Isogenic strain of Escherichia coli O157:H7 that has lost both Shiga toxin 1 and 2 genes

Pathogenomes of Shiga Toxin Positive and Negative Escherichia coli O157:H7 Strains TT12A and TT12B: Comprehensive Phylogenomic Analysis Using Closed Genomes

Shiga toxin-producing Escherichia coli are zoonotic pathogens that cause food-borne human disease. Among these, the O157:H7 serotype has evolved from an enteropathogenic O55:H7 ancestor through the displacement of the somatic gene cluster and recurrent toxigenic conversion by Shiga toxin-converting bacteriophages. However, atypical strains that lack the Shiga toxin, the characteristic virulence hallmark, are circulating in this lineage. For this study, we analyzed the pathogenome and virulence inventories of the stx+ strain, TT12A, isolated from a patient with hemorrhagic colitis, and its respective co-isolated stx- strain, TT12B. Sequencing the genomes to closure proved critical to the cataloguing of subtle strain differentiating sequence and structural polymorphisms at a high-level of phylogenetic accuracy and resolution. Phylogenomic profiling revealed SNP and MLST profiles similar to the near clonal outbreak isolates. Their prophage inventories, however, were notably different. The attenuated atypical non-shigatoxigenic status of TT12B is explained by the absence of both the ΦStx1a- and ΦStx2a-prophages carried by TT12A, and we also recorded further alterations in the non-Stx prophage complement. Phenotypic characterization indicated that culture growth was directly impacted by the strains' distinct lytic phage complement. Altogether, our phylogenomic and phenotypic analyses show that these intimately related isogenic strains are on divergent Stx(+/stx-) evolutionary paths.

Comparative Use of Quantitative PCR (qPCR), Droplet Digital PCR (ddPCR), and Recombinase Polymerase Amplification (RPA) in the Detection of Shiga Toxin-Producing E. coli (STEC) in Environmental Samples

E. coli O157:H7 is a foodborne pathogen that constitutes a global threat to human health. However, the quantification of this pathogen in food and environmental samples may be problematic at the low cell numbers commonly encountered in environmental samples. In this study, we used recombinase polymerase amplification (RPA) for the detection of E. coli O157:H7, real-time quantitative PCR (qPCR) for quantification, and droplet digital PCR (ddPCR) for absolute and accurate quantification of E. coli O157:H7 from spiked and environmental samples. Primer and probe sets were used for the detection of stx1 and stx2 using RPA. Genes encoding for stx1, stx2, eae, and rfbE were used to quantify E. coli O157:H7 in the water samples. Furthermore, duplex ddPCR assays were used to quantify the pathogens in these samples. Duplex assay set 1 used stx1 and rfbE genes, while assay set 2 used stx2 and eae genes. Droplet digital PCR was used for the absolute quantification of E. coli O15:H7 in comparison with qPCR for the spiked and environmental samples. The RPA results were compared to those from qPCR and ddPCR in order to assess the efficiency of the RPA compared with the PCR methods. The assays were further applied to the dairy lagoon effluent (DLE) and the high rate algae pond (HRAP) effluent, which were fed with diluted DLE. The RPA detected was <10 CFU/mL, while ddPCR showed quantification from 1 to 104 CFU/mL with a high reproducibility. In addition, quantification by qPCR was from 103 to 107 CFU/mL of the wastewater samples. Therefore, the RPA assay has potential as a point of care tool for the detection of E. coli O157:H7 from different environmental sources, followed by quantification of the target concentrations.

Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes

The toxigenic conversion of Escherichia coli strains by Shiga toxin-converting (Stx) bacteriophages were prominent and recurring events in the stepwise evolution of enterohemorrhagic E. coli (EHEC) O157:H7 from an enteropathogenic (EPEC) O55:H7 ancestor. Atypical, attenuated isolates have been described for both non-sorbitol fermenting (NSF) O157:H7 and SF O157:NM serotypes, which are distinguished by the absence of Stx, the characteristic virulence hallmark of Stx-producing E. coli (STEC). Such atypical isolates either never acquired Stx-phages or may have secondarily lost stx during the course of infection, isolation, or routine subculture; the latter are commonly referred to as LST (Lost Shiga Toxin)-isolates. In this study we analyzed the genomes of 15 NSF O157:H7 and SF O157:NM strains from North America, Europe, and Asia that are characterized by the absence of stx, the virulence hallmark of STEC. The individual genomic basis of the Stx (-) phenotype has remained largely undetermined as the majority of STEC genomes in public genome repositories were generated using short read technology and are in draft stage, posing a major obstacle for the high-resolution whole genome sequence typing (WGST). The application of LRT (long-read technology) sequencing provided us with closed genomes, which proved critical to put the atypical non-shigatoxigenic NSF O157:H7 and SF O157:NM strains into the phylogenomic context of the stepwise evolutionary model. Availability of closed chromosomes for representative Stx (-) NSF O157:H7 and SF O157:NM strains allowed to describe the genomic basis and individual evolutionary trajectories underlying the absence of Stx at high accuracy and resolution. The ability of LRT to recover and accurately assemble plasmids revealed a strong correlation between the strains' featured plasmid genotype and chromosomally inferred clade, which suggests the coevolution of the chromosome and accessory plasmids. The identified ancestral traits in the pSFO157 plasmid of NSF O157:H7 strain LSU-61 provided additional evidence for its intermediate status. Taken together, these observations highlight the utility of LRTs for advancing our understanding of EHEC O157:H7/NM pathogenome evolution. Insights into the genomic and phenotypic plasticity of STEC on a lineage- and genome-wide scale are foundational to improve and inform risk assessment, biosurveillance, and prevention strategies.

Isolation and characterisation of Shiga toxin-producing Escherichia coli from Norwegian bivalves

Only a few studies concerning Shiga toxin-producing E. coli (STEC) detection in bivalves and their harvesting areas have been reported, and to the best of our knowledge there are no outbreaks associated with STEC from bivalves described. The aim of the present study was to investigate the occurrence of STEC in Norwegian bivalves, and to characterize potential STEC isolated from the samples. A total of 269 samples of bivalves were screened for the presence of stx and eae genes, and markers for the serogroups O26, O103, O111, O145 and O157 by using ISO TS 13136 (2012). The screening returned 19 samples that were positive for stx and eae, and attempts of isolation of STEC were made from these samples. Presumptive STEC were obtained from three samples, and three isolates (one from each sample) were subjected to whole-genome-sequencing (WGS). The WGS revealed that one of the isolates did not carry the stx genes, while the other two were identified as stx_2i positive E. coli O9:H19 and stx_2g positive E. coli O96:H19. Neither of the two STEC isolates were positive for virulence markers such as eae and ehx. The results suggest that the occurrence of STEC in Norwegian bivalves is low.

Rapid and robust analytical protocol for E. coli STEC bacteria subspecies differentiation using whole cell MALDI mass spectrometry

Whole cell MALDI is regularly used for the identification of bacteria to species level in clinical Microbiology laboratories. However, there remains a need to rapidly characterize and differentiate isolates below the species level to support outbreak management. We describe the implementation of a modified preparative approach for MALDI-MS combined with a custom analytical computational pipeline as a rapid procedure for subtyping Shigatoxigenic E. coli (STEC) and accurately identifying strain-specifying biomarkers. The technique was able to differentiate E. coli O157:H7 from other STEC. Within O157 serotype O157:H7 isolates were readily distinguishable from Sorbitol Fermenting O157 isolates. Overall, nine homogeneous groups of isolates were distinguished, each exhibiting distinct profiles of defining mass spectra features. This offers a robust analytical tool useable in reference/diagnostic public health scenarios.

Rapid Flow Cytometry Detection of a Single Viable Escherichia coli O157:H7 Cell in Raw Spinach Using a Simplified Sample Preparation Technique

Very low cell count detection of Escherichia coli O157:H7 in foods is critical, since an infective dose for this pathogen may be only 10 cells, and fewer still for vulnerable populations. A flow cytometer is able to detect and count individual cells of a target bacterium, in this case E. coli O157:H7. The challenge is to find the single cell in a complex matrix like raw spinach. To find that cell requires growing it as quickly as possible to a number sufficiently in excess of matrix background that identification is certain. The experimental design for this work was that of a U.S. Food and Drug Administration (FDA) In-House Level 3 validation executed in the technology’s originating laboratory. Using non-selective enrichment broth, 6.5 h incubation at 42°C, centrifugation for target cell concentration, and a highly selective E. coli O157 fluorescent antibody tag, the cytometry method proved more sensitive than a reference regulatory method (p = 0.01) for detecting a single target cell, one E. coli O157:H7 cell, in 25 g of spinach. It counted that cell’s daughters with at least 38× signal-to-noise ratio, analyzing 25 samples in total-time-to-results of 9 h.

Is Shiga Toxin-Negative Escherichia coli O157:H7 Enteropathogenic or Enterohemorrhagic Escherichia coli? Comprehensive Molecular Analysis Using Whole-Genome Sequencing

The ability of Escherichia coli O157:H7 to induce cellular damage leading to disease in humans is related to numerous virulence factors, most notably the stx gene, encoding Shiga toxin (Stx) and carried by a bacteriophage. Loss of the Stx-encoding bacteriophage may occur during infection or culturing of the strain. Here, we collected stx-positive and stx-negative variants of E. coli O157:H7/NM (nonmotile) isolates from patients with gastrointestinal complaints. Isolates were characterized by whole-genome sequencing (WGS), and their virulence properties and phylogenetic relationship were determined. Because of the presence of the eae gene but lack of the bfpA gene, the stx-negative isolates were considered atypical enteropathogenic E. coli (aEPEC). However, they had phenotypic characteristics similar to those of the Shiga toxin-producing E. coli (STEC) isolates and belonged to the same sequence type, ST11. Furthermore, EPEC and STEC isolates shared similar virulence genes, the locus of enterocyte effacement region, and plasmids. Core genome phylogenetic analysis using a gene-by-gene typing approach showed that the sorbitol-fermenting (SF) stx-negative isolates clustered together with an SF STEC isolate and that one non-sorbitol-fermenting (NSF) stx-negative isolate clustered together with NSF STEC isolates. Therefore, these stx-negative isolates were thought either to have lost the Stx phage or to be a progenitor of STEC O157:H7/NM. As detection of STEC infections is often based solely on the identification of the presence of stx genes, these may be misdiagnosed in routine laboratories. Therefore, an improved diagnostic approach is required to manage identification, strategies for treatment, and prevention of transmission of these potentially pathogenic strains.

Multiplex real-time PCR and culture methods for detection of Shiga toxin-producing Escherichia coli and Salmonella Thompson in strawberries, a lettuce mix and basil

An appropriate approach of high throughput multi-screening was verified for Shiga toxin-producing Escherichia coli (STEC) and Salmonella spp. in strawberries, lettuce and basil. Sample replicates were inoculated with STEC O157 or O26 and Salmonella Thompson (ca. 10-70, 100-700 and 1000-7000 cfu/25 g) and analysed after 1 and 5 days of storage (strawberries and lettuce at 7 °C and basil at 10 °C). After 18-24 h of enrichment at 37 °C in buffered peptone water, detection was performed using the GeneDisc multiplex PCR (stx1, stx2, eae and iroB genes) and selective culture media for isolation of STEC (with immunomagnetic separation (IMS)) and Salmonella spp. in parallel. After 1 day, the pathogenic strains were recovered from all samples for all inoculum levels, whereas reduced detection rates of STEC O157 and S. Thompson were observed after 5 days of storage in case of strawberries, in particular for the lowest inoculums level, suggesting superior survival potential for STEC O26. Overall, this study indicates the ability of PCR based screening methods for reproducible multi-detection of low numbers (10-70 cfu/25 g) of STEC and Salmonella in this type of foods. However, for the basil samples, PCR needed twofold dilution of the DNA extract to overcome inhibition. It was noted that on several occasions growth of competitive microbiota obstructed finding presumptive colonies on the selective agar media, whereas the use of an additional agar medium such as CHROMagar STEC (without IMS) improved recovery rate of STEC.

Topological data analysis of Escherichia coli O157:H7 and non-O157 survival in soils

Shiga toxin-producing E. coli O157:H7 and non-O157 have been implicated in many foodborne illnesses caused by the consumption of contaminated fresh produce. However, data on their persistence in soils are limited due to the complexity in datasets generated from different environmental variables and bacterial taxa. There is a continuing need to distinguish the various environmental variables and different bacterial groups to understand the relationships among these factors and the pathogen survival. Using an approach called Topological Data Analysis (TDA); we reconstructed the relationship structure of E. coli O157 and non-O157 survival in 32 soils (16 organic and 16 conventionally managed soils) from California (CA) and Arizona (AZ) with a multi-resolution output. In our study, we took a community approach based on total soil microbiome to study community level survival and examining the network of the community as a whole and the relationship between its topology and biological processes. TDA produces a geometric representation of complex data sets. Network analysis showed that Shiga toxin negative strain E. coli O157:H7 4554 survived significantly longer in comparison to E. coli O157:H7 EDL 933, while the survival time of E. coli O157:NM was comparable to that of E. coli O157:H7 EDL 933 in all of the tested soils. Two non-O157 strains, E. coli O26:H11 and E. coli O103:H2 survived much longer than E. coli O91:H21 and the three strains of E. coli O157. We show that there are complex interactions between E. coli strain survival, microbial community structures, and soil parameters.

Persistence of Escherichia coli O157 and non-O157 strains in agricultural soils

Shiga toxin producing Escherichia coli O157 and non-O157 serogroups are known to cause serious diseases in human. However, research on the persistence of E. coli non-O157 serogroups in preharvest environment is limited. In the current study, we compared the survival behavior of E. coli O157 to that of non-O157 E. coli strains in agricultural soils collected from three major fresh produce growing areas of California (CA) and Arizona (AZ). Results showed that the nonpathogenic E. coli O157:H7 4554 survived longer than the pathogenic E. coli O157:H7 EDL933 in Imperial Valley CA and Yuma AZ, but not in soils from the Salinas area. However, E. coli O157:NM was found to persist significantly longer than E. coli O157:H7 EDL933 in all soil tested from the three regions. Furthermore, two non-O157 (E. coli O26:H21 and E. coli O103:H2) survived significantly longer than E. coli O157:H7 EDL933 in all soils tested. Pearson correlation analysis showed that survival of the E. coli strains was affected by different environmental factors. Our data suggest that survival of E. coli O157 and non-O157 may be strain and soil specific, and therefore, care must be taken in data interpretation with respect to survival of this pathogen in different soils.

Genetic diversity and virulence potential of shiga toxin-producing Escherichia coli O113:H21 strains isolated from clinical, environmental, and food sources

Shiga toxin-producing Escherichia coli strains of serotype O113:H21 have caused severe human diseases, but they are unusual in that they do not produce adherence factors coded by the locus of enterocyte effacement. Here, a PCR microarray was used to characterize 65 O113:H21 strains isolated from the environment, food, and clinical infections from various countries. In comparison to the pathogenic strains that were implicated in hemolytic-uremic syndrome in Australia, there were no clear differences between the pathogens and the environmental strains with respect to the 41 genetic markers tested. Furthermore, all of the strains carried only Shiga toxin subtypes associated with human infections, suggesting that the environmental strains have the potential to cause disease. Most of the O113:H21 strains were closely related and belonged in the same clonal group (ST-223), but CRISPR analysis showed a great degree of genetic diversity among the O113:H21 strains.

Characterization of enterohemorrhagic Escherichia coli O111 and O157 strains isolated from outbreak patients in Japan

In April and May 2011, there was a serious food-poisoning outbreak in Japan caused by enterohemorrhagic Escherichia coli (EHEC) strains O111:H8 and O157:H7 from raw beef dishes at branches of a barbecue restaurant. This outbreak involved 181 infected patients, including 34 hemolytic-uremic syndrome (HUS) cases (19%). Among the 34 HUS patients, 21 developed acute encephalopathy (AE) and 5 died. Patient stool specimens yielded E. coli O111 and O157 strains. We also detected both EHEC O111 stx2 and stx-negative E. coli O111 strains in a stock of meat block from the restaurant. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem-repeat analysis (MLVA) showed that the stx-negative E. coli O111 isolates were closely related to EHEC O111 stx2 isolates. Although the EHEC O157 strains had diverse stx gene profiles (stx1, stx2, and stx1 stx2), the PFGE and MLVA analyses indicated that these isolates originated from a single clone. Deletion of the Stx2-converting prophage from the EHEC O111 stx2 isolates was frequently observed during in vitro growth, suggesting that strain conversion from an EHEC O111 stx2 to an stx-negative strain may have occurred during infection.

Detection and enumeration of E. coli O157:H7 in water samples by culture and molecular methods

The performances of three chromogenic agars were evaluated for the recovery of Escherichia coli O157:H7 from spiked dechlorinated tap, ground and surface water, and treated drinking water samples. The chromogenic agars: ChromAgar O157 (CHROM), Rainbow Agar O157 (RB) and HiCrome EC O157 (HC) were compared to cefixime-tellurite Sorbitol MacConkey (CT-SMAC), commonly used for the isolation of E. coli O157:H7. Confirmation of suspect E. coli O157:H7 colonies were performed by colony real-time PCR (C-RTi-PCR) based on the presence of Shiga-toxin genes (stx1 and stx2). Recovery of inoculated E. coli O157:H7 from dechlorinated tap water indicated that RB and CHROM agars demonstrated improved recovery when compared to HC or CT-SMAC. There was a significant drop in recovery on all agars tested after 120h (day 5). Twenty dechlorinated tap and/or treated drinking water samples were inoculated with a pure culture of E. coli O157:H7 (ATCC 43894), and a mixed culture of E. coli O157:H7 (ATCC 43894), E. coli strain K-12, and Enterococcus faecalis (ATCC 063589). After a 48-hour holding time, the recovery using CHROM (99%) and HC (12%) from samples contaminated with the pure culture were found to be significantly different (p<0.05). Recovery results using CHROM (39%) and CT-SMAC (32%) from samples contaminated with the mixed culture after a 48-hour holding time were not significantly different (p>0.05). Analysis by C-RTi-PCR of forty five environmental water samples (surface, sewage, and final effluents) which were negative for E. coli O157:H7 showed an incidence of false suspect positive colonies of 38% (CHROM), 53% (RB), 58% (HC), and 91% (CT-SMAC). Further analysis of eight of the environmental samples inoculated with E. coli (ATCC 43894) showed 100% recovery when utilizing CHROM, 50% when using RB and 40% when using HC. In addition, the C-RTi-PCR positive confirmation rate was 100% for CHROM and HC and 65% for RB. CHROM demonstrated improved recovery of E. coli O157:H7 over RB, HC, and CT-SMAC in terms of sensitivity and specificity.

Clonal relations of atypical enteropathogenic Escherichia coli O157:H16 strains isolated from various sources from several countries

Atypical enteropathogenic Escherichia coli (aEPEC) is comprised of a large heterogeneous group of strains and serotypes that carry the intimin gene (eae) but no other EPEC virulence factors. In a previous study, we examined a few aEPEC strains of O157:H16 serotype from the U.S. and France and found these to be nearly homologous, and speculated that the same strain had been disseminated or perhaps they are part of a large clonal group that exists worldwide. To test that hypothesis, we examined additional 45 strains isolated from various sources from 4 other countries and determined that although there are a few eae-negative O157:H16 strains, most are aEPEC that carried eae and specifically, the ε-eae allele. Analysis by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing showed that as a whole, O157:H16 strains are phylogenetically diverse and have different sequence types and PFGE profiles. But the aEPEC strains within the O157:H16 serotype, regardless of the eae allele carried, are a highly conserved and homologous group of sequence type (ST)-171 strains that shared similar PFGE profiles. These aEPEC strains of O157:H16 serotype are not closely related to any of the major EPEC and enterohemorrhagic E. coli clonal lineages and appear to be part of a large clonal group that are prevalent worldwide.

The highly virulent 2006 Norwegian EHEC O103:H25 outbreak strain is related to the 2011 German O104:H4 outbreak strain

In 2006, a severe foodborne EHEC outbreak occured in Norway. Seventeen cases were recorded and the HUS frequency was 60%. The causative strain, Esherichia coli O103:H25, is considered to be particularly virulent. Sequencing of the outbreak strain revealed resemblance to the 2011 German outbreak strain E. coli O104:H4, both in genome and Shiga toxin 2-encoding (Stx2) phage sequence. The nucleotide identity between the Stx2 phages from the Norwegian and German outbreak strains was 90%. During the 2006 outbreak, stx₂-positive O103:H25 E. coli was isolated from two patients. All the other outbreak associated isolates, including all food isolates, were stx-negative, and carried a different phage replacing the Stx2 phage. This phage was of similar size to the Stx2 phage, but had a distinctive early phage region and no stx gene. The sequence of the early region of this phage was not retrieved from the bacterial host genome, and the origin of the phage is unknown. The contaminated food most likely contained a mixture of E. coli O103:H25 cells with either one of the phages.

Escherichia coli serotype O55:H7 diversity supports parallel acquisition of bacteriophage at Shiga toxin phage insertion sites during evolution of the O157:H7 lineage

Enteropathogenic Escherichia coli (EPEC) continues to be a leading cause of mortality and morbidity in children around the world. Two EPEC genomes have been fully sequenced: those of EPEC O127:H6 strain E2348/69 (United Kingdom, 1969) and EPEC O55:H7 strain CB9615 (Germany, 2003). The O55:H7 serotype is a recent precursor to the virulent enterohemorrhagic E. coli O157:H7. To explore the diversity of O55:H7 and better understand the clonal evolution of O157:H7, we fully sequenced EPEC O55:H7 strain RM12579 (California, 1974), which was collected 1 year before the first U.S. isolate of O157:H7 was identified in California. Phage-related sequences accounted for nearly all differences between the two O55:H7 strains. Additionally, O55:H7 and O157:H7 strains were tested for the presence and insertion sites of Shiga toxin gene (stx)-containing bacteriophages. Analysis of non-phage-associated genes supported core elements of previous O157:H7 stepwise evolutionary models, whereas phage composition and insertion analyses suggested a key refinement. Specifically, the placement and presence of lambda-like bacteriophages (including those containing stx) should not be considered stable evolutionary markers or be required in placing O55:H7 and O157:H7 strains within the stepwise evolutionary models. Additionally, we suggest that a 10.9-kb region (block 172) previously believed unique to O55:H7 strains can be used to identify early O157:H7 strains. Finally, we defined two subsets of O55:H7 strains that share an as-yet-unobserved or extinct common ancestor with O157:H7 strains. Exploration of O55:H7 diversity improved our understanding of the evolution of E. coli O157:H7 and suggested a key revision to accommodate existing and future configurations of stx-containing bacteriophages into current models.

Loss of vtx genes after the first subcultivation step of verocytotoxigenic Escherichia coli O157 and Non-O157 during isolation from naturally contaminated fecal samples

Verocytotoxins VT1 and VT2,produced by Verocytotoxigenic Escherichia coli (VTEC), are encoded on temperate bacteriophages. Several studies reported the loss of the vtx genes after multiple subcultivation steps or long preservation. The objective of this study was to determine if the loss of the verocytotoxin genes can already occur during the first subcultivation step. Consequently, the stability of the vtx genes were tested in 40 isolates originating from 40 vtx-positive fecal samples after the first subcultivation step following the isolation procedure. The loss occurred in 12 out of 40 strains tested and was rather rare among the O157 strains compared to the non-O157 strains. This is the first study demonstrating that the loss of the verocytotoxin genes can already occur after the first subcultivation step. This may lead to an underestimation of VTEC positive samples.

Chromosomal instability in enterohaemorrhagic Escherichia coli O157:H7: impact on adherence, tellurite resistance and colony phenotype

Tellurite (Tel) resistant enterohaemorrhagic Escherichia coli (EHEC) O157:H7 is a global pathogen. In strain EDL933 Tel resistance (Tel^R) is encoded by duplicate ter cluster in O islands (OI) 43 and 48, which also harbour iha, encoding the adhesin and siderophore receptor Iha. We identified five EHEC O157:H7 strains that differentiate into large (L) colonies and small (S) colonies with high and low Tel minimal inhibitory concentrations (MICs) respectively. S colonies (Tel-MICs ≤ 4 µg ml⁻¹) sustained large internal deletions within the Tel^R OIs via homologous recombination between IS elements and lost ter and iha. Moreover, complete excision of the islands occurred by site-specific recombination between flanking direct repeats. Complete excision of OI 43 and OI 48 occurred in 1.81 × 10⁻³ and 1.97 × 10⁻⁴ cells in culture, respectively; internal deletion of OI 48 was more frequent (9.7 × 10⁻¹ cells). Under iron limitation that promotes iha transcription, iha-negative derivatives adhered less well to human intestinal epithelial cells and grew slower than did their iha-positive counterparts. Experiments utilizing iha deletion and complementation mutants identified Iha as the major factor responsible for these phenotypic differences. Spontaneous deletions affecting Tel^R OIs contribute to EHEC O157 genome plasticity and might impair virulence and/or fitness.

Analysis of Escherichia coli O157 clinical isolates by multilocus sequence typing

Background

Although many strain typing methods exist for pathogenic Escherichia coli, most have drawbacks in terms of resolving power, interpretability, or scalability. For this reason, multilocus sequence typing (MLST) is an appealing alternative especially when applied to the typing of temporal and spatially separated isolates. This method relies on an unambiguous DNA sequence analysis of nucleotide polymorphisms in housekeeping genes and has shown a high degree of intraspecies discriminatory power for bacterial and fungal pathogens.

Results

Here we used the MLST method to study the genetic diversity among E. coli O157 isolates collected from humans from two different locations of USA over a period of several years (2000-2008). MLST analysis of 33 E. coli O157 patient isolates using the eBurst algorithm distinguished 26 different sequence types (STs), which were clustered into two clonal groups and 11 singletons. The predominant ST was ST2, which consisted of 5 isolates (14.28%) followed by ST1 (11.42%). All the isolates under clonal group I exhibited a virtually similar virulence profile except for two strains, which tested negative for the presence of stx genes. The isolates that were assigned to clonal group II in addition to the 11 singletons were found to be phylogenetically distant from clonal group I. Furthermore, we observed a positive correlation between the virulence profile of the isolates and their clonal origin.

Conclusions

Our data suggests the presence of genetic diversity among E. coli O157 isolates from humans shows no measurable correlation to the geographic origin of the isolates.

Molecular analysis of virulence profiles and Shiga toxin genes in food-borne Shiga toxin-producing Escherichia coli

In this study, 75 Shiga toxin (Stx)-producing Escherichia coli (STEC) strains originating from foods (n = 73) and drinking water (n = 2) were analyzed for their stx genotype, as well as for further chromosome-, phage-, and plasmid-encoded virulence factors. A broad spectrum of stx genes was detected. Fifty-three strains (70.7%) contained stx(2) or stx(2) variants, including stx(2d), mucus-activatable stx(2d), stx(2e), and stx(2g). Seven strains (9.3%) harbored stx(1) or stx(1c), and 15 strains (20.0%) carried both stx(2) and/or stx(2) variants and stx(1) or stx(1c). Beside stx, the most abundant accessory virulence markers in STEC food isolates were iha (57.3%), ehxA (40.0%), espP (28.0%), and subAB (25.3%). Only four strains were eae positive; three of these belonged to the serogroups O26, O103, and O157 and contained a typical enterohemorrhagic E. coli virulence spectrum. The results of this study show that a number of STEC strains that occur in foods appear to be pathogenic for humans, based on their virulence profiles. Analysis of stx subtypes and detection of additional virulence factors in eae-negative strains may help to better assess the risk of such strains for causing human infection.

Occurrence of non-sorbitol fermenting, verocytotoxin-lacking Escherichia coli O157 on cattle farms

Escherichia coli O157 is often associated with hemorrhagic colitis and the hemolytic uremic syndrome (HUS). The verocytotoxins are considered to be the major virulence determinants. However, vt-negative E. coli O157 were recently isolated from patients with HUS. Several transmission routes to humans are described, but cattle feces are the primary source from which both the food supply and the environment become contaminated with E. coli O157. In a prevalence study performed on dairy, beef, mixed dairy/beef and veal farms in the summer of 2007, vt-negative isolates were detected on 11.8% (8/68) of the positive farms. From these eight farms, a total of 43 sorbitol-negative E. coli O157:H7 were collected. On five farms, only strains negative for the vt genes were present whereas both vt-negative and vt-positive strains could be detected on three other farms. Further characterization revealed that all isolates carried the eaeA and hlyA genes. Pulsed-field gel electrophoresis (PFGE) of all isolates resulted in nine different PFGE types and within the vt-negative strains, four different genotypes were identified, indicating that certain genetic clones are widespread over the cattle population.

Outbreak of haemolytic uraemic syndrome in Norway caused by stx2-positive Escherichia coli O103:H25 traced to cured mutton sausages

BACKGROUND

On 20-21 February 2006, six cases of diarrhoea-associated haemolytic uraemic syndrome (HUS) were reported by paediatricians to the Norwegian Institute of Public Health. We initiated an investigation to identify the etiologic agent and determine the source of the outbreak in order to implement control measures.

METHODS

A case was defined as a child with diarrhoea-associated HUS or any person with an infection with the outbreak strain of E. coli O103 (defined by the multi-locus variable number tandem repeats analysis (MLVA) profile) both with illness onset after January 1st 2006 in Norway. After initial hypotheses-generating interviews, we performed a case-control study with the first fifteen cases and three controls for each case matched by age, sex and municipality. Suspected food items were sampled, and any E. coli O103 strains were typed by MLVA.

RESULTS

Between 20 February and 6 April 2006, 17 cases were identified, of which 10 children developed HUS, including one fatal case. After pilot interviews, a matched case-control study was performed indicating an association between a traditional cured sausage (odds ratio 19.4 (95% CI: 2.4-156)) and STEC infection. E. coli O103:H25 identical to the outbreak strain defined by MLVA profile was found in the product and traced back to contaminated mutton.

CONCLUSION

We report an outbreak caused by a rare STEC variant (O103:H25, stx2-positive). More than half of the diagnosed patients developed HUS, indicating that the causative organism is particularly virulent. Small ruminants continue to be important reservoirs for human-pathogen STEC. Improved slaughtering hygiene and good manufacturing practices for cured sausage products are needed to minimise the possibility of STEC surviving through the entire sausage production process.

Isolation of Escherichia coli O157:H7 strains that do not produce Shiga toxin from bovine, avian and environmental sources

AIMS

To determine the potential for naturally occurring Shiga toxin-negative Escherichia coli O157 to acquire stx(2) genes.

METHODS AND RESULTS

Multiple E. coli O157:H7 isolates positive for eae and ehxA, but not for stx genes, were isolated from cattle, water trough sediment, animal bedding and wild bird sources on several Ohio dairy farms. These isolates were experimentally lysogenized by stx(2)-converting bacteriophage.

CONCLUSIONS

Shiga toxin-negative strains of E. coli O157 are present in multiple animal and environmental sources.

SIGNIFICANCE AND IMPACT OF THE STUDY

Shiga toxin-negative strains of E. coli O157 present in the food production environment are able to acquire the stx genes, demonstrating their potential to emerge as new Shiga toxin-producing E. coli strains.

Human intestinal tissue tropism in Escherichia coli O157 : H7--initial colonization of terminal ileum and Peyer's patches and minimal colonic adhesion ex vivo

Enterohaemorrhagic Escherichia coli (EHEC) are an important cause of diarrhoeal and renal disease in man. Studies of a single prototypic O157 : H7 strain have shown tropism for follicle-associated epithelium (FAE) of distal ileal Peyer's patches without colonization of either small or large intestine. This study determined tropism in a range of Shiga toxin (Stx)-negative EHEC strains and looked for factors that might induce colonic colonization using human in vitro intestinal organ culture (IVOC). An FAE-restricted colonization was confirmed in two strains; four strains additionally colonized ileal villous surfaces, and adhesion to proximal small intestinal FAE was observed. All strains showed minimal adhesion to non-FAE regions of proximal small intestinal and to the transverse colon. Extensive large-bowel IVOC studies using three O157 : H7 strains, an O26 : H11 and an O103 : H2 strain, and tissue from caecum to rectum found colonization and attaching/effacing lesion formation in only 4 of 113 (3.5 %) IVOCs. Colonic adhesion was not enhanced by altering the IVOC technique or environment. Co-incubation of O157 : H7-infected ileal FAE with colonic samples enhanced colonic colonization, producing a novel, non-intimate adhesive phenotype. Thus, in the initial stages of colonization Stx-negative EHEC preferentially infect FAE and villi of the terminal ileal region ex vivo; colonic colonization is infrequently observed as an initial event but may represent a subsequent stage of infection.

Presence of Shiga toxin-producing E. coli O157:H7 in a survey of wild artiodactyls

This study was carried out to evaluate the role of wild artiodactyls as reservoirs of Escherichia coli O157:H7 for livestock and humans. Retroanal mucosal swabs samples from 206 red deer (Cervus elaphus), 20 roe deer (Capreolus capreolus), 6 fallow deer (Dama dama) and 11 mouflon (Ovis musimon), collected during the hunting season (autumn-winter) in South-western Spain, were screened. Samples were pre-enriched in modified buffered peptone water, concentrated by an immunomagnetic separation technique and cultured onto selective cefixime tellurite sorbitol MacConkey agar. Polymerase chain reaction (PCR) was used to detect the presence of genes coding O157 and H7 antigens and the virulence factors verocytotoxin, intimin and enterohaemolysin. Three E. coli O157:H7 isolates were obtained from red deer (1.5%). Two of them showed inability to ferment sorbitol and lack of beta-d-glucuronidase (GUD) activity, however, the other strain investigated was an atypical sorbitol-fermenting E. coli O157:H7 with GUD(+) activity. This is the first report pointing to red deer as a reservoir of E. coli O157:H7 in Spain.

Shiga toxin gene loss and transfer in vitro and in vivo during enterohemorrhagic Escherichia coli O26 infection in humans

Escherichia coli serogroup O26 consists of enterohemorrhagic E. coli (EHEC) and atypical enteropathogenic E. coli (aEPEC). The former produces Shiga toxins (Stx), major determinants of EHEC pathogenicity, encoded by bacteriophages; the latter is Stx negative. We have isolated EHEC O26 from patient stools early in illness and aEPEC O26 from stools later in illness, and vice versa. Intrapatient EHEC and aEPEC isolates had quite similar pulsed-field gel electrophoresis (PFGE) patterns, suggesting that they might have arisen by conversion between the EHEC and aEPEC pathotypes during infection. To test this hypothesis, we asked whether EHEC O26 can lose stx genes and whether aEPEC O26 can be lysogenized with Stx-encoding phages from EHEC O26 in vitro. The stx2 loss associated with the loss of Stx2-encoding phages occurred in 10% to 14% of colonies tested. Conversely, Stx2- and, to a lesser extent, Stx1-encoding bacteriophages from EHEC O26 lysogenized aEPEC O26 isolates, converting them to EHEC strains. In the lysogens and EHEC O26 donors, Stx2-converting bacteriophages integrated in yecE or wrbA. The loss and gain of Stx-converting bacteriophages diversifies PFGE patterns; this parallels findings of similar but not identical PFGE patterns in the intrapatient EHEC and aEPEC O26 isolates. EHEC O26 and aEPEC O26 thus exist as a dynamic system whose members undergo ephemeral interconversions via loss and gain of Stx-encoding phages to yield different pathotypes. The suggested occurrence of this process in the human intestine has diagnostic, clinical, epidemiological, and evolutionary implications.

Produce isolates of the Escherichia coli Ont:H52 serotype that carry both Shiga toxin 1 and stable toxin genes

Produce isolates of the Escherichia coli Ont:H52 serotype carried Shiga toxin 1 and stable toxin genes but only expressed Stx1. These strains had pulsed-field gel electrophoresis profiles that were 90% homologous to clinical Ont:H52 strains that had identical phenotypes and genotypes. All Ont:H52 strains had identical single nucleotide polymorphism profiles that are suggestive of a unique clonal group.

Chromosomal dynamism in progeny of outbreak-related sorbitol-fermenting enterohemorrhagic Escherichia coli O157:NM

Sorbitol-fermenting (SF) enterohemorrhagic Escherichia coli (EHEC) O157:NM (nonmotile) is a unique clone that causes outbreaks of hemorrhagic colitis and hemolytic-uremic syndrome. In well-defined clusters of cases, we have observed significant variability in pulsed-field gel electrophoresis (PFGE) patterns which could indicate coinfection by different strains. An analysis of randomly selected progeny colonies of an outbreak strain after subcultivation demonstrated that they displayed either the cognate PFGE outbreak pattern or one of four additional patterns and were <89% similar. These profound alterations were associated with changes in the genomic position of one of two Shiga toxin 2-encoding genes (stx2) in the outbreak strain or with the loss of this gene. The two stx2 alleles in the outbreak strain were identical but were flanked with phage-related sequences with only 77% sequence identity. Neither of these phages produced plaques, but one lysogenized E. coli K-12 and integrated in yecE in the lysogens and the wild-type strain. The presence of two stx2 genes which correlated with increased production of Stx2 in vitro but not with the clinical outcome of infection was also found in 14 (21%) of 67 SF EHEC O157:NM isolates from sporadic cases of human disease. The variability of PFGE patterns for the progeny of a single colony must be considered when interpreting PFGE patterns in SF EHEC O157-associated outbreaks.

Enterohemorrhagic Escherichia coli in Human Infection: In Vivo Evolution of a Bacterial Pathogen

BACKGROUND

Enterohemorrhagic Escherichia coli (EHEC) cause most cases of the hemolytic uremic syndrome (HUS) worldwide. To investigate genetic changes in EHEC during the course of human infection, we analyzed consecutive stool samples and shed isolates from patients with HUS, focusing on the genes encoding Shiga toxin (stx) and intimin (eae).

METHODS

Sequential stool samples from 210 patients with HUS were investigated for the persistence of E. coli strains harboring stx and/or eae. Initial stool samples were collected during the acute phase of HUS, and subsequent stool samples were collected 3-16 days later (median interval, 8 days).

RESULTS

Organisms that were stx and eae positive (stx+/eae+ strains; n=137) or stx negative and eae positive (stx-/eae+ strains; n=5) were detected in the initial stool samples from 142 patients. Subsequently, the proportion of those who shed stx+/eae+ strains decreased to 13 of 210 patients, whereas the proportion of those who shed strains that were stx-/eae+ increased to 12 of 210 patients. Seven patients who initially excreted strains that were stx+/eae+ shed, at second analysis, stx-/eae+ strains of the same serotypes; they had no free fecal Shiga toxin at follow-up. Comparison of the initial and follow-up isolates from these patients with use of molecular-epidemiological methods revealed loss of stx genes and genomic rearrangement.

CONCLUSIONS

We demonstrate the loss of a critical bacterial virulence factor from pathogens during very brief intervals in the human host. These genetic changes have evolutionary, diagnostic, and clinical implications. Generation of stx- mutants might contribute to subclonal evolution and evolutionary success.

Identifying new PCR targets for pathogenic bacteria using top-down LC/MS protein discovery

We have investigated the use of a top-down liquid chromatography/mass spectrometric (LC/MS) approach for the identification of specific protein biomarkers useful for differentiation of closely related strains of bacteria. The sequence information derived from the protein biomarker was then used to develop specific polymerase chain reaction primers useful for rapid identification of the strains. Shiga-toxigenic Escherichia coli (STEC) strains were used for this evaluation. The expressed protein profiles of two closely related serotype 0157:H7 strains, the predominant strain implicated in illness worldwide, and the nonpathogenic E. coli K-12 strain were compared with each other in an attempt to identify new protein markers that could be used to distinguish the 0157:H7 strains from each other and from the E. coli K-12 strain. Sequencing of a single protein unique to one of the 0157:H7 strains identified it as a cytolethal distending toxin, a potential virulence marker. The protein sequence information enabled the derivation of genetic sequence information for this toxin, thus allowing the development of specific polymerase chain reaction primers for its detection. In addition, the top-down LC/MS technique was able to identify other unique biomarkers and differentiate nearly identical 0157:H7 strains, which exhibited identical phenotypic, serologic, and genetic traits. The results of these studies demonstrate that this approach can be expanded to other serotypes of interest and provide a rational approach to identifying new molecular targets for detection.

DNA microarray for discrimination between pathogenic 0157:H7 EDL933 and non-pathogenic Escherichia coli strains

The primary technique currently used to detect biological agents is based on immunoassays. Although sensitive and specific, currently employed immunoassays generally rely on the detection of a single epitope, and therefore often cannot discriminate subtle strain-specific differences. Since DNA microarrays can hybridize hundreds to thousands of genomic targets simultaneously and do not rely on phenotypic expression of these genetic features for identification purposes, they have enormous potential to provide inexpensive, flexible and specific strain-specific detection and identification of pathogens. In this study, pathogenic Escherichia coli O157:H7-specific genes, non-pathogenic K12-specific genes, common E. coli genes, and negative control genes were polymerase chain reaction-amplified and spotted onto the surface of treated glass slides. After labeled bacterial cDNA samples were hybridized with probes on the microarray, specific fluorescence patterns were obtained, enabling identification of pathogenic E. coli O157:H7 and non-pathogenic E. coli K12. To test the utility of this microarray device to detect genetically engineered bacteria, E. coli BL21 (a B strain derivative with antibiotic resistance gene, ampR) and E. coli JM107 (a K12 strain derivative lacking the gene ompT) were also employed. The array successfully confirmed the strain genotypes and demonstrated that antibiotic resistance can also be detected. The ability to assess multiple data points makes this array method more efficient and accurate than a typical immunoassay, which detects a single protein product.

Characterization of O157:H7 and other Escherichia coli isolates recovered from cattle hides, feces, and carcasses

In a previous study, the seasonal prevalence was reported for stx+ Escherichia coli O157:H7 in feces and on hides and carcasses of cattle at processing. Overall, 1,697 O157:H7 isolates have now been characterized for the incidence of (i) eae(O157), hlyA, stx1, and stx2 in the recovered isolates and (ii) presumptive rough and presumptive nonmotile isolates. Seven O157:H7 isolates (0.4%) lacked stx genes, although they carried eae and hlyA. All but one of the isolates carried both eae and hlyA. Approximately two-thirds of the isolates (64% when one isolate per sample was considered) carried both stx1 and stx2. E. coli O157:H7 cells that harbored both stx1 and stx2 were more often recovered from hides in the fall (79% of the fall hide isolates) and winter (84% of the winter hide isolates) than in the spring (53%) and summer (59%). Isolates recovered from preevisceration carcasses showed a similar but not statistically significant trend. Twenty-three of the 25 O157:H7 isolates carrying stx1 but not stx2 were recovered during summer. Fifteen presumptive rough and 117 presumptive nonmotile stx+ O157:H7 isolates were recovered. Ten (67%) of the presumptive rough isolates were recovered during summer. Ninety-five of the presumptive nonmotile isolates (81%) were recovered during fall. Forty-eight percent of the false-positive isolates (175 of 363) tentatively identified as O157:H7 were O157+ H7- and lacked eae(O157), hlyA, and stx. These data suggest that in beef processing samples (i) there are minor seasonal variations in the prevalence of stx genes among E. coli O157:H7 isolates, (ii) presumptive rough and presumptive nonmotile stx+ O157:H7 isolates are present, (iii) E. coli O157:H7 isolates lacking stx genes may be rare, and (iv) O157+ H7- isolates lacking stx genes can result in many false-positive results.

Subtyping of foodborne and environmental isolates of Escherichia coli by multiplex-PCR, rep-PCR, PFGE, ribotyping and AFLP

A total of 54 isolates were characterized by multiplex-PCR for toxin genes and genotyped using several DNA fingerprinting methods: using repetitive extragenic palindromes (REP) and Box primers (rep-PCR), amplified fragment length polymorphism (AFLP), pulsed-field gel electrophoresis (PFGE) and ribotyping. The known-pathogenic strains tested were from food and clinical samples (34 strains) and included serovars O157:H7, O111:H8, O111:H11, O91:H21 and O55:H7. Two type cultures, Escherichia coli K12 (ATCC 29425) and DUP-101 (ATCC 51739), were included as known non-pathogenic strains and an additional 17 previously unclassified isolates from animal fecal samples. Comparisons of genomic DNA fingerprint patterns using unweighted pair group method with arithmetic averages (UPGMA) cluster analysis of Jaccard similarity indices indicated that all methods tested showed a greater similarity between the E. coli O157:H7 strains than to other isolates. On the basis of these studies, we propose that AFLP, REP-PCR, Box-PCR and ribotyping techniques can all be used for discriminating O157:H7 isolates and are preferred for large-scale screening because of the speed and ease of the methods. The PFGE method is the best to discriminate between subtypes of O157:H7 associated with specific outbreak investigations; however, it is more time consuming and unnecessary if subtyping is not required. There are differences between the dendrograms generated from each method and the relationship between the other strains analyzed. However, the fingerprint profiles of the O157:H7 isolates were virtually identical using REP-PCR and Box-PCR enabling easy distinction of the group. Thus, these typing methods have the potential to aid investigators in identifying the source of an outbreak to prevent or control further spread of E. coli O157:H7.

Isolation of Shiga toxin-producing Escherichia coli O103 from sheep using automated immunomagnetic separation (AIMS) and AIMS-ELISA: sheep as the source of a clinical E. coli O103 case?

AIMS

To investigate whether a sheep flock was the original reservoir of a Shiga toxin-producing Escherichia coli (STEC) O103 strain causing a clinical human case and to compare the two diagnostic methods automated immunomagnetic separation (AIMS) and AIMS-ELISA.

METHODS AND RESULTS

AIMS detected Escherichia coli O103 in 36.5% of the samples and AIMS-ELISA detected E. coli O103 in 52.1% of the samples. Polymerase chain reaction detected stx1 and eae in three of 109 E. coli O103 isolates. Pulsed field gel electrophoresis showed that the sheep and human STEC O103 were characterized by distinctly different profiles.

CONCLUSIONS

The sheep flock was shown to carry STEC O103, although an association between the sheep flock and the clinical human case could neither be proven nor eliminated. Substantial agreement was found between AIMS and AIMS-ELISA, but AIMS-ELISA was less time consuming and resulted in a higher recovery of E. coli O103.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study shows that sheep may be carriers of STEC that are associated with human disease and that the methods described can be used to increase the sensitivity of STEC detection.