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

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.