DNA sequencing technology yields new insights into German E. coli pathogen

July 28, 2011

An international team of scientists has successfully employed single molecule, real-time (SMRT™) DNA sequencing technology from Pacific Biosciences of California, Inc. (NASDAQ: PACB) to provide valuable insights into the pathogenicity and evolutionary origins of the highly virulent bacterium responsible for the German E. coli outbreak. Published online today in the New England Journal of Medicine, the results provide the most detailed genetic profile to date of the outbreak strain, including medically relevant information.

The researchers determined the outbreak strain was a member of the enteroaggregative pathotype of E. coli (EAEC) with serotype O104:H4. The outbreak isolates are distinguished from other O104:H4 strains because they contain genes encoding Shiga toxin 2 (Stx2) and a distinct set of additional virulence and antibiotic resistance factors. In addition, the team found that expression of the stx2 gene was increased by certain antibiotics including ciprofloxacin, suggesting caution should be used before using certain classes of antibiotics to counteract this newly emerged pathogen.

By sequencing the outbreak strain and 11 related strains with the PacBio RS, the team concluded that horizontal genetic exchange with the Shiga toxin-producing enterohemorrhagic E. coli (EHEC) strain enabled the emergence of the highly virulent Shiga toxin-producing O104:H4 EAEC strain. The genetic analysis also indicates that evolution of this new form was a relatively recent event.

The team identified many virulence factor genes commonly found in EAEC. Furthermore, the exceptionally long sequencing reads that are characteristic of PacBio SMRT DNA sequencing technology enabled the team to also detect larger-scale deletions, insertions, inversions and other structural variation between the O104:H4 outbreak samples and the other O104:H4 EAEC samples that were sequenced. Several of these structurally divergent regions house genes that encode virulence factors. Another feature in which the current outbreak diverges from common EAEC isolates is in the number and nature of SPATE proteases. Taken together, the results provide a possible explanation for the increased virulence of the German E. coli outbreak strain.

The authors included scientists in the U.S. and Denmark from Pacific Biosciences, the University of Maryland School of Medicine, the University of Virginia School of Medicine, the World Health Organization Collaborating Centre for Reference and Research on Escherichia coli and Klebsiella, the Statens Serum Institut, Hvidovre University Hospital, Brigham and Women's Hospital and Harvard Medical School.

"This multi-strain sequencing data and analysis significantly increases the amount of scientific information available for the study of this new deadly form of E. coli and has yielded critical insights into its causative agent," said co-author, David A. Rasko, Ph.D., Assistant Professor, University of Maryland School of Medicine, Institute for Genome Sciences and Department of Microbiology and Immunology. "Our results provide the most complete published genome of this strain to date and highlight the importance of DNA sequencing to understanding how the plasticity of bacterial genomes facilitates the emergence of new ."

Whole genome sequencing involves decoding the precise order of nucleotide bases that make up an organism's complete set of DNA and provides more comprehensive information than other analysis methods such as DNA fingerprinting or arrays. With advances in technology and decreasing cost, whole genome sequencing is emerging as the gold standard method for identifying and classifying infectious agents. SMRT technology is the latest advance in DNA sequencing, capable of generating long sequence reads to resolve structural variations and complex genomes at ultra-fast speeds by 'eavesdropping' on DNA replicating in real time.

Eric Schadt, Ph.D., Chief Scientific Officer of Pacific Biosciences and co-author of the paper commented: "We have reached a new era in which communities of researchers can rapidly share large-scale data sets and analyses vital for public health. Sequencing genomes in hours, as opposed to days or weeks, with unprecedented read lengths is the emerging hallmark of third generation DNA sequencing. The long PacBio RS reads enabled a PacBio-only de novo genome assembly, a key component of new pathogen characterization, as well as deeper insights into structural variants."

Explore further: EHEC 2011 outbreak: Scientists publish their prospective genomic characterization

Related Stories

EHEC 2011 outbreak: Scientists publish their prospective genomic characterization

July 20, 2011
Scientists of the Medical Faculty of the University Munster and the University Hospital Munster in collaboration with scientists of the enterprise 'Life Technologies Corporation' were the first to release a draft genome sequence ...

Researchers crack code of German E. Coli outbreak

July 27, 2011
A team led by University of Maryland School of Medicine Institute for Genome Sciences researchers has unraveled the genomic code of the E. coli bacterium that caused the ongoing deadly outbreak in Germany that began in May ...

BGI sequences genome of the deadly E. coli in Germany and reveals new super-toxic strain

June 2, 2011
The recent outbreak of an E. coli infection in Germany has resulted in serious concerns about the potential appearance of a new deadly strain of bacteria. In response to this situation, and immediately after the reports of ...

Recommended for you

Gene variant activity is surprisingly variable between tissues

August 21, 2017
Every gene in almost every cell of the body is present in two variants called alleles—one from the mother, the other one from the father. In most cases, both alleles are active and transcribed by the cells into RNA. However, ...

Genome analysis with near-complete privacy possible, say researchers

August 17, 2017
It is now possible to scour complete human genomes for the presence of disease-associated genes without revealing any genetic information not directly associated with the inquiry, say Stanford University researchers.

Science Says: DNA test results may not change health habits

August 17, 2017
If you learned your DNA made you more susceptible to getting a disease, wouldn't you work to stay healthy?

Genetic variants found to play key role in human immune system

August 16, 2017
It is widely recognized that people respond differently to infections. This can partially be explained by genetics, shows a new study published today in Nature Communications by an international collaboration of researchers ...

Phenotype varies for presumed pathogenic variants in KCNB1

August 16, 2017
(HealthDay)—De novo KCNB1 missense and loss-of-function variants are associated with neurodevelopmental disorders, with or without seizures, according to a study published online Aug. 14 in JAMA Neurology.

Active non-coding DNA might help pinpoint genetic risk for psychiatric disorders

August 16, 2017
Northwestern Medicine scientists have demonstrated a new method of analyzing non-coding regions of DNA in neurons, which may help to pinpoint which genetic variants are most important to the development of schizophrenia and ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.