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Relationship among Shigella spp. and enteroinvasive Escherichia coli (EIEC) and their differentiation


Shigellosis produces inflammatory reactions and ulceration on the intestinal epithelium followed by bloody or mucoid diarrhea. It is caused by enteroinvasive E. coli (EIEC) as well as any species of the genus Shigella, namely, S. dysenteriae, S. flexneri, S. boydii, and S. sonnei. This current species designation of Shigella does not specify genetic similarity. Shigella spp. could be easily differentiated from E. coli, but difficulties observed for the EIEC-Shigella differentiation as both show similar biochemical traits and can cause dysentery using the same mode of invasion. Sequencing of multiple housekeeping genes indicates that Shigella has derived on several different occasions via acquisition of the transferable forms of ancestral virulence plasmids within commensal E. coli and form a Shigella-EIEC pathovar. EIEC showed lower expression of virulence genes compared to Shigella, hence EIEC produce less severe disease than Shigella spp. Conventional microbiological techniques often lead to confusing results concerning the discrimination between EIEC and Shigella spp. The lactose permease gene (lacY) is present in all E. coli strains but absent in Shigella spp., whereas β-glucuronidase gene (uidA) is present in both E. coli and Shigella spp. Thus uidA gene and lacY gene based duplex real-time PCR assay could be used for easy identification and differentiation of Shigella spp. from E. coli and in particular EIEC.

diarrhea; E. coli; Shigella; real-time PCR


Relationship among Shigella spp. and enteroinvasive Escherichia coli (EIEC) and their differentiation

Abu Ud-DinI; Syeda WahidII

IIdentification and Subtyping of Enteric Pathogens, International Centre for Diarrhoeal Disease Research in Bangladesh, Dhaka, Bangladesh

IICenter for Food and Water Borne Disease, International Centre for Diarrhoeal Disease Research in Bangladesh, Dhaka, Bangladesh

Correspondence Correspondence: Abu Ud-Din International Centre for Diarrhoeal Disease Research in Bangladesh Identification and Subtyping of Enteric Pathogens Bangladesh E-mail:


Shigellosis produces inflammatory reactions and ulceration on the intestinal epithelium followed by bloody or mucoid diarrhea. It is caused by enteroinvasive E. coli (EIEC) as well as any species of the genus Shigella, namely, S. dysenteriae, S. flexneri, S. boydii, and S. sonnei. This current species designation of Shigella does not specify genetic similarity. Shigella spp. could be easily differentiated from E. coli, but difficulties observed for the EIEC-Shigella differentiation as both show similar biochemical traits and can cause dysentery using the same mode of invasion. Sequencing of multiple housekeeping genes indicates that Shigella has derived on several different occasions via acquisition of the transferable forms of ancestral virulence plasmids within commensal E. coli and form a Shigella-EIEC pathovar. EIEC showed lower expression of virulence genes compared to Shigella, hence EIEC produce less severe disease than Shigella spp. Conventional microbiological techniques often lead to confusing results concerning the discrimination between EIEC and Shigella spp. The lactose permease gene (lacY) is present in all E. coli strains but absent in Shigella spp., whereas β-glucuronidase gene (uidA) is present in both E. coli and Shigella spp. Thus uidA gene and lacY gene based duplex real-time PCR assay could be used for easy identification and differentiation of Shigella spp. from E. coli and in particular EIEC.

Key words: diarrhea, E. coli, Shigella, real-time PCR


Bacillary dysentery like shigellosis, endemic throughout the world, is one of the major causes of morbidity and mortality, especially among children > 5 years of age in low and middle income countries including Bangladesh (Bardhan et al., 2010; Wen et al., 2012). The disease is caused by enteroinvasive Escherichia coli (EIEC) or any of the four species or groups of Shigella: S. dysenteriae, S. flexneri, S. boydii, and S. sonnei. In the nineties, there are about 165 million cases of Shigella infection annually worldwide and 1.1 million Shigella-related deaths, with 98% of those cases in low income countries (Kotloff et al., 1999). According to a recent review on Asian countries (Bardhan et al., 2010), about 125 million cases of endemic shigellosis occur per year. The study showed that the incidence of shigellosis is similar to an earlier report (Kotloff et al., 1999), however, the overall mortality rate due to shigellosis has come down to ~ 0.01% and ~0.89% among the youngest age group. Although EIEC is one of the etiologic agents of diarrhea, very few epidemiologic studies have been done globally to estimate the actual disease burden due to EIEC, individual risk factors for infection or prospective reservoirs of EIEC. Adequate attention was not given to the epidemiology of EIEC, since it is often found to be rare etiological agent of diarrhea compared to other diarrhea-causing enteropathogens (Vieira et al., 2007; Moreno et al., 2010). Identification and differentiation of Shigella spp. and EIEC from environmental and clinical specimens by conventional culture and biochemical assays are complex and time consuming. This review focuses on phenotypic and genotypic relationship among EIEC and Shigella spp., and recent progress of clinical and practical research, and utility of currently available molecular methods for differentiation between Shigella spp. and E. coli, in particular emphasis on EIEC based on literature study.

Identification and Classification

The Japanese scientist Kioshi Shiga first identified Shigella in the 1898s. He termed it as Bacillus because it seemed to be related to Bacillus coli, which is now referred to as E. coli (Hale, 1991). In taxonomy, Shigella strains were classified into a different genus from E. coli in the 1940s due to their pathological significance. The genus is divided into four species and at least 54 serotypes based on their biochemical and/or the structure of the O-antigen component of LPS present on the cell wall outer membrane: S. dysenteriae (subgroup A, 16 serotypes), S. flexneri (subgroup B, 17 serotypes and sub-serotypes), S. boydii (subgroup C, 20 serotypes), and S. sonnei (subgroup D, 1 serotype) (Simmons and Romanowska, 1987; Talukder and Azmi, 2012).

On the other hand, EIEC was first reported as 'paracolon bacillus' in 1944, but it was later designated as E. coli O124. EIEC is associated with specific E. coli O-serotypes: O28ac:NM, O29:NM, O112ac:NM, O121:NM, O124:NM, O124:H30, O135:NM, O136:NM, O143:NM, O144:NM, O152:NM, O159:H2, O159:NM, O164:NM, O167:H4, O167:H5, O167:NM and O173:NM (Orskov et al., 1991; Matsushita et al., 1993; Nataro and Kaper, 1998; Martinez et al., 1999; Gibotti et al., 2004). All of the serotypes are nonmotile except few biotypes of O28ac, O29, O124, O136 and O143 (Silva et al., 1980; Martinez et al., 1999). Some of these EIEC-associated O antigens are identical or similar to O antigens present in Shigella spp., namely: O112ac, O124, O136, O143, O152, and O164 with Shigella O antigens of S. dysenteriae 2/S. boydii 15/S. boydii 1, S. dysenteriae 3/ provisional Shigella serovar 3615.53, S. dysenteriae 3/S. boydii 1, S. boydii 8, provisional Shigella serovar 3341:55, and S. dysenteriae 3, respectively (Cheasty and Rowe, 1983; Landersjo et al., 1996; Linnerborg et al., 1999). In fact, differentiation between Shigella and EIEC strains with the same serotype is often difficult due to their nearly identical physio-biochemical traits. EIEC strains can be differentiated from typical members of commensal E. coli strains by the Sereny test and/or the identification of bacterial invasion-associated proteins or genes via specific tests. However, these methods are not routinely used for laboratory diagnosis and EIEC strains are only provisionally identified by O serotyping with commercially available antisera in diagnostic laboratories (Beutin et al., 1997). Where a typable isolate additionally carries a serotype occurring in both EIEC and Shigella spp., a taxonomic classification could be at best possible on the basis of genes responsible for the higher metabolic activity of EIEC (Ewing, 1986; Kibbee et al., 2013).

Phenotypic and Genotypic Relationship

Although Shigella and E. coli are closely related, E. coli always show some different physio-biochemical properties than Shigella. More than 80% of E. coli are prototrophic, motile, able to decarboxylate lysine and ferment many sugars, produce gas from D-glucose and indole positive, whereas Shigella are auxotrophic, obligate pathogens, non-motile, unable to decarboxylate lysine, ferment few sugars and never produce gas from D-glucose, except Shigella flexneri 6, S. boydii 13 and S. dysenteriae 3 (Clayton and Warren, 1929; Downie et al., 1933; Stypulkowska, 1964; Rowe et al., 1975; Silva et al., 1980; Toledo and Trabulsi, 1983; Baumann and Schubert, 1984; Ewing, 1986; Scheutz F, 2005). Shigella spp. are unable to ferment salicine and hydrolyze esculine (Bopp et al., 2003) . Of four Shigella spp., only S. sonnei is able to ferment lactose slowly and can be mucate positive (Goodman and Pickett, 1966). However, some EIEC strains have remarkable phenotypic and genotypic similarity with Shigella species (Farmer et al., 1985; Lan et al., 2004). They are usually nonmotile, lactose negative and lysine-decarboxylase negative except for a few serotypes, which are the Sereny test negative and motile (Farmer et al., 1985). The few biochemical properties that enable differentiation of E. coli and Shigella spp. are mucate fermentation and acetate utilization. EIEC may be positive for one or both of the properties, in contrast Shigella strains are negative for both and more than 90% of other E. coli strains are positive for both with very few exceptions (Bopp et al., 2003; Lan et al., 2004).

It was reported that Shigella and E. coli show 80-90% similarity at the nucleotide level, while other Escherichia spp. have a much lower degree of similarity and are genetically distant (Brenner et al., 1972). Multilocus enzyme electrophoresis and ribotyping analyses revealed that Shigella genotypes are interspersed within E. coli genotypes, irrespective of their nomen-species (Rolland et al., 1998). Likewise, a high degree of relatedness between Shigella and E. coli is found based on 16S rDNA analysis (Christensen et al., 1998). DNA-DNA re-association studies, sequencing of numerous other housekeeping genes, virulence genes and complete genome sequencing showed that EIEC and Shigella spp. formed a distinctive E. coli pathovar (Brenner et al., 1972; Brenner, 1973; Lan et al., 2004). However, the discrimination between EIEC and Shigella spp. is necessary as both exhibit a number of clinical differences. For example, Shigella spp. can cause haemolytic uraemic syndrome (HUS), a clinical syndrome characterized by progressive renal failure associated with microangiopathic (nonimmune, Coombs-negative) hemolytic anemia and thrombocytopenia, whereas EIEC is not known to cause HUS (Johnson, 2000).

Genetic Structure of Shigella

Each of the Shigella genomes includes a single circular chromosome and /or a circular virulence plasmid (VP) that harbors conserved primary virulence determinants (Sasakawa et al., 1992). The whole-genome sequencing of all four Shigella spp. and E. coli revealed that they share a fundamental core genome of approximately 3 Mb (Lukjancenko et al., 2010). The Shigella chromosome has more than 200 pseudogenes, 300~700 copies IS-elements, numerous deletions, insertions, translocations and inversions. Although, Shigella chromosomes share most of their genes with E. coli K12 strain MG1655, bacteriophage-mediated horizontal gene transfer is the main contributor for the massive diversity of putative virulence genes (Venkatesan et al., 2001). Shigella spp. became highly virulent pathogens with distinct clinical and epidemiological features via gaining and loss of gene functions in adaptation and convergent evolution, by means of bacteriophage integration, IS-mediated transposition and formation of pseudogenes (Yang et al., 2005; Peng et al., 2006).

Phylogenetic Relationship

The sequencing of multiple housekeeping genes indicates that Shigella has risen on several different occasions from several independent ancestors by acquisition of the transferable forms of ancestral VPs within the group of nonpathogenic E. coli. Based on the analysis of sequence variation in eight housekeeping genes of Shigella, Pupo et al. proposed that Shigella strains fall into three main clusters and four outliers (Pupo et al., 2000). In 2007, Yang et al. showed a similar phylogenetic tree using the DNA sequences of 23 housekeeping genes, which corroborated the credibility of the previous conclusions (Yang et al., 2007). The most striking features are that each cluster includes strains from different Shigella species. The phylogenic tree shows that most of the Shigella strains belong to three clusters (C1, C2 and C3) leaving S. sonnei (SS), S. dysenteriae (D) serotype 1, 8, 10 and S. boydii serotype 13 (B13) as outliers. Cluster 1 can be sub-clustered to SC1, SC2, SC3, and a minor branch consisting of only S. dysenteriae 7. Sub-cluster 1 contains only D strains (D3-4, D6, D9, D11-13), SC2 contains mostly B strains (B1, B3, B6, B8, B10, and B18) but also D5, and SC3 contains three B strains (B2, B4, and B14) and F6. Cluster 2 is mainly composed of B strains (B5, B7, B9, B11, and B15-17) and D2. Cluster 3 consists of mostly S. flexneri (F) strains (F1a, F1b, F2a, F2b, F3, F4a, F4b, F5, Fx, and Fy) and B12. The most profound observation is that each of the five clusters/sub clusters contains strains mostly from only one serogroup indicates that serological classification is highly correlated with the genotypes and continues to be useful in epidemiologic and diagnostic investigations. In the phylogenetic tree, B13 is distant from all the E. coli/Shigella strains, which is consistent with a recent report that B13 and E. albertii strains form a distinct lineage of enteric pathogens that had separated from an E. coli-like ancestor about 28 million years ago (Hyma et al., 2005). MLST analysis revealed that EIEC strains grouped into four clusters with one outlier strain (which was found in Shigella cluster 2), indicating the independent derivation of EIEC several times (Lan et al., 2004). In comparison of EIEC with Shigella clusters, the authors showed that EIEC clusters have diverged less than Shigella clusters, although Shigella-EIEC forms one single pathovar of E. coli (Lan et al., 2004).

Pupo et al. proposed that the three main clusters of Shigella had independently evolved from multiple E. coli ancestors with diverse genetic backgrounds 35,000-270,000 years ago (Pupo et al., 2000). This indicated that dysentery existed long before civilization and was one of the early infectious diseases of human. S. sonnei had developed as a human-pathogenic clone of E. coli approximately 10,000 years ago (Shepherd et al., 2000). The descent times are relatively recent when one takes in account that a major nonpathogenic E. coli cluster diverged from other bacteria 8-22 million years ago. These data are probably no coincidence because pathogenesis of Shigella is based on surviving in the intestinal epithelial cells of humans only-a perfect host-adaptation (Pupo et al., 2000). Sequence variations in the clusters of Shigella and EIEC indicated that EIEC might have arisen from E. coli ancestors after Shigella developed. Based on this derivation of EIEC, two hypotheses about EIEC in relation to Shigella were stated. First, EIEC strains are in an intermediate stage and are a potential precursor of 'full-blown' Shigella strains. Second, like Shigella, EIEC is a distinct group of organisms that is adapted to human hosts, but is better equipped to survive outside the host (Lan et al., 2004).

The critical step for Shigella creation is the acquisition of the antecedent forms of the VP, which is a non self-transferable large single-copy plasmid of 180-230 kb (Hale et al., 1983). This VP is essential for invasiveness, cell survival and apoptosis of Macrophages (Harris et al., 1982; Sansonetti et al., 1982b; Sansonetti et al., 1983). The virulence associated genes on the pINV are probably acquired horizontally from another unrelated genus, because the A+T content of the nucleotides of these genes is 75%, while the A+T content of all Shigella and E. coli genomes is 50% (Adler et al., 1989; Hale, 1991). Based on the analysis of three virulence genes (ipgD, mxiA, and mxiC) that are located on the invasion region of VP in Shigella and EIEC strains, two forms of VPs (pINVA and pINVB) were found (Lan et al., 2001; Yang et al., 2007). Lan et al. extensively studied 32 EIEC strains and found that all but two EIEC strains have the pINV A form (Lan et al., 2004). S. sonnei has only pINVB and other serotypes have mixed form. The acquisition of the VP in an ancestral E. coli strain preceded the diversification by radiation of all Shigella and EIEC groups. The DNA sequence indicated that a 31-kb entry region of VP encodes components of the Mxi [membrane excretion of Ipa]-Spa[surface presentation of invasion plasmid antigens] TTSS [type three secretion system] apparatus, substrates of this apparatus (IpaA-D [invasion plasmid gene]), their dedicated chaperones (IpgA, IpgC, IpgE and Spa15) and two transcriptional activators (VirB and MxiE) (Buchrieser et al., 2000). Outside of the entry region, there are i) virG gene, encoding outer membrane protein (VirG), responsible for bacterial movement within the cytoplasm of infected cells, ii) virF gene, encoding a transcriptional activator (VirF), controls expression of icsA and virB, and iii) the sepA gene encodes a secreted serine protease of the autotransporter family. Moreover, the virulence plasmid also contains two copies of the shet2 gene encoding a putative enterotoxin, and genes encoding several secreted proteins (VirA, IpaH4.5, IpaH7.8, IpaH9.8) and six uncharacterized protein designated (outer Shigella proteins): OspB, OspC1, OspD1, OspE1, OspF, and OspG (Harris et al., 1982; Sansonetti et al., 1982a; Sansonetti et al., 1983). The plasmid encoded proteins are directly involved in the entry into host epithelial cells. With the acquisition of the pINV, Shigella and EIEC were able to live in the human intestinal epithelial cells. For the invasion and maintaining in the host, Shigella and EIEC need a combined expression of genes located on the pINV and chromosome (Sansonetti et al., 1982b; Maurelli et al., 1998).

The Shigella genome has adapted to the acquisition of invasion plasmid by multiple different events, such as: (i) controlling at promoter level, (ii) mutations within genes, (iii) the suppression or over expression of certain genes, or (iv) deletion of anti-virulence genes which is called "black hole" to evolve toward a pathogenic lifestyle (Maurelli et al., 1998). For example, the loss of cadA gene is a black hole in EIEC and Shigella. CadA encodes for lysine decarboxylase activity (LDC), which is present in almost all non-enteroinvasive E. coli. Cadaverine produced by lysine decarboxylase has been shown to attenuate the bacteria's ability to induce polymorphonuclear leucocytes transepithelial migration. Because of the inhibiting influence of cadaverin on the virulence of Shigella, LDC activity was lost by genome deletion (Maurelli et al., 1998). Consequently, LDC is a biochemical trait which can be used to differentiate between other E. coli vs. Shigella and EIEC, but not between EIEC and Shigella.

Pathogenesis Process

The illness caused by Shigella or EIEC is characterized by the destruction of the colonic epithelium caused by the inflammatory response induced upon invasion of the mucosa by bacteria (Parsot, 2005). It is well established that the disease induced by EIEC is generally less severe than Shigella does (DuPont et al., 1989; Moreno et al., 2009; Bando et al., 2010; Moreno et al., 2012). Recombination techniques and the sequencing of the invasion plasmid and chromosomal genes associated with virulence, gave insight of the precise mechanism of infection by Shigella. First, the bacteria in the intestinal lumen invade the colon by transcytosis through microfold cells (M-cells) of the Follicle-Associated Epithelium (FAE) to reach the underlying submucosa (Croxen and Finlay, 2010). The disruption of tight junctions and the damage that is caused by inflammation also give Shigella entry to the submucosa. Although Shigella phagocytosed by resident macrophages, it can escape from the phagosome, and caspase-1-dependent inflammation activation resulting ultimate release from macrophages. After cell death, the bacteria, released in the submucosa, invade epithelial cells by endocytosis. During the invasion of the epithelial cells, ipaBCD and mxiAB genes of the ipa-mxi-spa island on the VP are brought to expression (Sansonetti et al., 1981; Sansonetti et al., 1982b; Buysse et al., 1987; Venkatesan et al., 2001; Moreno et al., 2009; Croxen and Finlay, 2010). IpaD is believed to play a role in attaching to host cell membranes, and subsequently IpaB plays a role in the endocytic uptake of the bacteria. The roles of the other known virulence genes associated with invasion of the cell have yet to be discovered. Once internalized, the phagocytic vacuole is quickly lysed by the invading bacterium, thereby allowing its escape into the host cell cytoplasm, where it nucleates and assembles an F-actin comet at one of its poles (Bernardini et al., 1989). This result in the bacterium moving inside epithelial cells and passing from cell to cell, thereby is causing a very efficient process of intracellular colonization. Shigella actin based motility is mediated by a single outer membrane protein, IcsA (VirG) (Lett et al., 1989). Glycine-rich repeats in the amino terminal end of IcsA (VirG) bind neuronal Wiskoff-Aldrich Syndrome Protein (N-WASP) (Suzuki et al., 1998), a member of the WASP family of Cdc-42-dependent mediators of actin nucleation via the Arp 2/3 complex. Formation of a complex between IcsA, N-WASP, and Arp 2/3 at the bacterial surface is sufficient to cause actin nucleation/polymerization in the presence of actin monomers (Egile et al., 1999). Motile intracellular Shigella then involve components of the cell intermediate junction to form a protrusion that is internalized by the adjacent cell, thus causing cell-to-cell spread (Sansonetti et al., 1994). Invasion of epithelial cells by Shigella stimulates the release of proinflammatory cytokines and chemokines, such as IL-8 attacks polymorphonuclear leukocytes (PMN) to the infection site and their transmigration through the epithelium, which results in major tissue destruction and inflammation.

Difference in Pathogenecity and Virulence Genes Expression

EIEC produce less severe disease than S. flexneri (Moreno et al., 2009; Bando et al., 2010; Moreno et al., 2012). An inoculum of 106 EIEC cells is sufficient for infection, whereas as low as 102Shigella cells can cause successful infection (DuPont et al., 1971). S. flexneri induced keratoconjunctivitis quickly and more severely than the EIEC strains. One of the hypotheses for this phenomenon is the increased efficiency of Shigella in spreading through epithelial cells compared to EIEC. (Moreno et al., 2009). Moreover, it is noteworthy that Shigella and EIEC showed significant differences in the expression of regulatory and pathogenic genes (icsA, icsB, ipaA-D, virF and virB). It was found that S. flexneri expresses pathogenic genes at significantly higher levels than that of EIEC (Moreno et al., 2009; Bardhan et al., 2010). The virF and virB genes act in a regulatory cascade to trigger virulence genes transcription following the receipt of specific environmental signals by the bacterium (Adler et al., 1989; Prosseda et al., 1998). The VirF protein initiates the transcription of the virB regulatory gene, and the product of this gene (VirB) in turn activates the promoters of the structural virulence genes (Porter and Dorman, 2002). Among the studied genes, only the virF gene was more expressed by EIEC than by S. flexneri. All the other genes were less expressed in EIEC. The lower expression of these genes might lead to significant differences in virulence between EIEC and Shigella, leading to a weaken dissemination capacity of EIEC. These data also corroborated the differences in the mechanism by which EIEC and S. flexneri manipulate the host intestinal cells, and suggest that their genes respond specifically to the environment of the host cell milieu, resulting in different disease outcomes (Moreno et al., 2009). Regarding the immune response related to dendritic cells (DCs), the innate immune response upon EIEC infection are preserved although DCs fail to activate naive T lymphocytes (Moreno et al., 2012). Moreover, EIEC showed a late killing effect in J774 macrophage cultures in compare to S. flexneri (Bando et al., 2010). This data could explain why EIEC takes longer time than Shigella species to cause diarrhea.

Current Approaches to Differentiate Shigella spp. and EIEC

The above described characteristics suggest that Shigella/EIEC could be differentiated genetically from typical E. coli by targeting marker genes. But designing a rapid, sensitive and reliable molecular technique for identification and differentiation between EIEC and Shigella spp. is very difficult due to their close biochemical similarity. Till now few molecular methods have been described for identification of the members of Shigella-EIEC pathover from other typical E. coli. For example, apyrase-based colorimetric test (Sankaran et al., 2009), loop-mediated isothermal amplification method targeting the ipaH gene (Song et al., 2005), PCR-ELISA (Sethabutr et al., 2000), IpaC and IpaH gene -specific ELISA (Oberhelman et al., 1993; Pal et al., 1997), large invasive plasmid (120-140 MDa) analysis based method (Ud-Din et al., 2010), colony blotting using 2.5 kb HindIII fragment of invasion plasmid (Small and Falkow, 1988). Moreover, PCR based assay targeting- IS630-probes (Houng et al., 1997), virF gene (Wang and Chen, 2012), ipaH gene (Thiem et al., 2004) and IS1 region (Hsu et al., 2007), multiplex PCR (Antikainen et al., 2009; Fujioka et al., 2013) and singleplex real-time PCR (Liu et al., 2013) have been reported previously to detect the presence or absence of Shigella/EIEC. Most recently, Ojha et al. developed a pentaplex PCR which is able to detect and differentiate among Shigella spp. (Ojha et al., 2013). Unfortunately, this method is also unable to differentiate EIEC from Shigella spp.

Lactose fermentation is the biochemical hallmark of E. coli which is exploited extensively for its detection by conventional culture methods (Ito et al., 1991; Stoebel, 2005). The lacY gene, a gene encoding lactose permease, is present in different members of the family Enterobacteriaceae like E. coli, Enterobacter cloacae, Citrobacter freundii or Kluyvera ascorbata, while the b-glucuronidase gene (uidA), which encodes the beta-glucuronidase enzyme is present in E. coli and Shigella spp. (Horakova et al., 2008), Horakova et al. reported that the lacY gene is a putative genetic marker for differentiation of Shigella spp. from E. coli (Horakova et al., 2008). They developed a conventional multiplex PCR, which seemed to work well to differentiate Shigella from E. coli but not for EIEC-Shigella differentiation. Additionally, this conventional PCR failed to differentiate EIEC from Shigella due to presence of similar sized non-specific amplicons for Shigella spp. In consequence, Pavlovic M et al. developed a simple, rapid, reliable and specific probe-based duplex real-time PCR assay specific for the genes uidA and lacY to minimize the risk of detection of nonspecific targets (Pavlovic et al., 2011). They successfully differentiated ninety-six isolates including 11 EIEC isolates of different serotypes and at least three representatives of each Shigella species correctly. All the tested Shigella and E. coli including EIEC isolates were positive for the uidA gene. Additionally, all E. coli isolates were positive for the lacY gene, whereas none of the tested Shigella isolate harbored the lacY gene. Even cross reacting serotypes of EIEC (O112ac, O124 and O152) were clearly differentiated from Shigella as EIEC by the duplex real-time PCR. The selectivity of the lacY-uidA duplex real-time PCR was 100%.


In summary, Shigella and EIEC can be differentiated from commensal E. coli by testing for presence of the ipaH-gene. Since Shigella and EIEC have similar physio-biochemical characteristics, conventional identification systems will identify members of the Shigella-EIEC pathovar as either E. coli or Shigella. Conventional cultural techniques often lead to confusing results concerning the discrimination of EIEC and Shigella spp. The duplex real-time PCR assay, which is simple, rapid, reliable and specific, can be used for differentiation of Shigella spp. from E. coli and in particular EIEC.

Submitted: May 28, 2013

Approved: December 13, 2013

All the content of the journal, except where otherwise noted, is licensed under a Creative Commons License CC BY-NC.

  • Adler B, Sasakawa C, Tobe T, Makino S, Komatsu K, Yoshikawa M (1989) A dual transcriptional activation system for the 230 kb plasmid genes coding for virulence-associated antigens of Shigella flexneri Mol Microbiol 3:627-635.
  • Antikainen J, Tarkka E, Haukka K, Siitonen A, Vaara M, Kirveskari J (2009) New 16-plex PCR method for rapid detection of diarrheagenic Escherichia coli directly from stool samples. Eur J Clin Microbiol 28:899-908.
  • Bando SY, Moreno AC, Albuquerque JA, Amhaz JM, Moreira-Filho CA, Martinez MB (2010) Expression of bacterial virulence factors and cytokines during in vitro macrophage infection by enteroinvasive Escherichia coli and Shigella flexneri: a comparative study. Mem Inst Oswaldo Cruz 105:786-791.
  • Bardhan P, Faruque ASG, Naheed A, Sack DA (2010) Decreasing shigellosis-related deaths without Shigella spp.-specific interventions, Asia. Emerg Infect Dis 16:1718-1723.
  • Baumann P, Schubert R (1984) Vibrionaceae. In: Krieg NR, Holt JG (eds). Bergey's manual of systematic bacteriology Williams and Wilkins, Hagerstown, MD pp 440-445.
  • Bernardini ML, Mounier J, d'Hauteville H, Coquis-Rondon M, Sansonetti PJ (1989) Identification of icsA, a plasmid locus of Shigella flexneri that governs bacterial intra- and intercellular spread through interaction with F-actin. Proc Natl Acad Sci USA 86:3867-3871.
  • Beutin L, Gleier K, Kontny I, Echeverria P, Scheutz F (1997) Origin and characteristics of enteroinvasive strains of Escherichia coli (EIEC) isolated in Germany. Epidemiol Infect 118:199-205.
  • Bopp CA, Brenner FW, Fields PI, Wells JG, Strockbine NA. Escherichia, Shigella, and Salmonella In: Murray PR, Baron EJ, Jorgensen JH, Pfaller MA, Yolken RH, editors. Manual of clinical microbiology, 8th ed. Washington: ASM Press; 2003. p. 654-671.
  • Brenner DJ (1973) Deoxyribonucleic acid reassociation in the taxonomy of enteric bacteria. Int J Syst Bacteriol 23:298-307.
  • Brenner DJ, Fanning GR, Steigerwalt AG, Orskov I, Orskov F (1972) Polynucleotide sequence relatedness among three groups of pathogenic Escherichia coli strains. Infect Immun 6:308-315.
  • Buchrieser C, Glaser P, Rusniok C, Nedjari H, d'Hauteville H, Kunst F, Sansonetti P, Parsot C (2000) The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri Mol Microbiol 38:760-771.
  • Buysse JM, Stover CK, Oaks EV, Venkatesan M, Kopecko DJ (1987) Molecular cloning of invasion plasmid antigen (ipa) genes from Shigella flexneri: analysis of ipa gene products and genetic mapping. J Bacteriol 169:2561-2569.
  • Cheasty T, Rowe B (1983) Antigenic relationships between the enteroinvasive Escherichia coli O antigens O28ac, O112ac, O124, O136, O143, O144, O152, and O164 and Shigella O antigens. J Clin Microbiol 17:681-684.
  • Christensen H, Nordentoft S, Olsen JE (1998) Phylogenetic relationships of Salmonella based on rRNA sequences. Int J Syst Bacteriol 48:605-610.
  • Clayton F, Warren S (1929) An unusual Bacillus recovered from cases presenting symptoms of dysentery. J Hyg 28:355-362.
  • Croxen MA, Finlay BB (2010) Molecular mechanisms of Escherichia coli pathogenicity. Nat Rev Microbiol 8:26-38.
  • Downie A, Wade E, Young J (1933) An organism resembling the Newcastle type of dysentery bacillus associated with cases of dysentry. J Hyg 33:196-203.
  • DuPont HL, Formal SB, Hornick RB, Snyder MJ, Libonati JP, Sheahan DG, LaBrec EH, Kalas JP (1971) Pathogenesis of Escherichia coli diarrhea. N Engl J Med 285:1-9.
  • DuPont HL, Levine MM, Hornick RB, Formal SB (1989) Inoculum size in shigellosis and implications for expected mode of transmission. J Infect Dis 159:1126-1128.
  • Egile C, Loisel TP, Laurent V, Li R, Pantaloni D, Sansonetti PJ, Carlier MF (1999) Activation of the CDC42 effector N-WASP by the Shigella flexneri IcsA protein promotes actin nucleation by Arp2/3 complex and bacterial actin-based motility. J Cell Biol 146:1319-1332.
  • Ewing WH (1986) The genus Escherichia:Edwards & Ewing's identification of enterobacteriaceaes, Elsevier Science Publishing Co. Inc. New York.
  • Farmer JJ, Davis BR, Hickman-Brenner FW, McWhorter A, Huntley-Carter GP, Asbury MA, Riddle C, Wathen-Grady HG, Elias C, Fanning GR (1985) Biochemical identification of new species and biogroups of enterobacteriaceae isolated from clinical specimens. J Clin Microbiol 21:46-76.
  • Fujioka M, Otomo Y, Ahsan CR (2013) A novel single-step multiplex polymerase chain reaction assay for the detection of diarrheagenic Escherichia coli J Microbiol Meth 92:289-292.
  • Gibotti A, Tanaka TL, Oliveira VR, Taddei CR, Martinez MB (2004) Molecular characterization of enteroinvasive Escherichia coli ipa genes by PCR-RFLP analysis. Braz J Microbiol 35:74-80.
  • Goodman RE, Pickett MJ (1966) Delayed lactose fermentation by enterobacteriaceae. J Bacteriol 92:318-327.
  • Hale TL (1991) Genetic basis of virulence in Shigella species. Microbiol Rev 55:206-224.
  • Hale TL, Sansonetti PJ, Schad PA, Austin S, Formal SB (1983) Characterization of virulence plasmids and plasmid-associated outer membrane proteins in Shigella flexneri, Shigella sonnei, and Escherichia coli Infect Immun 40:340-350.
  • Harris JR, Wachsmuth IK, Davis BR, Cohen ML (1982) High-molecular-weight plasmid correlates with Escherichia coli enteroinvasiveness. Infect Immun 37:1295-1298.
  • Horakova K, Mlejnkova H, Mlejnek P (2008) Specific detection of Escherichia coli isolated from water samples using polymerase chain reaction targeting four genes: cytochrome bd complex, lactose permease, beta-D-glucuronidase, and beta-D-galactosidase. J Appl Microbiol 105:970-976.
  • Houng HS, Sethabutr O, Echeverria P (1997) A simple polymerase chain reaction technique to detect and differentiate Shigella and enteroinvasive Escherichia coli in human feces. Diagn Microbiol Infect Dis 28:19-25.
  • Hsu WB, Wang JH, Chen PC, Lu YS, Chen JH (2007) Detecting low concentrations of Shigella sonnei in environmental water samples by PCR. FEMS Microbiol Lett 270:291-298.
  • Hyma KE, Lacher DW, Nelson AM, Bumbaugh AC, Janda JM, Strockbine NA, Young VB, Whittam TS (2005) Evolutionary genetics of a new pathogenic Escherichia species: Escherichia albertii and related Shigella boydii strains. J Bacteriol 187:619-628.
  • Ito H, Kido N, Arakawa Y, Ohta M, Sugiyama T, Kato N (1991) Possible mechanisms underlying the slow lactose fermentation phenotype in Shigella spp. Appl Environ Microbiol 57:2912-2917.
  • Johnson JR (2000) Shigella and Escherichia coli at the crossroads: machiavellian masqueraders or taxonomic treachery? J Med Microbiol 49:583-585.
  • Kibbee R, Linklater N, Ormeci B (2013) Eliminating false positives in a qPCR assay for the detection of the uidA gene in Escherichia coli J Water Health 11:382-386.
  • Kotloff KL, Winickoff JP, Ivanoff B, Clemens JD, Swerdlow DL, Sansonetti PJ, Adak GK, Levine MM (1999) Global burden of Shigella infections: implications for vaccine development and implementation of control strategies. Bull World Health Organ 77:651-666.
  • Lan R, Alles MC, Donohoe K, Martinez MB, Reeves PR (2004) Molecular evolutionary relationships of enteroinvasive Escherichia coli and Shigella spp. Infect Immun 72:5080-5088.
  • Lan R, Lumb B, Ryan D, Reeves PR (2001) Molecular evolution of large virulence plasmid in Shigella clones and enteroinvasive Escherichia coli Infect Immun 69:6303-6309.
  • Landersjo C, Weintraub A, Widmalm G (1996) Structure determination of the O-antigen polysaccharide from the enteroinvasive Escherichia coli (EIEC) O143 by component analysis and NMR spectroscopy. Carbohydr Res 291:209-216.
  • Lett MC, Sasakawa C, Okada N, Sakai T, Makino S, Yamada M, Komatsu K, Yoshikawa M (1989) virG, a plasmid-coded virulence gene of Shigella flexneri: identification of the virG protein and determination of the complete coding sequence. J Bacteriol 171:353-359.
  • Linnerborg M, Weintraub A, Widmalm G (1999) Structural studies of the O-antigen polysaccharide from the enteroinvasive Escherichia coli O164 cross-reacting with Shigella dysenteriae type 3. Eur J Biochem 266:460-466.
  • Liu J, Gratz J, Amour C, Kibiki G, Becker S, Janaki L, Verweij JJ, Taniuchi M, Sobuz SU, Haque R, Haverstick DM, Houpt ER (2013) A laboratory-developed TaqMan Array Card for simultaneous detection of 19 enteropathogens. J Clin Microbiol 51:472-480.
  • Lukjancenko O, Wassenaar TM, Ussery DW (2010) Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol 60:708-720.
  • Martinez MB, Whittan TS, McGraw EA, Rodrigues J, Trabulsi LR (1999) Clonal relationship among invasive and non-invasive strains of enteroinvasive Escherichia coli serogroups. FEMS Microbiol Lett 172:145-151.
  • Matsushita S, Yamada S, Kai A, Kudoh Y (1993) Invasive strains of Escherichia coli belonging to serotype O121: NM. J Clin Microbiol 31:3034-3035.
  • Maurelli AT, Fernandez RE, Bloch CA, Rode CK, Fasano A (1998) "Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli Proc Natl Acad Sci USA 95:3943-3948.
  • Moreno AC, Ferreira KS, Ferreira LG, Almeida SR, Martinez MB (2012) Recognition of enteroinvasive Escherichia coli and Shigella flexneri by dendritic cells: distinct dendritic cell activation states. Mem Inst Oswaldo Cruz 107:138-141.
  • Moreno AC, Ferreira LG, Martinez MB (2009) Enteroinvasive Escherichia coli vs. Shigella flexneri: how different patterns of gene expression affect virulence. FEMS Microbiol Lett 301:156-163.
  • Moreno AC, Filho AF, Gomes Tdo A, Ramos ST, Montemor LP, Tavares VC, Filho Ldos S, Irino K, Martinez MB (2010) Etiology of childhood diarrhea in the northeast of Brazil: significant emergent diarrheal pathogens. Diagn Microbiol Infect Dis 66:50-57.
  • Nataro JP, Kaper JB (1998) Diarrheagenic Escherichia coli Clin Microbiol Rev 11:142-201.
  • Oberhelman RA, Kopecko DJ, Venkatesan MM, Salazar-Lindo E, Gotuzzo E, Yi A, Chea-Woo E, Ruiz R, Fernandez-Prada C, Leon-Barua R (1993) Evaluation of alkaline phosphatase-labelled ipaH probe for diagnosis of Shigella infections. J Clin Microbiol 31:2101-2104.
  • Ojha SC, Yean Yean C, Ismail A, Banga Singh K-K (2013) A pentaplex PCR assay for the detection and differentiation of Shigella species. BioMed Res Int 2013.
  • Orskov I, Wachsmuth IK, Taylor DN, Echeverria P, Rowe B, Sakazaki R, Orskov F (1991) Two new Escherichia coli O groups: O172 from Shigella-like toxin II-producing strains (EHEC) and O173 from enteroinvasive E. coli (EIEC). APMIS 99:30-32.
  • Pal T, Al-Sweih NA, Herpay M, Chugh TD (1997) Identification of enteroinvasive Escherichia coli and Shigella strains in pediatric patients by an IpaC-specific enzyme-linked immunosorbent assay. J Clin Microbiol 35:1757-1760.
  • Parsot C (2005) Shigella spp. and enteroinvasive Escherichia coli pathogenicity factors. FEMS Microbiol Lett 252:11-18.
  • Pavlovic M, Luze A, Konrad R, Berger A, Sing A, Busch U, Huber I (2011) Development of a duplex real-time PCR for differentiation between E. coli and Shigella spp. J Appl Microbiol 110:1245-1251.
  • Peng J, Zhang X, Yang J, Wang J, Yang E, Bin W, Wei C, Sun M, Jin Q (2006) The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella BMC Genomics 7:218.
  • Porter ME, Dorman CJ (2002) In vivo DNA-binding and oligomerization properties of the Shigella flexneri AraC-like transcriptional regulator VirF as identified by random and site-specific mutagenesis. J Bacteriol 184:531-539.
  • Prosseda G, Fradiani P, Di Lorenzo M, Falconi M, Micheli G, Casalino M, Nicoletti M, Colonna B (1998) A role for H-NS in the regulation of the virF gene of Shigella and enteroinvasive Escherichia coli Res Microbiol 149:15-25.
  • Pupo GM, Lan R, Reeves PR (2000) Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc Natl Acad Sci USA 97:10567-10572.
  • Rolland K, Lambert-Zechovsky N, Picard B, Denamur E (1998) Shigella and enteroinvasive Escherichia coli strains are derived from distinct ancestral strains of E. coli Microbiology 144:2667-2672.
  • Rowe B, Gross RJ, Van Oye E (1975) An organism differing from Shigella boydii 13 only in its ability to produce gas from glucose. Int J Syst Bacteriol 25:301-303.
  • Sankaran K, Banerjee S, Pavankumar AR, Jesudason M, Reissbrodt R, Williams pH (2009) Apyrase-based colorimetric test for detection of Shigella and enteroinvasive Escherichia coli in stool. Diagn Microbiol Infect Dis 63:243-250.
  • Sansonetti PJ, d'Hauteville H, Formal SB, Toucas M (1982a) Plasmid-mediated invasiveness of "Shigella-like" Escherichia coli Ann Microbiol (Paris) 133:351-355.
  • Sansonetti PJ, Hale TL, Dammin GJ, Kapfer C, Collins HH, Jr., Formal SB (1983) Alterations in the pathogenicity of Escherichia coli K-12 after transfer of plasmid and chromosomal genes from Shigella flexneri Infect Immun 39:1392-1402.
  • Sansonetti PJ, Kopecko DJ, Formal SB (1981) Shigella sonnei plasmids: evidence that a large plasmid is necessary for virulence. Infect Immun 34:75-83.
  • Sansonetti PJ, Kopecko DJ, Formal SB (1982b) Involvement of a plasmid in the invasive ability of Shigella flexneri Infect Immun 35:852-860.
  • Sansonetti PJ, Mounier J, Prevost MC, Mege RM (1994) Cadherin expression is required for the spread of Shigella flexneri between epithelial cells. Cell 76:829-839.
  • Sasakawa C, Buysse JM, Watanabe H (1992) The large virulence plasmid of Shigella Curr Top Microbiol Immunol 180:21-44.
  • Scheutz F SN, (2005) Genus I. Escherichia. In: Bergey's Manual of Systematic Bacteriology, Springer, USA.
  • Sethabutr O, Venkatesan M, Yam S, Pang LW, Smoak BL, Sang WK, Echeverria P, Taylor DN, Isenbarger DW (2000) Detection of PCR products of the ipaH gene from Shigella and enteroinvasive Escherichia coli by enzyme linked immunosorbent assay. Diagn Microbiol Infect Dis 37:11-16.
  • Shepherd JG, Wang L, Reeves PR (2000) Comparison of O-antigen gene clusters of Escherichia coli (Shigella) Sonnei and Plesiomonas shigelloides O17: Sonnei gained its current plasmid-borne O-antigen genes from P. shigelloides in a recent event. Infect Immun 68:6056-6061.
  • Silva RM, Toledo MR, Trabulsi LR (1980) Biochemical and cultural characteristics of invasive Escherichia coli J Clin Microbiol 11:441-444.
  • Simmons DA, Romanowska E (1987) Structure and biology of Shigella flexneri O antigens. J Med Microbiol 23:289-302.
  • Small PL, Falkow S (1988) Identification of regions on a 230-kilobase plasmid from enteroinvasive Escherichia coli that are required for entry into HEp-2 cells. Infect Immun 56:225-229.
  • Song T, Toma C, Nakasone N, Iwanaga M (2005) Sensitive and rapid detection of Shigella and enteroinvasive Escherichia coli by a loop-mediated isothermal amplification method. FEMS Microbiol Lett 243:259-263.
  • Stoebel DM (2005) Lack of evidence for horizontal transfer of the lac operon into Escherichia coli Mol Biol Evol 22:683-690.
  • Stypulkowska H (1964) Atypical strain of Shigella dysenteriae 3 isolated in Poland. Med Dosw Mikrobiol 16:147-154.
  • Suzuki T, Miki H, Takenawa T, Sasakawa C (1998) Neural Wiskott-Aldrich Syndrome Protein is implicated in the actin-based motility of Shigella flexneri EMBO J 17:2767-2776.
  • Talukder KA, Azmi IJ (2012) Population genetics and molecular epidemiology of Shigella species. In: Faruque SM (eds). Foodborne and waterborne bacterial pathogens epidemiology, evolution and molecular biology. Caister Academic Press, pp 63-76.
  • Thiem VD, Sethabutr O, Von Seidlein L, Van Tung T, Chien BT, Lee H, Houng HS, Hale TL, Clemens JD, Mason C (2004) Detection of Shigella by a PCR assay targeting the ipaH gene suggests increased prevalence of shigellosis in Nha Trang, Vietnam. J Clin Microbiol 42:2031-2035.
  • Toledo MR, Trabulsi LR (1983) Correlation between biochemical and serological characteristics of Escherichia coli and results of the Sereny test. J Clin Microbiol 17:419-421.
  • Ud-Din AIMS, Azmi IJ, Dutta DK, Wahid SUH, Iqbal MS, Faroque ASG, Endtz HP, Cravioto A, Talukder KA (2010) Plasmid profiling facilitates the detection of invasive Shigella and enteroinvasive E. coli directly from enriched stool culture broth of diarrheal patients. The 13th Annual Scientific Conference (ASCON XIII), icddr,b Dhaka, Bangladesh, pp 256.
  • Venkatesan MM, Goldberg MB, Rose DJ, Grotbeck EJ, Burland V, Blattner FR (2001) Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri Infect Immun 69:3271-3285.
  • Vieira N, Bates SJ, Solberg OD, Ponce K, Howsmon R, Cevallos W, Trueba G, Riley L, Eisenberg JN (2007) High prevalence of enteroinvasive Escherichia coli isolated in a remote region of northern coastal Ecuador. Am J Trop Med Hyg 76:528-532.
  • Wang SJ, Chen JH (2012) A rapid and specific PCR method for the detection of Shigella spp. in spiked samples. J Food Drug Anal 20:59-65.
  • Wen X, Wu Y, Bian F, Sun Y, Zheng X, Zhang Y, Jiang C, Yuan G (2012) High prevalence of atypical class 1 integrons and class 2 integrons in multi-drug resistance Shigella flexneri isolated from China. Afr J Microbiol Res 6:6987-6993.
  • Yang F, Yang J, Zhang X, Chen L, Jiang Y, Yan Y, Tang X, Wang J, Xiong Z, Dong J, Xue Y, Zhu Y, Xu X, Sun L, Chen S, Nie H, Peng J, Xu J, Wang Y, Yuan Z, Wen Y, Yao Z, Shen Y, Qiang B, Hou Y, Yu J, Jin Q (2005) Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res 33:6445-6458.
  • Yang J, Nie H, Chen L, Zhang X, Yang F, Xu X, Zhu Y, Yu J, Jin Q (2007) Revisiting the molecular evolutionary history of Shigella spp. J Mol Evol 64:71-79.
  • Correspondence:
    Abu Ud-Din
    International Centre for Diarrhoeal Disease Research in Bangladesh
    Identification and Subtyping of Enteric Pathogens
  • Publication Dates

    • Publication in this collection
      13 Feb 2015
    • Date of issue
      Dec 2014


    • Accepted
      13 Dec 2013
    • Received
      28 May 2013
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