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Services
  • Multi Locus Sequence Typing (MLST) from an assembled genome or from set of reads
    MLST typing

  • Identifcation of acquired antibiotic resistance genes from a file with sequence reads
    ResFinder

  • SNPs phylogenetic tree from assembled genomes or sets of reads
    snpTree

  • Reads2Type gives a fast and dirty prediction of bacterial taxonomy
    Reads2Type


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CGE
Welcome to the Center for Genomic Epidemiology

The cost of sequencing a bacterial genome is $50 and is expected to decrease further in the near future and the equipment needed cost less than $150 000. Thus, within a few years all clinical microbiological laboratories will have a sequencer in use on a daily basis. The price of genome sequencing is already so low that whole genome sequencing will also find worldwide application in human and veterinary practices as well as many other places where bacteria are handled. In Denmark alone this equals more than 1 million isolates annually in 15-20 laboratories and globally up to 1-2 billion isolates per year. The limiting factor will therefore in the future 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, especially for diagnostic and surveillance.

The aim of this center is to provide the scientific foundation for future internet-based solutions where a central database will enable simplification of total genome sequence information and comparison to all other sequenced including spatial-temporal analysis. We will develop algorithms for rapid analyses of whole genome DNA-sequences, tools for analyses and extraction of information from the sequence data and internet/web-interfaces for using the tools in the global scientific and medical community. The activity is being expanded to also include other microorganisms, such as vira and parasites as well as metagenomic samples.


News

Advisory Board meeting
March 2013
The annual advisory board meeting in the Center for Genomic Epidemiology took place at DTU on March 1st.

Global Microbial Identifier
December 2012
The initiative 'Global Microbial Identifier' focuses on the use of genome sequencing techniques in a global system for microbiological identification and epidemiological surveillance. Visit the homepage for further information

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes
December 2012
The use of whole genome sequencing will make it possible to eliminate, or at least reduce, the need for several typing steps used in traditional epidemiology. Link to article...

Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response
October 2012
Publications in the center...

Identification of acquired antimicrobial resistance genes
August 2012
We here present ResFinder, a web server that uses WGS data for identifying acquired antimicrobial resistance genes in bacteria. Publications in the center...

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium
May 2012
Combining three RNA-sequencing techniques and two sequencing platforms to generate transcriptional map of SL1344 advances our understanding of S. Typhimurium, arguably the most important bacterial infection model. Publications in the center...


Copyright DTU 2011 / All rights reserved
Center for Genomic Epidemiology, DTU, Kemitorvet, Building 204, 2800 Kgs. Lyngby, Denmark
Contact: Vibeke Dybdahl Hammer, Telephone: +45 3588 6420, E-mail: vdha@food.dtu.dk
Funded by: The Danish Council for Strategic Research