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The utility of multiple molecular methods including whole genome sequencing as tools to differentiate Escherichia coli O157:H7 outbreaks
- Source :
- Eurosurveillance. 20
- Publication Year :
- 2015
- Publisher :
- European Centre for Disease Control and Prevention (ECDC), 2015.
-
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.
- Subjects :
- Canada
Virulence Factors
Epidemiology
Virulence
Minisatellite Repeats
Multiple Loci VNTR Analysis
Biology
Escherichia coli O157
Polymerase Chain Reaction
Genome
Disease Outbreaks
law.invention
Tandem repeat
law
Virology
Pulsed-field gel electrophoresis
Humans
Escherichia coli Infections
Phylogeny
Polymerase chain reaction
Whole genome sequencing
Genetics
Shiga-Toxigenic Escherichia coli
Public Health, Environmental and Occupational Health
Electrophoresis, Gel, Pulsed-Field
Molecular Typing
Multilocus sequence typing
Genome-Wide Association Study
Multilocus Sequence Typing
Subjects
Details
- ISSN :
- 15607917
- Volume :
- 20
- Database :
- OpenAIRE
- Journal :
- Eurosurveillance
- Accession number :
- edsair.doi.dedup.....9537e73b864e536eefbf8eac06587c39
- Full Text :
- https://doi.org/10.2807/1560-7917.es.2015.20.47.30073