Two isolates from E. coli outbreak available

Jun 11, 2011

An outbreak of Escherichia coli causing a severe illness called hemolytic-uremic syndrome (HUS) began in Germany on May 2, 2011 and has killed more than 20 people and sickened more than 2,000. The organism causing the outbreak has been identified as a strain of E. coli O104:H4 that produces a Shiga toxin and causes an illness similar to infection with E. coli O157:H7. Two isolates from this outbreak have been sequenced. Both strains, TY-2482 and LB226692, have been annotated and are now available from Virginia Bioinformatics Institute's (VBI's) Pathosystems Resource Integration Center (PATRIC, patricbrc.org), which is funded by the National Institute of Allergy and Infectious Diseases.

In the rush to save lives, many laboratories are analyzing these genomes and providing data to the research community. Bruno Sobral, PATRIC's principal investigator, commented, "The PATRIC team is working around the clock to help the scientific community address this emergency. Analyses such as these provide insights into the origin of highly pathogenic strains and potential response strategies."

The two genomes have been annotated with Rapid Annotation using Subsystem Technology (RAST), making them consistent with the 184 E. coli genomes and the total 2,865 bacterial genomes available at PATRIC. The proteins conserved across all E. coli have been used to generate a preliminary that is based on 166640 characters across 527 genes in 354 taxa. This tree shows that the two new strains are most closely related to the pathogenic, enteroaggregative strain 559899, which may give additional insight into its origin. The tree is available in interactive form on the PATRIC website (http://patricbrc.org/portal/portal/patric/Phylogeny?cType=taxon&cId=561). For a comparison of the RAST annotations with the other publicized annotations, visit http://theseed.org/ecoli/.

As can be seen in the PATRIC Protein Family Sorter (http://patricbrc.org/portal/portal/patric/FIGfamSorterB?cType=taxon&cId=561&dm=result), the proteins from these two new pathogenic strains have several unique islands as compared to other E. coli genomes. Further investigation of these islands and unique proteins may yield clues as to virulence or intervention strategies for the new strains. The "heatmap" tab of the Protein Family Sorter presents a graphical view presence and absence of the proteins across the E. coli genomes.

Much of the information in PATRIC is updated on an ongoing basis including:

PATRIC is performing additional analyses, including collecting a list of the important genes identified, and will be providing gene trees and multiple sequence alignments of the genes with their closest homologs. Updates will be posted at http://enews.patricbrc.org/

Explore further: First step towards global attack on potato blight

Related Stories

Disease-causing Escherichia coli: 'I will survive'

Sep 09, 2009

Strains of Escherichia coli bacteria that cause food poisoning have been shown to have marked differences in the numbers of genes they carry compared to laboratory strains of E. coli. Some of these genes may enable them t ...

New Vaccines May Help Thwart E. coli O157:H7

Dec 18, 2009

(PhysOrg.com) -- Immunizing calves with either of two forms of a vaccine newly developed by Agricultural Research Service (ARS) scientists might reduce the spread of sometimes deadly Escherichia coli O157:H7 ...

Recommended for you

First step towards global attack on potato blight

1 hour ago

European researchers and companies concerned with the potato disease phytophthora will work more closely with parties in other parts of the world. The first move was made during the biennial meeting of the ...

Bacteria study could have agricultural impact

3 hours ago

Wichita State University microbiology professor Mark Schneegurt and ornithology professor Chris Rogers have discovered that one of North America's most common migratory birds – the Dark-eyed Junco – carries ...

Sex chromosomes—why the Y genes matter

14 hours ago

Several genes have been lost from the Y chromosome in humans and other mammals, according to research published in the open access journal Genome Biology. The study shows that essential Y genes are rescue ...

Better mouse model enables colon cancer research

May 27, 2015

Every day, it seems, someone in some lab is "curing cancer." Well, it's easy to kill cancer cells in a lab, but in a human, it's a lot more complicated, which is why nearly all cancer drugs fail clinical ...

How to get high-quality RNA from chemically complex plants

May 26, 2015

Ask any molecular plant biologist about RNA extractions and you might just open up the floodgates to the woes of troubleshooting. RNA extraction is a notoriously tricky and sensitive lab procedure. New protocols out of the ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.