Sequencing and analysis of the Escherichia coli serogroup O117, O126, and O146 O-antigen gene clusters and development of PCR assays targeting serogroup O117-, O126-, and O146-specific DNA sequences

Molecular and in silico analyses for detection of Shiga toxin-producing Escherichia coli (STEC) and highly pathogenic enterohemorrhagic Escherichia coli (EHEC) using genetic markers located on plasmid, O Island 57 and O Island 71

BACKGROUND

Due to the diversity of Shiga toxin-producing Escherichia coli (STEC) isolates, detecting highly pathogenic strains in foodstuffs is challenging. Currently, reference protocols for STEC rely on the molecular detection of eae and the stx1 and/or stx2 genes, followed by the detection of serogroup-specific wzx or wzy genes related to the top 7 serogroups. However, these screening methods do not distinguish between samples in which a STEC possessing both determinants are present and those containing two or more organisms, each containing one of these genes. This study aimed to evaluate ecf1, Z2098, Z2099, and nleA genes as single markers and their combinations (ecf1/Z2098, ecf1/Z2099, ecf1/nleA, Z2098/Z2099, Z2098/nleA, and Z2099/nleA) as genetic markers to detect potentially pathogenic STEC by the polymerase chain reaction (PCR) in 96 animal samples, as well as in 52 whole genome sequences of human samples via in silico PCR analyses.

RESULTS

In animal isolates, Z2098 and Z2098/Z2099 showed a strong association with the detected top 7 isolates, with 100% and 69.2% of them testing positive, respectively. In human isolates, Z2099 was detected in 95% of the top 7 HUS isolates, while Z2098/Z2099 and ecf1/Z2099 were detected in 87.5% of the top 7 HUS isolates.

CONCLUSIONS

Overall, using a single gene marker, Z2098, Z2099, and ecf1 are sensitive targets for screening the top 7 STEC isolates, and the combination of Z2098/Z2099 offers a more targeted initial screening method to detect the top 7 STEC isolates. Detecting non-top 7 STEC in both animal and human samples proved challenging due to inconsistent characteristics associated with the genetic markers studied.

Pathogenic potential to humans of Shiga toxin-producing Escherichia coli isolated from wild boars in Poland

The aim of the study was to investigate the presence of Shiga toxin-producing Escherichia coli (STEC) in the wild boar population of north-eastern Poland, and to evaluate the potential health risk associated with wild boars carrying STEC/AE-STEC strains. In Poland, the African Swine Fever (ASF) virus has been a growing problem in domestic pigs and wild boars, one of the main reservoirs of the virus, because of this hunters, veterinary practitioners and foresters thus face a greater risk of coming into contact with animals. Rectal swabs samples were obtained from 152 wild boars hunter-harvested in the 2017/2018 season (autumn-winter) in north-eastern Poland. The samples were enrichment in modified buffered peptone water. Polymerase chain reaction (PCR) assays were conducted to determine the virulence profile of stx1, stx2 and eae and aggR genes, identify subtypes of stx1 and stx2 genes, and perform O and H serotyping. STEC/AE-STEC virulence genes were detected in 43 isolates (28.29%): STEC in 17 isolates (11.18%) and AE-STEC in 26 isolates (17.11%), respectively. None of the tested isolates carried the aggR gene. The most dangerous AE-STEC virulence profile associated with HUS was found in 2 isolates (1.32%): stx1NS/stx2a/d/eae serotype ONT:H7 and stx2a/eae serotype O146:H7. Six of the 152 tested samples belonged to serogroup O157 (3.95%), including one AE-STEC isolate with virulence profile stx2g/eae and five EPEC isolates. The results of this study suggest that wild boars in north-eastern Poland can carry STEC/AE-STEC strains that are potentially pathogenic for humans. This is the first report documenting the virulence of STEC and AE-STEC isolates from wild boars in Poland.

Molecular serogrouping ofEscherichia coli

O-antigens present on the surface ofEscherichia coliprovide antigenic specificity for the strain and are the main components for O-serogroup designation. Serotyping using O-group-specific antisera for the identification ofE. coliO-serogroups has been traditionally the gold-standard for distinguishingE. colistrains. Knowledge of the O-group is important for determining pathogenic lineage, classifyingE. colifor epidemiological studies, for determining virulence, and for tracing outbreaks of diseases and sources of infection. However, serotyping has limitations, as the antisera generated against each specific O-group may cross-react, many strains are non-typeable, and others can autoagglutinate or be rough (lacking an O-antigen). Currently, the nucleotide sequences are available for most of the 187 designatedE. coliO-groups. Public health and other laboratories are considering whole genome sequencing to develop genotypic methods to determine O-groups. These procedures require instrumentation and analysis that may not be accessible and may be cost-prohibitive at this time. In this review, we have identified unique gene sequences within the O-antigen gene clusters and have targeted these genes for identification of O-groups using the polymerase chain reaction. This information can be used to distinguish O-groups by developing other platforms forE. colidiagnostics in the future.

Structures and gene clusters of the O-specific polysaccharides of the lipopolysaccharides of Escherichia coli O69 and O146 containing glycolactilic acids: ether conjugates of D-GlcNAc and D-Glc with (R)- and (S)-lactic acid

Based on the O-specific polysaccharides of the lipopolysaccharides (O-polysaccharides, O-antigens), strains of a clonal species Escherichia coli are classified into 184 O serogroups. In this work, structures of the O-polysaccharides of E. coli O69 and O146 were elucidated and gene clusters for their biosynthesis were characterized. The O-polysaccharides were released from the lipopolysaccharides by mild acid hydrolysis and studied by sugar analysis and one- and two-dimensional ¹H and ¹³C NMR spectroscopy before and after O-deacetylation. The O146 polysaccharide was also studied by Smith degradation. The O69 and O146 polysaccharides were found to contain ether conjugates of monosaccharides with lactic acid called glycolactilic acids: 2-acetamido-2-deoxy-4-O-[(R)-1-carboxyethyl]-D-glucose (D-GlcNAc4Rlac) and 3-O-[(S)-1-carboxyethyl]-D-glucose (D-Glc3Slac), respectively. Structures of the pentasaccharide repeats of the O-polysaccharides were established, and that of E. coli O69 was found to differ in the presence of D-GlcNAc4Rlac from the structure reported for this bacterium earlier (Erbing C, Kenne L, Lindberg B. 1977. Carbohydr Res. 56:371-376). The O-antigen gene clusters of E. coli O69 and O146 between conserved genes galF and gnd were analyzed taking into account the O-polysaccharide structures established, and functions of putative genes for synthesis of D-Glc3Slac and D-GlcNAc4Rlac and for glycosyltransferases were assigned based on homology with O-antigen biosynthesis genes of other enteric bacteria. It was found that in E. coli and Shigella spp. predicted enolpyruvate reductases of the biosynthesis pathway of glycolactilic acids, LarR and LarS, which catalyze formation of conjugates with (R)- or (S)-lactic acid, respectively, are distinguished by sequence homology and size.

The one-pot multienzyme (OPME) synthesis of human blood group H antigens and a human milk oligosaccharide (HMOS) with highly active Thermosynechococcus elongates α1-2-fucosyltransferase

A novel α1-2-fucosyltransferase from Thermosynechococcus elongatus BP-1 (Te2FT) with high fucosyltransferase activity and low donor hydrolysis activity was discovered and characterized. It was used in an efficient one-pot multienzyme (OPME) fucosylation system for the high-yield synthesis of human blood group H antigens containing β1-3-linked galactosides and an important human milk oligosaccharide (HMOS) lacto-N-fucopentaose I (LNFP I) on preparative and gram scales. LNFP I was shown to be selectively consumed by Bifidobacterium longum subsp. infantis but not Bifidobacterium animalis subsp. lactis and is a potential prebiotic.

Development of three multiplex PCR assays targeting the 21 most clinically relevant serogroups associated with Shiga toxin-producing E. coli infection in humans

Escherichia coli serogroups O5, O15, O26, O45, O55, O76, O91, O103, O104, O111, O113, O118, O121, O123, O128, O145, O146, O157, O165, O172, and O177 are the O-antigen forms of the most clinically relevant Shiga toxin-producing E. coli (STEC) serotypes. In this study, three multiplex PCR assays able to specifically detect these 21 serogroups were developed and validated. For this purpose, the O-antigen gene clusters of E. coli O5 and O76 were fully sequenced, their associated genes were identified on the basis of homology, and serogroup-specific primers were designed. After preliminary evaluation, these two primer pairs were proven to be highly specific and suitable for the development of PCR assays for O5 and O76 serogroup identification. Specific primers were also designed for serogroups O15, O45, O55, O91, O104, O113, O118, O123, O128, O146, O157, O165, O172, and O177 based on previously published sequences, and previously published specific primers for serogroups O26, O103, O111, O121, and O145 were also included. These 21 primer pairs were shown to be specific for their target serogroup when tested against E. coli type strains representing 169 known O-antigen forms of E. coli and Shigella and therefore suitable for being used in PCR assays for serogroup identification. In order to validate the three multiplex PCR assays, 22 E. coli strains belonging to the 21 covered serogroups and 18 E. coli strains belonging to other serogroups were screened in a double-blind test and their sensitivity was determined as 1 ng chromosomal DNA. The PCR assays developed in this study could be a faster, simpler, and less expensive strategy for serotyping of the most clinically relevant STEC strains in both clinical microbiology and public health laboratories, and so their development could benefit for clinical diagnosis, epidemiological investigations, surveillance, and control of STEC infections.

Pathotypes and probiotics: response to a commentary on the detection of a Shiga toxin producing Escherichia coli in a Crohn's disease patient

A recent report on the detection in a Crohn’s disease (CD) patient of an adherent and invasive Shiga toxin producing Escherichia coli (STEC) (Gut pathogens 2015, 7:2) prompted a commentary expressing some skepticism on the significance of the paper findings (Gut pathogens 2015, 7:15). Besides focusing on recurrent issues concerning the difficulties in defining a pathogen, the opinion considers recent data demonstrating the presence of virulence factors in a commercial probiotic. In response to the commentary’s observations, additional information on the described STEC strain, as well as a short discussion on CD associated E. coli are presented here.

WbgL: a novel bacterial α1,2-fucosyltransferase for the synthesis of 2'-fucosyllactose

Fucosyltransferases (FucTs) are essential tools for the synthesis of fucosylated glycoconjugates. Multistep enzyme catalysis of fucosylated glycans is not limited as long as isolated and well-characterized FucTs are available. The present paper introduces a novel bacterial α1,2-FucT of the glycosyltransferase family 11 encoded by the gene wbgL in the E. coli O126 genome, which only displays 25-30% homology to previously published α1,2-FucTs. A tailor made cloning and expression strategy allowed the successful production of active soluble enzyme in the cytoplasm of E. coli BL21(DE3) and E. coli JM109(DE3), respectively. The lack of a DxD motif and its high activity without divalent metal ions suggests that WbgL belongs to the GT-B fold superfamily. Substrate screening revealed the highest activity for β4-linked galactoside acceptor substrates, such as lactose and lactulose, making WbgL unique among other characterized α1,2-FucTs. Based on its excellent kinetic efficiency for lactose, we present here a sequential reaction strategy for the synthesis of α1,2-fucosyllactose in one pot including the synthesis of the donor substrate 3,3'-Diaminobenzidine (GDP)-β-l-fucose by the bifunctional l-fucokinase/GDP-β-l-Fuc pyrophosphorylase of Bacteroides fragilis 9343.

Evaluation of pathogenic Escherichia coli occurrence in vegetable samples from district bazaars in Istanbul using real-time PCR

In this study, a total of 180 vegetable samples collected from several district bazaars of Istanbul were investigated for the occurrence of Escherichia coli using a culture-based method. The isolates were subjected to real-time PCR detection of Shiga-toxin-producing E. coli (STEC) using primers specific for the Shiga toxin (stx1 and stx2) and intimin (eae) virulence genes. The prevalences of E. coli in the samples were 93·3% in spinach, 93·3% in lettuce, 86·6% in parsley, 43·3% in carrot, 33·3% in cucumber and 13·3% in tomato. Of 180 samples, 13 contained STEC (six parsley, three carrots, three lettuces and one cucumber of 30 samples of each). Among 13 STEC-positive isolates, presence of stx1, stx2 and eae was detected in only one sample, stx2 and eae in two samples, and stx2 in ten samples. Serotype O157 was found in parsley, lettuce and carrot; O26 in lettuce, parsley, cucumber and carrot; and O111 and O113 in parsley only. In conclusion, STEC was present in vegetable samples marketed in several district bazaars in Istanbul; this might represent a route of transmission of pathogenic STEC to humans and be harmful to public health.

SIGNIFICANCE AND IMPACT OF THE STUDY

We assessed the occurrence of virulent Escherichia (E.) coli and Shiga-toxin-producing E. coli (STEC) virulent populations in the vegetable samples collected from several district bazaars in Istanbul, Turkey. The results indicated that the vegetables from the bazaars had poor microbial quality and represented a potential health risk to customers.

Detection of O antigens in Escherichia coli

Lipopolysaccharide on the surface of Escherichia coli constitutes the O antigens which are important virulence factors that are targets of both the innate and adaptive immune systems and play a major role in host-pathogen interactions. O antigens are responsible for antigenic specificity of the strain and determine the O serogroup. The designation of O serogroups is important for classifying E. coli strains, for epidemiological studies, in tracing the source of outbreaks of gastrointestinal or other illness, and for linking the source to the infection. For conventional serogroup identification, serotyping by agglutination reactions against antisera developed for each of the O serogroups has been used. In the last decade, many O-antigen gene clusters that encode for the enzymes responsible for the synthesis of the variable oligosaccharide region on the surface of the bacteria have been sequenced and characterized. Unique gene sequences within the O-antigen gene clusters have been targeted for identification and detection of many O groups using the polymerase chain reaction and microarrays. This review summarizes current knowledge on the DNA sequences of the O-antigen gene clusters, genetic-based methods for O-group determination and detection of pathogenic E. coli based on O-antigen and virulence gene detection, and provides perspectives on future developments in the field.

Prevalence and characterization of non-O157 shiga toxin-producing Escherichia coli isolates from commercial ground beef in the United States

Escherichia coli O157:H7 is a Shiga toxin (stx)-producing E. coli (STEC) strain that has been classified as an adulterant in U.S. beef. However, numerous other non-O157 STEC strains are associated with diseases of various severities and have become an increasing concern to the beef industry, regulatory officials, and the public. This study reports on the prevalence and characterization of non-O157 STEC in commercial ground beef samples (n = 4,133) obtained from numerous manufacturers across the United States over a period of 24 months. All samples were screened by DNA amplification for the presence of Shiga toxin genes, which were present in 1,006 (24.3%) of the samples. Then, culture isolation of an STEC isolate from all samples that contained stx(1) and/or stx(2) was attempted. Of the 1,006 positive ground beef samples screened for stx, 300 (7.3% of the total of 4,133) were confirmed to have at least one strain of STEC present by culture isolation. In total, 338 unique STEC isolates were recovered from the 300 samples that yielded an STEC isolate. All unique STEC isolates were serotyped and were characterized for the presence of known virulence factors. These included Shiga toxin subtypes, intimin subtypes, and accessory virulence factors related to adherence (saa, iha, lifA), toxicity (cnf, subA, astA), iron acquisition (chuA), and the presence of the large 60-MDa virulence plasmid (espP, etpD, toxB, katP, toxB). The isolates were also characterized by use of a pathogenicity molecular risk assessment (MRA; based on the presence of various O-island nle genes). Results of this characterization identified 10 STEC isolates (0.24% of the 4,133 total) that may be considered a significant food safety threat, defined by the presence of eae, subA, and nle genes.

Characterization of Escherichia coli O3 and O21 O antigen gene clusters and development of serogroup-specific PCR assays

Escherichia coli O3 and O21 are associated with enteroaggregative E. coli (EAEC). EAEC strains are often non-typable using the routine agglutination method due to their aggregative phenotype. Typing of E. coli O3 and O21 may also be impeded by cross-reactions with O152 or O83. In this study, the O antigen gene clusters of E. coli O3 and O21 were characterized, and PCR assays based on O antigen specific genes wzx (encoding O unit flippase) and wzy (encoding O unit polymerase) from each strain were developed. By screening against all 186 known E. coli O serotypes, the PCR assays were shown to be highly specific to O3 and O21 respectively. The sensitivity of the assays was determined to be 1 pg per microl of chromosomal DNA and 2 CFU per 10 g of water samples. The PCR assays were also applied to 658 clinical E. coli isolates, and 100% of detection accuracy was obtained. The PCR assays developed here are suitable for the detection and identification of E. coli O3 and O21 strains in environmental and clinical samples.