Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

On Top of Outbreaks: Rapid Next Generation Sequencing for Diagnostics

16.08.2011
Combating the Superbug Klebsiella Oxa-48 Outbreak in a Dutch Hospital

Over 80 patients have become infected with a multiple antibiotic-resistant bacterium named Klebsiella pneumoniae Oxa-48 during an outbreak at Maasstad Hospital, Rotterdam, the Netherlands. The hospital has estimated that over 2000 people were at risk of infection. The Dutch National Institute for Public Health and the Environment (RIVM) was asked to assist the hospital in containing the outbreak.

Experts at RIVM teamed up with scientists of the Medical Faculty of the University Münster (Germany), and bioinformaticians from Life Technologies Corporation (United States of America) and the Wellcome Trust Sanger Institute (United Kingdom) to develop a highly specific, and rapid molecular screening test to detect and prevent further spread of the superbug.

Hajo Grundmann, epidemiologist at the RIVM, coordinated this joint task force. “It was essential to quickly bring together the right people and resources, so that we were able to respond to the potential spread of this multi-resistant bacterium among patients in Dutch hospitals. We are especially pleased about the role of rapid whole genome sequencing of the outbreak strain,” he explained.

Microbiologist Dag Harmsen from the Department of Periodontology at the University Münster led the team responsible for sequencing on an Ion Torrent Personal Genome Machine™. "When we first used the PGM™ during the German EHEC 2011 outbreak, this was just a proof of principle (PLoS ONE. 2011 6(7): e22751; PubMed; doi: 10.1371/journal.pone.0022751). However, this time the rapid bacterial whole genome sequencing will make a difference for the protection of patients’ health. The sequence data laid the ground for the development of a specific molecular test. That is a true first real-time ‘genomics for diagnostics’ application,” he said.

Bioinformaticans from Life Technologies used the data from a single Ion 316™ chip to assemble a draft genome of the K. pneumoniae Oxa-48 outbreak strain (isolate 1191100241), which is available to the public via NCBI. “Using our TaqMan® assay development pipeline, we were able to rapidly compare this genome to other publicly available Klebsiella genomes and identify 36 candidate signature sequences that could be used to develop an outbreak strain-specific multiplex PCR test,” said Craig Cummings from Life Technologies.

By comparing these candidate signature sequences against the publically available data for over two-hundred additional Klebsiella genomes from an ongoing worldwide population study, Thomas Connor and Nicholas Thomson from the Wellcome Trust Sanger Institute in Cambridge identified two regions that remain entirely specific for the Dutch hospital outbreak strain. PCR assays targeting these two unique sequences together with the antibiotic resistance genes were then evaluated and field-tested by Grundmann’s team at the RIVM to develop a multiplex molecular screening test. The protocol for this test and test kits have been made available to all Dutch hospitals.

“Overall, this is a good example of how rapid next generation sequencing can help controlling outbreaks and how joint forces from different countries and continents can achieve quick results to prevent further infections for the sake of the Dutch hospital patients,” commented Hajo Grundmann from the RIVM.

Contact:
Dr. Thomas Bauer
University Münster, Medical Faculty
Tel.: 0251 / 83-58937
E-mail: thbauer@uni-muenster.de
Resources available:
NCBI draft genome accession number: AFXH00000000
NCBI/SRA accession number: SRA043951.1

Dr. Christina Heimken | idw
Further information:
http://www.uni-muenster.de

More articles from Life Sciences:

nachricht First-of-its-kind chemical oscillator offers new level of molecular control
15.12.2017 | University of Texas at Austin

nachricht New technique could make captured carbon more valuable
15.12.2017 | DOE/Idaho National Laboratory

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: First-of-its-kind chemical oscillator offers new level of molecular control

DNA molecules that follow specific instructions could offer more precise molecular control of synthetic chemical systems, a discovery that opens the door for engineers to create molecular machines with new and complex behaviors.

Researchers have created chemical amplifiers and a chemical oscillator using a systematic method that has the potential to embed sophisticated circuit...

Im Focus: Long-lived storage of a photonic qubit for worldwide teleportation

MPQ scientists achieve long storage times for photonic quantum bits which break the lower bound for direct teleportation in a global quantum network.

Concerning the development of quantum memories for the realization of global quantum networks, scientists of the Quantum Dynamics Division led by Professor...

Im Focus: Electromagnetic water cloak eliminates drag and wake

Detailed calculations show water cloaks are feasible with today's technology

Researchers have developed a water cloaking concept based on electromagnetic forces that could eliminate an object's wake, greatly reducing its drag while...

Im Focus: Scientists channel graphene to understand filtration and ion transport into cells

Tiny pores at a cell's entryway act as miniature bouncers, letting in some electrically charged atoms--ions--but blocking others. Operating as exquisitely sensitive filters, these "ion channels" play a critical role in biological functions such as muscle contraction and the firing of brain cells.

To rapidly transport the right ions through the cell membrane, the tiny channels rely on a complex interplay between the ions and surrounding molecules,...

Im Focus: Towards data storage at the single molecule level

The miniaturization of the current technology of storage media is hindered by fundamental limits of quantum mechanics. A new approach consists in using so-called spin-crossover molecules as the smallest possible storage unit. Similar to normal hard drives, these special molecules can save information via their magnetic state. A research team from Kiel University has now managed to successfully place a new class of spin-crossover molecules onto a surface and to improve the molecule’s storage capacity. The storage density of conventional hard drives could therefore theoretically be increased by more than one hundred fold. The study has been published in the scientific journal Nano Letters.

Over the past few years, the building blocks of storage media have gotten ever smaller. But further miniaturization of the current technology is hindered by...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

See, understand and experience the work of the future

11.12.2017 | Event News

Innovative strategies to tackle parasitic worms

08.12.2017 | Event News

AKL’18: The opportunities and challenges of digitalization in the laser industry

07.12.2017 | Event News

 
Latest News

New technique could make captured carbon more valuable

15.12.2017 | Life Sciences

First-of-its-kind chemical oscillator offers new level of molecular control

15.12.2017 | Life Sciences

A chip for environmental and health monitoring

15.12.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>