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Journal of Clinical Microbiology, October 2005, p. 5143-5149, Vol. 43, No. 10
0095-1137/05/$08.00+0 doi:10.1128/JCM.43.10.5143-5149.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Division of Microbial Toxins, Robert Koch Institut, Nordufer 20, D-13353 Berlin, Germany,1 National Reference Laboratory for Escherichia coli, Federal Institute for Risk Assessment (BfR), D-12277 Berlin, Germany,2 TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hong Da Street, TEDA, Tianjin 300457, Peoples Republic of China,3 Tianjin Key Laboratory for Microbial Functional Genomics, TEDA College, Nankai University, 23 Hong Da Street, TEDA, Tianjin 300457, Peoples Republic of China,4 Freie Universität Berlin, Königin Luise Str. 12-16, D-14195 Berlin, Germany,5 Departamento de Microbiologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, 05508-900 São Paulo, Brazil,6 State Key Laboratory for Molecular Virology and Genetic Engineering, Beijing 100052, Peoples Republic of China7
Received 16 April 2005/ Returned for modification 13 June 2005/ Accepted 11 July 2005
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More recently, DNA-based typing methods were employed for the detection of E. coli O-antigen-encoding genes, and correspondent PCR protocols for the identification of pathogenic E. coli strains such as O157, O111, O114, and O172 were developed (12, 14, 28, 30). The O antigen, as a part of the lipopolysaccharide moiety of gram-negative bacteria, consists of many repeats of an oligosaccharide unit (O unit) (9). The genes for O-antigen synthesis are normally clustered between the two housekeeping genes galF and gnd on the E. coli chromosome, and a conserved 39-bp JUMPStart sequence, which is required for the regulation of downstream genes by RfaH (15), is located in the intergenic region between galF and the O-antigen gene cluster (18). The genes in the O-antigen gene cluster are normally classified into three main classes: genes for synthesis of nucleotide sugar precursors, genes encoding glycosyltransferases, and genes for O-unit processing, including the flippase (Wzx) and polymerase (Wzy) genes (9). Genes in the last two classes are O-antigen specific since they are specific to sugar donors, sugar acceptors, and linkages between the sugars (30). The differences between O-antigen forms are almost entirely due to genetic variations in the O-antigen gene clusters (9).
PCR methods for the detection of O-antigen-specific genes such as wzx and wzy represent a reliable, rapid, and sensitive alternative to serotyping, particularly for E. coli strains that belong to serogroups that are not covered by the panel of commercially available antisera (5, 14, 22, 27). Moreover, PCR detection of O-antigen-specific genes allows detection of strains which are serologically rough for their O antigens, and last but not least, serological cross-reactions between different O antigens that may cause difficulties in O typing are ruled out.
In this study, a collection of 13 E. coli O174 strains and 12 E. coli O177 strains was studied on the O:H serotypes and virulence markers. The O-antigen gene clusters of the E. coli reference strains for the newly defined serogroups O174 and O177 were sequenced, and the associated genes were identified on the basis of homology. By screening against all 186 E. coli O serotypes (including Shigella) strains, genes specific for E. coli serogroups O174 and O177 were identified. The PCR assays that were developed in this study for detection of O-antigen-specific genes were shown to be highly specific and sensitive and were shown to be useful for the detection of E. coli O174 and O177 strains from clinical, food, and environmental samples.
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TABLE 1. Relevant properties of E. coli O174 and O177 strains
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Phenotypical and genotypical characterization of virulence markers. The E. coli O174 and O177 strains were investigated for the production of cytotoxins with the Verocell assay and for hemolysins on enterohemolysin agar (Oxoid, Wesel, Germany) (6). Detection and subtyping of genes encoding the EPEC adherence factor (EAF) plasmid, intimins (eae), Shiga toxins (stx), and EHEC-hemolysin (ehxA) were performed by PCR and RFLP analysis using primers and restriction enzymes described previously (3, 13). An updated nomenclature of Shiga toxin types was used as described recently (3).
Construction of DNase I shotgun bank, sequencing, and analysis of O-antigen gene cluster. Chromosomal DNA was prepared as previously described (2). The primer pairs wl-1098 (5'-ATT GGT AGC TGT AAG CCA AGG GCG GTA GCG T-3') and wl-2211 (5'-CAC TGC CAT ACC GAC GAC GCC GAT CTG TTG CTT GG-3'), based on the JUMPStart sequence and gnd, respectively (30), were used to amplify the O-antigen gene clusters of E. coli O174 and O177 type strains 2531-54 and E40874-85 (Table 1). The PCR was performed for 30 cycles as follows: a denaturation step at 94°C for 10 s, an annealing step at 60°C for 30 s, and an extension step at 68°C for 15 min. Shotgun banks for each strain were constructed as described previously (30). Sequencing was carried out using an ABI 3730 automated DNA sequencer, and sequence data were analyzed using computer programs as described previously (11).
Specificity and sensitivity test of O-serogroup-specific PCR assay. Chromosomal DNA was prepared from each of 186 type strains to represent a broad range of O antigens of E. coli and Shigella and was used to make DNA pools as described previously (12). A total of 13 pools were made, each containing DNA from 12 to 19 strains (12). Either E. coli strain 2531-54 (O174) or strain E40874-85 (O177) and the strains of pool 12 were used to make up pool 13. Primer pairs (see Table 4) specific for wzx and wzy genes of E. coli O174 and O177 were used to screen the DNA pools. The PCR was performed as follows: a denaturation step at 95°C for 30 s, an annealing step at 45°C for 30 s, and an extension step at 72°C for 1 min for 30 cycles. Template DNA from 50 clinical E. coli isolates including 12 E. coli O174, 11 E. coli O177 (Table 1), and 26 E. coli strains belonging to other O serogroups (data not shown) were prepared as described previously (14) and screened with the primers listed in Table 4 in a double-blind test.
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TABLE 4. Primers used for PCR detection of strains of E. coli O serogroups O174 and O177
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Nucleotide sequence accession numbers. The DNA sequences of the E. coli O174 and O177 O-antigen gene clusters have been deposited in GenBank under the accession numbers DQ008592 and DQ008593, respectively.
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The 11 E. coli O177 strains originated from diarrheagenic humans and calves as well as from healthy cattle. They were distributed over three H types (H11, H25, and H26), except for two nonmotile strains, which could not be typed for their fliC genes (Table 1). In contrast to E. coli O174, all E. coli O177 strains investigated were positive for an eae gene. Those distributed over H types H11, H25, and H26 carried an eae-ß gene, and the two nonmotile strains carried an eae-
gene. Seven of the E. coli O177 strains produced Shiga toxins (types 1 and/or 2). Nine were positive for enterohemolysin and the ehxA gene. According to their virulence profiles, E. coli O177:H11 and O177:H25 were associated with two pathotypes such as atypical EPEC (eae positive) and EHEC (eae and stx positive) (24). None of the E. coli O177 and O174 strains were positive for sequences of the EAF plasmid, which is harbored by typical (class I) EPEC strains (24).
Nucleotide sequence analysis of the E. coli O174 O-antigen gene cluster. A sequence of 5,660 bases between the JUMPStart sequence and gnd was obtained from E. coli O174, and five open reading frames (ORFs) were found (Fig. 1). By comparing these to related genes in nucleotide sequence databases, all ORFs were assigned functions and shown to be related to O-antigen biosynthesis (Table 2).
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FIG. 1. O-antigen gene clusters of E. coli O174 and E. coli O177. All genes are transcribed in a direction from the JUMPStart sequence to gnd.
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TABLE 2. Putative genes in the E. coli O174 O-antigen gene cluster
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(ii) Glycosyltransferase genes. Orf1, Orf4, and Orf5 belong to the glycosyltransferase family 2 (pfam00535 E values, 5 x e5, 1.8 x e13, and 6.0 x e25, respectively) and share 43 to 70% similarity with other putative glycosyltransferases (Table 2). Therefore, orf1, orf4, and orf5 were proposed to be glycosyltransferase genes and were named wbcX, wbcY, and wbcZ, respectively.
The O-antigen structure of E. coli O174 has not been characterized. The absence of sugar synthesis genes in the O-antigen gene cluster indicates that the O unit of E. coli O174 consists of common sugars such as Glc, Gal, GlcNAc, and GalA. Genes for the synthesis of common sugars are outside the O-antigen gene cluster (9). Glycosyltransferase genes are highly specific to sugar donors, sugar receptors, and the linkages between them. The wecA gene, which is located outside the O-antigen gene cluster, is responsible for the transfer of GlcNAc presented as the first sugar in most E. coli O units (1). Three glycosyltransferase genes were found in the E. coli O174 O-antigen gene cluster. Therefore, E. coli O174 O antigen was predicted to be composed of tetrasaccharide repeating units.
A large nonencoding region between orf4 and orf5 (positions 4084 to 4668) was found. It contains numbers of stop codons and shares no similarity to other genes in the databases. It appears that this intergenic region underwent numerous changes under selection pressure.
Nucleotide sequence analysis of the E. coli O177 O-antigen gene cluster. A sequence of 13,198 bases between the JUMPStart sequence and gnd was obtained from E. coli O177, and 13 ORFs were found (Fig. 1). By comparing these to related genes in nucleotide sequence databases, all ORFs were assigned functions and were shown to be related to O-antigen biosynthesis (Table 3).
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TABLE 3. Putative genes in the E. coli O177 O-antigen gene cluster
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Orf9, Orf10, and Orf11 share 80, 55, and 70% identity to FnlA (WbjB), FnlB (WbjC), and FnlC (WbjD) of the Pseudomonas aeruginosa O11 O-antigen gene cluster, respectively, which were experimentally identified as UDP-L-FucNAc biosynthesis pathway enzymes (16). They also share 92, 96, and 98% identity to FnlA (Fnl1), FnlB (Fnl2), and FnlC (Fnl3) of the E. coli O26 O-antigen gene cluster, respectively. Therefore, orf9, orf10, and orf11 were identified as fnlA, fnlB, and fnlC and were named accordingly. The presence of the fnl genes indicates that the E. coli O177 O antigen contains a fucosamine moiety.
(ii) O-unit-processing genes. Orf4 has 10 predicted transmembrane segments and shares 74% similarity to Wzx of S. flexneri 2a strain 301. It belongs to the Pfam family PF01943 (E value, 3.1 x e52), and members of this family are involved in the export of the O antigen and teichoic acid. Therefore, orf4 was proposed to be an O-unit flippase gene (wzx) and was named accordingly. Orf6 has 10 predicted transmembrane segments and a large periplasmic loop of 56 amino acid residues. It also shares 52% similarity to Wzy of S. flexneri 2a. Therefore, orf6 was proposed to be an O-antigen polymerase gene (wzy) and was named accordingly.
(iii) Glycosyltransferase genes. Orf7 and Orf8 belong to glycosyltransferase family 2 (PF00535; E value, 1.7 x e2) and glycosyltransferase family 1 (PF00534; E value, 6.6 x e7). They also share 48 and 45% similarity to glycosyltransferases of Shigella dysenteriae type 1 and Shigella boydii type 13, respectively. orf7 and orf8 were proposed to be glycosyltransferase genes and were named wbdY and wbdZ, respectively. Orf12 belongs to glycosyltransferase family 1 (PF00534; E value, 4.5 x e3) and shares 96% identity to a putative L-fucosamine transferase, WbuB, of E. coli O26 (9); based on this high-level identity, orf12 was proposed to be an L-Fucosamine transferase gene and was named wbuB.
(iv) Nonfunctional gene. Orf13 shares 98% identity to a proposed remnant gene product, WbuC, of E. coli O26 (9). orf13 was proposed to be nonfunctional and was named wbuC.
The O-antigen structure of E. coli O177 has not been characterized. Based on the number of glycosyltransferase genes found in the O-antigen gene cluster, E. coli O177 O antigen was predicted to be composed of tetrasaccharide O-unit containing rhamnose and FucNAc.
Specific identification of E. coli O174 and O177 serogroup-specific genes by PCR. Two pairs of primers specific for wzx and wzy genes were designed for E. coli O174 (Table 4) and used to screen DNA pools containing representatives of the 186 known O-antigen forms of E. coli and Shigella strains. Except for the pools containing E. coli O174, which gave PCR products of the expected size, no PCR products were obtained with all other pools tested (Fig. 2). The same high primer specificity was found with primers designed for E. coli O177 (Table 4). The primer pairs listed in Table 4 were further used in double-blind tests on E. coli clinical isolates including 12 E. coli O174 strains, 11 E. coli O177 strains (Table 1), and 26 E. coli strains of other O serogroups (Fig. 3). All of the E. coli O174 and O177 strains gave the expected PCR products corresponding to primer pairs used, and no PCR products were obtained from strains belonging to other O serogroups. The PCR products amplified from all O174 and O177 strains by the primers wl-4421/wl-4422 and wl-4417/wl-4418 were sequenced, and it was found that all the sequences of different strains of O174 or O177 share identity of more than 99.5% (at most, 1 base different). The results show that the primers for E. coli O174 and O177 are highly specific and suitable for the development of PCR assays for the identification and detection of E. coli O174 or O177 strains.
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FIG. 2. Amplification products obtained by PCR of 13 pools of DNA including 186 E. coli and Shigella O-antigen type strains and E. coli O174 strain G1609 or E. coli O174 strain G1606 using primer pairs wl-4397/wl-4398 (a), wl-4421/wl-4422 (b), wl-4399/wl-4400 (c), wl-4423/wl-4424 (d), wl-4393/wl-4394 (e), wl-4417/wl-4418 (f), wl-4395/wl-4396 (g), and wl-4419/wl-4420 (h). Lanes 1 and 15, DNA marker, bands with lengths of 100 bp, 250 bp, 500 bp, 750 bp, 1 kb, and 2 kb; lanes 2 to 14, pool 1 to pool 13, respectively.
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FIG. 3. Amplification products obtained by PCR of 13 clinical isolated E. coli O174 strains using primer pairs wl-4397/wl-4398 (a), wl-4421/wl-4422 (b), wl-4399/wl-4400 (c), and wl-4423/wl-4424 (d). Lanes 1 and 15, DNA marker, bands with lengths of 100 bp, 250 bp, 500 bp, 750 bp, 1 kb, and 2 kb; lane 2, G1609; lane 3, G1610; lane 4, G1611; lane 5, G2032; lane 6, G2033; lane 7, G2034; lane 8, G2035; lane 9, G2036; lane 10, G2037; lane 11, G2038; lane 12, G2039; lane 13, G2040; lane 14, G2041. Also shown are amplification products obtained by PCR of 12 clinically isolated E. coli O177 strains using primer pairs wl-4393/wl-4394 (e), wl-4417/wl-4418 (f), 4395/wl-4396 (g), and wl-4419/wl-4420 (h). Lanes 1 and 14, DNA marker, bands with lengths of 100 bp, 250 bp, 500 bp, 750 bp, 1 kb, and 2 kb; lane 2, G1606; lane 3, G1607; lane 4, G1608; lane 5, G2042; lane 6, G2043; lane 7, G2044; lane 8, G2045; lane 9, G2046; lane 10, G2047; lane 11, G2048; lane 12, G2049; lane 13, G2068.
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wzx-specific primer pairs wl-4397/wl-4398/wl-4399/wl-4400 (O174) and wl-4393/wl-4394/wl-4395/wl-4396 (O177) were used for the detection of serogroup O174 and O177 reference strains from spiked samples of pork and water. By this, as few as 103 CFU per g was detected in samples that were examined directly, and 0.1 CFU per g was detected in samples that were further incubated at 37°C for 12 h.
The O-antigen gene-specific PCR assays developed in this study were found to be highly suitable for the detection of E. coli strains belonging to the novel serogroups O174 and O177. E. coli groups O174 and O177 were shown to comprise Shiga toxin-producing E. coli, EHEC, and atypical EPEC strains which were isolated from diseased humans, animals, and food in different parts of the world. At present, the O-antigen-specific PCR is the only method generally applicable for screening of E. coli O174 and O177 strains, since other diagnostic tools for their detection are not yet commercially available. Detection of O174 and O177 strains by PCR could be the method of choice for epidemiological investigations of outbreaks and sporadic infections and for the investigation of animals and the food chain. Last but not least, this method could be useful to investigate the association of certain O174 strains with specific animal hosts for the development of possible prevention strategies against the spread of these pathogens.
We are grateful to H. Steinrück, BfR, Berlin, Germany, for helpful discussions.
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). J. Clin. Microbiol. 42:645-651.
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