Involvement of CRISPR-Cas Systems in Salmonella Immune Response, Genome Editing, and Pathogen Typing in Diagnosis and Surveillance

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated cas genes (CRISPR-Cas) provide acquired immunity in prokaryotes and protect microbial cells against infection by foreign organisms. CRISPR regions are found in bacterial genomes including Salmonella which is one of the primary causes of bacterial foodborne illness worldwide. The CRISPR array is composed of a succession duplicate sequences (repeats) which are separated by similar sized variable sequences (spacers). This chapter will first focus on the CRISPR-Cas involved in Salmonella immune response. With the emergence of whole genome sequencing (WGS) in recent years, more Salmonella genome sequences are available, and various genomic tools for CRISPR arrays identification have been developed. Second, through the analysis of 115 Salmonella isolates with complete genome sequences, significant diversity of spacer profiles in CRISPR arrays. Finally, some applications of CRISPR-Cas systems in Salmonella are illustrated, which mainly includes genome editing, CRISPR closely relating to antimicrobial resistance (AMR), CRISPR typing and subtyping as improved laboratory diagnostic tools. In summary, this chapter provides a brief review of the CRISPR-Cas system in Salmonella, which enhances the current knowledge of Salmonella genomics, and hold promise for developing new diagnostics methods in improving laboratory diagnosis and surveillance endeavors in food safety.