The UM School of Medicine Institute for Genome Sciences deciphers the code of e. coli

BALTIMORE, July 28, 2011/PRNewswire /-

• the UM School of Medicine Institute for Genome Sciences decrypts the genomic code of the German deadly outbreak of e. coli

• quick study of high-tech ongoing epidemics creates a new paradigm for the investigation of the outbreak

A team led by researchers at the University of Maryland School of Medicine Institute for Genome Sciences has unveiled the cóI say genome of the bacterium e. coli that has caused the deadly outbreak in Germany that began in May 2011. So far have killed 53 people because of the outbreak, becoming ill at the same time thousands of people in Germany, Sweden and United States. The document, published on July 27 in the New England Journal of Medicine (NEJM), describes how researchers around the world have worked together to use this revolutionary technology to sequence and analysis of genomic samples of e. coli from the outbreak, as well as the types related closely in just a few days. They have combined discoveries with his knowledge of the biology and evolution of bacteria to learn more about the outbreak. The analysis produced fast enough to inform the doctors who treated infected persons, help epidemiologists at the time who were still the source of the pathogen.

The research could be the first time is a complete scientific analysis in the first days and weeks of an outbreak, according to the main author of the study, David a. Rasko, Ph.d., Assistant Professor of Microbiology and Immunology of the University of Maryland School of Medicine, as well as scientific researcher at the Institute for Genome Sciences.

This technology is evolving very quickly, and it has enabled us to achieve a more accurate analysis with unprecedented speed ”, commented Dr. Rasko. it took years and millions of dollars to make the sequence of the first genome of e. coli over one decade ago. Here are just a few months after the start of the German outbreak of e. coli, and have already published a paper about it. This document and the research that describes represent a new paradigm for investigations of outbreaks ”.

Researchers have collaborated with Pacific Biosciences of California, Inc., a company based in Menlo Park, California that uses its new Single Molecule Real Time technology for the secuenciacón of the genome of the variation of e. coli outbreak of Germany. The collaboration also includes scientists from the Statens Serum Institute, the World Health Organization Collaborating Centre for Reference and Research on Escherichia coli and Klebsiella Denmark and also at the universities of Harvard and the University of Virginia.

The University of Maryland School of Medicine has a global presence expanded by 23 countries, and we are proud that our Institute for Genome Sciences has held an Office in the investigation of this international health crisis and improved human health around the world ”, explained e. Albert Reece, Dr., Ph.d., M.B.A., Vice President of Medical Affairs of the University of Maryland and distinguished Professor John z. and Akiko k. Bowers and Dean of the Faculty of medicine.

Dr. Rasko and his colleagues at the Institute for Genome Sciences data analyzed genomic using computational tools, some of them developed in the Institute. The team of the Institute for Genome Sciences included researchers from postdoctoral Jason Sahl, Ph.d. and Susan Steyert, Ph.d., as well as Julia Redmond lab responsible for. The experience of Dr. Rasko within molecular pathogenesis and evolution of e. coli has helped his team to interpret the massive amount of genomic data involved and also to learn more about microbes and as integrated within the overall vision of e. coli.

Scientists have discovered that the German outbreak of variant of e. coli was mainly e. coli enteroagreada, a subtype of bacteria. After a careful review of the genome, have discovered that the variant of the outbreak was actually an unusual combination of e. coli enteroagregada and another subtype known as e. coli enterohemorrágica. Researchers also indicated that the variant developed a unique set of virulence and antibiotic-resistant factors, unlike other variants of the bacteria.

This is not only a document of the genome. Also examines the virulence and the Microbe biology ”, said doctor Rasko. At the beginning of the outbreak, scientists discovered the bacterium as a Variant ‘ hybrid ’. This variant is not the true hybrid type, it contains only a small number of the sequence of the DNA of e. coli enterohemorrágica. We have not seen this kind of unique combinations often in the past. I believe that we are seeing an increase in them, now that Pacific Biosciences technology has advanced to the point where we sequence more variations of form very quickly and relatively cost content ”.

The combination of speed, accuracy and cost will lead the Genomic sequencing to make it a tool of diagnosis quicker than the rest of environments currently used by any ”, said doctor Sahl, co-author of the document.

When the outbreak began in may, scientists from around the world began to consider the variation of e. coli as soon as the samples were available. Many groups published their discoveries for free for the people – the data in the current study are also publicly available – something that served to get a kind of crowd source ”. This indicates that the research was carried out through the collaboration of a large and disparate group throughout the world. Normally, science developed in relative isolation ”, explained Dr. Rasko. This is the first time we’ve seen analysis of truly ‘ open source ’ of the Microbial Genome ”.

Very early in the outbreak, the German scientists used other sequencing technology and a preliminary analysis to determine what was unique about the pathogen associated with the outbreak. In fact, they identified a gene that produced a toxin associated to the primary symptoms that doctors saw patients, such as diarrhoea. This gene, known as the Shiga toxin, occurs more when using some antibiotics. Findings indicated that the symptoms of the patients could worsen in case of treatment with antibiotics. These initial discoveries began to immediately inform clinical treatment, while doctors stopped using antibiotics to treat those infected. Our research is a more detailed and complete than the initial research analysis ”, explained Dr. Rasko. This has been an international collaboration performed together in just a few days. We hope to see more partnerships like these to deal with new emerging pathogens for the future ”.

The NEJM paper will provide further detailed information to help researchers and physicians at the time who are investigating the current outbreak of e. coli in Europe.

Is exciting to be at the forefront of a genomic like this ”, exclaimed doctor Rasko. this research has been an opportunity for us in order to evaluate the power of the Institute for Genome Sciences in relation to aid for the creation of a new paradigm for the study of microbes and outbreaks. It also has implications for Genomic tool within the routine diagnosis ”.

Founded in 1807, the University of Maryland School of Medicine is the first public school of medicine and one of the oldest in United States. As one of the fastest growing in the country research institutions, the School of Medicine performs research in basic science and clinical research aimed at the health problems in the world – evolving quickly discoveries to the clinical phase for the benefit of patients. School of Medicine serves as anchor for the great academic center of health. Faculty members teach doctors and treat patients at the University of Maryland Medical Center and the Baltimore VA Medical Center.