Basic Info

A tool for identifying and locating Pathogenicity Islands in Salmonella

More Details

Pathogenicity islands are relatively large DNA segments within bacterial genomes, typically carrying genes closely related to bacterial pathogenicity. In Salmonella, these pathogenicity islands are named Salmonella Pathogenicity Islands (SPIs for short). SPIs play a crucial role in the pathogenic mechanism of Salmonella. They encode a variety of virulence factors, including secretion systems, effector proteins, and toxins, which work together to facilitate the colonization, replication, and dissemination of Salmonella within the host. Utilizing the SPI Finder tool to identify and locate SPIs can enhance our understanding of the pathogenic mechanism of Salmonella and provide valuable information for the diagnosis, treatment, and prevention of Salmonella infections.

What's New

SPIFinder is capable of accurately identifying Salmonella pathogenicity islands (SPIs) from the whole genome sequences or genome drafts of bacteria. It effectively classifies 20 types of SPIs (including SPI1 to SPI14, SESS-LEE, SGI1, SGI2, C63PI, CS54_island, and HPI) across various Salmonella serotypes.

Map of Salmonella pathogenicity islands found in Salmonella enterica genomes. The genomes are ordered by their restriction-modification system profiles. Each SPI is defined by a circle and colored according to the variant of the SPI. From the inner circle outward, the order of the SPIs is C63PI, CS54 island, SGI1, SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-7, SPI-8, SPI-9, SPI-10, SPI-11, SPI-12, genes of SPI-13, and genes of SPI-14.

Additional Information

Related links:

https://cge.cbs.dtu.dk/services/SPIFinder/

https://bitbucket.org/genomicepidemiology/spifinder_db/

Literature

Roer L, Hendriksen RS, Leekitcharoenphon P, et al. Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems?. mSystems. 2016;1(3):e00009-16. Published 2016 Jun 21. doi:10.1128/mSystems.00009-16

Li Lingzhi, Gu Dan, Jiao Xin'an, Pan Zhiming. Role of pathogenicity islands in Salmonella during persistent infection. Microbiology China. 2022, 49(10): 4327-4336. doi:10.13344/j.microbiol.china.220410