Salmonella enterica serovar Heidelberg is the second most frequently occurring serovar in Quebec and the third-most prevalent in Canada. Given that conventional pulsed-field gel electrophoresis (PFGE) subtyping for common Salmonella serovars, such as S. Heidelberg, yields identical subtypes for the majority of isolates recovered, public health laboratories are desperate for new subtyping tools to resolve highly clonal S. Heidelberg strains involved in outbreak events. As PFGE was unable to discriminate isolates from three epidemiologically distinct outbreaks in Quebec, this study was conducted to evaluate whole-genome sequencing (WGS) and phylogenetic analysis as an alternative to conventional subtyping tools. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013, and 2014) supported by strong epidemiological evidence were sequenced and analyzed using a highquality core genome single-nucleotide variant (hqSNV) bioinformatics approach (SNV phylogenomics [SNVphyl] pipeline). Outbreaks were indistinguishable by conventional PFGE subtyping, exhibiting the same PFGE pattern (SHEXAI.0001/ SHEBNI.0001). Phylogenetic analysis based on hqSNVs extracted from WGS separated the outbreak isolates into three distinct groups, 100% concordant with the epidemiological data. The minimum and maximum number of hqSNVs between isolates from the same outbreak was 0 and 4, respectively, while >59 hqSNVs were measured between 2 previously indistinguishable outbreaks having the same PFGE and phage type, thus corroborating their distinction as separate unrelated outbreaks. This study demonstrates that despite the previously reported high clonality of this serovar, the WGS-based hqSNV approach is a superior typing method, capable of resolving events that were previously indistinguishable using classic subtyping tools.
Nontyphoidal Salmonella enterica strains are important bacterial agents of salmonellosis in humans and animals (1) and represent up to 125,000 cases annually of foodborne gastroenteric disease arising from sporadic and outbreak events in Canada (2). More than 2,500 Salmonella enterica serovars have been described, but only a few have been associated with cases of human illness (3, 4). Salmonella Heidelberg ranks third and fourth among serovars causing human illness in Canada (5) and the United States (6), respectively, and is commonly detected in retail meat samples and food animals. While the majority of Salmonella infections are mild and self-limiting, S. Heidelberg can cause more severe diseases, including septicemia, myocarditis, extraintestinal infections, and death (7,8).Pulsed-field gel electrophoresis (PFGE) is the gold standard method used by Canadian public health laboratories for the molecular typing of S. Heidelberg, following standardized procedures set out by the PulseNet Canada guidelines. A well-recognized limitation of this classic typing method is that strains bearing highly common PFGE patterns occasionally render PFGE ineffective at detecting foodborne outbreaks from background sporadic cases, thus li...