Analysis of Prophage Load and cas Genes in the Genomes of Salmonella enterica Serovars Enteritidis, Typhimurium, and Infantis

Salmonella enterica is a Gram-negative, facultatively anaerobic bacterium that causes intestinal infections in humans and animals. The species S. enterica includes over 2,600 serovars, among which Typhimurium, Enteritidis, and Infantis are widely distributed in the Russian Federation and often exhibit multidrug resistance to antibiotics. One promising approach to combatting such pathogens is targeted therapy using lytic phages. However, the genomic mechanisms underlying phage-bacterium interactions remain insufficiently understood. Like most bacteria, Salmonella genomes harbor prophages. Investigating prophage abundance in S. enterica genomes may be crucial for developing targeted phage therapy against this pathogen. This study conducted a bioinformatic analysis of prophage content in the genomes of three S. enterica subsp. enterica serovars: Enteritidis (n=50), Infantis (n=50), and Typhimurium (n=50) using the DBSCAN-SWA algorithm. A total of 805 prophage sequences were identified, including 274 in Enteritidis, 212 in Infantis, and 319 in Typhimurium. These sequences were classified into genera including Salmonella, Escherichia, Enterobacter, Cronobacter, Shigella, Klebsiella, and Moraxella. Additionally, cas genes associated with class 1, subtype I-E CRISPR-Cas systems were detected in all analyzed genomes. The strains were divided into two groups: 23 strains with mutations in cas genes and 127 strains without mutations. It was found that Typhimurium genomes contain more prophages compared to the other serovars. Furthermore, strains with mutations in cas genes exhibited higher prophage abundance, highlighting the role of CRISPR-Cas systems in regulating prophage dynamics and bacterial population adaptation. These findings may contribute to the development of more effective phage therapy strategies.