title: The utility of multiple molecular methods including whole genome sequencing as tools to differentiate Escherichia coli O157:H7 outbreaks.
abstract: A standardised method for determining Escherichia coli O157:H7 strain relatedness using whole genome sequencing or virulence gene profiling is not yet established. We sought to assess the capacity of either high-throughput polymerase chain reaction (PCR) of 49 virulence genes, core-genome single nt variants (SNVs) or k-mer clustering to discriminate between outbreak-associated and sporadic E. coli O157:H7 isolates. Three outbreaks and multiple sporadic isolates from the province of Alberta, Canada were included in the study. Two of the outbreaks occurred concurrently in 2014 and one occurred in 2012. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA) were employed as comparator typing methods. The virulence gene profiles of isolates from the 2012 and 2014 Alberta outbreak events and contemporary sporadic isolates were mostly identical; therefore the set of virulence genes chosen in this study were not discriminatory enough to distinguish between outbreak clusters. Concordant with PFGE and MLVA results, core genome SNV and k-mer phylogenies clustered isolates from the 2012 and 2014 outbreaks as distinct events. k-mer phylogenies demonstrated increased discriminatory power compared with core SNV phylogenies. Prior to the widespread implementation of whole genome sequencing for routine public health use, issues surrounding cost, technical expertise, software standardisation, and data sharing/comparisons must be addressed.
authors.affiliation: Alberta Provincial Laboratory for Public Health, Alberta, Canada.
authors.forename: Byron M
authors.initials: BM
authors.lastname: Berenger
authors.forename: Chrystal
authors.initials: C
authors.lastname: Berry
authors.forename: Trevor
authors.initials: T
authors.lastname: Peterson
authors.forename: Patrick
authors.initials: P
authors.lastname: Fach
authors.forename: Sabine
authors.initials: S
authors.lastname: Delannoy
authors.forename: Vincent
authors.initials: V
authors.lastname: Li
authors.forename: Lorelee
authors.initials: L
authors.lastname: Tschetter
authors.forename: Celine
authors.initials: C
authors.lastname: Nadon
authors.forename: Lance
authors.initials: L
authors.lastname: Honish
authors.forename: Marie
authors.initials: M
authors.lastname: Louie
authors.forename: Linda
authors.initials: L
authors.lastname: Chui
mesh_terms: D002170:Canada / Q000453:epidemiology; D004196:Disease Outbreaks; D016521:Electrophoresis, Gel, Pulsed-Field; D004927:Escherichia coli Infections / Q000175:diagnosis / Q000453:epidemiology*; D019453:Escherichia coli O157 / Q000235:genetics* / Q000302:isolation & purification; D055106:Genome-Wide Association Study; D006801:Humans; D018598:Minisatellite Repeats; D058889:Molecular Typing; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D054323:Shiga-Toxigenic Escherichia coli; D037521:Virulence Factors / Q000235:genetics*
chemical_list: D037521:Virulence Factors
keywords: Escherichia coli O157:H7; Shiga toxin-producing Escherichia coli; haemolytic uremic syndrome; laboratory surveillance; outbreaks; whole genome sequencing, pulsed-field gel electrophoresis, multiple-locus variable number tandem repeat analysis