Shigella sonnei

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When Shigella was first discovered by a Japanese microbiologist, Kiyoshi Shiga in 1896, it was initially called Bacillus dysenteries. The name described the production of toxic factors by the organism (2).


Kingdom: Bacteria Phylum: Proteobacteria Class: Gamma proteobacteria Order: Enterobacteriales Family: Enterobacteriaceae Genus: Shigella Species:Shigella sonnei (17)

There are 4 species of Shigella classified on the basis of biochemical serological differences. Shigella sonneiis in the serogroup D category consisting of 1 serotype.

Shigella species subdivision classification:

• Serogroup A: S. dysenteriae (12 serotypes) • Serogroup B: S. flexneri (6 serotypes) • Serogroup C: S. boydii (23 serotypes) • Sergoroup D: S. sonnei (1 serotype)

This classification is based on O-antigen component of the lipopolysaccharide (LSP) present on the outer membrane of the bacteria. Serogroups A, B, C are very similar physiologically while Shigella sonnei is different due to its positive beta-D-galatosidase and ornithine decarboxylase biochemical reactions assay (2).

Description and significance

Shigella sonnei is a non-motile, nonspore-forming, facultative anaerobic Gram-negative bacterium. Its non-motile characteristic means that this species doesn’t have flagella to facilitate its movement like many other human enterobacteria. Shigella sonnei is a rod-shape bacterium and is lactose-fermenting bacterium causing dysentery (4). Shigella sonnei is extremely fragile in experimental settings. Its natural habitat is in a low pH environment such as the human gastrointestinal tract. Its optimal environmental temperature is 37 degrees Celsius, similar to the temperature in the human body. Therefore, human’s gastrointestinal tract appears to be the only found natural host of Shigella sonnei that we know so far.

Shigella sonnei was first successfully isolated from a 5 year old patient in Japan(2). It is a bacterium that is closely related to E. coli. It was known from the beginning that Shigella sonnei is related to E. coli, however, Shigella has evolved from many different strains of E. coli. Since the evolutionary route away from the similarities of the E. coli genome, Shigella has been classified as another species. Due Shigella’s highly evolved genome, it has become a highly specific human pathogen due to its extensive evolutionary progress involving its continual gain and loss of function comparative to E. coli(4).

In both developed and developing countries, the enteric infectious disease shigellosis, caused by Shigella sonnei infection, has been the most common cause of endemic in those areas.S. sonnei continues to be a major food-borne threat to public health in many developed countries where the issues of sanitation are closely monitored. This enterobacterium is generally transmitted by uncooked food or contaminated water. In the U.S., 70% cases of Shigellosis are caused by Shigella sonnei (5).

Genome structure

Shigella sonnei has a circular DNA genome. It uses both chromosomal and plasmid coded gene for its virulence (9). This species has been subjected to complete genome sequencing. It has a ~4Mb size genome. Shigella sonnei's chromosome has the same replication origin and terminus as those of E. coli; this not only means that they are evolutionarily related but suggest that they most likely use the same cellular mechanism to replicate. There are very few biochemical properties that can distinguish Shigella sonnei from E. coli. In all Shigella genomes, the rRNA operons, a sequence that is highly conserved among the prokaryotes, map to approximately the same relative positions as in E. coli indicating that Shigella sonnei and E. coli did not go through DNA recombination between the rRNA operons(4).

The most fascinating feature about the strains of Shigella sonnei and all the other species of Shigella is that their genomes are highly dynamic (9). They exhaust the use of insertion sequence element (IS-element) in characterizing their genome dynamic in terms of causing constant DNA rearrangement such as deletions, translocation, and inversions (4). It is through the use of IS-elements that E. coil differs from other Shigella species. It is evident that Shigella chromosome has inversions sites at its origin of replication sites and termini that can be possible recombination “hotspots” for the insertion of other bacteria’s mobile genome elements(4). It is also through the use of IS-element that Shigella sonnei and other Shigella species can be characterized as highly virulent. Like all the other Shigella species, Shigella sonnei has plasmids that increase in the toxicity of the microbe to their host or other organisms around them. They produce a toxin called the “Shiga toxin”. It is a unique kind of toxin that works its toxicity in the body in multiple ways that will bring potential harm to the neurons, cytoplasm of the cells and enteric epithelial cells (2).

Cell structure and metabolism

Shigella sonnei is a rod-shape, Gram-negative bacterium. Its outer membrane is filled with lipopolyscharride (LPS), a common characteristic of Gram-negative bacteria. The O-antigen component of LPS in Shigella sonnei is characterized differently among the other species of Shigella. Moreover, LPS of this bacterium play an important role in the bacterial virulence.

So far we only know that Shigella sonnei can survive in the human body, therefore, its mechanism of infection defines S. sonnei’s ability to live. S. sonnei, like most Shigella species, spends most of the time intracellularly during infection and is very mobile within the cells by polymerizing actin (2).

Unlike many other pathogenic bacteria, S. sonnei does not use flagella for its chemotoxicity and tissue invasion. Without flagella, S. sonnei can often escape the human immune system of the TLR-5 (toll-like receptor) that usually mediate the innate and adaptive immunity by detecting the conserved domain on many bacteria that use flagellin for motility(3). Although S. sonnei cannot be considered as a motile bacterium as it lacks flagellin for movement, nevertheless, it facilitates movement by using an atypical mechanism of motility, by polymerizing actin. Such a mechanism is not recognizable to the human immune system and also is a type of motile mechanism that saves energy (3).


Lactose fermentation is a biochemical property commonly used for to distinguish Shigella from the closely related bacterium E. coli. However, S. sonnei isolates ferment lactose at a lot slower process than other species of Shigella (2). The unique biochemical property of S. sonnei can be explained genetically. In genome Sd197 and Ss046 the key gene lacZ, encoding beta-D-galactosidase, is attached to lacY gene encoding for galactose transport function. Many of the genes in S. sonnei are categorized as pseudogenes. Pseudogenes are genetic sequences sporadically located in the S. sonnei genome. They are subject to decay at any given time. The nature and purpose of pseudogene still remains elusive (1, 2). The result of this sporadic lost of galactoside transport functional gene in S. sonnei explains the slow lactose fermentation process due to the fact that pseudogene is subject to constant decay from its original site of the initial encoded region (1,2,4).

Much of the S. sonnei’s metabolic mechanism remains elusive because it is considered to be a more evolved species than other Shigella serogroups. S. sonnei is known to be less virulent than other Shigella species because it doesn’t kill its host immediately. Perhaps this also explains why S. sonnei is now the most common Shigellosis causing species that pervades most the developed countries.


The primary host and natural reservoir known at this point for Shigella sonnei and among all other species of Shigella is the human gastrointestinal tract (2, 3). Shigella can survive in fecal contaminated material but has a low survival rate without the optimal acidic environment in the intestinal tract as its surrounding. The bacterium is known to be able to survive in soiled linen for up to seven weeks. In fresh water environments, it can live up to 5 days and in salt water for 12-30 hours. It has been recorded that Shigella sonnei can not survive on the smooth surfaces of tomatoes(10).

No known cases of another natural reservoir have been proven to be the natural host Shigella sonnei other than human’s intestinal tract. Some investigations have researched the possibility of free-living amoebae engulfing Shigella bacteria as a mode of harvesting Shigella sonnei in an environment outside of the human host. Amoebas are unicellular microscopic life forms that have the ability to live in the environment without a host. They can change shapes and engulf other cells. Much is not yet known about of the origin and the formation of these phenomenal cells. It has been shown experimentally that free-living amoebae Acanthamoeba species have the ability to uptake virulent and non-virulent S. sonnei. These amoebas can promote growth of many different pathogenic bacteria inside their cysts in experimental settings, which gives the pathogenic bacterium like Shigella sonnei a microhabitat that protects them from the outside environment. However, natural finding of fee-living amoebae harvesting Shigella sonnei has not been found; therefore, the possible host for Shigella sonnei other than the human GI tract still remains an elusive factor (8).


Shigella sonnei cause an enterobacterium disease called Shigellosis. Shigella sonnei is the Shigella species has been responsible for most of the large shigellosis endemic in industrialized countries (12). Shigella sonnei is spread mostly by means of fecal-oral transmission. Other possible modes of transmission can be from ingestion of contaminated food or water, and subcutaneous contact with inanimate objects and, most rarely, sexual contact (18). Food prepared by the contaminated person may easily become contaminated with Shigella bacteria.

Shigella sonnei infection is characterized by invasion of the intestinal mucosa (18). S. sonnei bacterium utilizes the common enteric Gram-negative pathogen’s Type III secretion systems to inject designated Invasion Plasmid Antigen (Ipa) protein into the invaded cell. Ipa BC protein complex can cause the lysis of epithelial cell vacuoles and increase the uptake of Shigella sonnei by M cells and other epithelial cells (2, 15). The infection stays locally at the colon and rectal mucosa site where the bacteria cause major inflammatory destruction of the mucosal wall. Shigella sonnei’s infectivity dose is very low; as few as 100-200 bacteria are needed to cause a clinical infection, shigellosis.

Shigella pathogenic mechanism is very complex due to its different mechanisms that cause destruction to the intestinal wall. Shigella sonnei, like all the other Shigella species, excrete shiga toxin that causes inflammatory response to the enteric cell wall and necrotic cell death of the colonic epithelium (2). The necrotic cell death is an extremely messy death for the cell due to the massive spill-out of all the intracellular content upon its death; as the result, it attracts the body’s cytokine-mediated immune response to clean up the mess; however, the cleaning up process of cell debris also causes a large local enteric inflammatory response that contributes to the shigellosis disease progression (2).

Once Shigella sonnei enter into the colonic cell wall they can also invade other cells in the intestinal tract. After they enter into the intestinal tract, Shigella bacteria lyse the phagocytic vacuole and enter the epithelial cell’s cytoplasm where they multiply and move to invade other cells (13). Shigella is known for its promiscuity in terms of their ability to infect different cell types, such as enterocytes and M cells, and the intestinal epithelial cells (2). Shigella bacteria multiply within colonic epithelial cells, causing mucosal ulceration, inflammation and bleeding.

Shigella sonnei’s virulence can be largely understood in its genome versatility. Shigella sonnei unlike the species of most enteric pathogens, has no known natural reservoir other than human, therefore, this enterobacteria is highly expected to undergo gene transfer and selective pressures in the human intestinal tract (11). It has been found through genome sequence analysis that S. sonnei contains site of several different mobile genetic elements including plasmids, transposons, and integron involving gene cassettes that are all important factors in S. sonnei incorporation of antibiotic resistance abilities and increase its virulence (11). It has been found that S. sonnie bacteria can use contact-dependent conjugative plasmid transfer in obtaining antibiotic resistance factor from other bacteria (11).

Shigella sonnei has a circular chromosomal DNA and a large plasmid that contribute largely to its virulent factors. Class 1 and 2 integrons have been detected in S. sonnei encoding recombinase to induce the site of incorporation for the gene cassettes that can contribute to the virulence of the bacterium chromosomal genome. The gene cassettes are usually integrated between the two conserved segments at the 5’ and 3’ ends at the attI1 site (11). As for the large plasmid genome of S. sonnei, one encoded ability is cellular invasion. This large plasmid encodes for S. sonnei’s outer membrane protein, VirG (IcsA) to elicit polymerization of filamentous actin that's involved in intra and intercellular movement for the bacterium. This is one of the main mechanisms that S. sonnei use to form protruding pores at the colonic epithelial cell wall in order to invade other neighboring cells in the colon (13).

Knowing the many mobile genetic elements markers on the Shigella sonnei plasmid and chromosomal DNA, it would be expected that strains of Shigella sonnei would be resistant to multiple antibiotics; however, resistant to multiple antibiotics strains is quite uncommon in the United States (14). Clinical symptoms of shigellosis cause by Shigella sonnei in the United States are similar to all other the dysenteric diseases. The most common symptom is bloody stool and small to severe diarrhea. Other symptoms on some people are mild to high fever, malaise, and tenesmus. Tenesmus is the constant feeling of the need to empty the bowel, accompanied by pain and cramping. The passage of stool excretion can go for 3 or more per day either chronically or last for several days (2, 5, and 14).

Application to Biotechnology

Shigella sonnei is the cause of a human enteric infectious disease, shigellosis. Its natural reservoir is in the human intestinal tract, therefore, S. sonnei is only known for its disease causing ability. S. sonnei is not use for any known biotechnology to benefit society. Much is still needed to investigate the evolutionary development from E. coli to the Shigella species, in order to answer questions on the nature of Shigella choice of reservoir in the human intestinal tract.

Current Research

S. sonnei's disease causing ability has given much attention to recent research on the epidemiology of the bacteria and the techniques to disinfect the disease causing bacteria on food products. New outbreaks and disease patterns of the different strains of Shigella sonnei have been detected and updated by epidemiologists around the world. Most recent research papers on shigellosis outbreak cause by Shigella sonnei are from countries outside the United States.

The shigellosis outbreak that happened in Taiwan during 2001 to 2003 has now been found to be a Shigella sonnei strain outside of Taiwan. The Taiwanese researchers and epidemiologists have been using the technique of pulse-field gel electrophoresis (PFGE) technique to genotype and tract the bacteria’s mobile genetic element marker, the IS sites, on the large plasmid virulent factor of S. sonnei. After the genotyping and characterization of S. sonnei's genome, they found that the first wave of the outbreak happened in 2001 was a foreign strain. In the year 2007, this particular ancestral strain from the 2001 outbreak continues to be widespread in the central region of Taiwan even though there are several new strains that have arisen from the 2001 outbreak. The Taiwanese epidemiologists are on watch for the new emerging strain to arise in Taiwan to cause another outbreak (12).

The Korean epidemiologists have recently published a paper on the tracking of their own shigellosis endemic cause by Shigella sonnei. Shigella sonnei first appeared in Korea in 1951 and since then there have been sporadic reports of the bacteria causing the disease shigellosis over many decades. Looking at the trends of the disease since the first emergence of S. sonnei in Korea, the scientists saw that S. sonnei disease causing ability have been zoning in and out of the Korean population. Current genotyping of the recent antibiotic resistance strains of S. sonnei using PFGE technique have revealed the genetic changes of S. sonnei over the decade of shigellosis emergence in Korea. The scientists have found multiple antibiotic resistance strains of S. sonnei. A high proportion of the resistant strains were found to be resistant to some of the most commonly used antibiotics such as tetracycline and streptomycin. These reports have alerted the Korean epidemiologists to develop a more comprehensive report of the genetic changes in S. sonnei since the beginning of its emergence in the 1951, knowing that the use of many antibiotics that we currently have pervasively today throughout the world will soon become obsolete (3).

It was previously known by the Spanish epidemiologists that several shigellosis outbreaks in Spain were caused by the consumption of fresh-cut vegetables. Since then fresh produce has been treated with chlorine-based agents to kill the Shigella sonnei bacteria responsible for the outbreaks since the beginning. However, most recent reports have been found that chlorine-based agent treatment of fresh produce can be carcinogenic. Therefore, new techniques have been investigated in Spain to find an alternative approach to decontaminate. A research study of quality, safety and bioactivity of plant foods under the Spanish department of Food Science and Technology has found that ozone can inactive S. sonnei. The research group inoculated S. sonnei on lettuce and in water and exposed them to UV-C. As the result of this experiment, the growth of S. sonnei bacteria was halted. This means that there is a safer alternative to decompose S. sonnei’s toxic products from fresh produce (16).


1. Mammina, C., Aleo, A., Romani, C., and Natasi, A. “Shigella sonnei biotype G carrying class 2 integrins in southern Italy: a retrospective typing study by pulsed field gel electrophoresis”. BMC Infectious Diseases. 2006. 6:117.

2. Niyogi, SK. “Shigellosis”. Journal of Microbiology (2005 Apr). 43(2): 133-143.

3. Seol, SY. “Molecular characteristic of antimicrobial resistance of Shigella sonnei isolates in Korea”. Journal of Medical Microbiology (2006) 55:871-877.

4. Yang, F., Yang, J. “Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery”. Nucleic Acid Research, 2005. Vol 33 No.9: 6445-6458.

5. Shiferaw, B., Shallow, S., Marcus, R., Segler, S., Soderlund, D., Hardnett, FP., and Van Gilder, T. “Trends in population-based active surveillance for shigellosis and demographic variability in FoodNet sites, 1996-1999”. Clinical Infectious Diseases, 2004. Volume 38. pp. 175-180. 6. Stothard P, Van Domselaar G, Shrivastava S, Guo A, O'Neill B, Cruz J, Ellison M, Wishart DS (2005) BacMap: an interactive picture atlas of annotated bacterial genomes. Nucleic Acids Res 33:D317-D320

7. Keusch GT, Jacewicz, M., Acheson DW, Donohue-Rolfe, A., Kane AV, McCluer RH. “Globotriaosyleramide, Gb3, is an alternative functional receptor for Shiga-like 2e.” Infectious Immun. 1995; 63(3): 1138-1141.

8. Jeong, HJ., Jang ES., Han, BI., Lee, KH., Ock, MS. “Acathamoeba: Could it be an environmental host of Shigella?” Experimental Parasitolog. Volume 115 (2007) pp 181-186.

9. Chiou, CS., Wei, HL., Wang, YW., Liao, JC., and Li, CC. “Usefulness of Inter-IS1 Spacer Polymorphisms for Subtyping of Shigella sonnei Isolates.” Jounral of Clinical Microbiology. Volume 44, No.11 pp 3928-3933.

10. Warren, BR., Yuk, HG., Schneider, KR. “Survival of Shigella sonnei on smooth tomato surfaces, in potato salad and in raw ground beef.” International Journal of Food Microbiology Volume 116 (2007) pp 400-404.

11. DeLappe N., O’Halloran, F., Fanning, S., Corbett-Feeney, G., Cheasty, T., and Cormican M. “Antimicrobial Resistance and Genetic Diversity of Shigella sonnei isolated from Western Ireland, an Area of Low Incidence of Infection.” Journal of Clinical Microbiology. May 2003. Volume 41, No.5 pp1919-1924.

12. Wei, HL., Wang, YW., Li, CC., Tung, SK., Chiou, CS. “Epidemiology and evolution of genotype and antimicrobial resistance of an imported Shigella sonnei clone circulating in central Taiwan.” Diagnostic Microbiology and Infectious Disease. (2007).

13. Miura, M., Terajiuma, J., Izumiya, H., Mitobe, J., Komano, T. “OspE2 of Shigella sonnei is Required for the Maintenance of Cell Architecture of Bacterium-Infected Cells.” Infection and Immunity. 2006 volume 74, No.5. pp2587-2595.

14. Brain, MJ., Van, R., Townsend, I., Murray, BE., Cleary, TG., and Pickering, LK. “Evaluation of the Molecular Epidemiology of an Outbreak of Multiply Resistant Shigella sonnei in a Day-Care Center by Using Pulse-Field Gel Electrophoresis and Plasmid DNA Analysis” Journal of Clinical Microbiology. (1993) Volume 31, No.8 pp2152-2156.

15. Zahrl, D., Wagner, M., Bishof, K., Bayer, M., Zavecz, B., Beranek, A., Ruckenstuhl, C., Zarfel, GE., Koraimann, G. “Paptidoglycan degradation by specialized lytic transglycosylases associated with type III and type secretion systems.” Microbiology. (2005) Volume 151, pp 3455-3467.

16. Selma, MV., Beltran, D., Allende, A., Chacon-Vera, E., Gil, MI. “Elimination by ozone of Shigella sonnei in shredded lettuce and water” Food Microbiology volume 24 (2007) pp492-499.

17. Shigella sonnei, genus, enterobacteria NCBI reference:

18. Shigella eMedicine electronic reference: Sureshbabu, J., Venugopalan P. “Shigella Infection – Infectious Disease” eMedicine – webMD (2006)

Edited by Susan Cheng, student of Rachel Larsen and Kit Pogliano