Abstract
Whole-genome sequencing (WGS) is the method of choice for bacterial subtyping and it is rapidly replacing the more traditional methods such as pulsed-field gel electrophoresis (PFGE). Here we used the high-resolution core genome single nucleotide variant (cgSNV) typing method to characterize clinical and food from Salmonella enterica serovar Heidelberg isolates in the context of source attribution. Additionally, clustered regularly interspaced short palindromic repeats (CRISPR) analysis was included to further support this method. Our results revealed that cgSNV was highly discriminatory and separated the outbreak isolates into distinct clusters (0–4 SNVs). CRISPR analysis was also able to distinguish outbreak strains from epidemiologically unrelated isolates. Specifically, our data clearly demonstrated the strength of these two methods to determine the probable source(s) of a 2012 epidemiologically characterized outbreak of S. Heidelberg. Using molecular cut-off of 0–10 SNVs, the cgSNV analysis of 246 clinical and food isolates of S. Heidelberg collected in Québec, in the same year of the outbreak event, revealed that retail and abattoir chicken isolates likely represent an important source of human infection to S. Heidelberg. Interestingly, the isolates genetically related by cgSNV also harbored the same CRISPR as outbreak isolates and clusters. This indicates that CRISPR profiles can be useful as a complementary approach to determine source attribution in foodborne outbreaks. Use of the genomic analysis also allowed to identify a large number of cases that were missed by PFGE, indicating that most outbreaks are probably underestimated. Although epidemiological information must still support WGS-based results, cgSNV method is a highly discriminatory method for the resolution of outbreak events and the attribution of these events to their respective sources. CRISPR typing can serve as a complimentary tool to this analysis during source tracking.
Highlights
Non-typhoidal Salmonella (NTS) enterica serovars are the most important causes of bacterial gastroenteritis (Acheson and Hohmann, 2001; Rabsch et al, 2001)
The genetic distance interpretation was based on the Public Health Agency of Canada (PHAC)/PulseNet Canada guidelines used to interpret the relatedness of the outbreak isolates (0–10 SNVs)
Our analysis revealed two non-documented cases (NDC) [ID119099 (ST81) and ID119764 (ST89)], differentiated from CL1 based on clustered regularly interspaced short palindromic repeats (CRISPR) profile, exhibiting CP9 which lost 12 spacers in the CRISPR2 locus compared to CRISPR profile 1 (CP1)
Summary
Non-typhoidal Salmonella (NTS) enterica serovars are the most important causes of bacterial gastroenteritis (Acheson and Hohmann, 2001; Rabsch et al, 2001). Heidelberg typing owing to the extremely low genetic diversity of this serovar (Bekal et al, 2016; Vincent et al, 2018) This lack of adequate discriminatory power makes it difficult to track the source of a specific clone of S. Whole genome sequence (WGS) based methods, owing to their growing availability and high genomic resolution, are rapidly replacing traditional typing methods such as PFGE within major public health laboratories including PulseNet Canada (PNC) (Nadon et al, 2017). WGS-based methods include the high resolution core genome single nucleotide variant analysis typing method (cgSNV) The utility of this typing method in surveillance and outbreak detection has been already demonstrated in several Salmonella serovars in Canada, United States, and Australia (Hoffmann et al, 2014; Fu et al, 2017; Nadon et al, 2017). Variation in spacer content has been exploited for bacterial subtyping and epidemiological investigations in major Salmonella serovars (Shariat and Dudley, 2014)
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