Salmonella enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. This serovar ranks second and third among serovars that cause human infections in Québec and Canada, respectively, and has been associated with severe infections. Traditional typing methods such as PFGE do not display adequate discrimination required to resolve outbreak investigations due to the low level of genetic diversity of isolates belonging to this serovar. This study evaluates the ability of four whole genome sequence (WGS)-based typing methods to differentiate among 145 S. Heidelberg strains involved in four distinct outbreak events and sporadic cases of salmonellosis that occurred in Québec between 2007 and 2016. Isolates from all outbreaks were indistinguishable by PFGE. The core genome single nucleotide variant (SNV), core genome multilocus sequence typing (MLST) and whole genome MLST approaches were highly discriminatory and separated outbreak strains into four distinct phylogenetic clusters that were concordant with the epidemiological data. The clustered regularly interspaced short palindromic repeats (CRISPR) typing method was less discriminatory. However, CRISPR typing may be used as a secondary method to differentiate isolates of S. Heidelberg that are genetically similar but epidemiologically unrelated to outbreak events. WGS-based typing methods provide a highly discriminatory alternative to PFGE for the laboratory investigation of foodborne outbreaks.
Comparison of advanced whole genome sequence-based methods to distinguish strains of Salmonella enterica serovar Heidelberg involved in foodborne outbreaks in Québec.
C. Vincent,V. Usongo,Chrystal Berry,D. Tremblay,S. Moineau,K. Yousfi,F. Doualla-Bell,É. Fournier,C. Nadon,L. Goodridge,S. Bekal
Published 2018 in Food microbiology
ABSTRACT
PUBLICATION RECORD
- Publication year
2018
- Venue
Food microbiology
- Publication date
2018-08-01
- Fields of study
Biology, Medicine, Environmental Science
- Identifiers
- External record
- Source metadata
Semantic Scholar, PubMed
CITATION MAP
EXTRACTION MAP
CLAIMS
CONCEPTS
- core genome multilocus sequence typing
A genome typing method that compares allelic profiles across loci in the core genome.
Aliases: cgMLST, core genome MLST
- core genome single nucleotide variant typing
A genome typing method that compares isolates by single-nucleotide variants across the core genome.
Aliases: core genome SNV typing, SNV typing
- crispr typing
A typing method that compares clustered regularly interspaced short palindromic repeat loci among bacterial isolates.
Aliases: clustered regularly interspaced short palindromic repeats typing
- pulsed-field gel electrophoresis
A gel-based bacterial typing method used as the traditional comparison standard in outbreak investigation.
Aliases: PFGE
- salmonella enterica serovar heidelberg
A Salmonella enterica serovar analyzed here as the organism causing the outbreak and sporadic isolates.
Aliases: S. Heidelberg
- whole genome mlst
A multilocus sequence typing approach that uses loci distributed across the whole genome for isolate comparison.
Aliases: wgMLST
- whole genome sequence-based typing methods
Typing approaches that use whole-genome sequence data to compare bacterial isolates at high resolution.
Aliases: WGS-based typing methods, WGS-based approaches
REFERENCES
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