Featured Research

from universities, journals, and other organizations

Metagenomics used to identify organisms in outbreaks of serious infectious disease

Date:
April 10, 2013
Source:
University of Warwick
Summary:
Researchers have been able to reconstruct the genome sequence of an outbreak strain of Shiga-toxigenic Escherichia coli (STEC), which caused over 50 deaths in Germany, using an approach known as metagenomics which bypasses the need for growing bacteria in the lab.

Researchers have been able to reconstruct the genome sequence of an outbreak strain of Shiga-toxigenic Escherichia coli (STEC), which caused over 50 deaths in Germany, using an approach known as metagenomics which bypasses the need for growing bacteria in the lab.

An international team coordinated by Mark Pallen, Professor of Microbial Genomics at Warwick Medical School, was able to reconstruct the genome sequence through the direct sequencing of DNA extracted from microbiologically complex samples. The study, published in a genomics-themed issue of JAMA on 10 April, highlights the potential of this approach to identify and characterise bacterial pathogens directly from clinical specimens.

Metagenomics has been used previously in a clinical diagnostic setting to identify the cause of outbreaks of viral infection, but this is its first reported use in an outbreak of bacterial infection.

Professor Pallen explained the significance of the STEC outbreak, “The outbreak of Shiga-toxigenic Escherichia coli illustrated the effects of a bacterial epidemic on a wealthy, modern, industrialized society, with more than 3,000 cases and more than 50 deaths reported in Germany between May and June of 2011.”

He added, “During an outbreak such as this, rapid and accurate pathogen identification and characterisation is essential for the management of individual cases and the outbreak as a whole. Traditionally, clinical bacteriology has relied primarily on laboratory isolation of bacteria in pure culture to identify and characterise an outbreak strain. Often, however laboratory culture proves slow, difficult, or even impossible and recognition of an outbreak strain can be difficult if it belongs to an unknown variety or species for which specific laboratory tests and diagnostic criteria don’t already exist.”

Professor Pallen led the team, which included two other recently appointed Warwick microbiologists, Chrystala Constantinidou and Jacqueline Chan, together with scientists from the University of Birmingham, the University of Glasgow, the University Medical Centre Hamburg-Eppendorf in Germany and the sequencing company Illumina, to develop and exploit novel sequencing and analytic approaches.

In this retrospective investigation, 45 samples were selected from faecal specimens obtained from patients in Germany with diarrhoea during the 2011 STEC outbreak. Samples were sequenced in summer 2012, followed by a 3-phase analysis in late 2012-early 2013.

In phase 1, a draft genome of the outbreak strain was constructed, using data obtained the HiSeq 2500 instrument in rapid-run mode. In an innovative new approach devised by Nick Loman (Birmingham) and Chris Quince (Glasgow), outbreak-specific sequences were identified by subtracting sequences from the outbreak metagenome that were present in faecal samples from healthy individuals.

In phase 2, the depth of coverage of the outbreak strain genome was determined in each sample. 10 samples gave greater than 10-fold coverage and 26 samples yielded greater than 1-fold coverage. Sequences from the Shiga-toxin genes were detected in two-thirds of the STEC-positive samples. In phase 3, sequences from each sample were compared with sequences from known bacteria to identify potential pathogens other than the outbreak strain, including Clostridium difficile, Campylobacter jejuni, Campylobacter concisus, and Salmonella enterica.

Professor Pallen summarises what this means for the identification of future outbreaks, “There are numerous drawbacks to the use of nineteenth-century approaches such as microscopy and culture when it comes to classification. Our results illustrate the potential of metagenomics as an open-ended, culture-independent approach for the identification and characterization of bacterial pathogens during an outbreak.

“There are challenges, of course, including speeding up and simplifying workflows, reducing costs and improving diagnostic sensitivity. However, given the dizzying pace of progress in high-throughput sequencing, these are not likely to remain problems for very long.”


Story Source:

The above story is based on materials provided by University of Warwick. Note: Materials may be edited for content and length.


Journal Reference:

  1. Nicholas J. Loman et al. A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4Outbreak of Shiga-toxigenic Escherichia coli. JAMA, 2013; 309 (14): 1502 DOI: 10.1001/jama.2013.3231

Cite This Page:

University of Warwick. "Metagenomics used to identify organisms in outbreaks of serious infectious disease." ScienceDaily. ScienceDaily, 10 April 2013. <www.sciencedaily.com/releases/2013/04/130410094137.htm>.
University of Warwick. (2013, April 10). Metagenomics used to identify organisms in outbreaks of serious infectious disease. ScienceDaily. Retrieved August 22, 2014 from www.sciencedaily.com/releases/2013/04/130410094137.htm
University of Warwick. "Metagenomics used to identify organisms in outbreaks of serious infectious disease." ScienceDaily. www.sciencedaily.com/releases/2013/04/130410094137.htm (accessed August 22, 2014).

Share This




More Health & Medicine News

Friday, August 22, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Drug Used To Treat 'Ebola's Cousin' Shows Promise

Drug Used To Treat 'Ebola's Cousin' Shows Promise

Newsy (Aug. 21, 2014) An experimental drug used to treat Marburg virus in rhesus monkeys could give new insight into a similar treatment for Ebola. Video provided by Newsy
Powered by NewsLook.com
Two US Ebola Patients Leave Hospital Free of the Disease

Two US Ebola Patients Leave Hospital Free of the Disease

AFP (Aug. 21, 2014) Two American missionaries who were sickened with Ebola while working in Liberia and were treated with an experimental drug are doing better and have left the hospital, doctors say on August 21, 2014. Duration: 01:05 Video provided by AFP
Powered by NewsLook.com
Cadavers, a Teen, and a Medical School Dream

Cadavers, a Teen, and a Medical School Dream

AP (Aug. 21, 2014) Contains graphic content. He's only 17. But Johntrell Bowles has wanted to be a doctor from a young age, despite the odds against him. He was recently the youngest participant in a cadaver program at the Indiana University NW medical school. (Aug. 21) Video provided by AP
Powered by NewsLook.com
American Ebola Patients Released: What Cured Them?

American Ebola Patients Released: What Cured Them?

Newsy (Aug. 21, 2014) It's unclear whether the American Ebola patients' recoveries can be attributed to an experimental drug or early detection and good medical care. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins