Center for genomic epidemiology

Within five years the costs for a total bacterial genome sequencing will be less than 5 000 DKK and the equipment needed will cost less than 500 000 DKK. Thus, in 5 to 10 years most clinical and industrial microbiological laboratories will have a sequencer in use on a daily basis. As prices decline to less than 1000 DKK whole genome sequencing will also find worldwide application in human and veterinary practices, in the biotech industry, as well as many other places where bacteria are handled.

In Denmark alone this equals more than 100,000 isolates annually in 15-20 laboratories and globally up to half a billion isolates per year. Thus, in the future, the limiting factor will not be the cost of the sequencing, but how to assemble, process and handle the large amount of data in a standardized way that will make the information useful for diagnosis, outbreak investigation, source tracking and surveillance.

The biotechnology industry and environmental microbiology will have a similar need. The proposed center will provide the bioinformatic and scientific foundation for future web-based solutions where a central database will provide simplified whole genome sequence information and enable rapid whole genome comparisons to all other sequences including spatial-temporal analysis. Thus, we will develop algorithms for rapid whole genome sequence analyses, tools for extraction of biologically and epidemiologically relevant information from the sequence data, and web-based interfaces to enable use of the system by the global scientific, public health and medical communities.

The activity can be expanded to also include other microorganisms, such as viruses and parasites. To build up such a service and have it accepted by the medical and scientific community it must be a well-organized and stably funded project; therefore, we are applying for 6 years of funding in order to develop a strategic research centre. Following this period, we expect that these functions will be imbedded in the basic activities of the project partners.