RECSALMO: Rapid typing and characterization tool for whole genome sequencing data of Salmonella

Abstract

Salmonella is one of the most prevalent foodborne pathogens. Endemic events involving Salmonella now occur more frequently and must be handled efficiently and quickly. Whole genome sequencing (WGS) cost and speed have improved significantly during the past decades, with the number of bioinformatics tools based on WGS data also increasing. This research presented the “RECSALMO” tool, designed specifically to analyze Salmonella genome assemblies. This tool can quickly type and characterize a collection of Salmonella genomes, providing extensive information and assist related healthcare personnel to effectively and timely manage a Salmonella epidemic. The essential outputs of the tool include sequence-based typing comprising serotyping, MLST and cgMLST, antibiotic resistance genes with their associated classes/subclasses of antibiotic drugs, Salmonella pathogenicity islands (SPIs) from SPI-1 to SPI-17, and spacer profiles (CRISPR locus 1 and 2). Moreover, the tool generates SNP-based trees, CRISPR-based dendrograms and pie charts of serotypes and ST indexes. Due to the superior resolution, quick operational time, and low processing cost of WGS, RECSALMO is considered a practical bioinformatics tool for comprehensive and rapid examination of Salmonella genomes.