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Imprint
Total genome sequencing of S. aureus, B. cereus and clostridia by NGS: Genetic structures of antibiotic resistance, virulence factors and species demarcation
Project
Project code: BfR-BIOS-08-1322-688
Contract period: 01.01.2018
- 31.12.2019
Purpose of research: Experimental development
The unit "Microbial Toxins" uses whole genome sequencing (WGS) to characterize isolates of the pathogenic species groups presumptive Bacillus (B.) cereus, Clostridia (C.), and coagulase-positive Staphylococci (S.). In the field of Bacilli, the focus is on issues concerning species differentiation within the B. cereus group, fine typing of isolates (e.g. outbreak strains, biopesticidal strains) and new virulence markers. With regard to virulence markers, an analysis of total genome sequences, combined with findings on the cytotoxicity of strains, should provide new insights. Regarding Clostridia phylogenetic analyzes are central. Strains from food but also from humans and animals shall be examined regarding their genetic relationship. For this purpose, mainly SNP-based analyzes and core genome (cg-) MLST are carried out and the results are compared. In the area of Staphylococci, methicillin-resistant S. aureus (MRSA), which display unusual or non-typeable antibiotic resistance genes (SCCmec elements), will be investigated in more detail during the project year. Furthermore, S. aureus isolates are analyzed which have phenotypic resistance to cefoxitin, but whose resistance mechanism is unclear. The data and insights gained may help to extend or adapt detection or typing procedures for MRSA. For the characterization of toxin formers, a validation should be carried out, comparing the results of sequencing and microarray analysis using strains from the strain collection and new isolates submitted to the NRL Staph. This is intended to prepare an accreditation of the WGS procedure. In this sense, a comparison between the results of existing methods and results based on WGS should also be carried out for the other groups of pathogens with a large number of strains. By means of this comparison, the method of WGS shall be validated with regard to various analyzes/evaluations in order to replace certain methods in the long term with WGS in the accreditation system.
Section overview
Subjects
- Biotechnology
- Food microbiology
- Toxicology
