Hemorrhagic colitis associated with a rare Escherichia coli serotype

Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of Shiga toxin-producing Escherichia coli O157:H7 in the UK

Over the last 35 years in the UK, the burden of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infection has, during different periods of time, been associated with five different sub-lineages (1983-1995, Ia, I/IIa and I/IIb; 1996-2014, Ic; and 2015-2018, IIb). The acquisition of a stx2a-encoding bacteriophage by these five sub-lineages appears to have coincided with their respective emergences. The Oxford Nanopore Technologies (ONT) system was used to sequence, characterize and compare the stx-encoding prophages harboured by each sub-lineage to investigate the integration of this key virulence factor. The stx2a-encoding prophages from each of the lineages causing clinical disease in the UK were all different, including the two UK sub-lineages (Ia and I/IIa) circulating concurrently and causing severe disease in the early 1980s. Comparisons between the stx2a-encoding prophage in sub-lineages I/IIb and IIb revealed similarity to the prophage commonly found to encode stx2c, and the same site of bacteriophage integration (sbcB) as stx2c-encoding prophage. These data suggest independent acquisition of previously unobserved stx2a-encoding phage is more likely to have contributed to the emergence of STEC O157:H7 sub-lineages in the UK than intra-UK lineage to lineage phage transmission. In contrast, the stx2c-encoding prophage showed a high level of similarity across lineages and time, consistent with the model of stx2c being present in the common ancestor to extant STEC O157:H7 and maintained by vertical inheritance in the majority of the population. Studying the nature of the stx-encoding bacteriophage contributes to our understanding of the emergence of highly pathogenic strains of STEC O157:H7.

Development and Evaluation of a Novel VHH-Based Immunocapture Assay for High-Sensitivity Detection of Shiga Toxin Type 2 (Stx2) in Stool Samples

Shiga toxin (Stx)-producing Escherichia coli (STEC) is the main cause of postdiarrheal hemolytic-uremic syndrome (HUS), a life-threatening clinical complication characterized by hemolytic anemia, thrombocytopenia, and acute renal failure that mainly affects children. A relevant feature of STEC strains is the production of Stx, and all of them express Stx1 and/or Stx2 regardless of the strain serotype. Therefore, Stx detection assays are considered the most suitable methods for the early detection of STEC infections. Single-domain antibodies from camelids (VHHs) exhibit several advantages in comparison with conventional antibodies, making them promising tools for diagnosis. In this work, we have exploited VHH technology for the development of an immunocapture assay for Stx2 detection. Thirteen anti-Stx2 VHHs previously obtained from a variable-domain repertoire library were selected and evaluated in 130 capture-detection pair combinations for Stx detection. Based on this analysis, two VHHs were selected and a double VHH-based biotin-streptavidin capture enzyme-linked immunosorbent assay (ELISA) with spectrophotometric detection was developed and optimized for Stx2 detection. This assay showed an excellent analytical and clinical sensitivity in both STEC culture supernatants and stool samples even higher than the sensitivity of a commercial ELISA. Furthermore, based on the analysis of stool samples, the VHH-based ELISA showed high correlation with stx ₂ detection by PCR and a commercial rapid membrane-based immunoassay. The intrinsic properties of VHHs (high target affinity and specificity, stability, and ease of expression at high yields in recombinant bacteria) and their optimal performance for Stx detection make them attractive tools for the diagnosis of HUS related to STEC (STEC-HUS).

Intimate Attachment of Escherichia coli O157:H7 to Urinary Bladder Epithelium in the Gnotobiotic Piglet Model

Enterohemorrhagic Escherichia coli (EHEC), a pathogenic subset of Shiga toxin-producing E. coli (STEC), is an important cause of hemorrhagic colitis and hemolytic–uremic syndrome (HUS), and a rare cause of urinary tract infections (UTIs) with associated HUS. EHEC strains attach intimately to intestinal epithelium with formation of actin pedestals (attaching-effacing (A/E) lesions); however, the mechanism of EHEC attachment to the uroepithelium is unknown. We conducted a retrospective study on archived urinary bladder specimens from gnotobiotic piglets that naturally developed cystitis associated with EHEC O157:H7 infection following oral inoculation and fecal shedding. Paraffin-embedded bladder tissues from three piglets with cystitis and immunohistochemical evidence of EHEC O157:H7 adherence to the uroepithelium were processed for and examined by transmission electron microscopy. EHEC O157:H7 bacteria were found in one of three piglets, intimately attached to pedestals on the apical surfaces of the superficial urothelium (umbrella cells). Cystitis was significantly associated with the length of survival of the piglets post-inoculation (p = 0.0339; estimated odds ratio = 2.6652). This is the first report of E. coli causing A/E-like lesions in the uroepithelium, and also evidence of the utility of the gnotobiotic piglet as a model for studies of the pathogenesis of EHEC UTIs.

The ea22 gene of lambdoid phages: preserved prolysogenic function despite of high sequence diversity

The exo-xis region of lambdoid phages contains open reading frames and genes that appear to be evolutionarily important. However, this region has received little attention up to now. In this study, we provided evidence that ea22, the largest gene of this region, favors the lysogenic pathway over the lytic pathway in contrast to other characterized exo-xis region genes including ea8.5, orf61, orf60a, and orf63. Our assays also suggest some functional analogies between Ea22 and the phage integrase protein (Int). While it is unsurprising that Ea22 operates similarly in both λ and Stx phages, we have observed some distinctions that may arise from considerable sequence dissimilarity at the carboxy termini of each protein.

Shiga Toxin-Associated Hemolytic Uremic Syndrome: A Narrative Review

The severity of human infection by one of the many Shiga toxin-producing Escherichia coli (STEC) is determined by a number of factors: the bacterial genome, the capacity of human societies to prevent foodborne epidemics, the medical condition of infected patients (in particular their hydration status, often compromised by severe diarrhea), and by our capacity to devise new therapeutic approaches, most specifically to combat the bacterial virulence factors, as opposed to our current strategies that essentially aim to palliate organ deficiencies. The last major outbreak in 2011 in Germany, which killed more than 50 people in Europe, was evidence that an effective treatment was still lacking. Herein, we review the current knowledge of STEC virulence, how societies organize the prevention of human disease, and how physicians treat (and, hopefully, will treat) its potentially fatal complications. In particular, we focus on STEC-induced hemolytic and uremic syndrome (HUS), where the intrusion of toxins inside endothelial cells results in massive cell death, activation of the coagulation within capillaries, and eventually organ failure.

Facile Route of Fabricating Long-Term Microbicidal Silver Nanoparticle Clusters against Shiga Toxin-Producing Escherichia coli O157:H7 and Candida auris

Microbial contamination remains a significant issue for many industrial, commercial, and medical applications. For instance, microbial surface contamination is detrimental to numerous aspects of food production, infection transfer, and even marine applications. As such, intense scientific interest has focused on improving the antimicrobial properties of surface coatings via both chemical and physical routes. However, there is a lack of synthetic coatings that possess long-term microbiocidal performance. In this study, silver nanoparticle cluster coatings were developed on copper surfaces via an ion-exchange and reduction reaction, followed by a silanization step. The durability of the microbiocidal activity for these develped surfaces was tested against pathogenic bacterial and fungal species, specifically Escherichia coli O157:H7 and Candida auris, over periods of 1- and 7-days. It was observed that more than 90% of E. coli and C. auris were found to be non-viable following the extended exposure times. This facile material fabrication presents as a new surface design for the production of durable microbicidal coatings which can be applied to numerous applications.

Preparation of Fluorescent Recombinant Shiga Toxin B Subunit and Its Application to Flow Cytometry

Shiga toxin (Stx) is a major virulence factor of enterohemorrhagic Escherichia coli (E. coli). Stx consists of one enzymatic A subunit and five B subunits (StxB) that are involved in binding. The StxB pentamer specifically recognizes a glycosphingolipid, globotriaosylceramide (Gb3), as a receptor; therefore, it can be used as a probe to detect Gb3. This chapter describes the preparation of recombinant Stx1B proteins using E. coli, their conjugation with fluorescent dyes, and their application for flow cytometry. The prepared fluorescent StxB proteins bound to cells of several lines, including the HeLa human cervix adenocarcinoma cell line and the THP-1 human monocytic leukemia cell line. Furthermore, the probe was useful for confirmation of several sphingolipid-deficient HeLa cell lines that were constructed using genome editing.

A Putative Microcin Amplifies Shiga Toxin 2a Production of Escherichia coli O157:H7

Escherichia coli O157:H7 is a foodborne pathogen implicated in various multistate outbreaks. It encodes Shiga toxin on a prophage, and Shiga toxin production is linked to phage induction. An E. coli strain, designated 0.1229, that amplified Stx2a production when cocultured with E. coli O157:H7 strain PA2 was identified. Growth of PA2 in 0.1229 cell-free supernatants had a similar effect, even when supernatants were heated to 100°C for 10 min, but not after treatment with proteinase K. The secreted molecule was shown to use TolC for export and the TonB system for import. The genes sufficient for production of this molecule were localized to a 5.2-kb region of a 12.8-kb plasmid. This region was annotated, identifying hypothetical proteins, a predicted ABC transporter, and a cupin superfamily protein. These genes were identified and shown to be functional in two other E. coli strains, and bioinformatic analyses identified related gene clusters in similar and distinct bacterial species. These data collectively suggest that E. coli 0.1229 and other E. coli strains produce a microcin that induces the SOS response in target bacteria. Besides adding to the limited number of microcins known to be produced by E. coli, this study provides an additional mechanism by which stx _2a expression is increased in response to the gut microflora.IMPORTANCE How the gut microflora influences the progression of bacterial infections is only beginning to be understood. Antibiotics are counterindicated for E. coli O157:H7 infections, limiting treatment options. An increased understanding of how the gut microflora directs O157:H7 virulence gene expression may lead to additional treatment options. This work identified E. coli strains that enhance the production of Shiga toxin by O157:H7 through the secretion of a proposed microcin. Microcins are natural antimicrobial peptides that target specific species, can act as alternatives to antibiotics, and mediate microbial competition. This work demonstrates another mechanism by which non-O157 E. coli strains may increase Shiga toxin production and adds to our understanding of microcins, a group of antimicrobials less well understood than colicins.

Cattle intestinal microbiota shifts following Escherichia coli O157:H7 vaccination and colonization

Vaccination-induced Escherichia coli O157:H7-specific immune responses have been shown to reduce E. coli O157:H7 shedding in cattle. Although E. coli O157:H7 colonization is correlated with perturbations in intestinal microbial diversity, it is not yet known whether vaccination against E. coli O157:H7 could cause shifts in bovine intestinal microbiota. To understand the impact of E. coli O157:H7 vaccination and colonization on intestinal microbial diversity, cattle were vaccinated with two doses of different E. coli O157:H7 vaccine formulations. Six weeks post-vaccination, the two vaccinated groups (Vx-Ch) and one non-vaccinated group (NonVx-Ch) were orally challenged with E. coli O157:H7. Another group was neither vaccinated nor challenged (NonVx-NonCh). Fecal microbiota analysis over a 30-day period indicated a significant (FDR corrected, p <0.05) association of bacterial community structure with vaccination until E. coli O157:H7 challenge. Shannon diversity index and species richness were significantly lower in vaccinated compared to non-vaccinated groups after E. coli O157:H7 challenge (p < 0.05). The Firmicutes:Bacteroidetes ratio (p > 0.05) was not associated with vaccination but the relative abundance of Proteobacteria was significantly lower (p < 0.05) in vaccinated calves after E. coli O157:H7 challenge. Similarly, Vx-Ch calves had higher relative abundance of Paeniclostridium spp. and Christenellaceae R7 group while Campylobacter spp., and Sutterella spp. were more abundant in NonVx-Ch group post-E. coli O157:H7 challenge. Only Vx-Ch calves had significantly higher (p < 0.001) E. coli O157:H7-specific serum IgG but no detectable E. coli O157:H7-specific IgA. However, E. coli O157:H7-specific IL-10-producing T cells were detected in vaccinated animals prior to challenge, but IFN-γ-producing T cells were not detected. Neither E. coli O157:H7-specific IgG nor IgA were detected in blood or feces, respectively, of NonVx-Ch and NonVx-NonCh groups prior to or post vaccinations. Both Vx-Ch and NonVx-Ch animals shed detectable levels of challenge strain during the course of the study. Despite the lack of protection with the vaccine formulations there were detectable shifts in the microbiota of vaccinated animals before and after challenge with E. coli O157:H7.

Application of kernel smoothing to estimate the spatio-temporal variation in risk of STEC O157 in England

Identifying geographical areas with significantly higher or lower rates of infectious diseases can provide important aetiological clues to inform the development of public health policy and interventions designed to reduce morbidity. We applied kernel smoothing to estimate the spatial and spatio-temporal variation in risk of STEC O157 infection in England between 2009 and 2015, and to explore differences between the residential locations of cases reporting travel and those not reporting travel. We provide evidence that the distribution of STEC O157 infection in England is non-uniform with respect to the distribution of the at-risk population; that the spatial distribution of the three main genetic lineages infecting humans (I, II and I/II) differs significantly and that the spatio-temporal risk is highly dynamic. Our results also indicate that cases of STEC O157 reporting travel within or outside the UK are more likely to live in the south/south-east of the country, meaning that their residential location may not reflect the location of exposure that led to their infection. We suggest that the observed variation in risk reflects exposure to sources of STEC O157 that are geographically prescribed. These differences may be related to a combination of changes in the strains circulating in the ruminant reservoir, animal movements (livestock, birds or wildlife) or the behavior of individuals prior to infection. Further work to identify the importance of behaviours and exposures reported by cases relative to residential location is needed.

Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain ATCC 43888

Escherichia coli serotype O157:H7 strain ATCC 43888 is a Shiga toxin-deficient human fecal isolate. Due to its reduced toxicity and its availability from a curated culture collection, the strain has been used extensively in applied research studies. Here, we report the Illumina-corrected PacBio whole-genome sequence of E. coli O157:H7 strain ATCC 43888.

Escherichia coli serotype O157:H7 strain ATCC 43888 is a Shiga toxin-deficient human fecal isolate. Due to its reduced toxicity and its availability from a curated culture collection, the strain has been used extensively in applied research studies. Here, we report the Illumina-corrected PacBio whole-genome sequence of E. coli O157:H7 strain ATCC 43888.

Escherichia coli O157:H7: distribution, molecular characterization, antimicrobial resistance patterns and source of contamination of sheep and goat carcasses at an export abattoir, Mojdo, Ethiopia

BACKGROUND

Cattle have been identified as a major reservoir of E. coli O157:H7 for human infection; the ecology of the organism in sheep and goats is less understood. This study was carried out to determine prevalence, source of infection, antibiotic resistance and molecular characterization of Escherichia coli O157: H7 isolated from sheep and goat.

METHODS

Systematic random sampling was carried out at Modjo export abattoir, Ethiopia, from November 2012 to April 2013 to collect 408 samples from 72 sheep and 32 goats. Samples collected were skin swabs, fecal samples, intestinal mucosal swabs and the inside and outside part of carcasses as well as carcass in contacts such as workers hands, knife, hook and carcass washing water. Then, samples were processed following standard bacteriological procedures. Non-Sorbitol fermenting colonies were tested on latex agglutination test and the positives are subjected to PCR for detection of attaching and effacing genes (eaeA) and shiga toxin producing genes (stx1 and stx2). All E. coli O157:H7 isolates were checked for their susceptibility pattern towards 15 selected antibiotics.

RESULTS

E. coli O157:H7 were detected in only 20/408 samples (4.9%). Among these 20 positive samples, 70% (14/20), 25% (5/20) and 5% (1/20) were from sheep, goats and knife samples, respectively. No significant associations were found between carcasses and the assumed sources of contaminations. Of all the 20 isolates virulence genes were found in 10 (50%) of them; 3 (15%) with only the eaeA gene and 7(35%) expressing eaeA and stx2 genes. All the isolates were susceptible to Norfloxacin (NOR) (100%).

CONCLUSIONS

The presence of virulence genes shows E. coli O157:H7 is a potential source of human infection in Ethiopia.

Shiga toxin-producing Escherichia coli in British Columbia, 2011-2017: Analysis to inform exclusion guidelines

Background

Shiga toxin-producing Escherichia coli (STEC) can cause severe illness including bloody diarrhea and hemolytic-uremic syndrome (HUS) through the production of Shiga toxins 1 (Stx1) and 2 (Stx2). E. coli O157:H7 was the most common serotype detected in the 1980s to 1990s, but improvements in laboratory methods have led to increased detection of non-O157 STEC. Non-O157 STEC producing only Stx1 tend to cause milder clinical illness. Exclusion guidelines restrict return to high-risk work or settings for STEC cases, but most do not differentiate between STEC serogroups and Stx type.

Objective

To analyze British Columbia (BC) laboratory and surveillance data to inform the BC STEC exclusion guideline.

Methods

For all STEC cases reported in BC in 2011-2017, laboratory and epidemiological data were obtained through provincial laboratory and reportable disease electronic systems, respectively. Incidence was measured for all STEC combined as well as by serogroup. Associations were measured between serogroups, Stx types and clinical outcomes.

Results

Over the seven year period, 984 cases of STEC were reported. A decrease in O157 incidence was observed, while non-O157 rates increased. The O157 serogroup was significantly associated with Stx2. Significant associations were observed between Stx2 and bloody diarrhea, hospitalization and HUS.

Conclusion

The epidemiology of STEC has changed in BC as laboratories increasingly distinguish between O157 and non-O157 cases and identify Stx type. It appears that non-O157 cases with Stx1 are less severe than O157 cases with Stx2. The BC STEC exclusion guidelines were updated as a result of this analysis.

Development and Validation of Shiga Toxin-Producing Escherichia coli Immunodiagnostic Assay

Shiga toxin (Stx)-producing Escherichia coli (STEC) and its subgroup enterohemorrhagic E. coli are important pathogens involved in diarrhea, which may be complicated by hemorrhagic colitis and hemolytic uremic syndrome, the leading cause of acute renal failure in children. Early diagnosis is essential for clinical management, as an antibiotic treatment in STEC infections is not recommended. Previously obtained antibodies against Stx1 and Stx2 toxins were employed to evaluate the sensitivity and specificity of the latex Agglutination test (LAT), lateral flow assay (LFA), and capture ELISA (cEIA) for STEC detection. The LAT (mAb Stx1 plus mAb stx2) showed 99% sensitivity and 97% specificity. Individually, Stx1 antibodies showed 95.5% and 94% sensitivity and a specificity of 97% and 99% in the cEIA and LFA assay, respectively. Stx2 antibodies showed a sensitivity of 92% in both assays and a specificity of 100% and 98% in the cEIA and LFA assay, respectively. These results allow us to conclude that we have robust tools for the diagnosis of STEC infections.

Transposon-insertion sequencing screens unveil requirements for EHEC growth and intestinal colonization

Enterohemorrhagic Escherichia coli O157:H7 (EHEC) is an important food-borne pathogen that colonizes the colon. Transposon-insertion sequencing (TIS) was used to identify genes required for EHEC and E. coli K-12 growth in vitro and for EHEC growth in vivo in the infant rabbit colon. Surprisingly, many conserved loci contribute to EHEC's but not to K-12's growth in vitro. There was a restrictive bottleneck for EHEC colonization of the rabbit colon, which complicated identification of EHEC genes facilitating growth in vivo. Both a refined version of an existing analytic framework as well as PCA-based analysis were used to compensate for the effects of the infection bottleneck. These analyses confirmed that the EHEC LEE-encoded type III secretion apparatus is required for growth in vivo and revealed that only a few effectors are critical for in vivo fitness. Over 200 mutants not previously associated with EHEC survival/growth in vivo also appeared attenuated in vivo, and a subset of these putative in vivo fitness factors were validated. Some were found to contribute to efficient type-three secretion while others, including tatABC, oxyR, envC, acrAB, and cvpA, promote EHEC resistance to host-derived stresses. cvpA is also required for intestinal growth of several other enteric pathogens, and proved to be required for EHEC, Vibrio cholerae and Vibrio parahaemolyticus resistance to the bile salt deoxycholate, highlighting the important role of this previously uncharacterized protein in pathogen survival. Collectively, our findings provide a comprehensive framework for understanding EHEC growth in the intestine.

Virulence Characteristics and Antimicrobial Resistance Profiles of Shiga Toxin-Producing Escherichia coli Isolates from Humans in South Africa: 2006-2013

Shiga toxin-producing Escherichia coli (STEC) isolates (N = 38) that were incriminated in human disease from 2006 to 2013 in South Africa were characterized by serotype, virulence-associated genes, antimicrobial resistance and pulsed-field gel electrophoresis (PFGE). The isolates belonged to 11 O:H serotypes. STEC O26:H11 (24%) was the most frequent serotype associated with human disease, followed by O111:H8 (16%), O157:H7 (13%) and O117:H7 (13%). The majority of isolates were positive for key virulence-associated genes including stx1 (84%), eaeA (61%), ehxA (68.4%) and espP (55%), but lacked stx2 (29%), katP (42%), etpD (16%), saa (16%) and subA (3%). stx2 positive isolates carried stx2c (26%) and/or stx2d (26%) subtypes. All pathogenicity island encoded virulence marker genes were detected in all (100%) isolates except nleA (47%), nleC (84%) and nleD (76%). Multidrug resistance was observed in 89% of isolates. PFGE revealed 34 profiles with eight distinct clusters that shared ≥80% intra-serotype similarity, regardless of the year of isolation. In conclusion, STEC isolates that were implicated in human disease between 2006 and 2013 in South Africa were mainly non-O157 strains which possessed virulence genes and markers commonly associated with STEC strains that have been incriminated in mild to severe human disease worldwide. Improved STEC monitoring and surveillance programs are needed in South Africa to control and prevent STEC disease in humans.

Identification and characterization of atypical enteropathogenic and Shiga toxin-producing Escherichia coli isolated from ground beef and poultry breast purchased in Botucatu, Brazil

Atypical enteropathogenic (serotypes O4:H16, O8:H25, O68:H2, O105:H7, and OR:H25) and Shigatoxigenic (ONT:H46) Escherichia coli were isolated from samples of ground beef and poultry breast purchased in Botucatu, Brazil. Phenotypic and molecular characterization indicated the potential of these isolates to adhere to host epithelial cells and cause damage.

Characterization of a Lytic Bacteriophage as an Antimicrobial Agent for Biocontrol of Shiga Toxin-Producing Escherichia coli O145 Strains

Shiga toxin-producing Escherichia coli (STEC) O145 is one of the most prevalent non-O157 serogroups associated with foodborne outbreaks. Lytic phages are a potential alternative to antibiotics in combatting bacterial pathogens. In this study, we characterized a Siphoviridae phage lytic against STEC O145 strains as a novel antimicrobial agent. Escherichia phage vB_EcoS-Ro145clw (Ro145clw) was isolated and purified prior to physiological and genomic characterization. Then, in vitro antimicrobial activity against an outbreak strain, E. coli O145:H28, was evaluated. Ro145clw is a double-stranded DNA phage with a genome 42,031 bp in length. Of the 67 genes identified in the genome, 21 were annotated with functional proteins, none of which were stx genes. Ro145clw had a latent period of 21 min and a burst size of 192 phages per infected cell. The phage could sustain a wide range of pH (pH 3 to pH 10) and temperatures (-80 °C to -73 °C). Ro145clw was able to reduce E. coli O145:H28 in lysogeny broth by approximately 5 log at 37 °C in four hours. These findings indicate that the Ro145clw phage is a promising antimicrobial agent that can be used to control E. coli O145 in adverse pH and temperature conditions.

Anti-biofilm and Antibacterial Activity of Allium sativum Against Drug Resistant Shiga-Toxin Producing Escherichia coli (STEC) Isolates from Patient Samples and Food Sources

Escherichia coli (E. coli) colonizes human intestinal tract and is usually harmless to the host. However, several strains of E. coli have acquired virulent genes and could cause enteric diseases, urinary tract and even brain infections. Shiga toxin producing Escherichia coli (STEC) is an enterohaemorrhagic E. coli (EHEC) which can result in bloody diarrhoea and could potentially lead to deadly heamolytic uremic syndrome (HUS). STEC is one of the important food borne pathogens that causes food poisoning leading to diarrhoea and number of STEC outbreaks have occurred across the world. The use of standard antibiotics to treat STEC infection is not recommended as it increases the production of shiga toxin which could lead to HUS. Therefore, use of alternative approaches which include use of plant products to treat STEC infections have been gaining attention. The objective of this study was to evaluate the antibacterial and anti-biofilm activity of garlic (Allium sativum) against STEC strains isolated from various patient and food samples using in vitro assays. The microbiological isolation of STEC from various patient and food samples resulted in eight STEC isolates of which seven strains were multidrug resistant. Antibacterial assay results indicated that all the strains exhibited dose dependent sensitivity towards garlic with zone of inhibition diameters ranging from 7 to 24 mm with 15 µl of fresh garlic extract (FGE). Minimum inhibitory  concentration (MIC) of FGE for isolates ranged from 30 to 140 µl/ml. Interestingly, the biofilm formation of all isolates in presence of 4% of FGE decreased by 35 to 59%. FTIR analysis indicated that treatment with 1% FGE results in compositional and content changes in the biofilm. In addition, the total carbohydrate content of biofilm was reduced by 40% upon 1% FGE treatment. The results of the present study report for the first time the antibacterial and anti-biofilm activity of garlic against STEC. The findings will enable development of novel garlic organosulfide based drugs for the prevention and treatment of STEC infections.

The Prophages of Citrobacter rodentium Represent a Conserved Family of Horizontally Acquired Mobile Genetic Elements Associated with Enteric Evolution towards Pathogenicity

Prophage-mediated horizontal gene transfer (HGT) plays a key role in the evolution of bacteria, enabling access to new environmental niches, including pathogenicity. Citrobacter rodentium is a host-adapted intestinal mouse pathogen and important model organism for attaching and effacing (A/E) pathogens, including the clinically significant enterohaemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC, respectively). Even though C. rodentium contains 10 prophage genomic regions, including an active temperate phage, ΦNP, little was known regarding the nature of C. rodentium prophages in the bacterium's evolution toward pathogenicity. In this study, our characterization of ΦNP led to the discovery of a second, fully functional temperate phage, named ΦSM. We identify the bacterial host receptor for both phages as lipopolysaccharide (LPS). ΦNP and ΦSM are likely important mediators of HGT in C. rodentium Bioinformatic analysis of the 10 prophage regions reveals cargo genes encoding known virulence factors, including several type III secretion system (T3SS) effectors. C. rodentium prophages are conserved across a wide range of pathogenic enteric bacteria, including EPEC and EHEC as well as pathogenic strains of Salmonella enterica, Shigella boydii, and Klebsiella pneumoniae Phylogenetic analysis of core enteric backbone genes compared against prophage evolutionary models suggests that these prophages represent an important, conserved family of horizontally acquired enteric-bacterium-associated pathogenicity determinants. In addition to highlighting the transformative role of bacteriophage-mediated HGT in C. rodentium's evolution toward pathogenicity, these data suggest that the examination of conserved families of prophages in other pathogenic bacteria and disease outbreaks might provide deeper evolutionary and pathological insights otherwise obscured by more classical analysis.IMPORTANCE Bacteriophages are obligate intracellular parasites of bacteria. Some bacteriophages can confer novel bacterial phenotypes, including pathogenicity, through horizontal gene transfer (HGT). The pathogenic bacterium Citrobacter rodentium infects mice using mechanisms similar to those employed by human gastrointestinal pathogens, making it an important model organism. Here, we examined the 10 prophages of C. rodentium, investigating their roles in its evolution toward virulence. We characterized ΦNP and ΦSM, two endogenous active temperate bacteriophages likely important for HGT. We showed that the 10 prophages encode predicted virulence factors and are conserved within other intestinal pathogens. Phylogenetic analysis suggested that they represent a conserved family of horizontally acquired enteric-bacterium-associated pathogenic determinants. Consequently, similar analysis of prophage elements in other pathogens might further understanding of their evolution and pathology.

Two putative MmpL homologs contribute to antimicrobial resistance and nephropathy of enterohemorrhagic E. coli O157:H7

Background

The serious human pathogen, E. coli serotype O157:H7, continues to gain antibiotic resistance, posing a public health threat. While this serotype’s genome has been sequenced, the role of 25% of its genes remains unknown, including genes conferring additional resistance. A prominent bacterial resistance mechanism is acquiring genes encoding efflux pumps, among which are the mycobacterial membrane proteins (Mmp), which contribute to virulence and membrane transport in mycobacteria. Here, we identified two potential mmp homologs (z4861 and yegN) in E. coli O157:H7, and we aimed to investigate their distribution among E. coli strains and their potential functions.

Methods and results

By screening different E. coli strains in vitro and in silico, we observed that yegN is more conserved than z4861. Using knockout mutants lacking either or both genes, we found that the mutants were more susceptible to fluoroquinolones than the parent strain and their secretomes included fewer virulence-related proteins. Moreover, histopathological examination of the kidneys of CD-1 mice infected by the wild-type or knockout strains indicated a greater impact of z4861 on pathogenesis and kidney damage than yegN, since both mutants lacking z4861 caused less severe kidney damage. The growth pattern of the wild-type was similar to that of mutant strains under aerobic and anaerobic conditions; yet, the mutant strains grew less when treated with subinhibitory dose of ciprofloxacin.

Conclusion

The previously unannotated gene product, Z4861, and its more conserved homolog, YegN, contribute to the kidney damage and resistance of E. coli O157:H7.

Electronic supplementary material

The online version of this article (10.1186/s13099-019-0296-7) contains supplementary material, which is available to authorized users.

An enterohaemorrhagic Escherichia coli outbreak spread through the environment at an institute for people with intellectual disabilities in Japan in 2005

OBJECTIVE

An enterohaemorrhagic Escherichia coli (EHEC) outbreak at an institute with multiple facilities for children and adults with intellectual disabilities was investigated to characterize the cases and identify risk factors for infection.

METHODS

A case was defined as a resident, a staff member or a visitor at the institute from 16 May through 30 June 2005 testing positive for type 2 Vero toxin-producing EHEC O157:H7 (confirmed case) or exhibiting bloody diarrhoea for two or more days (probable case). We collected and analysed demographic, clinical, laboratory and individual behaviour data to identify possible risk factors for infection and infection routes.

RESULTS

We recorded 58 confirmed cases, of which 13 were symptomatic. One probable case was also found. The median age of the patients was 37 years (range: 6-59 years). Thirty-six patients (61%) were male. Thirteen patients (93%) had diarrhoea and six (43%) had abdominal pain. Two developed haemolytic-uraemic syndrome but recovered. All the patients were treated with antibiotics and tested negative after treatment. Some residents had problems with personal hygiene. The residents of one of the facilities who cleaned a particular restroom had 18.0 times higher odds of being infected with EHEC (95% confidence interval: 4.0-102.4) than those who did not.

DISCUSSION

The source of the outbreak could not be identified; however, the infection may have spread through environmental sources contaminated with EHEC. We recommend that institutional settings, particularly those that accommodate people with intellectual disabilities, clean restrooms as often as possible to reduce possible infection from contact with infected surfaces.

Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7

Background

Escherichia coli O157:H7 (O157) has been linked to numerous foodborne disease outbreaks. The ability to rapidly sequence and analyze genomes is important for understanding epidemiology, virulence, survival, and evolution of outbreak strains. In the current study, we performed comparative genomics to determine structural and functional features of the genome of a foodborne O157 isolate NADC 6564 and infer its evolutionary relationship to other O157 strains.

Results

The chromosome of NADC 6564 contained 5466 kb compared to reference strains Sakai (5498 kb) and EDL933 (5547 kb) and shared 41 of its 43 Linear Conserved Blocks (LCB) with the reference strains. However, 18 of 41 LCB had inverse orientation in NADC 6564 compared to the reference strains. NADC 6564 shared 18 of 19 bacteriophages with reference strains except that the chromosomal positioning of some of the phages differed among these strains. The additional phage (P19) of NADC 6564 was located on a 39-kb insertion element (IE) encoding several hypothetical proteins, an integrase, transposases, transcriptional regulators, an adhesin, and a phosphoethanolamine transferase (PEA). The complete homologs of the 39-kb IE were found in E. coli PCN061 of porcine origin. The IE-encoded PEA showed low homology (32–33%) to four other PEA in NADC 6564 and PEA linked to mobilizable colistin resistance in E. coli but was highly homologous (95%) to a PEA of uropathogenic, avian pathogenic, and enteroaggregative E. coli. NADC 6564 showed slightly higher minimum inhibitory concentration of colistin compared to the reference strains. The 39-kb IE also contained dndBCDE and dptFGH operons encoding DNA S-modification and a restriction pathway, linked to oxidative stress tolerance and self-defense against foreign DNA, respectively. Evolutionary tree analysis grouped NADC 6564 with lineage I O157 strains.

Conclusions

These results indicated that differential phage counts and different chromosomal positioning of many bacteriophages and genomic islands might have resulted in recombination events causing altered chromosomal organization in NADC 6564. Evolutionary analysis grouped NADC 6564 with lineage I strains and suggested its earlier divergence from these strains. The ability to perform S-DNA modification might affect tolerance of NADC 6564 to various stressors.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5568-6) contains supplementary material, which is available to authorized users.

Comparative Performance Evaluation of Real-Time PCR and Dual-Labeled Fluorescence Resonance Energy Transfer Probe-Based Melt Peak Analysis for the Detection of Escherichia coli O157:H7 in Beef Products

Contaminated beef and beef products remain a frequent vehicle for the transmission of Escherichia coli O157:H7. The current U.S. Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS) regulatory testing for E. coli O157:H7 uses the method described in the USDA-FSIS Microbiology Laboratory Guidebook (MLG), chapter 5. At times, described presumptive test results are nonconfirmable, suggesting that recent PCR technological advancements and presumed enhanced sensitivity and specificity may offer beneficial changes. Here, we have evaluated the precision and sensitivity of a fluorescence resonance energy transfer-based real-time PCR assay called ECO for the detection of E. coli O157:H7. ECO detects the gene target specific to both E. coli O157:H7 and E. coli O157:non-H7 but distinguishes the two by using a melt curve analysis. A total of 3,113 O157:H7 and O157:non-H7 isolates were used to define this melting temperature-based criteria. The simulated comparative performance evaluation in the spiked beef samples indicated detection of 3 of 3 samples by ECO at <3.3 log CFU/mL, whereas MLG only detected 1 of 3 (<3.3 log CFU/mL). Using modified tryptic soy broth-enriched natural beef and veal product samples ( n = 452), the comparative sensitivity, specificity, false-positive rate, and false-negative rate against culture between MLG and ECO were 75 versus 92%, 91 versus 99%, 8.9 versus 0.77%, and 25 versus 8.3%, respectively. Positive predictive value, negative predictive value, and the overall accuracy were found to be 56 versus 94%, 96 versus 98%, and 88 versus 98%, for MLG and ECO, respectively. These data demonstrate that the ECO assay is comparable to MLG detection of E. coli O157:H7 and offers improved sensitivity.

Research and molecular characteristic of Shiga toxin-producing Escherichia coli isolated from sheep carcasses

Domestic ruminants are regarded as the major reservoir of Shiga toxin-producing Escherichia coli (STEC) closely related to human infection. A total of 363 ovine carcasses were swabbed in an Algiers city slaughterhouse for research on STEC. First of all, screening of the STECs was carried out by a multiplex PCR searching for the genes coding for the virulence factors stx₁ , stx₂ and eae. This step was followed by STEC isolation and serotyping. The presence of stx⁺ /stx⁺ eae⁺ genes was shown in 116 sheep carcasses (31·95%). From the 116 positive samples, 20 bacterial strains (17·24%) were isolated. Nineteen strains belonged to the species E. coli (STEC), and 1 belonged to Citrobacter braakii (eae⁺ stx₁ ⁺ ). During this study, the presence of potentially pathogenic STEC for humans on the surface of sheep carcasses was confirmed. Corrective measures should be considered at the slaughterhouse level to avoid outbreaks of STEC in Algeria. SIGNIFICANCE AND IMPACT OF THE STUDY: PCR screening revealed the significant presence of the genetic markers of Shiga toxin-producing Escherichia coli (STEC) (stx⁺ /stx⁺ eae⁺ ) on the surfaces of sheep carcasses. Citrobacter braakii (stx₁ ⁺ eae⁺ ) was isolated for the first time in this study. The risk of foodborne diseases due to STEC must be taken into account in Algeria. To prevent the emergence of epidemic outbreaks among children and older by people, preventive measures should be taken.

Salmonella and Enterohemorrhagic Escherichia coli Serogroups O45, O121, O145 in Wheat Flour: Effects of Long-Term Storage and Thermal Treatments

Salmonella and enterohemorrhagic Escherichia coli (EHEC) are of serious concern in wheat flour and its related products but little is known on their survival and thermal death kinetics. This study was undertaken to determine their long-term viability and thermal inactivation kinetics in flour. Inoculation was performed using mixtures of EHEC serogroups O45, O121, O145 and Salmonella followed by storage at room temperature (23°C) or 35°C (for Salmonella). Plate counting on tryptic soy agar (TSA) and enrichment were used to assess long-term survival. For thermal studies, wheat flour samples were heated at 55, 60, 65, and 70°C and cell counts of EHEC and Salmonella were determined by plating. The δ-values were calculated using the Weibull model. At room temperature, EHEC serovars and Salmonella were quantifiable for 84 and 112 days, and were detectable for the duration of the experiment after 168 and 365 days, respectively. The δ-values were 2.0, 5.54, and 9.3 days, for EHEC O121, O45, and O145, respectively, and 9.7 days for Salmonella. However, the only significant difference among all values was the δ-value for Salmonella and serogroup O121 (p ≤ 0.05). At 35°C, Salmonella counts declined to unquantifiable levels after a week and were not detected upon enrichment after 98 days. Heat treatment of inoculated wheat flour at 55, 60, 65, and 70°C resulted in δ-value ranges of 20.0-42.9, 4.9-10.0, 2.4-3.2, and 0.2-1.6 min, respectively, for EHEC. The δ-values for Salmonella at those temperatures were 152.2, 40.8, 17.9, and 17.4 min, respectively. The δ-values obtained for Salmonella at each temperature were significantly longer than for EHEC (p ≤ 0.05). Weibull model was a good fit to describe the thermal death kinetics of Salmonella and EHEC O45, O121 and O145 in wheat flour. HIGHLIGHTS -EHEC and Salmonella can survive for extended periods of time in wheat flour.-Long-term storage inactivation curves of EHEC and Salmonella were similar.-EHEC was more sensitive to heat than Salmonella.-Weibull model was a good fit to describe thermal death kinetics of EHEC and Salmonella.-Flour storage at 35°C may be a feasible method for microbial reduction.

Inhibition of enterohemorrhagic Escherichia coli O157:H7 infection in a gnotobiotic mouse model with pre-colonization by Bacteroides strains

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 has been known to cause outbreaks of hemorrhagic colitis and hemolytic uremic syndrome. We previously demonstrated that intestinal flora contribute to the prevention of EHEC infection in a mouse model. However, it has not yet been determined whether Bacteroides, a predominant genus in the human intestine, contributes to the prevention of EHEC infection. The aim of the present study was to investigate the effect of Bacteroides fragilis (B. fragilis) and Bacteroides vulgatus (B. vulgatus) on EHEC O157:H7 infection in vivo using gnotobiotic mice. These strains were inoculated into germ-free mice to create a gnotobiotic mouse model. EHEC was inoculated into the mice, which were then monitored for 7 days for any change in symptoms. The mice that had been pre-colonized with the Bacteroides strains did not develop lethal EHEC infection, although several inflammatory symptoms were observed in the B. vulgatus pre-colonized group. However, no inflammatory symptoms were identified in the B. fragilis pre-colonized group. Moreover, B. fragilis exerted an inhibitory effect on enterocyte-like cell apoptosis. B. fragilis protected HT29 cells from apoptosis caused by Shiga toxin. In conclusion, the findings of the present study demonstrated that colonization by Bacteroides strains can inhibit EHEC infection.

Novel Antibiotic Testing Approaches Reveal Reduced Antibiotic Efficacy Against Shiga Toxin-Producing Escherichia coli O157:H7 Under Simulated Microgravity

As a foodborne and environmental pathogen, Shiga toxin-producing Escherichia coli O157:H7 could pose a health threat to immunocompromised astronauts during a space mission. In this study, novel approaches, including real-time testing and direct evaluation of resistance mechanisms, were used to evaluate antibiotic efficacy against E. coli O157:H7 under low-shear modeled microgravity (LSMMG) produced using a rotary cell culture system. When compared with normal gravity (NG), bacterial growth was increased under LSMMG in the presence of sub-inhibitory nalidixic acid concentrations and there was an accompanying up-regulation of stress-related genes. LSMMG also induced transcriptional changes of the virulence genes stx1 and stx2, highlighting the potential risk of inappropriate antibiotic use during a spaceflight. The degree of bacterial cell damage induced by the antibiotics was reduced under LSMMG, suggesting low induction of reactive oxygen species. Efflux pumps were also shown to play an important role in these responses. Increased cell filamentation was observed under LSMMG upon ampicillin treatment, possibly reflecting a protective mechanism against exposure to antibiotics. These observations indicate that, in the presence of antibiotics, the survival of E. coli O157:H7 is greater under LSMMG than under NG, indicating that antibiotic therapies may need to be adjusted during space missions.

Development of a bacteriophage-based Method for Detection of Escherichia Coli O157:H7 in Fresh Vegetables

In this study, a method using a recombinant phage for detection of E. coli O157:H7 in fresh vegetables was investigated. Four kinds of fresh vegetables, i.e. lettuce (Lactuca sativa), mustard greens (Brassica juncea), coriander (Coriandrum sativum), and soybean sprouts were selected since they are commonly used in meals in Vietnam. Firstly, a phage-based method was investigated for detection of E. coli O157:H7 in the four types of vegetables. To support the detection by suppressing growth of background bacteria in vegetables, selective antibiotics, i.e. novobiocin (N) and vancomycin (V) in combination with BHI medium were examined. Secondly, quality of the method was evaluated in terms of sensitivity, specificity, and rapidity. The method enabled the detection of E. coli O157:H7 inoculated at 10³, 10², or 10¹ CFU/ 10 mL of sterile 0.8% NaCl containing 5 g of vegetable and in the presence of several Gram-positive and Gram-negative bacteria inoculated at 10⁷ CFU/10 mL. The time for detection was approximately 16.5 hours for E. coli O157:H7 inoculated at 10 CFU/10 mL of sterile 0.8% NaCl containing 5 g of vegetable. The limit of detection was considered to be 2 CFU g^-1 vegetable.

Characterization of Diarrheagenic Strains of Escherichia coli Isolated From Cattle Raised in Three Regions of Mexico

Intestinal infections represent an important public health concern worldwide. Escherichia coli is one of the main bacterial agents involved in the pathogenesis of different diseases. In 2011, an outbreak of hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS) in Germany was related to a non-O157 STEC strain of O104:H4 serotype. The difficulty in identifying the origin of the bacteria related to the outbreak showed the importance of having epidemiological information from different parts of the world. The aim of this study was to perform a retrospective analysis to determine if E. coli strains isolated from cattle from different locations in Mexico have similar characteristics to those isolated in other countries. Samples obtained in different years from 252 cows belonging to 5 herds were analyzed. A total of 1,260 colonies were selected from the 252 samples, 841 (67%) of which corresponded to E. coli and 419 (33%) to other enterobacteria. In total, 78% (656) of the E. coli strains could be serotyped, of which 393 (59.9%) belonged to 5 diarrheagenic (DEC) pathotypes. Serotyping showed STEC (40.7%) and ETEC (26.7%) strains were more common. PCR assays were used to determine the presence of STEC (eae, stx1, stx2, and ehxA) and EAEC (aatA, aggR, and aapA) genes, and phylogenetic groups. The results showed that 70 strains belonging to 23 serogroups were stx1 and stx2 positive, while 13 strains from the O9 serogroup were ehxA, aggR, and eae positive. Phylogenetic analysis showed 58 (82.9%) strains belonged to A and B1 commensal phylogroups and 12 (17.1%) to B2, D and E virulent phylogroups. An assay to evaluate cross-antigenic reactivity in the serum of cattle between K9 capsular antigen and O104 LPS by ELISA showed similar responses against both antigens (p > 0.05). The antimicrobial sensitivity assay of the strains showed resistance to AM, CEP, CXM, TE, SXT, cephalosporins and fluoroquinolones. The results show that cattle are carriers and potential transmitters of STEC and ETEC strains containing virulence genes. Epidemiological retrospective studies in different countries are of great help for identifying virulent bacterial strains with the potential to cause outbreaks that may have epidemiological impact in susceptible countries.

De-O-Acetylation of mucin-derived sialic acids by recombinant NanS-p esterases of Escherichia coli O157:H7 strain EDL933

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain EDL933 encodes the single chromosomal 9-O-acetylesterase NanS, and several copies of prophage-encoded 9-O-acetylesterases (NanS-p). These enzymes have recently been shown to cleave 5-N-acetyl-9-O-acetyl neuraminic acid (Neu5,9Ac₂) to yield de-O-acetylated Neu5Ac, the latter of which may serve as a carbon and/or nitrogen source.

In the current study, we investigated the NanS- and NanS-p-mediated digestion of synthetic O-acetylated neuraminic acids and bovine submaxillary glands mucin (BSM)-derived O-acetylneuraminic acids by high-performance thin-layer chromatography (HPTLC) and nano electrospray ionization mass spectrometry (nanoESI MS). Initial HPTLC analyses showed the expected activity of NanS and NanS-p variants for Neu5,9Ac₂. However, all tested enzymes were unable to de-O-acetylate 5-N-acetyl-4-O-acetylneuraminic acid (Neu5,4 Ac₂) in our test system. The nanoESI MS analysis of neuraminic acids after treatment of BSM with NanS-p gave evidence that NanS-p variants of EHEC O157:H7 strain EDL933 cleave off O-acetyl groups from mono-, di-, and tri-O-acetylated Neu5Ac and N-glycolylneuraminic acid (Neu5Gc), regardless of the carbon positions C7, C8 or C9 of the acetate esters. This enzyme activity leads to neuraminidase-accessible Neu5Ac and Neu5Gc on mucin glycans.

Moreover, we could demonstrate by HPTLC analyses that recombinant Bacteroides thetaiotaomicron sialidase (BTSA-His) was able to cleave Neu5Ac and Neu5,9Ac₂ from BSM and that the combination of BTSA-His with both NanS-His and NanS-p-His derivatives enhanced the release of de-O-acetylated core Neu5Ac and Neu5Gc from mammalian mucin O-glycans.

Growth experiments with EHEC wildtype strain EDL933, its nanS and nanS/nanS-p1a-p7 mutant and exogenous BTSA-His in BSM demonstrated that the presence of BTSA-His enhanced growth of EDL933 and the nanS deletion mutant but not the nanS/nanS-p1a-p7 mutant.

Thus, we hypothesize that the expression of sialic acid O-acetylesterases with a broad specificity could be an advantage in competition with the gut microbiota for nutrients and facilitate EHEC colonization in the human large intestine.

Acquired Resistance to Shiga Toxin-Induced Apoptosis by Loss of CD77 Expression in Human Myelogenous Leukemia Cell Line, THP-1

Shiga toxin (Stx) is a main virulence factor of Enterohemorrhagic Escherichia coli (EHEC) that causes diarrhea and hemorrhagic colitis and occasionally fatal systemic complications. Stx induces rapid apoptotic cell death in some cells, such as human myelogenous leukemia THP-1 cells expressing CD77, a receptor for Stx internalization, and the induction of apoptotic cell death is thought to be crucial for the fatal systemic complications. Therefore, in order to suppress the fatal toxicity, it is important to understand the mechanism how cells can escape from apoptotic cell death in the presence of Stx. In this study, we isolated resistant clones to Stx-induced apoptosis from highly sensitive THP-1 cells by continuous exposure with lethal dose of Stx. All of the ten resistant clones lost the expression of CD77 as a consequence of the reduction in CD77 synthase mRNA expression. These results suggest that downregulation of CD77 or CD77 synthase expression could be a novel approach to suppress the fatal toxicity of Stx in EHEC infected patient.

Whole genome shotgun sequencing revealed highly polymorphic genome regions and genes in Escherichia coli O157:H7 isolates collected from a single feedlot

Escherichia coli serotype O157:H7 continues to pose a serious health threat to human beings. Cattle, a major reservoir of the pathogen, harbor E. coli O157:H7 in their gastrointestinal tract and shed variable concentrations of E. coli O157:H7 into the environment. Genetic characterization of cattle-shed E. coli O157 strains is of interest to the livestock industry, food business, and public health community. The present study applied whole genome shotgun sequencing (WGS) and single nucleotide variant (SNV) calling to characterize 279 cattle-shed E. coli O157:H7 strains isolated from a single feedlot located in southwestern region of the US. More than 4,000 SNVs were identified among the strains and the resultant phylogenomic tree revealed three major groups. Using the Sakai strain genome as reference, more than 2,000 SNVs were annotated and a detailed SNV map generated. Results clearly revealed highly polymorphic loci along the E. coli O157:H7 genome that aligned with the prophage regions and highly variant genes involved in processing bacterial genetic information. The WGS data were further profiled against a comprehensive virulence factor database (VFDB) for virulence gene identification. Among the total 285 virulence genes identified, only 132 were present in all the strains. There were six virulence genes unique to single isolates. Our findings suggested that the genome variations of the E. coli O157:H7 were mainly attributable to dynamics of certain phages, and the bacterial strains have variable virulence gene profiles, even though they came from a single cattle population, which may explain the differences in pathogenicity, host prevalence, and transmissibility by E. coli O157:H7.

Factors in the emergence of serious human infections associated with highly pathogenic strains of shiga toxin-producing Escherichia coli

The appearance of highly pathogenic strains of Shiga toxin (Stx)-producingEscherichia. coli (STEC) has owed largely to the acquisition of Stx-encoding prophages by strains of E. coli that have pre-existing potential as enteric pathogens, such as atypical enteropathogenic E. coli (aEPEC) and enteroaggregative E. coli (EAEC). However, while high pathogenic potential is necessary, it is not sufficient for such strains to have a serious public health impact (i.e., large outbreaks, many cases of HUS, or both). To do so requires susceptible hosts and additional elements related to transmission, such as, socio-economic, societal, and lifestyle, factors. Two examples are discussed to illustrate this. The factors involved in the emergence of serious disease associated with E. coli O157:H7 in the 1980s probably included a massive increase in population exposure to this pathogen, likely as a result of the introduction of factory farming of cattle in the 1960s, and the development and wide patronage of fast food hamburger restaurants, and, potentially, waning immunity to intimin as a result of the reduction of incidence of enteropathogenic E. coli (EPEC) infection. In the devastating outbreak of Stx2-positiveEAEC O104:H4 in 2011, the wide distribution of the proposed vehicle of transmission, imported fenugreek seeds, was decisive in the exposure of a large population in Central Europe to this pathogen. Contributing factors likely included a preference for eating raw sprouts as a healthy food choice by the affected cases, many of whom were women. Low population levels of immunity to Stx2 probably contributed to the severe clinical outcome. A better understanding of the factors responsible for the emergence of potentially dangerous STEC pathogens as well as of extensive and serious disease associated with them can enhance public health strategies to respond to them.

Pathogenic and phylogenetic characteristics of non-O157 Shiga toxin-producing Escherichia coli isolates from retail meats in South Korea

Herein, we report the pathogenic and phylogenetic characteristics of seven Shiga toxin (Stx)-producing Escherichia coli (STEC) isolates from 434 retail meats collected in Korea during 2006 to 2012. The experimental analyses revealed that all isolates (i) were identified as non-O157 STEC, including O91:H14 (3 isolates), O121:H10 (2 isolates), O91:H21 (1 isolate), and O18:H20 (1 isolate), (ii) carried diverse Stx subtype genes (stx₁, stx_2c, stx_2e, or stx₁ + stx_2b) whose expression levels varied strain by strain, and (iii) lacked the locus of enterocyte effacement (LEE) pathogenicity island, a major virulence factor of STEC, but they possessed one or more alternative virulence genes encoding cytotoxins (Cdt and SubAB) and/or adhesins (Saa, Iha, and EcpA). Notably, a significant heterogeneity in glutamate-induced acid resistance was observed among the STEC isolates (p < 0.05). In addition, phylogenetic analyses demonstrated that all three STEC O91:H14 isolates were categorized into sequence type (ST) 33, of which two beef isolates were identical in their pulsotypes. Similar results were observed with two O121:H10 pork isolates (ST641; 88.2% similarity). Interestingly, 96.0% of the 100 human STEC isolates collected in Korea during 2003 to 2014 were serotyped as O91:H14, and the ST33 lineage was confirmed in approximately 72.2% (13/18 isolates) of human STEC O91:H14 isolates from diarrheal patients.