ACTIVITY 4. DEVELOPMENT AND APPLICATION OF WHOLE GENOME, SEQUENCE-BASED BACTERIAL STRAIN TYPING TOOLS FOR SALMONELLA, HARMONIZED WITH PULSENET INFRASTRUCTURE AND HUMAN SURVEILLANCE IN CANADA
Activity Leader: Sadjia Bekal, Institut National de Santé Publique du Québec, firstname.lastname@example.org, T. (514) 457-2070, ext.2336
Co-leader: Céline Nadon, Public Health Agency of Canada, email@example.com, T. (204) 784-7507
To demonstrate the innovative use of next generation sequencing and efficient algorithm in developing guidelines for strain typing relevant for human surveillance and outbreak investigations.
The lack of genetic discrimination among Salmonella strains, when analyzed by PFGE, is a major problem during outbreaks and sporadic case investigations. This usually leads to failure to promptly identify the source of exposure and to control outbreaks. Thus, tracing the source of Salmonella (and other foodborne pathogens) during foodborne outbreaks is a significant health concern of Canadians and requires more specialized genomic approaches capable of typing specific strains within Salmonella serovars.
The following sub-objectives will be instrumental to reach the main goal:
Obj. 4.1 Assessment of core/phage-based WGS methods for their genetic discriminatory power
We will interrogate the Salmonella whole genome sequences obtained from Objective 1 using four recognized and emerging methods, in order to determine the best approach to the use of WGS data for Salmonella typing purposes. Those methods are:
4.1.1 Core genome high quality single nucleotide polymorphism (hqSNP)
4.1.2 Whole/core genome multi-locus sequence typing (wgMLST)
4.1.3 Development and validation of a prophage sequence typing method (PST)
4.1.4 Clustered regularly interspaced short palindromic repeats (CRISPR)
Obj. 4.2 Validation of a Salmonella typing algorithm and development of interpretation guidelines
The current algorithm used by PulseNet laboratories is based on PFGE and include criteria for its interpretation (enzymes, mismatching bands, prevalence of the pattern etc.). Interpretation guidelines for hqSNP should include genome assembly criteria, phylogenetic analysis parameters and provide data on the number of SNPs allowing for inclusion or exclusion of a given strain from the outbreak.
Obj. 4.3 Genomic comparison in the context of source attribution
Source attribution for Salmonella strains remains a big challenge in public health due mainly to the lack of a discriminatory tool for source identification during outbreak and/or foodborne illness. The validated molecular tool will be used to compare human data available at PulseNet-Canada and LSPQ with whole genome sequence data from food and environmental isolates of Salmonella generated mainly in Activity 1.
1) Identification of hqSNP positions in Salmonella genomes that allow better isolate discrimination.
2) Identification of relevant genes sets for WgMLST analysis.
3) Cataloguing of prophages present in available Salmonella genomes.
4) Development and validation of PST.
5) Identification of spacers for CRISPR-based tool application for epidemiological investigations.
6) Elaboration of an algorithm and interpretation guidelines for real-time surveillance.
7) Generation of a clinical/food/environmental database in the context of source attribution.