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Real-time genome sequencing helps control hospital outbreak

BioMed Central

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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Research

Genomic Epidemiology of a Protracted Hospital Outbreak caused by Multi-Drug-Resistant Acinetobacter baumannii in Birmingham, England
Mihail R Halachev, Jacqueline Z-M Chan, Chrystala I Constantinidou, Nicola Cumley, Craig Bradley, Matthew Smith-Banks, Beryl Oppenheim and Mark J Pallen
Genome Medicine

For a copy of the research article during embargo period please contact Shane Canning.

After embargo, article available at journal website here: http://genomemedicine.com/content/6/11/70

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Genome Medicine publishes peer-reviewed research articles, new methods, software tools, reviews and comment articles in all areas of medicine studied from a post-genomic perspective. Areas covered include, but are not limited to, disease genomics (including genome-wide association studies and sequencing-based studies), disease epigenomics, pathogen and microbiome genomics, immunogenomics, translational genomics, pharmacogenomics and personalized medicine, proteomics and metabolomics in medicine, systems medicine, and ethical, legal and social issues.

BioMed Central is an STM (Science, Technology and Medicine) publisher which has pioneered the open access publishing model. All peer-reviewed research articles published by BioMed Central are made immediately and freely accessible online, and are licensed to allow redistribution and reuse. BioMed Central is part of Springer Science+Business Media, a leading global publisher in the STM sector.

The National Institute for Health Research (NIHR)

The NIHR is funded by the Department of Health to improve the health and wealth of the nation through research. Since its establishment in April 2006, the NIHR has transformed research in the NHS. It has increased the volume of applied health research for the benefit of patients and the public, driven faster translation of basic science discoveries into tangible benefits for patients and the economy, and developed and supported the people who conduct and contribute to applied health research. The NIHR plays a key role in the Government's strategy for economic growth, attracting investment by the life-sciences industries through its world-class infrastructure for health research. Together, the NIHR people, programmes, centres of excellence and systems represent the most integrated health research system in the world. For further information, visit the NIHR website.

The NIHR Centre for Surgical Reconstruction and Microbiology

The NIHR SRMRC is a national centre for trauma research, transferring innovation used in the treatment of injured military personnel to improve outcomes for all patients. It brings together the pioneering advances in surgery and infection control made by military and civilian scientists and medics working together. Launched in January 2011, the national trauma research centre will share its discoveries with the wider NHS to support delivery of excellence in a complex area of acute care. Based at the Queen Elizabeth Hospital Birmingham (QEHB), the centre harnesses expertise from the Ministry of Defence (MoD), University of Birmingham (UoB) and QEHB and has been funded over five years with a total £15 million investment (£5 million QEHB and UoB; £5 million MoD; £5 million DH). For more information, go to http://www.srmrc.nihr.ac.uk.

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