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Appl Environ Microbiol. 2010 Jan; 76(1): 203–211.
Published online 2009 Oct 30. doi:  10.1128/AEM.01921-09
PMCID: PMC2798666

Low-Density Macroarray Targeting Non-Locus of Enterocyte Effacement Effectors (nle Genes) and Major Virulence Factors of Shiga Toxin-Producing Escherichia coli (STEC): a New Approach for Molecular Risk Assessment of STEC Isolates[down-pointing small open triangle]


Rapid and specific detection of Shiga toxin-producing Escherichia coli (STEC) strains with a high level of virulence for humans has become a priority for public health authorities. This study reports on the development of a low-density macroarray for simultaneously testing the genes stx1, stx2, eae, and ehxA and six different nle genes issued from genomic islands OI-122 (ent, nleB, and nleE) and OI-71 (nleF, nleH1-2, and nleA). Various strains of E. coli isolated from the environment, food, animals, and healthy children have been compared with clinical isolates of various seropathotypes. The eae gene was detected in all enteropathogenic E. coli (EPEC) strains as well as in enterohemorrhagic E. coli (EHEC) strains, except in EHEC O91:H21 and EHEC O113:H21. The gene ehxA was more prevalent in EHEC (90%) than in STEC (42.66%) strains, in which it was unequally distributed. The nle genes were detected only in some EPEC and EHEC strains but with various distributions, showing that nle genes are strain and/or serotype specific, probably reflecting adaptation of the strains to different hosts or environmental niches. One characteristic nle gene distribution in EHEC O157:[H7], O111:[H8], O26:[H11], O103:H25, O118:[H16], O121:[H19], O5:H−, O55:H7, O123:H11, O172:H25, and O165:H25 was ent/espL2, nleB, nleE, nleF, nleH1-2, nleA. (Brackets indicate genotyping of the flic or rfb genes.) A second nle pattern (ent/espL2, nleB, nleE, nleH1-2) was characteristic of EHEC O103:H2, O145:[H28], O45:H2, and O15:H2. The presence of eae, ent/espL2, nleB, nleE, and nleH1-2 genes is a clear signature of STEC strains with high virulence for humans.

Since the early 1980s, Shiga toxin-producing Escherichia coli (STEC) has emerged as a major cause of food-borne infections (17, 30). STEC can cause diarrhea in humans, and some STEC strains may cause life-threatening diseases, such as hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). On the basis of its human pathogenicity, this subset of STEC strains was also designated enterohemorrhagic E. coli (EHEC) (22, 25). Numerous cases of HC and HUS have been attributed to EHEC serotype O157:H7 strains, but it has now been recognized that other serotypes of STEC belong to the EHEC group. The STEC seropathotype classification is based upon the serotype association with human epidemics, HUS, and diarrhea and has been developed as a tool to assess the clinical and public health risks associated with non-O157 EHEC and STEC strains (18). Only a few serotypes of STEC have been reported as most frequently associated with severe disease in humans. Besides E. coli O157:[H7], five other serotypes, namely O26:[H11], O103:H2, O111:[H8], O121:[H19], and O145:[H28], account for the group of typical EHEC (25). (Brackets indicate genotyping of the flic or rfb genes; the absence of brackets indicates data obtained with the conventional serotyping approach using specific antisera, as described in Materials and Methods.) Atypical EHEC group strains of serotypes O91:[H21], O113:H21, and O104:H21 are less frequently involved in hemorrhagic diseases than typical EHEC but are a frequent cause of diarrhea (8, 12, 25). Recent data from Enter-Net, a global surveillance consortium of 35 countries that tracks enteric infectious diseases, showed that the number of human cases of illness caused by non-O157 EHEC increased globally by 60.5% between 2000 and 2005, while at the same time the number of cases linked to EHEC O157 increased by only 13% (1). In the past few years, new serotypes of EHEC that differ from those previously known as typical and atypical EHEC have emerged (6, 8, 23, 24, 31). These EHEC strains were identified as important causes of food-borne infections in humans and were described as “new emerging EHEC.”

The production of Shiga toxin (Stx) by EHEC is the primary virulence trait responsible for HUS, but many E. coli non-O157:H7 strains that produce Stx do not cause HUS. Identification of human-virulent STEC by detection of unique stx genes may be misleading, since not all STEC strains are clinically significant for humans (11). Besides the ability to produce one or more types of Shiga toxins, typical EHEC strains harbor a genomic island called the “locus of enterocyte effacement” (LEE). Atypical EHEC strains are negative for the LEE but may carry other factors for colonization of the human intestine (6, 25). The LEE carries genes encoding functions for bacterial colonization of the gut and for destruction of the intestinal mucosa, thus contributing to the disease process (25). The LEE eae gene product intimin is directly involved in the attaching and effacing (A/E) process (37). The LEE includes regulatory elements, a type III secretion system (TTSS), secreted effector proteins, and their cognate chaperon (13, 29). In addition to the intimin, most of the typical EHEC strains harbor the plasmid-borne enterohemolysin (ehxA), which is considered an associated virulence factor (6, 25).

A number of other pathogenicity island (PAI) candidates, including O island 122 (OI-122) and O island 71 (OI-71), have been found in EHEC and EPEC strains, but their role in disease is not fully clear. Within the EHEC group, both O157:H7 strains (19, 34) and non-O157 strains (18, 35) present a variable repertoire of virulence determinants, including a collection of non-LEE-encoded effector (nle) genes that encode translocated substrates of the type III secretion system (9, 20). Our objective was to identify type III secreted virulence factors that distinguish EHEC O157 and non-O157 strains constituting a severe risk for human health from STEC strains that are not associated with severe and epidemic disease, a concept called “molecular risk assessment” (MRA) by Coombes et al. (9). Supporting the MRA approach requires the development of diagnostic tests based on multiplex nucleic acid amplification and microfluidics-based detection using standardized platforms applicable in hospital service or public health laboratories. It is now feasible to develop low-density DNA arrays that can be used to examine the gene inventory from isolated strains, offering a genetic bar coding strategy. A recent innovation in this field is the introduction of the GeneSystems PCR technology (5, 36). In this study, we have developed a GeneDisc array designed for simultaneous detection of genes encoding Shiga toxins 1 and 2 (stx1 and stx2), intimins (eae), enterohemolysin (ehxA), and six different nle genes derived from genomic islands OI-71 and OI-122. We focused our efforts on the detection of the OI-122 genes, ent/espL2 (Z4326), nleB (Z4328), and nleE (Z4329), and the OI-71 genes, nleF (Z6020), nleH1-2 (Z6021), and nleA (Z6024). The macroarray presented here was evaluated for its specificity and ability to discriminate between STEC causing serious illness in humans and other E. coli strains.


Principle of the GeneDisc array.

The principle of the GeneDisc array (Gene Systems, Bruz, France) has been previously described (5). It is based on real-time PCR applications of multiple targets in a plastic reaction tray engraved with reaction microchambers preloaded with desiccated PCR primers and TaqMan probes labeled with either the reporter dye 6-carboxyfluorescein (6-FAM; 490 to 520 nm) or carboxy-X-rhodamine (ROX; 580 to 620 nm).

Properties of the GeneDisc array developed in this study.

The “virulotyping GeneDisc” was designed for simultaneous examination of six different samples, each being tested for 10 EHEC-specific gene targets, together with negative and inhibition controls. It has the following settings: microwell 1, negative PCR control (6-FAM label) and PCR inhibition control (ROX-label); microwell 2, stx2 (FAM) and stx1 (ROX); microwell 3, ent/espL2 (FAM) and nleF (ROX); microwell 4, nleB (FAM) and nleH1-2 (ROX); microwell 5, nleE (FAM) and nleA (ROX); and microwell 6, ehxA (FAM) and eae (ROX). The oligonucleotide primers and gene probes used in the GeneDisc are listed in Table Table1.1. Primers and probes used for detecting stx1, stx2, and eae were described previously (26, 28) and were evaluated for their specificity and sensitivity (5). All oligonucleotides were purchased from Sigma-Aldrich (St. Quentin Fallavier, France). GeneDisc spotting and manufacturing were performed by GeneSystems (Bruz, France).

Primers and probes preloaded in the GeneDisc

Bacterial strains investigated with the GeneDisc array.

Strains of E. coli and other Enterobacteriaceae that were investigated for their virulence gene content with the virulotyping GeneDisc were from the collection of the National Reference Laboratory for E. coli (NRL-E. coli) at the Federal Institute for Risk Assessment (BfR) in Berlin, Germany, and from the French Food Safety Agency (AFSSA) in Maisons-Alfort, France. We used eae-positive attaching and effacing E. coli strains that were characterized by their eae alleles as previously described (21). STEC strains used in this study have been characterized by their stx genotypes as previously reported (2, 4, 21). All strains investigated in this work were identified for the E. coli O (lipopolysaccharide) and H (flagellar) antigens with specific antisera produced at the NRL-E. coli at the BfR as previously described (21). For reference strains of EHEC O groups O26, O103, O111, O145, and O157, we used strains previously identified by serotyping of their O and H antigens and by fliC genotyping (3). The characteristics and origin of EHEC reference strains H19 (O26:H11), PMK5 (O103:H2), CL37 (O111:[H8]), CB7874 (O145:[H28]), and EDL933 (O157:H7) had been described in other publications (3, 27, 32). The EHEC strain EDL933 (O157:H7) and the EPEC strain E2348/69 (O127:H6) were used as positive controls for testing the complete set of nle genes, i.e., ent/espL2 (Z4326), nleB (Z4328), nleE (Z4329), nleF (Z6020), nleH1-2 (Z6021), and nleA (Z6024). Strain C600 (E. coli K-12) was taken as a negative control for all genes investigated in this work (4). In addition, 97 enterobacteriaceal strains (from Cronobacter sakazakii, Yersinia spp., Escherichia spp., Salmonella spp., Shigella spp., Citrobacter spp., Hafnia spp., Klebsiella spp., and Proteus spp.) that were characterized by standard methods (14) were used for evaluation of the GeneDisc array. Except for Shigella dysenteriae type 1 (stx1), the Shigella sonnei strain CB7888 (stx1) (4), and the Citrobacter rodentium strain 10835 (eae), all other Enterobacteriacae isolates were negative for stx and eae genes. For examination, bacteria were cultured to single colonies on Luria broth plates and grown overnight at 37°C. A small aliquot of the colony corresponding to approximately 2 × 106 bacteria was either DNA extracted using the InstaGene matrix (Bio-Rad Laboratories, Marnes La Coquette, France) or directly added to 200 μl sterile water and vortexed thoroughly. Thirty-six microliters of the resuspended bacteria or DNA extracts was tested by the GeneDisc array.


Association of eae types, ehxA gene, and nle genes with typical and atypical EHEC strains.

243 EHEC strains, including typical EHEC (n = 183), atypical EHEC (n = 18), and new emerging EHEC strains (n = 41) as well as stx-negative strains belonging to the same serotype as the EHEC strains (n = 65), were investigated with the virulotyping GeneDisc array (Tables (Tables2,2, ,3,3, and and4).4). All EHEC strains tested positive for stx1 and/or stx2 genes, giving a total concordance with data previously published (3, 5, 15, 28). eae genes were detected in the strains belonging to the classical EHEC groups O26, O103, O111, O121, O145, and O157 as well as in emerging EHEC type O5, O15, O45, O55, O118, O123, O165, and O172 strains. Only one EHEC O103:H2 strain tested negative for the eae genes (Table (Table2).2). eae genes were absent in all other STEC strains investigated, including atypical EHEC O91:H21 and O113:H21; these strains are frequently isolated from food and from human patients (33). All eae-negative STEC strains as well as the atypical EHEC strains were also negative for the set of nle genes investigated in this study (Table (Table4).4). nle genes borne by islands OI-71 and OI-122 were present in typical EHEC strains, including the new emerging serotypes. One characteristic pattern of nle genes (ent/espL2, nleB, nleE, nleF, nleH1-2, and nleA) was found in EHEC strains belonging to serotypes O157:[H7], O111:[H8], O26:[H11], O103:H25, O118:[H16], O121:[H19], O5:H−, O55:H7, O123:H11, O172:H25, and O165:H25 (Table (Table2).2). Among the 76 EHEC O157:[H7] strains, six were sorbitol-fermenting (SF) O157:HNM stx2 strains; these showed the same nle pattern as the non-SF O157:[H7] strains. Two O-rough:[H7] (stx2, eae-gamma) strains, previously identified as positive for the rfbEO157 gene, had the same nle pattern as serologically typeable O157:[H7] strains.

Virulotyping of the eae and nle genes in EHEC strains
Virulotyping of the eae and nle genes in stx-negative strains
Virulotyping of strains that tested negative for the eae and nle genes

Another type of nle pattern was found with EHEC strains belonging to serotypes O103:H2, O145:[H28], O45:H2, and O15:H2. These were positive for all nle genes investigated except for OI-71-borne genes nleA and nleF (Table (Table2).2). Our results indicate that typical EHEC strains are highly conserved for the distribution of nle genes and point to an association of eae genotype, nle pattern, and serotype. Exceptions were rarely observed, such as an absence of the nleH1-2 gene in one of the 34 examined EHEC O26:H11 strains (Table (Table2).2). Most (93.25%) of the typical EHEC strains were positive for the plasmid-located ehxA gene encoding enterohemolysin; this marker was also present in 87% of new emerging EHEC, in 73% of the atypical EHEC, and in 42.66% of the other STEC strains investigated in this study.

Identification and characterization of stx-negative strains resembling EHEC for serotype and other properties.

It was previously reported that EHEC strains can lose their stx genes spontaneously during infection and upon subculturing (16). We were interested in investigating stx-negative, eae-positive E. coli strains belonging to EHEC-associated serotypes for their similarity with EHEC strains in regard to their eae genotypes and their nle genes. The results obtained with 65 strains are presented in Table Table3.3. We could identify three stx-negative O157:[H7], 10 O26:[H11], one O103:[H2], three O121:[H19], one O121:H−, and one O15:H2 strain that showed eae genotypes and nle patterns similar to those exhibited by Stx-producing EHEC strains belonging to the same serotypes (Table (Table3).3). It seems likely that these strains represent variants of EHEC strains belonging to these serotypes that have lost their stx genes. In contrast, stx-negative strains belonging to the same O groups but showing H types other than those of the classical EHEC strains differed also with respect to their eae genotypes and the presence and types of nle genes (Table (Table3),3), indicating that these were not variants of classical EHEC strains. EHEC O111:[H8] strains were usually positive for eae-theta and for all OI-71- and OI-122-encoded nle genes. Only one of 25 strains was negative for nleF (Table (Table2).2). Three stx-negative strains (O111:H11 and O111:[H25]) showed nle genotypes similar to those of EHEC O111:[H8]. The differences in the H type and in the eae genotype indicate that these were not closely related to strains of the EHEC O111:[H8] group. All other O111 strains, including EPEC O111:H2, were different from EHEC O111:[H8] with respect to their nle genotypes (Table (Table33).

EHEC O145:[H28] strains are characterized by possession of the complete set of OI-122 module 2-associated nle genes ent, nleB, and nleE (Table (Table2).2). Interestingly, these genes were absent in two Stx-negative O145:[H28] strains which resemble O145:[H28] EHEC with respect to all other traits that were investigated (Table (Table3).3). It cannot be excluded that these strains have lost their stx genes and the OI-122 PAI. All EPEC O145 strains differed significantly from EHEC O145:[H28] as they do not possess any nle gene and carry other eae genotypes.

In the group of O103:H2 strains, the rabbit EPEC strain E22 was similar to all EHEC O103:H2 strains for the set of nle genes but differed in the eae-beta subtype, as EHEC O103:H2 strains carry eae-epsilon. In contrast, the EHEC O103:H25 strain which caused an outbreak of HUS in Norway in 2006 (31) was found to be different from the classical EHEC O103:H2 clone by its H type, its eae type, and the set of nle genes.

We additionally investigated representatives of classical EPEC groups. The EPEC O55:H7 strain was similar in its eae genotype and nle genes to EHEC O157:[H7] and EHEC O55:H7 strains. All nle genes investigated were also present in the EPEC O127:H6 reference strain E2348/69. EPEC O84:H2 harbored all nle genes except nleE. EPEC O156:H8 was negative only for the OI-71 nleF and nleA genes. EPEC O128:H2 and O113:H6 were positive only for nleH and lacked the OI-122 module 2-associated nle genes. EPEC O55:H6 also lacked the OI-122 module 2-associated nle genes but carried nleH and nleF. In contrast, EPEC O86:H40 carried the OI-122 module 2-associated nle genes but none of those located on OI-71 (Table (Table3).3). Some other EPEC strains (O125:H6, O126:H6, O51, and O76:H51) did not possess any nle genes and usually carried the eae-alpha genotype.

Identification and characterization of eae- and nle-negative strains.

Numerous types of STEC are isolated from animals and food, but only 5% of these are positive for an eae gene or belong to serogroups O26, O103, O111, O145, and O157 (2). Some of the eae-negative STEC strains are known to cause diarrhea in humans but are rarely involved in hemorrhagic diseases such as HC and HUS (3, 16, 33). We were interested in investigating representative strains of the eae-negative STEC types that are frequently isolated from food (O8, O91, O100, O113, O146, O128, and O174). A total of 149 STEC strains that were isolated from food, animals, and humans as well as 29 fecal E. coli isolates from healthy children (FEC) were investigated with the virulotyping GeneDisc. The results show that the eae-negative STEC strains also tested negative for the nle genes (Table (Table4).4). All the E. coli strains issued from fecal flora of healthy infants were also found negative for stx, eae, and the nle genes. These data corroborate previous findings (18) indicating the absence of the LEE as well as the OI-122- and OI-71-associated nle genes in nonpathogenic E. coli strains.

In order to examine the possible spread of the OI-122- and OI-71-associated nle genes to other Enterobacteriaceae, we have investigated 68 strains of bacteria comprising Escherichia, Cronobacter, Yersinia, Salmonella, Shigella, Citrobacter, Hafnia, Klebsiella, and Proteus species. Except for the two strains of Shigella dysenteriae type 1 (stx1), the Shigella sonnei strain CB7888 (stx1), and the Citrobacter rodentium strain CB10835 (eae, nleE, nleA) (data not shown), all other Enterobacteriacae isolates tested negative for stx1, stx2, eae, ehxA, and the nle genes (Table (Table44).


The emergence of O157 and non-O157 EHEC in severe and epidemic human disease is a global health problem (11). The concept of MRA employing the presence of effector genes to diagnose HUS and identify outbreak-associated EHEC strains (9) has opened up new tools to assess the public health risks associated with STEC strains from food, animals, and the environment. In this study, we have evaluated a low-density DNA array that was designed for this purpose.

The detection systems for the major virulence genes of EHEC, i.e., stx1, stx2, eae, and ehxA, were previously evaluated for their specificity (5). Accordingly, stx genes were detected only in STEC, EHEC, S. dysenteriae type 1, and the S. sonnei strain CB7888, which were previously investigated for Stx production and for stx genes with block cycler PCR systems (2, 3, 5, 15). Similar findings were made for the ehxA gene. Its prevalences were significantly different between STEC (42.66%) and EHEC (90%). ehxA was not present in other E. coli strains tested in this study. The eae gene was detected in typical EHEC strains, as well as in all EPEC strains and in C. rodentium (strain 10835). Distribution of the nle genes was found to be closely associated with certain serotypes and intimin genotypes in typical EHEC strains, including the new emerging EHEC strains. Remarkably, nle genes carried by the module 2 of the O island OI-122 were detected in all typical and new emerging EHEC. In contrast, the nle genes issued from the O island OI-71 were not detected in all isolates of EHEC strains. The presence of nleF (72.8%) and nleA (79%) was less associated with EHEC than the presence of nleH1-2 (99.5%).

Our approach allows the identification of new emerging EHEC strains that were recently reported as severe human pathogens. One of these is the EHEC O103:H25 type strain, responsible for a food-borne outbreak of HUS in patients from Norway in 2006 (31). Interestingly, this strain had the same nle profile as EHEC O157:H7. O5:HNM, as another emerging EHEC type isolated from beef, dairy products, and human patients with HC (24), also shows the nle pattern ent/espL2, nleB, nleE, nleF, nleH1-2, nleA. A third type of emerging EHEC O118:H16/HNM (23) shows this same nle pattern (ent/espL2, nleB, nleE, nleF, nleH1-2 nleA), which is characteristic for EHEC O157:H7 and most of the typical EHEC strains.

On the other hand, not all EHEC strains possess the complete nle pattern investigated in this study. Thus, EHEC strains of serotypes O103:H2 and O145:H28 show a second characteristic nle pattern with positive signals for only ent/espL2, nleB, nleE, and nleH1-2 genes. These data are in accordance with the results of Creuzburg and Schmidt, who reported the presence of genetic variants of nleA in EHEC O103:H2 (espI-like) and in EHEC O145:H28 (nleA3, nleA5, nleA6-1, and nleA11) which differ significantly from nleA (Z6024) (10). A total of 15 nleA variants have been described with sequence identities at the amino acid level ranging from 71% to 96% (10). Moreover, we found that new emerging EHEC type O15:H2 and O45:H2 strains possess the same nle pattern (ent/espL2, nleB, nleE, nleH1-2) as EHEC O103:H2 and O145:H28 strains.

We report a number of stx-negative, eae-positive E. coli strains belonging to EHEC-associated serotypes which resemble EHEC strains in terms of their eae genotypes and their nle gene pattern. nle typing could thus be useful to identify EHEC variants which have lost their stx genes, as is reported to occur upon subculturing (16). It is also of diagnostic value for identification of the causative agent in HUS patients, since it was reported that many of these excrete stx-negative variants of the original EHEC strains in the course of the disease (7). The nle genes, in different distributions, were also detected in some EPEC strains. Contrary to the results reported by Creuzburg and Schmidt (10), the EPEC strain E2348/69 (O127:H6) tested positive for nleA (Z6024) in our study. The fact that EPEC strains carry multiple types of nle genes indicates that these effectors might play a role in EPEC-induced diarrhea in infants. The nle genes were absent in other species of Enterobacteriaceae that are frequently isolated from human feces and in fecal E. coli from the stool flora of healthy infants. This was taken as evidence that the nle virulotyping is specific and suitable for a rapid identification of human-virulent EHEC and possibly EPEC strains.

Data reported in the present study have shown that the simultaneous detection of stx1 and/or stx2, eae, and ehxA genes, together with some non-LEE effector genes located on PAI OI-71 and OI-122, provides a thorough approach for molecular risk assessment of STEC virulence. In summary, the results indicate that EHEC constitutes a heterogeneous group of pathogens sharing a common core of nle virulence determinants but may also harbor various distributions of nle genes that are strain or serotype specific. It is noteworthy that the presence in the same strain of a core of virulence determinants (eae, ent/espL2, nleB, nleE, and nleH1-2) is a strong signature of a human-pathogenic EHEC that can cause life-threatening diseases such as HC and HUS. Detection of these genetic markers in all typical EHEC, called the “gang of five” (6), but also in new emerging EHEC types such as O5:H− (24), O15:H2 (8), O118:H16 (23), and O103:H25 (31), shows the importance of monitoring routinely these markers in STEC isolated from the environment, animals, foods, and humans.


We are grateful to Gad Frankel (Imperial College, London, England) for providing an isolate of Citrobacter rodentium, to Reiner Helmuth (BfR, Berlin, Germany) and Anne Brisabois (AFSSA, Maisons-Alfort, France) for supplying us with Salmonella reference strains, to Alex Gill (Health Canada, Ottawa, Canada) for providing DNA from EHEC O165:H25, and to Eckhard Strauch (BfR) for supplying us with Yersinia reference strains.


[down-pointing small open triangle]Published ahead of print on 30 October 2009.


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