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Imprint
Integrated genome-based surveillance of salmonellae (GenoSalmSurv)
Project
Project code: BfR-BIOS-08-1368-1676
Contract period: 01.03.2019
- 28.02.2022
Purpose of research: Experimental development
Keywords: Salmonellosis, zoonotic agent, genome sequencing analysis, pathogen monitoring
Salmonellosis is a disease caused by enterobacteriae of the genus Salmonella. After campylobacteriosis, it is the second most frequently reported bacterial diarrhoea in humans in Germany, but the hospitalization rate in salmonellosis is significantly higher than in campylobacter enteritidiae. It is also of particular importance in health policy and socio-economic terms that this zoonotic agent causes many food-borne outbreaks. In the proposed project a model for an integrated genome-based surveillance of Salmonella shall be established, which is based on the use of modern high-resolution genome-sequencing methods. The reference laboratories of human medicine and food authorities of the federal government will collaborate with other institutions of the public health service (ÖGD) as well as the authorities for food safety and animal health of the federal countries. In the project, 1) typing methods including genome sequence analysis methods for salmonellae are to be collected, harmonised and bottlenecks identified, 2) licence-free (open-source) sequence analysis programmes for the cluster recognition and typing of Salmonella are to be evaluated and submitted to the authorities on a cross-sectoral basis, 3) prospective genome sequencing is to be carried out and the sequence data results are to be combined, and 4) the new concept is to be presented to the authorities and multipliers trained. This serves the purpose of making the high-resolution procedure of genome analysis for cluster recognition, pathogen monitoring and infection source analysis accessible to all participating authorities in a simple form and thus accelerating its establishment across sectors (One Health concept) and realising it on a broad scale.
BfR part of the project: Work Package 2: Development of Standard Procedures for Integrated Genome-Based Salmonella Surveillance (BfR) This focus will include the development of a model for integrated genome-based surveillance for laboratories and public authorities (including the further approach to cluster recognition), the coordination of laboratory protocols for WGS and the development and harmonization of standard bioinformatics workflows. Common criteria should guarantee a consistent data quality agreed between the partners. The resulting fine typing includes recognition of serotypes, multilocus sequence types (7-gene MLST), antimicrobial resistance genes, virulence genes and plasmids. Furthermore, tools are being established that allow for subtyping below the serovar level, allowing for the surveillance of dominant or emerging phylogenetic lineages (e.g., ribosomal MLST). Work package 4: Organisation of a WGS performance comparison test (BfR) It is planned to carry out a benchmarking test of selected laboratories of the ÖGD, veterinary medicine and food control of the countries. The participants are provided with isolates and DNA from Salmonella isolates, and the laboratories then reflect their generated sequence raw data. This test verifies the performance of the sequencing laboratories to ensure defined genome sequence qualities. The results should be incorporated into training measures.
Section overview
Subjects
- Food microbiology
