CRISPR Typing of Clinical Strains of Salmonella spp. Isolated in Tehran, Iran
Abstract
Background: Salmonella is one of the most leading causes of food-born infection and death among infants and people with the poor immunity system. Because Salmonella spp. have diversity in the genome composition and pathogenicity, access to rapid identification and genotyping is necessary to control of salmonellosis. The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) typing is a genotyping method that checks these variable sequences in the bacterial genome in a specific species. This study aimed to differentiate Salmonella strains using CRISPR region.
Methods: Salmonella isolates, previously identified via standard microbiological and molecular tests, were subjected to the study. Bacterial DNA was extracted and PCR was done using specific primers. The different PCR products were sequenced and the repeats patterns were used to identify additional or degenerate repeat clusters in the CRISPR region. All different sequences were analyzed using CRISPRtionary tool for dendrogram generation using the binary file.
Results: Overall, 119 strains of various Salmonella serovars were used. The result showed unique CRISPR and diversity in spacer both in sequence and the number. Analysis of the extracted sequence and band patterns illustrated that, except for S. infantis, both S. enteritidis and S. typhimurium isolates were classified as a separate cluster.
Conclusion: CRISPR genotyping could provide serotype/spacers dictionary and it is performed at low cost and high speed in comparison to the other typing methods. Therefore, the assessment of CRISPR and spacer content can be considered as a powerful and practical discriminatory method for subtyping of Salmonella isolates.
2. Shariat N, Dudley EG (2014). CRISPRs: molecular signatures used for pathogen subtyping. Appl Environ Microbiol,80(2):430-9.
3. Farshad S, Ranjbar R, Hosseini M (2015). Molecular genotyping of Shigella sonnei strains isolated from children with bloody diarrhea using pulsed field gel electrophoresis on the total genome and PCR-RFLP of IpaH and IpaBCD genes. Jundishapur J Microbiol,8(1) ): e14004.
4. Ranjbar R, Dallal MMS, Talebi M, Pourshafie MR (2008). Increased isolation and characterization of Shigella sonnei obtained from hospitalized children in Tehran, Iran. J Health Popul Nutr.,26(4):426-30.
5. Ranjbar R, Aleo A, Giammanco GM, Dionisi AM, Sadeghifard N, Mammina C (2007). Genetic relatedness among isolates of Shigella sonnei carrying class 2 integrons in Tehran, Iran, 2002–2003. BMC Infect Dis,7(1):62.
6. Sabat A, Budimir A, Nashev D, et al (2013). Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro surveillance : bulletin Europeen sur les maladies transmissibles. Euro Surveill, 18(4):20380.
7. Barrangou R (2013). CRISPR‐Cas systems and RNA‐guided interference. Wiley Interdiscip Rev RNA, 4(3):267-78.
8. Karimi Z, Ahmadi A, Najafi A, Ranjbar R (2018). Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies. Open Microbiol J,12:59-70.
9. Grissa I, Vergnaud G, Pourcel C (2007). The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinform,8(1):172.
10. Ranjbar R, Mortazavi SM, Tavana AM, Sarshar M, Najafi A, Zanjani RS (2017). Simultaneous molecular detection of Salmonella enterica serovars Typhi, enteritidis, infantis, and Typhimurium. Iran J Public Health, 46(1):103-111.
11. Bachmann NL, Petty NK, Zakour NLB, Szubert JM, Savill J, Beatson SA (2014). Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow. BMC Genom,15(1):389.
12. Fabre L, Le Hello S, Roux C, Issenhuth-Jeanjean S, Weill FX (2014). CRISPR is an optimal target for the design of specific PCR assays for salmonella enterica serotypes Typhi and Paratyphi A. PLoS Negl Trop Dis,8(1):e2671.
13. Li H, Li P, Xie J, et al (2014). New clustered regularly interspaced short palindromic repeat locus spacer pair typing method based on the newly incorporated spacer for Salmonella enterica. J Clin Microbiol,52(8):2955-62.
| Files | ||
| Issue | Vol 52 No 8 (2023) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijph.v52i8.13415 | |
| Keywords | ||
| Salmonella spp. Genotyping CRISPR-Cas Systems | ||
| Rights and permissions | |
|
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
