Public Release: 

BGI reports rapid open-source genomic analyses accelerated global studies on deadly E. coli O104:H4

BGI Shenzhen

July 28, 2011, Shenzhen, China - BGI, the world's largest genomic organization in the world, today announced that the study on Genomic Analysis of Shiga Toxin-Producing Escherichia coli O104:H4, conducted by BGI and its collaborators, was published online today in The New England Journal of Medicine (NEJM). The study involved the use of rapid, bench-top DNA sequencing technology, open-source data release and fast crowd-sourced analyses, and revealed for the first time that rapid open-source analysis of an outbreak-associated bacterial pathogen can play a significant role in public health emergencies.

An outbreak caused by an unusual Shiga toxin-producing E. coli O104:H4 occurred in Germany beginning in May 2011. As of July 21, more than 4,000 people were infected, 50 of whom died. BGI sequenced the genome of E. coli isolate within three days, using the Ion Torrent Personal Genome Machine and in less than a week, researchers found that the strain belonged to an enteroaggregative E. coli lineage containing genes for Shiga toxin 2 and resistant to several types of antibiotics. Scores of scientists all over the world rushed to the genomic studies of the lethal bacterium sequenced and analyzed by BGI and its collaborators in University Medical Centre Hamburg-Eppendorf, Beijing Institute of Microbiology and Epidemiology, China CDC, among others.

Dr. Junjie Qin, PI of the E. coli project at BGI and one of the co-leading authors of the study said: "In order to reveal the mechanisms of infection and control the spread of this epidemic as soon as possible, we together with our partners launched a rapid open-source genomics program for immediate data release and to provide more available genome data to the global researchers."

Professor Ruifu Yang, Research fellow at the Beijing Institute of Microbiology and Epidemiology, said, "This study not only lays an important foundation for tracing down the evolutionary origins and pathogenic potential of this epidemics strain but also opens a way to countermeasure infectious diseases by a new model of international collaboration."

The genomic analysis suggests that the E. coli O104:H4 evolved from a progenitor of enteroaggregative E. coli through acquisition of an stx2-encording prophage and a plasmid encoding a CTX-M15 extended-spectrum beta-lactamase (ESBL) gene. "Genome sequencing provides the foundation to identify and characterize novel pathogens, while the open-source genomic analysis via data sharing in the community can greatly accelerate the process and facilitate diagnostic and treatment applications in public health problems," said professor Jun Wang, Executive Director of BGI.


This work was supported by grants from the State Key Development Program for Basic Research of China, the National Key Program for Infectious Diseases of China, Shenzhen Biological Industry Development Special Foundation-Basic Research Key Projects, Key Laboratory Project Supported by Shenzhen City, the European Union Microme program, the Alexander von Humboldt Foundation, and the Medical Faculty of the University Medical Center Hamburg-Eppendorf, as well as a BBSRC grant supporting the xBASE project.

About BGI

BGI (formerly known as Beijing Genomics Institute) was founded in 1999 and has since become the largest genomic organization in the world. With a focus on research and applications in the healthcare, agriculture, conservation and bio-energy fields, BGI has a proven track record of innovative, high profile research, which has generated over 178 publications in top-tier journals such as Nature and Science. BGI's distinguished achievements have made a great contribution to the development of genomics in both China and the world. Our goal is to make leading-edge genomics highly accessible to the global research community by leveraging industry's best technology, economies of scale and expert bioinformatics resources. BGI and its affiliates, BGI Americas and BGI Europe, have established partnerships and collaborations with leading academic and government research institutions, as well as global biotechnology and pharmaceutical companies. At BGI, we have built the infrastructure and scientific expertise to enable our customers and collaborators to quickly migrate from samples to discovery. For more information, visit or

Contact Information:

Dr. Junjie Qin,
Group Leader, Metabolomics Research Group

Dr. Bicheng Yang
Director of Global Marketing Department

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