Researchers from the University of California, San Diego, and the University of Cairo have fully decoded the Escherichia coli EDL933 genome — a representative of E. coli serotype O157: H7, which can cause food poisoning and has been implicated in cases that occurred at Jack-in-the-Box restaurants in the US in 1993 and a Japanese school in 1996. This particular strain was isolated ground beef that was linked to a 1982 outbreak in Michigan.
The E. coli EDL933 genome was first published in 2001, but UCSD's Ramy Aziz and his colleagues note that that genome has more than 6,000 ambiguous base calls and a 4,000 basepair gap.
In Genome Announcements, they report their gapless sequence of the strain, which they generated through a combination of PacBio and Illumina sequencing. They were able to eliminate those ambiguous base calls and close that gap, yielding a 5,547,323-basepair chromosome and a 92,076-basepair plasmid. In a statement, the researchers add that they were also able to identify jumping genes that move around the E. coli genome.
"With a complete genome sequence, we can now pinpoint the precise location of all such elements, which might help to track and treat future outbreaks," Aziz says in a statement.