Genomic analysis of the correlation between CRISPR self-targeting spacers and prophage-related pathogenicity in Vibrio cholerae and Staphylococcus aureus

Abstract

The interactions between bacteria and phages are intricate and dynamic, manifesting through two main life cycles: the lytic cycle, in which phages destroy their hosts via cell lysis, and the lysogenic cycle, where phage DNA integrates into the bacterial genome, allowing for stable coexistence without immediate harm to the host. This interaction is often described as a competitive struggle, where bacteria evolve various defense strategies to evade phage attacks. In response, phages have developed strategies to bypass these defenses, securing their survival and replication. This investigation employed an in-silico approach to examine the pathogenicity of bacteria in relation to the CRISPR-Cas system and self-targeting spacers. For the analysis, two bacterial species were chosen: Vibrio cholerae, comprising 1794 strains, and Staphylococcus aureus, consisting of 16286 strains. Both strains demonstrated significantly distinct results across almost all parameters. The average pathogenic gene count with CRISPR and pathogenic gene count with STS demonstrated a notable decrease in V. cholerae strains. In contrast, S. aureus displayed a minor reduction in average pathogenic gene count with CRISPR (1.55), while revealing a significantly elevated average count in the presence of STS (2.50). A significant decrease in the pathogenic gene count of V. cholerae was recorded with CRISPR (from 1.12 to 0.13) and with STS (to 0.024), suggesting that the active CRISPR-Cas system may effectively target and interfere with the expression of genes linked to pathogenicity. Self-targeting spacers (STS) indicate a potential disruption of essential or pathogenicity-related genes, leading to a notable decrease in the count of pathogenic genes, which may be linked to auto-immunity or self-destruction mechanisms. In S. aureus, the CRISPR-Cas system appears to demonstrate a less pronounced suppression of pathogenic gene expression when contrasted with V. cholerae, as evidenced by a reduced count with CRISPR, suggesting a minimal regulatory influence on virulence factors. The significant increase in pathogenic gene count in S. aureus with STS indicates that STS could promote horizontal gene transfer or activate pathogenicity islands, leading to heightened virulence. This may occur if STS disrupts regulatory elements that govern the integration of virulence genes or if the bacteria compensate for STS by acquiring additional virulence factors. In addition, the S. aureus bacteria might employ some unknown mechanism to co-exist with STS-containing systems, increasing the overall pathogenic gene count of this bacteria.