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Assemblies of E. coli Genome Yield Information Important for Dx Development, Tracing Outbreak


By Monica Heger

Since the initial
sequencing of the genome of Escherichia coli O104 by two teams at the University of Münster and BGI, a number of additional groups have stepped in to characterize the genome of the bacteria responsible for killing at least 35 people and sickening thousands in Europe.

The Münster and BGI teams independently sequenced the genome of the deadly bacteria two weeks ago. Both groups used the Life Technologies Ion Torrent PGM to sequence the genome in a matter of days (IS 6/7/2011).

Since then, researchers have continued to do additional sequencing on the Ion Torrent, Illumina, and 454 platforms, and have also done de novo assemblies of the genome in order to aid public health officials in identifying the origin of the strain and in developing diagnostics.

This week, OpGen said that it used its Argus Optical Mapping system to produce whole-genome optical maps of six of the isolates. It also used the maps to order and orient sequence contigs to produce a complete, whole-genome sequence of the pathogen.

Rich Moore, OpGen's vice president of diagnostic systems, told In Sequence in an e-mail that the company worked with the University of Münster team to do an assembly based on the Ion Torrent PGM sequence data. Additionally, the company also used publicly available data generated by BGI from both the PGM and the Illumina HiSeq.

Meantime, researchers at the Health Protection Agency in Colindale, UK, said this week that they have sequenced and assembled the E. coli strain using Roche's 454 GS Junior machine. The data is publicly available on the National Center for Biotechnology Information website and on the HPA's website.

Moore said that OpGen has also done an assembly from HPA's 454 reads.

Meanwhile, the BGI team has been using its SOAPdenovo tool to assemble reads, which it has been making publicly available on its website as well as on the NCBI site.

While the initial sequencing of the bacteria was completed in just three days, and enabled researchers to quickly identify that it was a new, hybrid strain of E. coli, the additional sequencing and assembly is helpful for pinpointing the location of specific genes.

For instance, according to OpGen, the optical mapping and technology shows which "virulence and toxin genes are on chromosomes and which are on plasmids — information which has implications for the development of diagnostic tests."

Patrick Tang, a medical microbiologist at the British Columbia Center for Disease Control, who was not affiliated with any of the sequencing efforts, said that assembly must be done in order to glean information about the regions in the genome researchers are interested in.

Each platform and technology has its advantages and disadvantages, he added, but all can do good job with enough time and money.

Have topics you'd like to see covered by In Sequence? Contact the editor at mheger [at] genomeweb [.] com.

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