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Integrated genome based surveillance of salmonellae (GenoSalmSurv)

03/2019-02/2022

This third-party funded project is conducted in the framework of the BfR research programme on human, animal and environmental health (One Health).

Support programme of the Federal Ministry of Health (BMG): Zoonotic infectious diseases and pathogens with specific resistances

BMG grant number: ZMVI1-2518FSB709

Project homepage: -

Project description:

Salmonellosis is a disease caused by enterobacteria of the genus Salmonella. It is the second most frequently reported bacterial diarrheal disease in humans in Germany after campylobacteriosis, but the hospitalization rate for salmonellosis is significantly higher than for Campylobacter enteritidia. Of particular health and socio-economic importance is that this zoonotic agent causes many food-borne outbreaks. The GenoSalmSurv project aims to establish a model for integrated genome-based surveillance of salmonellae based on the use of modern high-resolution genome sequencing techniques. The reference laboratories of human medicine and food monitoring of the federal government are to cooperate with other institutions of the public health service (ÖGD) or the authorities for food safety and animal health of the federal states.

In the project

1. typing methods including genome sequence analysis methods for salmonellae are collected, harmonized and bottlenecks are recognized,
2. possible open-source analysis programs for cluster recognition and typing of Salmonella are evaluated,
3. prospective genome sequencing is performed and the sequence data results are brought together and
4. the new concept is presented to the supervisory authorities and multipliers are trained.

This serves the purpose of making the high-resolution method of genome analysis for cluster recognition, pathogen monitoring and infection source analysis accessible in a simple form to all authorities involved and thus to accelerate and widely implement its establishment across sectors (one-health concept).

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.

Project partners:

• Robert Koch-Institut
• Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL)

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