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Genome maps
 
S. dysenteriae Sd197
S. flexneri Sf301
S. boydii Sb227
S. sonnei Ss046

Comparison
 
General features
Linear alignment
Orthologs order
Metabolic pathway
Virulence factors
CGH results

Analysis tools
 
Text query
BLAST search
Shi-align service

Links
 
GenomeComp
VFDB database




About Shigella
Shigella is a group of Gram-negative, facultative intracellular pathogens. Recognised as the etiologic agents of bacillary dysentery or shigellosis in the 1890s, Shigella was adopted as a genus in the 1950s and subgrouped into four species: S. dysenteriae, S. flexneri, S. boydii and S. sonnei (also designated as serogroups A to D).

Shigella grows only in the intestinal tract of humans. It's transmitted by the fecal-oral route. Fliers, fingers, and food are the usual vehicles. But because Shigella cells survive for a long time in contaminated water or on fomites, they transmit it too. People who live in crowded conditions where cleanliness is difficult are particularly likely to contract shigellosis.
Children are far more likely than adults to get shigellosis. Those under 5 year old account for about half the reported cases, because they are too young to follow good hygiene habits and they are more susceptible to Shigella infection.
Many fecal-oral infections, including cholera and typhiod fever, have been nearly eradicated from industrialized countries, but not shigellosis. Shigellosis is difficult to eradicate partly because it is so infectious. A person must ingest thousands to millions of bacterial cells to contract typhoid fever or cholera, but only 200 cells are sufficient to cause shigellosis.
It is well-established that the virulence plasmid (VP) carries the primary virulence genes that enable the invasiveness of the bacteria in the colon and the rectum and the induction of apoptosis to resident macrophages and dentritic cells, leading to inflammatory infection.

For more detailed information about the pathogenesis, epidemiology, diagnosis and clinical aspects of Shigella, please refer the recent comprehensive reviews:
Jennison AV, Verma NK, 2004. Shigella flexneri infection: pathogenesis and vaccine development. FEMS Microbiol Rev.28(1):43-58.
Phalipon A, Sansonetti PJ, 2003. Shigellosis: innate mechanisms of inflammatory destruction of the intestinal epithelium, adaptive immune response, and vaccine development. Crit Rev Immunol. 23(5-6):371-401.
Fernandez MI, Sansonetti PJ, 2003. Shigella interaction with intestinal epithelial cells determines the innate immune response in shigellosis. Int J Med Microbiol. 293(1):55-67.
Sansonetti P, 2002. Host-pathogen interactions: the seduction of molecular cross talk. Gut. Suppl 3:III2-8.
Nhieu GT, Enninga J, Sansonetti P, Grompone G, 2005. Tyrosine kinase signaling and type III effectors orchestrating Shigella invasion. Curr Opin Microbiol. 8(1):16-20.


About ShiBASE
As shigellosis remains to be the top one diarrhoeal disease in China, the Chinese government has given strong support to the genome sequence project of Shigella. During the past five years, we determined the genomes of representative strains of all four Shigella species, and then completed the comparative genomic hybridization (CGH) of 43 different serotypes of Shigella strains by microarray.

So in order to better organize and present the large amount of data, we built the integrated database for comparative genomics of Shigella, named ShiBASE. It focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format.
ShiBASE devotes to provide the scientific community a workbench for the comparative genomics studies of Shigella, which is one of the most efficient ways to reveal the extremely diversity and dynamics features of Shigella genomes. The intra-species comparison of Shigella genomes are presented at several different levels in the database, including not only basic genome features, structure of genomes and orthologs ordering, but also metabolic pathways and virulence factors. Moreover, the CGH results on 43 different serotypes of Shigella strains were also integrated into ShiBASE. The newly developed online sequence comparison visualization service, Shi-align, offers an easy way for biologists to perform comparative analysis on their own data.


Related publications
Yang J., Chen L.H., Yu J., Sun L.L., Jin Q., 2006. ShiBASE: an integrated database for comparative genomics of Shigella. Nucleic Acids Res. 34, D398-D401.
Yang F., Yang J., Zhang X.B., Chen L.H., Jiang Y., Yan Y.L., Tang X.D., Wang J., Xiong Z.H., Dong J., Xue Y., Zhu Y.F., Xu X.Y., Sun L.L., Chen S.X., Nie H., Peng J.P., Xu J.G., Wang Y., Yuan Z.H., Wen Y.M., Yao Z.J., Shen Y., Qiang B.Q., Hou Y.D., Yu J., Jin Q., 2005. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 33, 6445-6458.
Jin Q., Yuan Z.H., Xu J.G., Wang Y., Shen Y., Lu W.C., Wang J.H., Liu H., Yang J., Yang F., Zhang X.B., Zhang J.Y., Yang G.W., Wu H.T., Qu D., Dong J., Sun L.L., Xue Y., Zhao A.L., Gao Y., Zhu J.P., Kan B., Ding K.Y., Chen S.X., Cheng H., Yao Z.J., He B., Chen R.S., Ma D.L., Qiang B.Q., Wen Y.M., Hou Y.D., Yu J., 2002. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30, 4432-4441.
Peng J.P., Zhang X.B., Yang J., Wang J., Yang E., Bin W., Wei C.D., Sun M.S., Jin Q., 2006. The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella. BMC Genomics 7, 218.
Nie H., Yang F., Zhang X.B., Yang J., Chen L.H., Wang J., Xiong Z.H., Peng J.P., Sun L.L., Dong J., Xue Y., Xu X.Y., Chen S.X., Yao Z.J., Shen Y., Jin Q., 2006. Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a. BMC Genomics 7, 173.
Jiang Y., Yang F., Zhang X.B., Yang J., Chen L.H., Yan Y.L., Nie H., Xiong Z.H., Wang J., Dong J., Xue Y., Xu X.Y., Zhu Y.F., Chen S.X., Jin Q., 2005. The complete sequence and analysis of the large virulence plasmid pSS of Shigella sonnei. Plasmid 54, 149-159.
Zhang J.Y., Liu H., Zhang X.B., Yang J., Yang F., Yang G.W., Shen Y., Hou Y.D., Jin Q., 2003. Complete DNA sequence and gene analysis of the virulence plasmid pCP301 of Shigella flexneri 2a. Sci. China C Life Sci. 46, 513-522.

Gao X., Zou T., Mu Z., Qin B., Yang J., Waltersperger S., Wang M., Cui S., Jin Q., 2013. Structural insights into VirB-DNA complexes reveal mechanism of transcriptional activation of virulence genes. Nucleic Acids Res. 41, 10529-10541.
Chang Z., Lu S., Chen L., Jin Q., Yang J., 2012. Causative species and serotypes of shigellosis in mainland China: systematic review and meta-analysis. PLoS One 7, e52515.
Fu H., Liu L.G., Zhang X.B., Zhu Y.F., Zhao L.N., Peng J.P., He H., Jin Q., 2012. Common changes in global gene expression induced by RNA polymerase inhibitors in Shigella flexneri. PLoS One 7, e33240.
Zhao L.N., Liu L.G., Leng W.C., Wei C.D., Jin Q., 2011. A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF. BMC Genomics 12, 528.
Peng J.P., Yang J., Jin Q., 2011. An integrated approach for finding overlooked genes in Shigella. PLoS One 6, e18509.
Peng J.P., Yang J., Jin Q., 2010. Research progress in Shigella in the postgenomic era. Sci. China Life Sci. 53, 1284-1290.
Fu H., Liu L.G., Peng J.P., Leng W.C., Yang J., Jin Q., 2010. Transcriptional profile of the Shigella flexneri response to an alkaloid: berberine. FEMS Microbiol. Lett. 303, 169-175.
Peng J.P., Yang J., Jin Q., 2009. The molecular evolutionary history of Shigella spp. and enteroinvasive Escherichia coli. Infect. Genet. Evol. 9, 147-152.
Wei C.D., Peng J.P., Xiong Z.H., Yang J., Wang J., Jin Q., 2008. Subproteomic tools to increase genome annotation complexity. Proteomics 8, 4209-4213.
Fu H., Leng W.C., Wang J., Zhang W.L., Peng J.P., Wang L.L., Jin Q., 2007. Transcriptional profile induced by furazolidone treatment of Shigella flexneri. Appl. Microbiol. Biotechnol. 77, 657-667.
Cheng F., Wang J., Peng J.P., Yang J., Fu H., Zhang X.B., Xue Y., Li W.J., Chu Y.L., Jin Q., 2007. Gene expression profiling of the pH response in Shigella flexneri 2a. FEMS Microbiol. Lett. 270, 12-20.
Yang J., Nie H., Chen L.H., Zhang X.B., Yang F., Xu X.Y., Zhu Y.F., Yu J., Jin Q., 2007. Revisiting the Molecular Evolutionary History of Shigella spp. J. Mol. Evol. 64, 71-79.
Wei C.D., Yang J., Zhu J.P., Zhang X.B., Leng W.C., Wang J., Xue Y., Sun L.L., Li W.J., Wang J., Jin Q., 2006. Comprehensive Proteomic Analysis of Shigella flexneri 2a Membrane Proteins. J. Proteome. Res. 5, 1860-1865.
Bin W., Liu M.Q., Peng J.P., Sun L.L., Xu X.Y., Zhang J.H., Jin Q., 2006. Construction, detection and microarray analysis on Shigella dysenteriae A1 IroN, ShuA single, double mutants. Sci.China C Life Sci. 49, 251-258.
Xiong Z.H., Tang X.D., Yang F., Zhang X.B., Yang J., Chen L.H., Nie H., Yan Y.L., Jiang Y., Wang J., Xue Y., Xu X.Y., Zhu Y.F., Dong J., An L.Z., Wang X.L., Jin Q., 2006. Comparison of the virulence plasmid genomes of two strains of Shigella which lost the ability to bind Congo red. Sci.China C Life Sci. 49, 141-148.
Wang J., Zhang X.B., Peng J.P., Yang E., Bin W., Yang J., Dong J., Sun L.L., Xu X.Y., Jin Q., 2006. Genomic compositions and phylogenetic analysis of Shigella boydii subgroup. Sci.China C Life Sci. 49, 46-52.
Yang E., Bin W., Peng J.P., Zhang X.B., Wang J., Yang J., Dong J., Chu Y.L., Zhang J.H., Jin Q., 2005. Comparative genomics and phylogenetic analysis of S. dysenteriae subgroup. Sci.China C Life Sci. 48, 406-413.
Liu M.Q., Liu H., Sun L.L., Dong J., Xue Y., Chen S.X., Jin Q., 2005. Construction, detection and microarray analysis on the Shigella flexneri 2a sitC mutant. Sci.China C Life Sci. 48, 228-240.
Liu H., Peng J.P., Yang J., Sun L.L., Chen S.X., Jin Q., 2004. Analysis of components of conserved "backbone sequences" among genomes of Shigella spp. strains. Chinese Sci. Bull. 49, 152-160.
Yang J., Wang J.H., Chen L.H.,Yu J., Dong J., Yao Z.J., Shen Y., Jin Q., Chen R.S., 2003. Identification and Characterization of Simple Sequence Repeats in the Genomes of Shigella Species. Gene 322, 85-92.
Yang J., Wang J.H., Yao Z.J., Jin Q., Shen Y., Chen R.S., 2003. GenomeComp: a visualization tool for microbial genome comparison. J. Microbiol. Meth.54, 423-426.
Zhang X.B., Liu H., Yang F., Yang J., Xue Y., Dong J., Sun L.L., Yang G.W., Zhu J.P., Chu Y.L., Jin Q., 2003. Comparative genome analysis of deleted genes in Shigella flexneri 2a strain 301. Chinese Sci. Bull. 48, 846-852.

Contact us

The ShiBASE was created by the State Key Laboratory for Moleclular Virology and Genetic Engineering, Institue of Pathogen Biology, CAMS. If you have any suggestions or comments to the database, please use the following address or e-mail:
Jian YANG
6 Rongjing Eastern Street, BDA
Beijing 100176
P.R.China
Tel: 86-10-67877735
Fax: 86-10-67877736
E-Mail: yangj#ipbcams.ac.cn

Acknowledgements
This project was supported by the State Key Basic Research Program and High Technology Project from the Ministry of Science and Technology of China.


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Copyright © 2005 State Key Laboratory for Molecular Virology and Genetic Engineering, Beijing, China