Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the...

Area of Science:

• Microbiology
• Genomics
• Epidemiology

Background:

• Salmonella enterica serovar Heidelberg is a significant public health concern in Canada and Quebec.
• Conventional subtyping methods like pulsed-field gel electrophoresis (PFGE) struggle to differentiate highly clonal Salmonella Heidelberg strains, limiting outbreak investigations.
• PFGE was insufficient to distinguish isolates from three distinct Salmonella Heidelberg outbreaks in Quebec.

Purpose of the Study:

• To evaluate whole-genome sequencing (WGS) and phylogenetic analysis as a superior alternative to conventional subtyping for Salmonella Heidelberg.
• To assess the utility of a high-quality core genome single-nucleotide variant (hqSNV) approach for resolving outbreaks.

Main Methods:

• Whole-genome sequencing (WGS) of 46 Salmonella Heidelberg isolates from three Quebec outbreaks (2012, 2013, 2014).
• Analysis using a high-quality core genome single-nucleotide variant (hqSNV) bioinformatics pipeline (SNVphyl).
• Comparison of WGS-based phylogenetic analysis with conventional PFGE subtyping.

Main Results:

• Phylogenetic analysis based on hqSNVs successfully separated the outbreak isolates into three distinct groups, aligning perfectly with epidemiological data.
• Conventional PFGE was unable to differentiate isolates, showing identical patterns (SHEXAI.0001/SHEBNI.0001) for all outbreaks.
• Minimal genetic variation (0-4 hqSNVs) was observed within outbreaks, while significant differences (>59 hqSNVs) distinguished previously indistinguishable outbreaks.

Conclusions:

• Whole-genome sequencing (WGS) combined with hqSNV phylogenetic analysis is a powerful and accurate method for subtyping Salmonella Heidelberg.
• This WGS-based approach overcomes the limitations of PFGE in resolving outbreaks caused by highly clonal bacterial strains.
• The SNVphyl pipeline provides a robust tool for public health laboratories to enhance surveillance and outbreak investigations for Salmonella Heidelberg.