A Simplified Guide to Whole-Genome Sequence Analysis of Salmonella on the Command Line

With the rapid development of sequencing technologies, whole-genome sequencing (WGS) is now easily accessible across various domains. Bacterial WGS has started to be routinely used in research and public health laboratories for clinical diagnostics, outbreak risk prediction, and pathogen characterization. WGS of foodborne pathogens allows for rapid, accurate identification and typing of pathogens, and detailed characterization of genomic features such as antimicrobial resistance genes, virulence genes, and plasmids. Salmonella, an important foodborne pathogen, is the leading cause of deaths associated with foodborne illness in the United States, with almost 420 deaths reported annually. Due to the affordability of short-read WGS and its higher discriminatory power, many public health laboratories and regulatory agencies have replaced traditional identification and typing techniques with WGS of Salmonella. However, there is a lack of easy-to-follow guides to analyze WGS datasets and generate reproducible results. This chapter provides detailed step-by-step commands for the analysis of the short-read WGS data of Salmonella, from quality control, trimming of unwanted sequences, genome assembly and annotation, to multi-locus sequence typing, serotyping, antimicrobial resistance gene identification, virulence gene identification, and phylogenetic tree construction, all using programs executed from the Unix shell command line. As such, this chapter serves as a user-friendly guide for WGS data analysis in Salmonella. Moreover, most of the bioinformatics programs described in this chapter can also be used to analyze WGS data of other Gram-positive and Gram-negative bacteria.