Center for Genomic Epidemiology

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Center for Genomic Epidemiology spinout
June 2016
A spinout company has recently been founded on the basis of Center for Genomic Epidemiology. One of the main activities of the company will be to conduct workshops on the topic of whole genome sequencing and analysis for microbial diagnostics with special focus on the tools developed by Center for Genomic Epidemiology.
Please visit GoSeqIt for more information...

Consortium to combat infectious disease outbreaks
January 2015
The COMPARE project has been funded with 20 million Euro from the EU. COMPARE (COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe) is a collaboration of founding members of the Global Microbial Identifier (GMI) initiative and institutions with hands-on experience in outbreak detection and response. The COMPARE project will establish a ‘one serves all’ analytical framework and data exchange platform that will allow real-time analysis and interpretation of sequence-based pathogen data in combination with associated data. The Consortium consists of 29 partners with multidisciplinary expertise in human health, animal health and food safety. How to optimally determine taxonomy from whole genome sequences.
For further information, please contact Frank M. Aarestrup...

Benchmarking of Methods for Genomic Taxonomy
April 2014
How to optimally determine taxonomy from whole genome sequences.
Link to publications...

Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica
March 2014
We evaluated WGS for outbreak detection of Salmonella enterica including different approaches for analyzing and comparing with a traditional typing, PFGE.
Link to publications...

Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads
January 2014
Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA.
Link to article...

Pathogenic bacteria identified and described directly from clinical samples within a day
December 2013
The CGE project has demonstrated how, within the space of a single day, pathogenic bacteria can be identified and described directly from clinical samples. In the long term, this will help doctors treat patients more quickly with the right medicine, thus reducing periods of illness and saving lives.
Link to article...

Internet-Based Solutions for Analysis of Next-Generation Sequence Data
August 2013
As a response to a paper published in Journal of Clinical Microbiology earlier this year, in which the authors wish for user-friendly and clinically focused platforms for analysis of next-generation sequence data, we here highlight the tools that we have already developed and made available, as well as future tools that are currently being developed.
Link to Letter to editor...

Advisory Board meeting
February 2013
The annual advisory board meeting in the Center for Genomic Epidemiology will take place at DTU on March 1st. At the meeting we will discuss the progress in the center.

Global Microbial Identifier
December 2012
GMI focuses on the use of genome sequencing techniques in a global system for microbiological identification and epidemiological surveillance.The vision is to develop a global system to aggregate, share, mine and use microbiological genomic data to address global public health and clinical challenges, a high impact area in need of focused effort.
Visit the homepage for further info

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...(e-published ahead of print)

Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response.
October 2012
Link to article...(e-published ahead of print)

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.
Link to article...

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.
Maj 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
Link to article...

Genomic variation in Salmonella enterica core genes for epidemiological typing.
March 2012
The variation within core genome is useful for investigating evolution and providing candidate genes from bacterial genome typing
Link to article...

Staphylococcus aureus CC398. Host Adaptation and Emergence of Methicillin Resistance in Livestock
February 2012
Publications in the center...

Comparative Genomics of Bifidobacterium, Lactobacillus and Related Probiotic Genera
January 2012
Genome diversity within a set of 'good bacteria' have been examined by a team from the CGE.
Publications in the center...

Multilocus Sequence Typing of Total Genome Sequenced Bacteria
January 2012
Publications in the center...

Characterization of Salmonella enterica serovar Stanley isolates; a serovar endemic to Asia and associated with travel
December 2011
Link to article...

The CGE is quoted in the Science article: Outbreak Detectives Embrace The Genome Era
September 2011
Doctors could soon be sequencing bacterial samples from virtually every patient. The avalanche of data will help fight disease outbreaks

Denmark leads the way in the global battle against infectious diseases
September 2011
DTU organized an expert meeting on microbiological genomic identification systems in September in Bruxelles. Please find more information and download the presentations from the meeting
Information and presentations...

Population Genetics of Vibrio cholerae from Nepal in 2010: Evidence on the Origin of the Haitian Outbreak
August 2011
In combination with evolutionary theory and advanced statistical methods, WGST represents the most powerful molecular approach imaginable and is setting a new standard for infectious disease epidemiology.

Defining the Pseudomonas Genus: Where do We Draw the Line with Azotobacter?
August 2011
Classifying bacteria is important for keeping track of outbreaks. How does one define a bacterial genus? Azotobacter was originally classified as belonging to the 'Pseudomonas' genus, but then later moved to its own genus, based on phenotypic behavior. Using several different genome-based methods, we find that the Azotobacter is most closely related to Pseudomonas, and perhaps is better understand as a different species within this genus.

Microbial Forensics and Molecular Epidemiology and the Population Genetics of High Homogeneous Bacteria
August, 2011
Paul Keim, Director of The Pathogen Genomics Division, TGen, USA gives a talk on the subject at DTU monday August 15th.
Bacterial pathogens frequently emerge in high virulent waves that sweep across regions, continents or even the globe. Whether this is due to a fitness advantage or simply due to stochastic opportunities isn't always clear, but these populations are highly clonal and highly homogeneous. The analytical challenges include the identification of rare genetic variation to discriminate among isolates and the subsequent genotyping of large sample sets to track the disease. Whole genome sequencing can now identify nucleotide differences, even if vanishingly rare. Genotyping assay development and implementation strategies are many, but need to fit particular applications in expense, speed, and sensitivity. Dr. Keim will discuss the state of this science and give examples from bioterrorism (anthrax), laboratory safety (plague) and public health (cholera).
For further information please contact: David Ussery

Molecular characterization and antimicrobial susceptibility testing of Escherichia coli isolates from patients with urinary tract infections in 20 Chinese hospitals
July 2011

New paper is published about the Salmonella enterica Pan-genome
June 2011
We have compared 45 sequenced S. enterica genomes that are publicly available (22 complete and 23 draft genome sequences) along with two Escherichia coli strains and estimated the core and pan-genome of Salmonella to be around 2,800 and 10,000 gene clusters, respectively. Pan-genomic dendrograms suggest that gene content is often, but not uniformly correlated to serotype. Any given Salmonella strain has a large stable core, which is extended with an abundance of variable accessory genes, typically localized in specific flexible genomic regions or islands, such as transposable elements, phages, and integrated plasmid DNA. These islands were typically well conserved in some, but not all, isolates - a difference which could have implications in, e.g., host specificity.

CGE supercomputer becomes operational
February 25, 2011
The new CGE supercomputer today became operational. The computer has 512 cores and will be used to analyse bacterial genomes. The computer will also act as server for CGE's webservices

CGE reserchers publish paper about predicting bacterial pathogenecity
October 10, 2010

Center for genomic Epidemiology officially opens
April 1, 2010

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