title: Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak.
abstract: In 2009, an outbreak of enterohemorrhagic Escherichia coli (EHEC) on an open farm infected 93 persons, and approximately 22% of these individuals developed hemolytic-uremic syndrome (HUS). Genome sequencing was used to investigate outbreak-derived animal and human EHEC isolates. Phylogeny based on the whole-genome sequence was used to place outbreak isolates in the context of the overall E. coli species and the O157:H7 sequence type 11 (ST11) subgroup. Four informative single nucleotide polymorphisms (SNPs) were identified and used to design an assay to type 122 other outbreak isolates. The SNP phylogeny demonstrated that the outbreak strain was from a lineage distinct from previously reported O157:H7 ST11 EHEC and was not a member of the hypervirulent clade 8. The strain harbored determinants for two Stx2 verotoxins and other putative virulence factors. When linked to the epidemiological information, the sequence data indicate that gross contamination of a single outbreak strain occurred across the farm prior to the first clinical report of HUS. The most likely explanation for these results is that a single successful strain of EHEC spread from a single introduction through the farm by clonal expansion and that contamination of the environment (including the possible colonization of several animals) led ultimately to human cases.
authors.affiliation: Health Protection Agency, London, United Kingdom. anthony.underwood@hpa.org.uk
authors.forename: Anthony P
authors.initials: AP
authors.lastname: Underwood
authors.forename: Tim
authors.initials: T
authors.lastname: Dallman
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
authors.forename: Michaela
authors.initials: M
authors.lastname: Williams
authors.forename: Katy
authors.initials: K
authors.lastname: Harker
authors.forename: Neil
authors.initials: N
authors.lastname: Perry
authors.forename: Bob
authors.initials: B
authors.lastname: Adak
authors.forename: Geraldine
authors.initials: G
authors.lastname: Willshaw
authors.forename: Tom
authors.initials: T
authors.lastname: Cheasty
authors.forename: Jonathan
authors.initials: J
authors.lastname: Green
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: John
authors.initials: J
authors.lastname: Wain
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques / Q000379:methods*; D016000:Cluster Analysis; D004196:Disease Outbreaks; D054324:Enterohemorrhagic Escherichia coli / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D004927:Escherichia coli Infections / Q000453:epidemiology* / Q000382:microbiology*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D011635:Public Health Administration / Q000379:methods