Center for Microbial Genome Sequencing

The Center for Microbial Genome Sequencing originates from the Research Unit for Clinical Microbiology and the Department of Clinical Microbiology, Odense University Hospital. We develop and use molecular biological genome sequencing methods and bioinformatics solutions to improve the diagnostics of infectious diseases, the characterization of disease-causing microorganisms and the detection of cases of infection associated with health sector-associated infections. Furthermore, sequencing is used to describe the composition of microorganisms in sample material, for example microbiome / microflora in stool samples. We collaborate with other research groups at Odense University Hospital, University of Southern Denmark and others in Denmark and abroad.

Methods

Whole genome sequencing of bacteria, viruses, and fungi with Illumina and Oxford Nanopore technologies. We have great capacity and have Illumina Nextseq 2000, Oxford Nanopore GridIon and P2i at our disposal. Automated cleaning robots and library-preparation robots.
Amplicon-based sequencing for example bacterial DNA, 16S, microbiome, fungal DNA, 18S, parasites.
Metagenome sequencing (mNGS) for unbiased detection of all microbial DNA in sample materials.

Research projects

Characteristics of faecal microbiome from patients on immunosuppressive treatment (Collaborative project with Frontline Center ICITox, Research Unit for Oncology, Odense University Hospital).
Optimization of amplicon-based diagnostics of bacterial infections (16S).Uncovering the incidence of healthcare-associated blood poisoning.
Decentralized typing of Salmonella infections using whole genome sequencing.
Optimizing the identification of yeast and mold infections.
FastTrax – Fast methods for tracing bacterial outbreaks (Collaborative project with Department for Bacteria, Parasites and Fungi, Statens Serum Institut)