Comparison of advanced whole genome sequence-based methods to distinguish strains of Salmonella enterica serovar Heidelberg involved in foodborne outbreaks in Québec
Caroline Vincenta, b, 1, Valentine Usongoa, e, 1, Chrystal Berryc, Denise M. Tremblayd, Sylvain Moineaud,Khadidja Yousfia, Florence Doualla-Bella, Eric Fourniera, Céline Nadonc, Lawrence Goodridgee, Sadjia Bekala, b
a Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
b Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
c Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
d Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC, Canada
e Department of Food Science and Agricultural Chemistry, Food Safety and Quality Program, McGill University, 21, 211 Lakeshore Dr., Ste Anne de Bellevue, QC, H9X 3V9, Canada
1 Both sharing first authorship
Abstract
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.
DOI: 10.1016/j.fm.2018.01.004