Structural analysis of CRISPR interference (CRISPRi) system of Salmonella enterica species

The classification and molecular typing of pathogenic bacteria is an important issue in modern microbiology. The main objective of microbial typing is to evaluate the relationships between microbial isolates. These techniques play a major role to determine the origin and routes of infections, confirm or exclude outbreaks, assess the cross-over of health-related pathogens especially identify virulence, and finally to determine the effectiveness of control measures. Conventional methods have limitations which do not allow for the more appropriate and accurate typing of the bacterial population to understand genetics, evolution and molecular epidemiology. Since 2000, high-throughput and high-resolution molecular typing methods have been deeply integrated into epidemiological molecular studies, most of which are DNA-based and PCR-based methods. CRISPR regions analysis is used as a new and powerful method for molecular typing and genetic comparative analysis of bacterial strains. Prokaryotes develop in spite of a large number and variety of viruses. This is partly due to the development of mechanisms for inactivating or silencing the effect of exogenous DNA. Among them, Clustered Regular Short Palindromic Repeats (CRISPR) is unique in providing adaptive immunity to elements of high local similarity to the genome of previously infected agents. In this study, we analyzed the CRISPR loci of different genotypes of 81 Salmonella enterica with PCR. Two pairs of primers were used to target the regions of CRISPR I and CRISPR II which were specific to Salmonella enterica species were used. CRISPR is a single pair in Salmonella, each pair showing a similar rate of rotation, repetition sequence, and a default connection for a common Cas gene set. The spacer locus analysis of CRISPR loci was performed using the NCBI-Blast and CRISPRFinder databases. According to these analyzes, they show a wide variety of exogenous DNA that infects bacteria and is not specific pathogens of Salmonella enterica serovars. Different isolate serovars isolated from the same location in the Aegean region in 2013 and 2014 showed the same spacer gain. All these results demonstrate high, sensitive and dynamic spacers in the immune system, which aims to protect bacteria from phages, and show the alternative evolutionary roles of CRISPR. In this study, we aimed to explain the nature, history and epidemiological applications of CRISPR region analysis. Key words: Salmonella enterica, CRISPR, PCR, Molecular typing, Immune system