UEA research could revolutionise genomic sequencing of drug-resistant bacteria

via University of East Anglia

via University of East Anglia

New nanopore DNA sequencing technology on a device the size of a USB stick could be used to diagnose infection – according to new research from the University of East Anglia and Public Health England.

Researchers tested the new technology with a complex problem – determining the cause of antibiotic resistance in a new multi-drug resistant strain of the bacterium that causes Typhoid.

The results, published today in the journal Nature Biotechnology, reveal that the small, accessible and cost effective technology could revolutionise genomic sequencing.

Current technology for ‘long read’ detailed genomic sequencing can be performed using expensive instrumentation (around £500,000). It is complex to perform, and generally only available in specialist laboratories.

The research team tested a new device called MinION, produced by Oxford Nanopore Technologies Ltd. The machine produces long sequencing reads using a different methodology that does not require optical imaging – but at a small fraction of the instrument cost (expected to be around £650 per device). These long reads are important when trying to determine where resistance genes are.

Researchers proved its utility by successfully mapping the multi-drug resistance genes in a strain called Salmonella Typhi haplotype H58 – which has recently emerged globally.

They successfully pinpointed the exact spot in the chromosomal structure that is home to the genes which makes it drug-resistant, known as an antibiotic resistance island. The MinION took just 18 hours to produce the results, with similar accuracy to current technologies.

Lead researcher Dr Justin O’Grady, from UEA’s Norwich Medical School, said: “This type of technology will revolutionise the way that we characterise the rapid spread of emerging antibiotic-resistant infectious diseases.

“This analysis would previously have taken months using traditional methods, due to extensive post-sequencing lab-based analysis. By the time the results are available, they might well be irrelevant for clinical diagnostics and guiding public health interventions.

“This is the first published research in the world to demonstrate the huge potential of MinION sequencing to solve important and complex biological problems.

“Public health and clinical laboratories could soon have easy access to this rapid, cheap technology which, in combination with short read sequencing, is capable of providing fully assembled bacterial genomes. Further improvements to the system are likely to remove the need for short read sequence data.

“MinION technology could potentially enable bacterial identification, diagnosis of infectious diseases and detection of drug-resistance at the point of clinical need.

“This type of technology makes next generation sequencing accessible to scientists everywhere.”

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Copper Surfaces Reduce the Rate of Healthcare-Acquired Infections in the ICU

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Placement of copper objects in intensive care unit (ICU) hospital rooms reduced the number of healthcare-acquired infections (HAIs) in patients by more than half

Placement of copper objects in intensive care unit (ICU) hospital rooms reduced the number of healthcare-acquired infections (HAIs) in patients by more than half, according to a new study published in the May issue of Infection Control and Hospital Epidemiology, the journal of the Society for Healthcare Epidemiology of America, in a special topic issue focused on the role of the environment in infection prevention.

In the United States, HAIs result in 100,000 deaths annually and add an estimated $45 billion to healthcare costs. HAIs often contaminate items within hospital rooms, allowing bacteria to transfer from patient to patient. Common microbes include methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE). While several strategies have been developed to decrease HAIs, few have been clinically proven to reduce the spread of these infections. The researchers tested the capability of copper surfaces to reduce environmental contamination of these germs and thereby decrease HAIs in patients. Copper surfaces have an inherent ability to continuously kill environmental microbes on these surfaces.

The study was performed from July 12, 2010 to June 14, 2011 at three medical centers including the Medical University of South Carolina, the Memorial Sloan-Kettering Cancer Center, and the Ralph H. Johnson Veterans Affairs Medical Center. Patients who were admitted to the ICU of these hospitals were randomly assigned to receive care in a traditional patient room or in a room where items such as bed rails, tables, IV poles, and nurse’s call buttons were made solely from copper-based metals. Both traditional patient rooms and rooms with copper surfaces at each institution were cleaned using the same practices.

The proportion of patients who developed HAI and/or colonization with MRSA or VRE was significantly lower among patients in rooms with copper surfaces (7.1%) compared with patients in traditional rooms (12.3%). The proportion of patients developing HAI was significantly lower among those assigned to copper rooms (3.4%) compared with those in traditional rooms (8.1%).

“Patients who suffer HAIs often stay in the hospital longer, incur greater costs, and unfortunately suffer a greater likelihood of dying while hospitalized,” said Cassandra D. Salgado, MD, Associate Professor at the Medical University of South Carolina and lead author of the study. “Our study found that placement of items with copper surfaces into ICU rooms as an additional measure to routine infection control practices could reduce the risk of HAI as well as colonization with multidrug resistant microbes.”

Read more . . .

via Society for Healthcare Epidemiology of America
 

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An ICU Monitor That Fits On Your Wrist

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A new medical device wants to make patient vitals more portable and networked, but designing devices for the medical field is nothing like the consumer electronics sector.

Anyone who’s been unfortunate enough to spend time in an ICU knows: It’s a horribly confining experience. Even for patients who are physically capable of walking around, they’re often so tethered to tubes and devices that it’s impossible. Everyone becomes bedbound.

The ViSi Mobile Monitor, by Sotera Wireless, is a pretty exciting prospect in the medical space. About the size of a flip phone, the monitor straps to your wrist to allow patients to move about without unplugging their electronics. It gets measurements from sensors placed on your body, including blood pressure, heart rate, ECG, oxygen saturation, respiration rate, and skin temperature. And just as important, it sends these measurements via Wi-Fi to a nearby nurses station, allowing medical staff to follow an average of eight to 16 patients at once through a PC.

If none of that made sense at all, know this: The ViSi Monitor allows you to go to the bathroom without triggering an alarm that your heart has stopped.

On one hand, the ViSi Monitor has a lot of potential for disruption. It’s portable and networked–two words that aren’t so common in the medical world. On the other hand, it’s no sleek and sexy iPod touch. It’s a clunky little piece of hardware, with a 160×128 pixel screen and an interface that looks inspired by the medical field itself. I wondered, where is the white space? Where is the aluminum and glass? Where is the gorgeous typography? Where are the high-resolution images?

“These guys aren’t cheap, this is something that’s going to live on a person. It has to deal with all sorts of real-life situations no one wants to talk about,” explains Greg Martin, Ziba’s senior interaction designer, who designed the platform’s software. Immediately, I consider the difficulties Jawbone had crafting their Up, while simultaneously having flashbacks to the three people I know who’ve broken their iPhone 5 screens in the past month. It makes sense. But what about that, can I say, sort of ugly display?

“This project wasn’t about innovation, it was about very clear information design in a compacted space,” Martin says. “In the medical space, you’re not innovating for innovation’s sake, which you may be doing on a consumer product. You’re actually looking very carefully on how to maintain the status quo while enhancing the experience.”

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via FastCoDesign – Mark Wilson
 

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