was that the evaluation and interpretation of Salmonella sequence data in Germany had previously been carried out on the basis of different analysis platforms at the respective partner institutes. This posed a corresponding hurdle for the processing of cross-sectoral outbreaks and a corresponding surveillance. These obstacles were identified, work processes optimized and a model for an integrated genome-based surveillance of Salmonella was developed and tested.
The evaluation of the available typing methods and genome sequence analysis methods showed that some of the WGS technology has already reached the state authorities and is being used. Other state-level institutions are also planning to use this technology for typing and surveillance of food-borne pathogens [Bundesgesundheitsblatt, Pietsch et al.short foret alii (lat. "and others"), 2023].
A core aspect was the creation of license-free sequence analysis programs for genome analysis, cluster recognition and typing of Salmonella [Frontiers in Microbiology, Uelze et al.short foret alii (lat. "and others"), 2021; Genes, Deneke et al.short foret alii (lat. "and others"), 2021; Frontiers in Microbiology, Deneke et al.short foret alii (lat. "and others"), 2021] and the evaluation of these tools. In the evaluation phase it could be shown that all project participants were able to use the developed tools successfully and comparably, that data exchange is feasible and cross-sectoral clusters could be identified. Using the analysis tools available, almost 500 cgMLST-based clusters could be identified from the approximately 4,500 Salmonella genomes, of which 48 cross-sector clusters were preselected using prioritization algorithms and then examined in detail in the cross-sector outbreak investigation. The decisive factor here was the linking of the WGS-based data with a minimal set of epidemiological data and the subsequent automated prioritization.

Experiences from the survey and the laboratory performance comparison test carried out have been incorporated into the training materials (presentations, screencasts, workshops) for the state authorities (https://www.lgl.bayern.de/forschung/forschung_gesundheit/fp_genosalmsurf_geno mbasis_surveillance_von_salmonellen.htm).
The knowledge gained in this project about the integrated genome-based surveillance of Salmonella forms a valuable basis for the further development of molecular surveillance of food-borne pathogens in Germany. The investigations provide insights into the dynamics of Salmonella clusters, and highlight the need to link whole-genome-based data with epidemiological data, which not only allows for easier prioritization, but also plays an important role in the efficient identification of infection vehicles and sources.