The scripts presented in this repository are to be used to perform in silico serotyping of Salmonella enterica in accordance with MMS136. It takes as input a draft assembly and outputs a serotype inference. The draft assembly is obtained by performing a de novo assembly on FASTQ data found to have passed MMS103 and to be identified as Salmonella enterica by kmer ID and by a wet laboratory method.
- Serotype: A form of classification of bacteria below the species level. Usually involves some sort of reactive between specific sera and antigens on the bacteria's wall.
- Serovar: In this case, a synonym of serotype.
- Serogroup: A group of serovars with common antigens.
- WGS: whole-genome sequence data. Usually, DNA sequence data comprised of short reads (between 35 and 300 bp in length) coded in the FASTQ format.
sistr will only call serotypes that are valid under the WHO Collaborating Centre for Reference and Research on Salmonella table of antigenic formulas for Salmonella serovars, which can be found here. The table follows the Kauffmann-White-Le Minor scheme (which is the Kauffmann-White scheme, but for historical reasons the WHOCC-Salm added Le Minor's name to the scheme's name). According to the document, about 30 serovars are expected to account for about 90% of the Salmonella in a country. The scheme, as presented in the document, describes a total of 2,579 serovars of Salmonella, of which 2,557 are of the species S. enterica and 22 are of the species S. bongori (data on pg. 13).
The genus Salmonella is now known to have two species: S. enterica and S. bongori. The species S. enterica has six subspecies: enterica, salamae, arizonae, diarizonae, houtenae, and indica. By far the most commonly found in human cases of Salmonellosis is S. enterica subsp enterica.
Originally, the subspecies were believed to be subgenera named with roman numerals: I (now S. enterica subsp enterica), II (S. enterica subsp salamae), III (former genus Arizona: subdivided in to IIIa S. enterica subsp arizonae and IIIb S. enterica subsp diarizonae), IV (S. enterica subsp houtenae), V (S. bongori), and VI (S. enterica subsp indica).
In the case of serotypes of Salmonella enterica subsp. enterica the serotype is typically reported by a single name (e.g., Enteritidis, Typhi, Typhimurium). This is kept for historical reasons. Serotypes of all other subspecies of S. enterica and S. bongori are typically reported with the antigenic formula.
To perform Salmonella enterica serotyping we use the tool sistr [1] developed by Public Health Agency of Canada and held here. The tool has been extensively validated by others [2].
sistr uses a combination of approaches to infer serotype from draft assemblies of WGS data. For the purposes of MDU work, we have validated the use of the combination of antigen detection and cgMLST typing:
- It uses BLAST to identify the presence of annotated O- and H- antigen sequences. As such, it comes with curated multiFASTA files for the fliC, fliB, and wzx and wzy genes.
- It has a cgMLST scheme with 330 loci, and a database of 52 790 genomes (mostly comprising subspecies I) that have been typed at these loci and annotated with a serotype. It uses BLAST to genotype the input assembly across as many of the 330 loci, and then calculates the pairwise distance of the input isolate to the database of curated genomes.
At the moment salmonella_typing installation is limited to installation from this repository
pip3 install git+https://github.com/MDU-PHL/salmonella_typing
Dependencies
- You will also need to ensure that
sistr v1.1.1is installed, instructions for this can be found here csvtkinstallation instructions can be found here
stype run --help
usage: stype run [-h] [--contigs CONTIGS] [--prefix PREFIX] [--jobs JOBS]
optional arguments:
-h, --help show this help message and exit
--contigs CONTIGS, -c CONTIGS
Tab-delimited file with sample ID as column 1 and path to assemblies as column 2 OR path to a contig file (used if only doing a single sample - should provide value for -pfx). (default: )
--prefix PREFIX, -px PREFIX
If running on a single sample, please provide a prefix for output directory (default: abritamr)
--jobs JOBS, -j JOBS Number of AMR finder jobs to run in parallel. (default: 16)
Salmonella_typing can be on a single sample run by
stype -c <path_to_contigs> -px <name_of_sample>
Or in batch mode
stype -c input.tab -j 16
Where input.tab is a tab-delimited file with column 1 being sample ID and column 2 is path to the assemblies.
usage: stype mdu [-h] [--runid RUNID] [--sistr SISTR]
optional arguments:
-h, --help show this help message and exit
--runid RUNID, -r RUNID
MDU RunID (default: Run ID)
--sistr SISTR, -s SISTR
Path to concatentated output of sistr (default: sistr_concatenated.csv)
In order to generate a LIMS friendly spreadsheet, collate all stype results
csvtk concat sample_1/sistr_filtered.csv sample_2/sistr_filtered.csv ... > sistr_concatenated.csv
Then run stype in mdu mode
stype mdu -r RUNID -s sistr_concatenated.csv
| File | Contents |
|---|---|
sample_directory/sistr.csv |
raw output of sistr |
sample_directory/sistr_filtered.csv |
sistr output that has been filtered based on MDU business logic per sample |
sistr_filtered.csv |
sistr output that has been collated and filtered based on MDU business logic for batch |
<RUNID>_sistr.xlsx |
a spreadsheet ready for upload into MDU LIMS only output if mdu used |
[1] Yoshida, C. E., Kruczkiewicz, P., Laing, C. R., Lingohr, E. J., Gannon, V. P. J., Nash, J. H. E., & Taboada, E. N. (2016). The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PloS One, 11(1), e0147101.
[2] Yachison, C. A., Yoshida, C., Robertson, J., Nash, J. H. E., Kruczkiewicz, P., Taboada, E. N., … Nadon, C. (2017). The Validation and Implications of Using Whole Genome Sequencing as a Replacement for Traditional Serotyping for a National Salmonella Reference Laboratory. Frontiers in Microbiology, 8, 1044.