Two-tool Serotyping with SISTR & SeqSero2
This two-tool serotyping method is available to some initiatives (e.g. PATH-SAFE)
Last updated
This two-tool serotyping method is available to some initiatives (e.g. PATH-SAFE)
Last updated
Serotyping is an important aspect of subtyping and classifying Salmonella genomes.
In practice, serotypes provide a useful label for a group of genomes and have historically been used to enable various epidemiological and microbial population analyses. In the age of whole genome sequencing, more sophisticated and accurate tools provide a higher resolution view of the dynamics of infectious disease, but serotyping still provides a critical link to organisation and places where WGS is not available or practical.
PATH-SAFE uses two serovar assignment tools, both of which use whole-genome sequence assemblies as input.
Example of results in Typing Table & Genome Report:
Validation testing showed that overall, SISTR provides more accurate results, and it can be generally assumed to be more likely to be correct when it conflicts with SeqSero2. However, where they conflict the result might need further cross-checking using an orthogonal approach (e.g. phenotyping or clustering with other genomes).
On the basis of these results, we have decided to include the output of both tools, giving the user confidence when they are in agreement, and the means to disambiguate conflicting results through the complementary tools provided by Pathogenwatch.
SISTR (Salmonella In Silico Typing Resource) produces serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST.
For PATH-SAFE, Pathogenwatch runs the docker image with and uses the cgmlst_subspecies and serovar fields from the JSON output.
Notes on the JSON output:
SISTR - The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada. PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
SeqSero2 takes the whole-genome sequence assemblies and performs rapid serotype prediction based on unique k-mers of serotype determinants.
Notes on interpretation:
The full validation report is available .
