Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variations in microbial strains. In recent years, molecular methods based on analysis of informative sets of SNPs have gained increased application in bacterial genotyping. The SNPT web platform and databases are designed to assist in analysis of SNP typing data of common bacterial pathogens.
The SNPT web application provides the following functionality:
- allows querying the isolate database according to specific criteria;
- allows defining custom sets of SNP positions from any loci used in the commonly accepted Multilocus Sequence Typing (MLST) schemes for querying the SNP-profile database (this functionality may be extended in the future to include other chromosomal loci);
- calculates the theoretical Simpson’s index of diversity (D-value) for the defined SNP set with respect to the existing MLST schemes;
- takes the input of isolates SNP profiles and finds matching or similar sequence types (STs) from MLST databases, genome sequences from GenBank, and isolates profiles from SNPT database;
- performs cluster analysis of SNP profiles and allelic profiles of matching STs (by using PHYLOViZ Online platform or PHYLOViZ desktop program);
- displays geographic distribution of isolates matching the defined SNP profiles on an interactive map;
- provides two-way interface with AMRmap platform that allows displaying the antibiotic susceptibility data (MIC distributions) of isolates according to their SNP types.
The SNPT species-specific databases contain the data on:
- isolate characteristics (e.g. source, geographical origin, date of isolation etc.) and SNP profiles;
- definitions of MLST alleles and allele sequences of MLST loci automatically retrieved from PubMLST and BIGSdb databases.
To speed up identification of genomes matching the defined SNP profiles, SNPT also extracts and stores in a local database the sequences of MLST loci from WGSs available in GenBank. The data are automatically retrieved and updated on a weekly basis.