Daily Archives: November 20, 2014

PUBLIC RELEASE DATE:

19-Nov-2014

Contact: Shane Canning shane.canning@biomedcentral.com 44-203-192-2243 BioMed Central @biomedcentral

Pioneering use of whole genome sequencing in real time to help control a hospital outbreak is reported in an article published in the open access journal Genome Medicine. The research corroborates the use of the technique as a rapid and cost-effective way of tracking and controlling the spread of drug-resistant hospital pathogens.

Acinetobacter baumannii is a multi-drug resistant pathogen found in hospitals across the globe and emerged as a significant threat to casualties in the Iraq and Afghanistan wars. It affects severely ill patients, particularly trauma and burns patients, often leading to pneumonia and bloodstream infections. Healthcare-associated infections (HAIs) are estimated to cost the UK 1 billion a year and, at any given time, one in every 15 patients will have a HAI.

Whole genome sequencing, which sequences an organism's entire DNA, is thought to be a promising new addition to the toolkit for controlling HAIs. Conventional methods are often applied retrospectively and yield limited information about a pathogen's DNA, making it difficult to compare whether patients are carrying the same bacteria and track transmission of outbreaks.

In this paper the researchers from the University of Birmingham, University of Warwick, and the National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, report how whole genome sequencing was used to control an outbreak of A. baumannii at Queen Elizabeth Hospital Birmingham in 2011. The outbreak began following the admittance of a military patient from Afghanistan with blast injuries and lasted for 80 weeks - making it one of the longest outbreaks ever described for this pathogen. The patient was carrying a novel strain of the bacterium that had not previously been observed in the region's hospitals. After first using traditional methods to try and contain the pathogen, the researchers decided to switch to whole genome sequencing mid-way through the outbreak.

Sampling patients and the environment, the researchers were able to identify 74 patients belonging to the outbreak. They then determined the detailed genetic makeup of the bacteria carried by each of these patients and used this data, with information about the ward that the patients were housed in, and the date of their first positive tests, to identify nearly 70 possible transmission events. Armed with this detailed information, the researchers were able to pinpoint transmission hot spots within the hospital, which included an operating theatre and a specialised bed for burns patients.

Deep cleaning of these transmission sites followed and new decontamination protocols were put in place by the hospital. In May 2013 the outbreak was declared closed. Lead author of the study, Mark Pallen from the University of Warwick, said: "We have demonstrated how whole genome sequencing can be applied in a clinically helpful timeframe to track and control the spread of drug-resistant hospital pathogens. In this case, it helped understand and control what was probably longest running A. baumannii outbreak ever seen in this country."

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Real-time genome sequencing helps control hospital outbreak

Chuck Bednar for redOrbit.com Your Universe Online

An international research consortium investigating the functional genome of the mouse have managed to map the creatures so-called mission control centers, and found new clues as to why certain processes and systems in the rodents prevent the results of mouse studies from being successfully replicated in humans.

Members of the Mouse ENCODE project, a project designed to complement the National Human Genome Research Institutes (NHGRI) Encyclopedia of DNA Elements (ENCODE) program, were able to produce an exhaustive description of the functional genome elements of mice, and compared that information to the human genome. Their findings produced similarities between the two mammals, as well as some significant differences.

ENCODE, which began in 2003, analyzed specific components in the human genome responsible for gene expression, or the process of coding for proteins that carry out a cells function. The Mouse ENCODE study looked at 100 mouse cell types and tissues to annotate the regulatory elements of the mouse genome and compared them to the human genome useful research, since mice are so often used as model organisms in clinical studies.

According to the National Institutes of Health (NIH), which oversees the NHGRI, the researchers reported their findings in four separate studies published in the journal Nature and other prominent scientific journals. In those papers, the authors examined the genetic and biochemical programs involved in regulating both mouse and human genomes, finding that the systems responsible for controlling gene activity in each have many similarities that have been conserved through the evolutionary process.

Their findings could provide new insight into genetic regulation and other systems essential to mammalian biology, the NIH said. Furthermore, their work could provide new information to determine in which cases the mouse will continue to be an appropriate model for studies involving the effect of drugs and disease on humans, as well as help explain some of the limitations of this model and why the results of such studies sometimes fail to translate to people.

The mouse has long been a mainstay of biological research models, said NHGRI Director Dr. Eric Green. These results provide a wealth of information about how the mouse genome works, and a foundation on which scientists can build to further understand both mouse and human biology. The collection of mouse ENCODE data is a tremendously useful resource for the research community.

This is the first systematic comparison of the mouse and human at the genomic level, added Dr. Bing Ren, a professor of cellular and molecular medicine at University of California, San Diego (UCSD) and co-senior author of the Consortiums primary Nature study. We have known that the mouse was mostly a good model for humans [and] this allows us to study human disease by studying those aspects of mouse biology that reflect human biology.

Among the discoveries made during the course of the research was the discovery as to why the immune system, metabolism and stress response of mice are so different from humans, the Centre for Genome Regulation (CGR), one of the institutions involved in the project, explained. They compared various processes involved in gene expression, including gene transcription and chromatin modification, and repeated those investigations in various different tissues and cell types from both mice and humans.

Our lab took part in analyzing the group of RNA or transcriptome, that results from transcription, the process by which the instructions in the genes are read, said Alessandra Breschi, a CGR researcher and one of the first co-authors of the main study. We have discovered that human and mice transcriptome contains both preserved and divergent elements. Surprisingly we have found that the differences seem bigger between species rather than between fabrics when initially we thought that the gene activity in the same kinds of tissues would be similar.

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Comparing The Genomes Of Mice And Humans To Aid Clinical Research