The enemy within us: lessons from the 2011 European Escherichia coli O104:H4 outbreak

Developing the PIP-eco: An integrated genomic pipeline for identification and characterization of Escherichia coli pathotypes encompassing hybrid forms

Pathogenic Escherichia coli (E. coli) strains are distinguished by their diverse virulence factors, which contribute to a wide spectrum of diseases. These pathogens evolve through the horizontal transfer of virulence factors, resulting in the emergence of hybrid pathotypes with complex and heterogeneous characteristics. Recognizing their profound impact on public health, this study introduces the PIP-eco pipeline, a comprehensive analytical tool designed for the precise identification and characterization of E. coli pathotypes. This PIP-eco pipeline advances beyond traditional molecular techniques by facilitating detailed analysis of both single and hybrid pathotypes. It integrates targeted marker gene analysis, virulence factor-based phylogenetic analysis, and pathogenicity islands (PAIs) profiling to elucidate the genetic diversity of E. coli pathotypes and support their accurate classification. This integrative approach enables PIP-eco to uncover connections among various E. coli pathotypes, highlight shared virulence factors, and provide insights into their evolutionary trajectories. By utilizing experimentally validated marker genes, the pipeline ensures robust identification of pathotypes, particularly those of hybrid pathotypes. Additionally, PAI analysis offers comprehensive genetic investigations, revealing strain-specific variations and potential virulence mechanisms. As a result, the PIP-eco pipeline emerges as a useful tool for dissecting the evolutionary dynamics of E. coli and characterizing complex pathotypes, addressing the critical need for accurate detection and understanding of hybrid pathotypes.

Enteroaggregative Escherichia coli: Frequent, yet underdiagnosed pathotype among E. coli O111 strains isolated from children with gastrointestinal disorders in the Czech Republic

Enteroaggregative Escherichia coli (EAEC) strains including those of serogroup O111 are important causes of diarrhea in children. In the Czech Republic, no information is available on the etiological role of EAEC in pediatric diarrhea due to the lack of their targeted surveillance. To fill this gap, we determined the proportion of EAEC among E. coli O111 isolates from children with gastrointestinal disorders ≤ 2 years of age submitted to the National Reference Laboratory for E. coli and Shigella during 2013-2022. EAEC accounted for 177 of 384 (46.1 %) E. coli O111 isolates, being the second most frequent E. coli O111 pathotype. Most of them (75.7 %) were typical EAEC that carried aggR, usually with aaiC and aatA marker genes; the remaining 24.3 % were atypical EAEC that lacked aggR but carried aaiC and/or aatA. Whole genome sequencing of 11 typical and two atypical EAEC O111 strains demonstrated differences in serotypes, sequence types (ST), virulence gene profiles, and the core genomes between these two groups. Typical EAEC O111:H21/ST40 strains resembled by their virulence profiles including the presence of the aggregative adherence fimbriae V (AAF/V)-encoding cluster to such strains from other countries and clustered with them in the core genome multilocus sequence typing (cgMLST). Atypical EAEC O111:H12/ST10 strains lacked virulence genes of typical EAEC and differed from them in cgMLST. All tested EAEC O111 strains displayed stacked-brick aggregative adherence to human intestinal epithelial cells. The AAF/V-encoding cluster was located on a plasmid of 95,749 bp or 93,286 bp (pAAO111) which also carried aggR, aap, aar, sepA, and aat cluster. EAEC O111 strains were resistant to antibiotics, in particular to aminopenicillins and cephalosporins; 88.3 % produced AmpC β-lactamase, and 4.1 % extended spectrum β-lactamase. We conclude that EAEC are frequent among E. coli O111 strains isolated from children with gastrointestinal disorders in the Czech Republic. To reliably assess the etiological role of EAEC in pediatric diarrhea, a serotype-independent, PCR-based pathotype surveillance system needs to be implemented in the future.

TRS-PCR profiles correlate with polymorphisms of the genomic o454-nlpD region, virulence factors repertoire, and phylogenetic groups among uropathogenic Escherichia coli strains isolated from patients from Lodz region, Poland

Extraintestinal urinary tract infections are mainly caused by uropathogenic strains of E. coli. UPECs are a heterogeneous group of strains possessing various genes associated with virulence traits. It was demonstrated that changes in the composition of the o454-nlpD region and genetic variation in the mutS-rpoS chromosomal region in ExPEC strains are correlated with their virulence, particularly in those with the pattern III o454-nlpD region and belonging to phylogenetic group B2. In this study, we investigated the presence and distribution of the o454-nlpD genomic polymorphism in our collection of 124 uropathogenic E. coli strains, examining the correlation of o454-nlpD region types with the virulence factors studied. Our findings revealed a positive association between certain virulence factors in UPEC strains and the presence of pattern III in the o454-nlpD region. Additionally, all these strains were classified under phylogenetic group B2. We also showed that the highly pathogenic group of E. coli identified by examining the polymorphism of the o454-nlpD region coincides with the highly pathogenic group of uropathogens we identified in the averaged TRS-PCR analysis.

Phage Tail Fiber Protein as a Specific Probe for Recognition of Shiga Toxin-Producing Escherichia coli O91, O103, and O111

The ability to quickly identify specific serotypes of Shiga toxin-producing Escherichia coli (STEC) could facilitate the monitoring and control of STEC pathogens. In this study, we identified the receptors and receptor-binding proteins (RBPs) of three novel phages (pO91, pO103, and pO111) isolated from hospital wastewater. Recombinant versions of these RBPs (pO91-ORF43, pO103-ORF42, and pO111-ORF8) fused to a fluorescent reporter protein were then constructed. Both fluorescence microscopy and transmission electron microscopy showed that all three recombinant RBPs were bound to the bacterial surface. Indirect enzyme-linked immunosorbent assay was used to verify that each recombinant RBP bound specifically to E. coli O91, O103, or O111, but not to any of the 83 strains of E. coli with different O-antigens, nor to 10 other bacterial species that were tested. The recombinant RBPs adsorbed to their respective host bacteria within 10 min of incubation. The minimum concentration of bacteria required for detection by the recombinant RBPs was 33 colony-forming units (CFU)/mL (range: 3.3 × 10 to 3.3 × 108 CFU/mL). Furthermore, each recombinant RBP was also able to detect bacteria in lettuce, chicken breast meat, and infected mice, indicating that their usage will facilitate the detection of STEC and may help to reduce the spread of STEC-related infections and diseases.

Nordihydroguaiaretic Acid (NDGA) Inhibits CsgA Polymerization, Bacterial Amyloid Biogenesis, and Biofilm Formation

Escherichia coli and other Enterobacteriaceae thrive in robust biofilm communities through the coproduction of curli amyloid fibers and phosphoethanolamine cellulose. Curli promote adhesion to abiotic surfaces and plant and human host tissues and are associated with pathogenesis in urinary tract infection and food-borne illness. The production of curli in the host has also been implicated in the pathogenesis of neurodegenerative diseases. We report that the natural product nordihydroguaiaretic acid (NDGA) is effective as a curlicide in E. coli. NDGA prevents CsgA polymerization in vitro in a dose-dependent manner. NDGA selectively inhibits cell-associated curli assembly and inhibits uropathogenic E. coli biofilm formation. More broadly, this work emphasizes the ability to evaluate and identify bioactive amyloid assembly inhibitors by using the powerful gene-directed amyloid biogenesis machinery in E. coli.

A chimeric protein-based vaccine elicits a strong IgG antibody response and confers partial protection against Shiga toxin-producing Escherichia coli in mice

Background

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen that causes gastrointestinal infections, ranging from acute diarrhea and dysentery to life-threatening diseases such as Hemolytic Uremic Syndrome. Currently, a vaccine to prevent STEC infection is an unmet medical need.

Results

We developed a chimeric protein-based vaccine targeting seven virulence factors of STEC, including the Stx2B subunit, Tir, Intimin, EspA, Cah, OmpT, and AggA proteins. Immunization of mice with this vaccine candidate elicited significant humoral and cellular immune responses against STEC. High levels of specific IgG antibodies were found in the serum and feces of immunized mice. However, specific IgA antibodies were not detected in either serum or feces. Furthermore, a significantly higher percentage of antigen-specific CD4+ T cells producing IFN-γ, IL-4, and IL-17 was observed in the spleens of immunized mice. Notably, the immunized mice showed decreased shedding of STEC O157:H7 and STEC O91:H21 strains and were protected against weight loss during experimental infection. Additionally, infection with the STEC O91:H21 strain resulted in kidney damage in control unimmunized mice; however, the extent of damage was slightly lower in immunized mice. Our findings suggest that IgG antibodies induced by this vaccine candidate may have a role in inhibiting bacterial adhesion and complement-mediated killing.

Conclusion

This study provides evidence that IgG responses are involved in the host defense against STEC. However, our results do not rule out that other classes of antibodies also participate in the protection against this pathogen. Additional work is needed to improve the protection conferred by our vaccine candidate and to elucidate the relevant immune responses that lead to complete protection against this pathogen.

Boundaries That Prevent or May Lead Animals to be Reservoirs of Escherichia coli O104:H4

Escherichia coli O104:H4, a hybrid serotype carrying virulence factors from enteroaggregative (EAEC) and Shiga toxin-producing (STEC) pathotypes, is the reported cause of a multicountry outbreak in 2011. Evaluation of potential routes of human contamination revealed that this strain is a foodborne pathogen. In contrast to STEC strains, whose main reservoir is cattle, serotype O104:H4 has not been commonly isolated from animals or related environments, suggesting an inability to naturally colonize the gut in hosts other than humans. However, contrary to this view, this strain has been shown to colonize the intestines of experimental animals in infectious studies. In this minireview, we provide a systematic summary of reports highlighting potential evolutionary changes that could facilitate the colonization of new reservoirs by these bacteria.

Coliform pollution mapping in major watersheds along Jhelum River Basin of Kashmir Himalaya

Coliform pollution for the last three decades in major river systems of the world has resulted in far ranging impacts on water quality. In this context, the present study aimed to assess the levels of indicator bacteria like total Coliform (TC), fecal Coliform (FC) and fecal Streptococcus (FS) in major watersheds of Kashmir valley. Sampling was carried out for a period of 2 years (summer 2017 to spring 2019) along several upstream, midstream and downstream reaches of Jhelum River Basin (JRB), while analysis was carried out by multiple tube fermentation technique involving Most Probable Number (MPN). Major highlights of the results revealed high levels of TC, FC and FS among downstream sites with pronounced seasonal variations between summer and winter. TC was highest at all the reaches and during all the seasons followed by FC and FS. Non-metric multidimensional scaling (NMDS) revealed more variation in Coliform count among reaches as compared to seasons. Mantle test revealed that environmental factors like observable environmental pressure (OEP) (r: 0.235, p < 0.0001), DO (r: 0.2815, p < 0.0001) and temperature (r: 0.04419, p = 0.0104) had prominent effect on Coliform distribution as compared to geographical factors. The study thus highlights the prevalence of Coliform bacteria along JRB resulting from fecal sources. Due to growing urbanization and lack of adequate sewage treatment facilities, there is an increase in the levels of Coliform bacteria along downstream reaches especially those residing within lower Jhelum and Dara watershed, which could jeopardize water quality and public health.

Review of Escherichia coli O157:H7 Prevalence, Pathogenicity, Heavy Metal and Antimicrobial Resistance, African Perspective

Escherichia coli O157:H7 is an important food-borne and water-borne pathogen that causes hemorrhagic colitis and the hemolytic-uremic syndrome in humans and may cause serious morbidity and large outbreaks worldwide. People with bloody diarrhea have an increased risk of developing serious complications such as acute renal failure and neurological damage. The hemolytic-uremic syndrome (HUS) is a serious condition, and up to 50% of HUS patients can develop long-term renal dysfunction or blood pressure-related complications. Children aged two to six years have an increased risk of developing HUS. Clinical enteropathogenic Escherichia coli (EPEC) infections show fever, vomiting, and diarrhea. The EPEC reservoir is unknown but is suggested to be an asymptomatic or symptomatic child or an asymptomatic adult carrier. Spreading is often through the fecal-oral route. The prevalence of EPEC in infants is low, and EPEC is highly contagious in children. EPEC disease in children tends to be clinically more severe than other diarrheal infections. Some children experience persistent diarrhea that lasts for more than 14 days. Enterotoxigenic Escherichia coli (ETEC) strains are a compelling cause of the problem of diarrheal disease. ETEC strains are a global concern as the bacteria are the leading cause of acute watery diarrhea in children and the leading cause of traveler’s diarrhea. It is contagious to children and can cause chronic diarrhea that can affect the development and well-being of children. Infections with diarrheagenic E. coli are more common in African countries. Antimicrobial agents should be avoided in the acute phase of the disease since studies showed that antimicrobial agents may increase the risk of HUS in children. The South African National Veterinary Surveillance and Monitoring Programme for Resistance to Antimicrobial Drugs has reported increased antimicrobial resistance in E. coli. Pathogenic bacterial strains have developed resistance to a variety of antimicrobial agents due to antimicrobial misuse. The induced heavy metal tolerance may also enhance antimicrobial resistance. The prevalence of antimicrobial resistance depends on the type of the antimicrobial agent, bacterial strain, dose, time, and mode of administration. Developing countries are severely affected by increased resistance to antimicrobial agents due to poverty, lack of proper hygiene, and clean water, which can lead to bacterial infections with limited treatment options due to resistance.

A Robust One-Step Recombineering System for Enterohemorrhagic Escherichia coli

Enterohemorrhagic Escherichia coli (EHEC) can cause severe diarrheic in humans. To improve therapy options, a better understanding of EHEC pathogenicity is essential. The genetic manipulation of EHEC with classical one-step methods, such as the transient overexpression of the phage lambda (λ) Red functions, is not very efficient. Here, we provide a robust and reliable method for increasing recombineering efficiency in EHEC based on the transient coexpression of recX together with gam, beta, and exo. We demonstrate that the genetic manipulation is 3–4 times more efficient in EHEC O157:H7 EDL933 Δstx1/2 with our method when compared to the overexpression of the λ Red functions alone. Both recombineering systems demonstrated similar efficiencies in Escherichia coli K-12 MG1655. Coexpression of recX did not enhance the Gam-mediated inhibition of sparfloxacin-mediated SOS response. Therefore, the additional inhibition of the RecFOR pathway rather than a stronger inhibition of the RecBCD pathway of SOS response induction might have resulted in the increased recombineering efficiency by indirectly blocking phage induction. Even though additional experiments are required to unravel the precise mechanistic details of the improved recombineering efficiency, we recommend the use of our method for the robust genetic manipulation of EHEC and other prophage-carrying E. coli isolates.

Enterohemorrhagic Escherichia coli and a Fresh View on Shiga Toxin-Binding Glycosphingolipids of Primary Human Kidney and Colon Epithelial Cells and Their Toxin Susceptibility

Enterohemorrhagic Escherichia coli (EHEC) are the human pathogenic subset of Shiga toxin (Stx)-producing E. coli (STEC). EHEC are responsible for severe colon infections associated with life-threatening extraintestinal complications such as the hemolytic-uremic syndrome (HUS) and neurological disturbances. Endothelial cells in various human organs are renowned targets of Stx, whereas the role of epithelial cells of colon and kidneys in the infection process has been and is still a matter of debate. This review shortly addresses the clinical impact of EHEC infections, novel aspects of vesicular package of Stx in the intestine and the blood stream as well as Stx-mediated extraintestinal complications and therapeutic options. Here follows a compilation of the Stx-binding glycosphingolipids (GSLs), globotriaosylceramide (Gb3Cer) and globotetraosylceramide (Gb4Cer) and their various lipoforms present in primary human kidney and colon epithelial cells and their distribution in lipid raft-analog membrane preparations. The last issues are the high and extremely low susceptibility of primary renal and colonic epithelial cells, respectively, suggesting a large resilience of the intestinal epithelium against the human-pathogenic Stx1a- and Stx2a-subtypes due to the low content of the high-affinity Stx-receptor Gb3Cer in colon epithelial cells. The review closes with a brief outlook on future challenges of Stx research.

The microbial ecology of Escherichia coli in the vertebrate gut

Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.

Multi-Criteria Decision Analysis in Food Safety Risk Management: The Case of Dioxins in Baltic Fish

The Swedish risk management case of Baltic fatty fishes, in which dioxin levels may be too high, is a typical multidimensional food safety decision problem involving public health, economic, environmental and socio-cultural aspects. To effectively address the dioxin food safety problem, the multiple dimensions and conflicting interests of stakeholders have to be considered systematically when evaluating competing risk management options. The objectives of this study were to illustrate the applicability of the Multi-Criteria Decision Analysis (MCDA) method for multidimensional food safety risk management problems, and to evaluate the Swedish dioxin risk management using MCDA. The results show that the MCDA method is indeed a relevant tool for modelling the multifactorial Swedish dioxin problem and for initiating discussions amongst stakeholders to increase the acceptance of chosen strategies. Abolishing the derogation from the European Commission’s maximum limits for the presence of dioxins in Swedish fish is the dominant strategy for risk assessors, whereas the preferences provided by the other stakeholders would suggest a continuation of the derogation without providing consumer information. However, the preferences of female consumers match with the 2011 decision of the Swedish government to ask for a derogation in combination with consumer information. The conclusion drawn from our MCDA analysis is comparable to the government’s decision that—given the gradual reduction in dioxin concentrations in Baltic fish—the decision to continue providing consumer information or not mainly depends on how risk managers balance the preferences of the different stakeholders.

STxB as an Antigen Delivery Tool for Mucosal Vaccination

Immunotherapy against cancer and infectious disease holds the promise of high efficacy with minor side effects. Mucosal vaccines to protect against tumors or infections disease agents that affect the upper airways or the lung are still lacking, however. One mucosal vaccine candidate is the B-subunit of Shiga toxin, STxB. In this review, we compare STxB to other immunotherapy vectors. STxB is a non-toxic protein that binds to a glycosylated lipid, termed globotriaosylceramide (Gb3), which is preferentially expressed by dendritic cells. We review the use of STxB for the cross-presentation of tumor or viral antigens in a MHC class I-restricted manner to induce humoral immunity against these antigens in addition to polyfunctional and persistent CD4⁺ and CD8⁺ T lymphocytes capable of protecting against viral infection or tumor growth. Other literature will be summarized that documents a powerful induction of mucosal IgA and resident memory CD8⁺ T cells against mucosal tumors specifically when STxB-antigen conjugates are administered via the nasal route. It will also be pointed out how STxB-based vaccines have been shown in preclinical cancer models to synergize with other therapeutic modalities (immune checkpoint inhibitors, anti-angiogenic therapy, radiotherapy). Finally, we will discuss how molecular aspects such as low immunogenicity, cross-species conservation of Gb3 expression, and lack of toxicity contribute to the competitive positioning of STxB among the different DC targeting approaches. STxB thereby appears as an original and innovative tool for the development of mucosal vaccines in infectious diseases and cancer.

Low incidence of colonic complications after severe Shiga toxin-producing E. coli O104:H4 infection

BACKGROUND

In summer 2011, Shiga toxin producing Escherichia coli (EHEC) serotype O104:H4 caused the most severe EHEC outbreak in Germany to date. The case of a previously recovered patient with symptomatic postinflammatory colonic stenosis following EHEC- infection prompted us to conduct a prospective study to assess the macro- and microscopic intestinal long-term damage in a cohort of patients who had suffered from severe EHEC colitis.

METHODS

Following EHEC infection in 2011, 182 patients were offered to participate in this study between January 2013 and October 2014 as part of the post-inpatient follow-up care at the University Medical Center Hamburg-Eppendorf and to undergo colonoscopy with stepwise biopsies. Prior to colonoscopy, medical history and persistent post-infectious complaints were assessed.

RESULTS

Out of 182 patients, 22 (12%) participated in the study, 18 (82%) were female. All patients had been hospitalized due severe EHEC enterocolitis: 20 patients (90%) had subsequently developed hemolytic uremic syndrome (HUS), 16 patients (72%) had additionally required dialysis. On assessment prior to colonoscopy, all patients denied any abdominal complaints before EHEC-infection but 8 (36%) patients reported persistent post-infectious symptoms. According to the ROME IV criteria, 4 (18%) patients met the definition for post-infectious irritable bowel syndrome (PI-IBS). In all patients with persistent symptoms, colonoscopies and histological examination were unremarkable. Only in one symptom-free patient, biopsy revealed a locally limited cryptitis of the caecum, while all patients without complaints had inconspicuous histological and endoscopical findings.

CONCLUSION

Following infection colonic stenosis is a serious but rare long-term complication in patients who had suffered from severe enterocolitis. However, a significant proportion of these patients develop PI-IBS.

Methods to perform risk-based inspections of food companies

Risk‐based monitoring programs are increasingly applied for cost‐effective monitoring of food safety. Such programs ideally consist of three steps: risk‐ranking, risk‐based inspections, and cost‐effective monitoring. Various methods have been described to perform the first step of risk‐based monitoring. However, once the risk‐ranking has been completed, identifying the hazard‐food combinations to monitor, the frequency of inspection needs to be established based on a prioritization of food business operators (FBOs). The aim of this paper is to provide an overview of methods available for risk‐based inspections. Literature shows that FBO's food safety compliance can be assessed based on company size, historical monitoring data, and socio‐economic factors influencing compliance behavior. Non‐compliance can either be intentional or unintentional. The latter can be assessed by evaluating the food safety culture of a company. Various models—ranging from qualitative (e.g., focus groups) to quantitative (e.g., scoring)—can be used for this purpose. These models usually include an evaluation of the organizational structure (e.g., management control, communication, commitment), the technical food safety environment (e.g., hygienic design, zoning), and employee characteristics (e.g., knowledge, risk awareness). Intentional non‐compliance can be assessed using food fraud vulnerability tools. These tools incorporate factors influencing the likelihood of food fraud at the company, that is, opportunity, motivation, and (lack of) control measures. The literature indicates that either self‐assessment tools or risk matrices are applied. There is no global consensus on the methods to apply for risk‐based inspections. Depending on time and budget available as well as preferred output, one of the presented methods may be applied for prioritizing FBOs.

Transmission of Escherichia coli from Manure to Root Zones of Field-Grown Lettuce and Leek Plants

Pathogenic Escherichia coli strains are responsible for food-borne disease outbreaks upon consumption of fresh vegetables and fruits. The aim of this study was to establish the transmission route of E. coli strain 0611, as proxy for human pathogenic E. coli, via manure, soil and plant root zones to the above-soil plant compartments. The ecological behavior of the introduced strain was established by making use of a combination of cultivation-based and molecular targeted and untargeted approaches. Strain 0611 CFUs and specific molecular targets were detected in the root zones of lettuce and leek plants, even up to 272 days after planting in the case of leek plants. However, no strain 0611 colonies were detected in leek leaves, and only in one occasion a single colony was found in lettuce leaves. Therefore, it was concluded that transmission of E. coli via manure is not the principal contamination route to the edible parts of both plant species grown under field conditions in this study. Strain 0611 was shown to accumulate in root zones of both species and metagenomic reads of this strain were retrieved from the lettuce rhizosphere soil metagenome library at a level of Log 4.11 CFU per g dry soil.

Diversity of Potentially Pathogenic Escherichia coli O104 and O9 Serogroups Isolated before 2011 from Fecal Samples from Children from Different Geographic Regions

In 2011, an outbreak of hemorrhagic colitis and hemolytic uremic syndrome (HUS) was reported in Europe that was related to a hybrid STEAEC of Escherichia coli (E. coli) O104:H4 strain. The current study aimed to analyze strains of E. coli O104 and O9 isolated before 2011. The study included 47 strains isolated from children with and without diarrhea between 1986 and 2009 from different geographic regions, as well as seven reference strains. Serotyping was carried out on 188 anti-O and 53 anti-H sera. PCR was used to identify DEC genes and phylogenetic groups. Resistance profiles to antimicrobials were determined by diffusion in agar, while PFGE was used to analyze genomic similarity. Five serotypes of E. coli O104 and nine of O9 were identified, as well as an antigenic cross-reaction with one anti-E. coli O9 serum. E. coli O104 and O9 presented diarrheagenic E. coli (DEC) genes in different combinations and were located in commensal phylogenetic groups with different antimicrobial resistance. PFGE showed that O104:H4 and O9:(H4, NM) strains from SSI, Bangladesh and México belong to a diverse group located in the same subgroup. E. coli O104 and O9 were classified as commensal strains containing DEC genes. The groups were genetically diverse with pathogenic potential making continued epidemiologic surveillance important.

Primary Human Renal Proximal Tubular Epithelial Cells (pHRPTEpiCs): Shiga Toxin (Stx) Glycosphingolipid Receptors, Stx Susceptibility, and Interaction with Membrane Microdomains

Tubular epithelial cells of the human kidney are considered as targets of Shiga toxins (Stxs) in the Stx-mediated pathogenesis of hemolytic–uremic syndrome (HUS) caused by Stx-releasing enterohemorrhagic Escherichia coli (EHEC). Analysis of Stx-binding glycosphingolipids (GSLs) of primary human renal proximal tubular epithelial cells (pHRPTEpiCs) yielded globotriaosylceramide (Gb3Cer) and globotetraosylceramide (Gb4Cer) with Cer (d18:1, C16:0), Cer (d18:1, C22:0), and Cer (d18:1, C24:1/C24:0) as the dominant lipoforms. Investigation of detergent-resistant membranes (DRMs) and nonDRMs, serving as equivalents for the liquid-ordered and liquid-disordered membrane phase, respectively, revealed the prevalence of Gb3Cer and Gb4Cer together with cholesterol and sphingomyelin in DRMs, suggesting lipid raft association. Stx1a and Stx2a exerted strong cellular damage with half-maximal cytotoxic doses (CD₅₀) of 1.31 × 10² pg/mL and 1.66 × 10³ pg/mL, respectively, indicating one order of magnitude higher cellular cytotoxicity of Stx1a. Surface acoustic wave (SAW) real-time interaction analysis using biosensor surfaces coated with DRM or nonDRM fractions gave stronger binding capability of Stx1a versus Stx2a that correlated with the lower cytotoxicity of Stx2a. Our study underlines the substantial role of proximal tubular epithelial cells of the human kidney being associated with the development of Stx-mediated HUS at least for Stx1a, while the impact of Stx2a remains somewhat ambiguous.

Interactions between risk assessors and risk managers during three major food incidents in Europe

Risk analysis consists of risk assessment (RA), risk management (RM), and risk communication (RC). In most countries, RA and RM of food safety are separated to achieve a high scientific integrity, and typically occur in sequential order. However, in case of a food safety incident, even though being separate processes, RA and RM are performed simultaneously due to great time pressure and expected high impacts. The aim of this study was to analyze and evaluate the observed interactions between RA and RM processes, during three major food incidents in Europe, and to provide suggestions for possible improvement. Based on the differences observed between the three cases, strengths and weaknesses of each system have been identified. The enterohemorrhagic Escherichia coli (EHEC) crisis in 2011 in Germany, the horsemeat scandal in 2013 in Ireland, and the fipronil incident in 2017 in the Netherlands were used as case studies. Timelines of these incidents and crisis management procedures in place in each of the three countries provided the basis for further analysis. First, results showed that details of the communication processes between RA and RM bodies were frequently lacking in crisis management protocols. Second, RA, RM, and RC processes differed for each incident, due to differences in estimated risk for public health, but also due to differences in the organization within a country. Based on our results, we recommend that crisis management protocols should contain a section on communication between RA, RM, and on communication between member states in the EU.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

The Cellular and Chemical Biology of Endocytic Trafficking and Intracellular Delivery-The GL-Lect Hypothesis

Lipid membranes are common to all forms of life. While being stable barriers that delimitate the cell as the fundamental organismal unit, biological membranes are highly dynamic by allowing for lateral diffusion, transbilayer passage via selective channels, and in eukaryotic cells for endocytic uptake through the formation of membrane bound vesicular or tubular carriers. Two of the most abundant fundamental fabrics of membranes-lipids and complex sugars-are produced through elaborate chains of biosynthetic enzymes, which makes it difficult to study them by conventional reverse genetics. This review illustrates how organic synthesis provides access to uncharted areas of membrane glycobiology research and its application to biomedicine. For this Special Issue on Chemical Biology Research in France, focus will be placed on synthetic approaches (i) to study endocytic functions of glycosylated proteins and lipids according to the GlycoLipid-Lectin (GL-Lect) hypothesis, notably that of Shiga toxin; (ii) to mechanistically dissect its endocytosis and intracellular trafficking with small molecule; and (iii) to devise intracellular delivery strategies for immunotherapy and tumor targeting. It will be pointed out how the chemical biologist's view on lipids, sugars, and proteins synergizes with biophysics and modeling to "look" into the membrane for atomistic scale insights on molecular rearrangements that drive the biogenesis of endocytic carriers in processes of clathrin-independent endocytosis.

Whole-genome characterization of hemolytic uremic syndrome-causing Shiga toxin-producing Escherichia coli in Sweden

Shiga toxin-producing Escherichia coli, a foodborne bacterial pathogen, has been linked to a broad spectrum of clinical outcomes ranging from asymptomatic carriage to fatal hemolytic uremic syndrome (HUS). Here, we collected clinical data and STEC strains from HUS patients from 1994 through 2018, whole-genome sequencing was performed to molecularly characterize HUS-associated STEC strains, statistical analysis was conducted to identify bacterial genetic factors associated with severe outcomes in HUS patients. O157:H7 was the most predominant serotype (57%) among 54 HUS-associated STEC strains, followed by O121:H19 (19%) and O26:H11 (7%). Notably, some non-predominant serotypes such as O59:H17 (2%) and O109:H21 (2%) also caused HUS. All O157:H7 strains with one exception belonged to clade 8. During follow-up at a median of 4 years, 41% of the patients had renal sequelae. Fifty-nine virulence genes were found to be statistically associated with severe renal sequelae, these genes encoded type II and type III secretion system effectors, chaperones, and other factors. Notably, virulence genes associated with severe clinical outcomes were significantly more prevalent in O157:H7 strains. In contrast, genes related to mild symptoms were evenly distributed across all serotypes. The whole-genome phylogeny indicated high genomic diversity among HUS-STEC strains. No distinct cluster was found between HUS and non-HUS STEC strains. The current study showed that O157:H7 remains the main cause of STEC-associated HUS, despite the rising importance of other non-O157 serotypes. Besides, O157:H7 is associated with severe renal sequelae in the follow-up, which could be a risk factor for long-term prognosis in HUS patients.

Identification, Shiga toxin subtypes and prevalence of minor serogroups of Shiga toxin-producing Escherichia coli in feedlot cattle feces

Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens that cause illnesses in humans ranging from mild to hemorrhagic enteritis with complications of hemolytic uremic syndrome and even death. Cattle are a major reservoir of STEC, which reside in the hindgut and are shed in the feces, a major source of food and water contaminations. Seven serogroups, O26, O45, O103, O111, O121, O145 and O157, called ‘top-7’, are responsible for the majority of human STEC infections in North America. Additionally, 151 serogroups of E. coli are known to carry Shiga toxin genes (stx). Not much is known about fecal shedding and prevalence and virulence potential of STEC other than the top-7. Our primary objectives were to identify serogroups of STEC strains, other than the top-7, isolated from cattle feces and subtype stx genes to assess their virulence potential. Additional objective was to develop and validate a novel multiplex PCR assay to detect and determine prevalence of six serogroups, O2, O74, O109, O131, O168, and O171, in cattle feces. A total of 351 strains, positive for stx gene and negative for the top-7 serogroups, isolated from feedlot cattle feces were used in the study. Of the 351 strains, 291 belonged to 16 serogroups and 60 could not be serogrouped. Among the 351 strains, 63 (17.9%) carried stx1 gene and 300 (82.1%) carried stx2, including 12 strains positive for both. The majority of the stx1 and stx2 were of stx1a (47/63; 74.6%) and stx2a subtypes (234/300; 78%), respectively, which are often associated with human infections. A novel multiplex PCR assay developed and validated to detect six serogroups, O2, O74, O109, O131, O168, and O171, which accounted for 86.9% of the STEC strains identified, was utilized to determine their prevalence in fecal samples (n = 576) collected from a commercial feedlot. Four serogroups, O2, O109, O168, and O171 were identified as the dominant serogroups prevalent in cattle feces. In conclusion, cattle shed in the feces a number of STEC serogroups, other than the top-7, and the majority of the strains isolated possessed stx2, particularly of the subtype 2a, suggesting their potential risk to cause human infections.

Effects of Pulsed Electric Fields and Ultrasound Processing on Proteins and Enzymes: A Review

There is increasing demand among consumers for food products free of chemical preservatives, minimally processed and have fresh-like natural flavors. To meet these growing demands, the industries and researchers are finding alternative processing methods, which involve nonthermal methods to obtain a quality product that meets the consumer demands and adheres to the food safety protocols. In the past two decades’ various research groups have developed a wide range of nonthermal processing methods, of which few have shown potential in replacing the traditional thermal processing systems. Among all the methods, ultrasonication (US) and pulsed electric field (PEF) seem to be the most effective in attaining desirable food products. Several researchers have shown that these methods significantly affect various major and minor nutritional components present in food, including proteins and enzymes. In this review, we are going to discuss the effect of nonthermal methods on proteins, including enzymes. This review comprises results from the latest studies conducted from all over the world, which would help the research community and industry investigate the future pathway for nonthermal processing methods, especially in preserving the nutritional safety and integrity of the food.

Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Escherichia coli Strains From Healthy Food Animals Across Europe

The role of livestock animals as a putative source of ESBL/pAmpC E. coli for humans is a central issue of research. In a large-scale pan-European surveillance, 2,993 commensal Escherichia spp. isolates were recovered from randomly collected fecal samples of healthy cattle, pigs and chickens in various abattoirs. One-hundred Escherichia spp. isolates (0.5% from cattle, 1.3% pigs, 8.0% chickens) fulfilled the criteria for cefotaxime and ceftazidime non-wildtype (EUCAST). In silico screening of WGS data of 99 isolates (98 E. coli and 1 E. fergusonii) revealed bla_SHV–12 (32.3%), bla_CTX–M–1 (24.2%), and bla_CMY–2 (22.2%) as predominant ESBL/pAmpC types. Other types were bla_SHV–2 (1.0%), bla_{CTX–M–2/–14/–15} (1.0/6.1/1.0%), and bla_TEM–52 (5.1%). Six isolates revealed AmpC-promoter mutations (position −42 (C > T) and one carried mcr-1. The majority (91.3%) of ESBL/pAmpC genes were located on plasmids. SHV-12 was mainly (50%) encoded on IncI1α plasmids (pST-3/-26/-95), followed by IncX3 (12.5%) and IncK2 (3.1%). The bla_TEM–52 genes were located on IncI1α-pST-36 (60%) and IncX1 plasmids (20%). The dominant plasmid lineage among CTX-M-1 isolates was IncI1α (pST-3/-295/-317) (87.5%), followed by IncN-pST-1 (8.3%). CMY-2 was mostly identified on IncI1α (pST-12/-2) (54.5%) and IncK2 (31.8%) plasmids. Several plasmids revealed high similarity to published plasmids from human and animal Enterobacteriaceae. The isolates were assigned to phylogroups A/C (34.7/7.1%), B1 (27.6%), B2 (3.1%), D/F (9.2/10.2%), E (5.1%), and to E. clades (3.0%). With 51 known and 2 novel MLST types, a wide variety of STs was found, including STs previously observed in human isolates (ST10/38/117/131/648). ESBL/AmpC types or STs were rarely correlated with the geographic origin of the isolates or animal species. Virulence gene typing identified extraintestinal pathogenic E. coli (ExPEC; 2.0%), avian pathogenic E. coli (APEC; 51.5%), and atypical enteropathogenic E. coli (EPEC; 6.1%). In conclusion, the high diversity of STs and phylogenetic groups provides hardly any hint for clonal spread of single lineages but hints toward the dissemination of cephalosporin resistance genes in livestock via distinct, globally successful plasmid lineages. Even though a number of isolates could not be assigned to a distinct pathotype, our finding of combined multidrug-resistance and virulence in this facultative pathogen should be considered an additional threat to public health.

Bacteriophages of Shiga Toxin-Producing Escherichia coli and Their Contribution to Pathogenicity

Shiga toxins (Stx) of Shiga toxin-producing Escherichia coli (STEC) are generally encoded in the genome of lambdoid bacteriophages, which spend the most time of their life cycle integrated as prophages in specific sites of the bacterial chromosome. Upon spontaneous induction or induction by chemical or physical stimuli, the stx genes are co-transcribed together with the late phase genes of the prophages. After being assembled in the cytoplasm, and after host cell lysis, mature bacteriophage particles are released into the environment, together with Stx. As members of the group of lambdoid phages, Stx phages share many genetic features with the archetypical temperate phage Lambda, but are heterogeneous in their DNA sequences due to frequent recombination events. In addition to Stx phages, the genome of pathogenic STEC bacteria may contain numerous prophages, which are either cryptic or functional. These prophages may carry foreign genes, some of them related to virulence, besides those necessary for the phage life cycle. Since the production of one or more Stx is considered the major pathogenicity factor of STEC, we aim to highlight the new insights on the contribution of Stx phages and other STEC phages to pathogenicity.

Digital Insights Into Nucleotide Metabolism and Antibiotic Treatment Failure

Nucleotide metabolism plays a central role in bacterial physiology, producing the nucleic acids necessary for DNA replication and RNA transcription. Recent studies demonstrate that nucleotide metabolism also proactively contributes to antibiotic-induced lethality in bacterial pathogens and that disruptions to nucleotide metabolism contributes to antibiotic treatment failure in the clinic. As antimicrobial resistance continues to grow unchecked, new approaches are needed to study the molecular mechanisms responsible for antibiotic efficacy. Here we review emerging technologies poised to transform understanding into why antibiotics may fail in the clinic. We discuss how these technologies led to the discovery that nucleotide metabolism regulates antibiotic drug responses and why these are relevant to human infections. We highlight opportunities for how studies into nucleotide metabolism may enhance understanding of antibiotic failure mechanisms.

Integrating evolutionary aspects into dual-use discussion: the cases of influenza virus and enterohemorrhagic Escherichia coli

Research in infection biology aims to understand the complex nature of host–pathogen interactions. While this knowledge facilitates strategies for preventing and treating diseases, it can also be intentionally misused to cause harm. Such dual-use risk is potentially high for highly pathogenic microbes such as Risk Group-3 (RG3) bacteria and RG4 viruses, which could be used in bioterrorism attacks. However, other pathogens such as influenza virus (IV) and enterohemorrhagic Escherichia coli (EHEC), usually classified as RG2 pathogens, also demonstrate high dual-use risk. As the currently approved therapeutics against these pathogens are not satisfactorily effective, previous outbreaks of these pathogens caused enormous public fear, media attention and economic burden. In this interdisciplinary review, we summarize the current perspectives of dual-use research on IV and EHEC, and further highlight the dual-use risk associated with evolutionary experiments with these infectious pathogens. We support the need to carry out experiments pertaining to pathogen evolution, including to gain predictive insights on their evolutionary trajectories, which cannot be otherwise achieved with stand-alone theoretical models and epidemiological data. However, we also advocate for increased awareness and assessment strategies to better quantify the risks-versus-benefits associated with such evolutionary experiments. In addition to building public trust in dual-use research, we propose that these approaches can be extended to other pathogens currently classified as low risk, but bearing high dual-use potential, given the particular pressing nature of their rapid evolutionary potential.

The Superior Adherence Phenotype of E. coli O104:H4 is Directly Mediated by the Aggregative Adherence Fimbriae Type I

Whereas the O104:H4 enterohemorrhagic Escherichia coli (EHEC) outbreak strain from 2011 expresses aggregative adherence fimbriae of subtype I (AAF/I), its close relative, the O104:H4 enteroaggregative Escherichia coli (EAEC) strain 55989, encodes AAF of subtype III. Tight adherence mediated by AAF/I in combination with Shiga toxin 2 production has been suggested to result in the outbreak strain’s exceptional pathogenicity. Furthermore, the O104:H4 outbreak strain adheres significantly better to cultured epithelial cells than archetypal EAEC strains expressing different AAF subtypes. To test whether AAF/I expression is associated with the different virulence phenotypes of the outbreak strain, we heterologously expressed AAF subtypes I, III, IV, and V in an AAF-negative EAEC 55989 mutant and compared AAF-mediated phenotypes, incl. autoaggregation, biofilm formation, as well as bacterial adherence to HEp-2 cells. We observed that the expression of all four AAF subtypes promoted bacterial autoaggregation, though with different kinetics. Disturbance of AAF interaction on the bacterial surface via addition of α-AAF antibodies impeded autoaggregation. Biofilm formation was enhanced upon heterologous expression of AAF variants and inversely correlated with the autoaggregation phenotype. Co-cultivation of bacteria expressing different AAF subtypes resulted in mixed bacterial aggregates. Interestingly, bacteria expressing AAF/I formed the largest bacterial clusters on HEp-2 cells, indicating a stronger host cell adherence similar to the EHEC O104:H4 outbreak strain. Our findings show that, compared to the closely related O104:H4 EAEC strain 55989, not only the acquisition of the Shiga toxin phage, but also the acquisition of the AAF/I subtype might have contributed to the increased EHEC O104:H4 pathogenicity.

Stochastic determination of the spatial variation of potentially pathogenic bacteria communities in a large subtropical river

Understanding the composition and assembly mechanism of waterborne pathogen is essential for preventing the pathogenic infection and protecting the human health. Here, based on 16S rRNA sequencing, we investigated the composition and spatial variation of potentially pathogenic bacteria from different sections of the Pearl River, the most important source of water for human in Southern China. The results showed that the potential pathogen communities consisted of 6 phyla and 64 genera, covering 11 categories of potential pathogens mainly involving animal parasites or symbionts (AniP), human pathogens all (HumPA), and intracellular parasites (IntCelP). Proteobacteria (75.87%) and Chlamydiae (20.56%) were dominant at the phylum level, and Acinetobacter (35.01%) and Roseomonas (8.24%) were dominant at the genus level. Multivariate analysis showed that the potential pathogenic bacterial community was significantly different among the four sections in the Pearl River. Both physicochemical factors (e.g., NO₃-N, and suspended solids) and land use (e.g., urban land and forest) significantly shaped the pathogen community structure. However, spatial effects contributed more to the variation of pathogen community based on variation partitioning and path analysis. Null model based normalized stochasticity ratio analysis further indicated that the stochastic process rather than deterministic process dominated the assembly mechanisms by controlling the spatial patterns of potential pathogens. In conclusion, high-throughput sequencing shows great potential for monitoring the potential pathogens, and provided more comprehensive information on the potentially pathogenic community. Our study highlighted the importance of considering the influences of dispersal-related processes in future risk assessments for the prevention and control of pathogenic bacteria.

The population genetics of pathogenic Escherichia coli

Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.

The prevalence and genomic context of Shiga toxin 2a genes in E. coli found in cattle

Shiga toxin-producing Escherichia coli (STEC) that cause severe disease predominantly carry the toxin gene variant stx2a. However, the role of Shiga toxin in the ruminant reservoirs of this zoonotic pathogen is poorly understood and strains that cause severe disease in humans (HUSEC) likely constitute a small and atypical subset of the overall STEC flora. The aim of this study was to investigate the presence of stx2a in samples from cattle and to isolate and characterize stx2a-positive E. coli. In nationwide surveys in Sweden and Norway samples were collected from individual cattle or from cattle herds, respectively. Samples were tested for Shiga toxin genes by real-time PCR and amplicon sequencing and stx2a-positive isolates were whole genome sequenced. Among faecal samples from Sweden, stx1 was detected in 37%, stx2 in 53% and stx2a in 5% and in skin (ear) samples in 64%, 79% and 2% respectively. In Norway, 79% of the herds were positive for stx1, 93% for stx2 and 17% for stx2a. Based on amplicon sequencing the most common stx2 types in samples from Swedish cattle were stx2a and stx2d. Multilocus sequence typing (MLST) of 39 stx2a-positive isolates collected from both countries revealed substantial diversity with 19 different sequence types. Only a few classical LEE-positive strains similar to HUSEC were found among the stx2a-positive isolates, notably a single O121:H19 and an O26:H11. Lineages known to include LEE-negative HUSEC were also recovered including, such as O113:H21 (sequence type ST-223), O130:H11 (ST-297), and O101:H33 (ST-330). We conclude that E. coli encoding stx2a in cattle are ranging from strains similar to HUSEC to unknown STEC variants. Comparison of isolates from human HUS cases to related STEC from the ruminant reservoirs can help identify combinations of virulence attributes necessary to cause HUS, as well as provide a better understanding of the routes of infection for rare and emerging pathogenic STEC.

Dissemination of the blaCTX-M-15 gene among Enterobacteriaceae via outer membrane vesicles

Background

Bacterial outer membrane vesicles (OMVs) are an emerging source of antibiotic resistance transfer but their role in the spread of the blaCTX-M-15 gene encoding the most frequent CTX-M ESBL in Enterobacteriaceae is unknown.

Objectives

To determine the presence of blaCTX-M-15 and other antibiotic resistance genes in OMVs of the CTX-M-15-producing MDR Escherichia coli O104:H4 outbreak strain and the ability of these OMVs to spread these genes among Enterobacteriaceae under different conditions.

Methods

OMV-borne antibiotic resistance genes were detected by PCR; OMV-mediated transfer of blaCTX-M-15 and the associated blaTEM-1 was quantified under laboratory conditions, simulated intraintestinal conditions and under ciprofloxacin stress; resistance to antibiotics and the ESBL phenotype were determined by the CLSI disc diffusion methods and the presence of pESBL by plasmid profiling and Southern blot hybridization.

Results

E. coli O104:H4 OMVs carried blaCTX-M-15 and blaTEM-1 located on the pESBL plasmid, but not chromosomal antibiotic resistance genes. The OMVs transferred blaCTX-M-15, blaTEM-1 and the associated pESBL into Enterobacteriaceae of different species. The frequencies of the OMV-mediated transfer were significantly increased under simulated intraintestinal conditions and under ciprofloxacin stress when compared with laboratory conditions. The ‘vesiculants’ (i.e. recipients that received the blaCTX-M-15- and blaTEM-1-harbouring pESBL via OMVs) acquired resistance to cefotaxime, ceftazidime and cefpodoxime and expressed the ESBL phenotype. They were able to further spread pESBL and the blaCTX-M-15 and blaTEM-1 genes via OMVs.

Conclusions

OMVs are efficient vehicles for dissemination of the blaCTX-M-15 gene among Enterobacteriaceae and may contribute to blaCTX-M-15 transfer in the human intestine.

Valid Presumption of Shiga Toxin-Mediated Damage of Developing Erythrocytes in EHEC-Associated Hemolytic Uremic Syndrome

The global emergence of clinical diseases caused by enterohemorrhagic Escherichia coli (EHEC) is an issue of great concern. EHEC release Shiga toxins (Stxs) as their key virulence factors, and investigations on the cell-damaging mechanisms toward target cells are inevitable for the development of novel mitigation strategies. Stx-mediated hemolytic uremic syndrome (HUS), characterized by the triad of microangiopathic hemolytic anemia, thrombocytopenia, and acute renal injury, is the most severe outcome of an EHEC infection. Hemolytic anemia during HUS is defined as the loss of erythrocytes by mechanical disruption when passing through narrowed microvessels. The formation of thrombi in the microvasculature is considered an indirect effect of Stx-mediated injury mainly of the renal microvascular endothelial cells, resulting in obstructions of vessels. In this review, we summarize and discuss recent data providing evidence that HUS-associated hemolytic anemia may arise not only from intravascular rupture of erythrocytes, but also from the extravascular impairment of erythropoiesis, the development of red blood cells in the bone marrow, via direct Stx-mediated damage of maturing erythrocytes, leading to “non-hemolytic” anemia.

Strategies to reduce Gram-negative infections: a community perspective

Infections caused by Gram-negative bacteria continue to be on the rise, despite efforts by the Government and health service to curb their numbers. Most of these infections arise in the community. The case for targeting community-onset healthcare-associated infections is stark and requires a shift in focus from traditionally providing increased efforts in the hospital setting to a diversion of attention to the community. This article describes the challenges faced with increasing Gram-negative bloodstream infections and explores measures being taken to reduce transmission. As recent guidance has highlighted a proliferation within the community setting this article particularly focuses on a three-point plan for primary care. The strategies laid out are to reduce urinary tract infections, improve hydration and control antibiotic usage. Adopting these strategies will assist in reducing infection and targeting efforts where they are needed most.

Food-to-Humans Bacterial Transmission

Microorganisms vehiculated by food might benefit health, cause minimal change within the equilibrium of the host microbial community or be associated with foodborne diseases. In this chapter we will focus on human pathogenic bacteria for which food is conclusively demonstrated as their transmission mode to human. We will describe the impact of foodborne diseases in public health, the reservoirs of foodborne pathogens (the environment, human and animals), the main bacterial pathogens and food vehicles causing human diseases, and the drivers for the transmission of foodborne diseases related to the food-chain, host or bacteria features. The implication of food-chain (foodborne pathogens and commensals) in the transmission of resistance to antibiotics relevant to the treatment of human infections is also evidenced. The multiplicity and interplay of drivers related to intensification, diversification and globalization of food production, consumer health status, preferences, lifestyles or behaviors, and bacteria adaptation to different challenges (stress tolerance and antimicrobial resistance) from farm to human, make the prevention of bacteria-food-human transmission a modern and continuous challenge. A global One Health approach is mandatory to better understand and minimize the transmission pathways of human pathogens, including multidrug-resistant pathogens and commensals, through food-chain.

Origin and Evolution of Hybrid Shiga Toxin-Producing and Uropathogenic Escherichia coli Strains of Sequence Type 141

Hybrid Shiga toxin-producing Escherichia coli (STEC) and uropathogenic E. coli (UPEC) strains of multilocus sequence type 141 (ST141) cause both urinary tract infections and diarrhea in humans and are phylogenetically positioned between STEC and UPEC strains. We used comparative genomic analysis of 85 temporally and spatially diverse ST141 E. coli strains, including 14 STEC/UPEC hybrids, collected in Germany (n = 13) and the United States (n = 1) to reconstruct their molecular evolution. Whole-genome sequencing data showed that 89% of the ST141 E. coli strains either were STEC/UPEC hybrids or contained a mixture of virulence genes from other pathotypes. Core genome analysis and ancestral reconstruction revealed that the ST141 E. coli strains clustered into two lineages that evolved from a common ancestor in the mid-19th century. The STEC/UPEC hybrid emerged ∼100 years ago by acquiring an stx prophage, which integrated into previously unknown insertion site between rcsB and rcsD, followed by the insertion of a pathogenicity island (PAI) similar to PAI II of UPEC strain 536 (PAI II536-like). The two variants of PAI II536-like were associated with tRNA genes leuX and pheU, respectively. Finally, microevolution within PAI II536-like and acquisition of the enterohemorrhagic E. coli plasmid were observed. Our data suggest that intestinal pathogenic E. coli (IPEC)/extraintestinal pathogenic E. coli (ExPEC) hybrids are widespread and that selection pressure within the ST141 E. coli population led to the emergence of the STEC/UPEC hybrid as a clinically important subgroup. We hypothesize that ST141 E. coli strains serve as a melting pot for pathogroup conversion between IPEC and ExPEC, contrasting the classical theory of pathogen emergence from nonpathogens and corroborating our recent phenomenon of heteropathogenicity among pathogenic E. coli strains.

Cumulative acquisition of pathogenicity islands has shaped virulence potential and contributed to the emergence of LEE-negative Shiga toxin-producing Escherichia coli strains

Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens causing severe gastroenteritis, which may lead to hemolytic uremic syndrome. The Locus of Enterocyte Effacement (LEE), a Pathogenicity Island (PAI), is a major determinant of intestinal epithelium attachment of a group of STEC strains; however, the virulence repertoire of STEC strains lacking LEE, has not been fully characterized. The incidence of LEE-negative STEC strains has increased in several countries, highlighting the relevance of their study. In order to gain insights into the basis for the emergence of LEE-negative STEC strains, we performed a large-scale genomic analysis of 367 strains isolated worldwide from humans, animals, food and the environment. We identified uncharacterized genomic islands, including two PAIs and one Integrative Conjugative Element. Additionally, the Locus of Adhesion and Autoaggregation (LAA) was the most prevalent PAI among LEE-negative strains and we found that it contributes to colonization of the mice intestine. Our comprehensive and rigorous comparative genomic and phylogenetic analyses suggest that the accumulative acquisition of PAIs has played an important, but currently unappreciated role, in the evolution of virulence in these strains. This study provides new knowledge on the pathogenicity of LEE-negative STEC strains and identifies molecular markers for their epidemiological surveillance.

Climate Change, Foodborne Pathogens and Illness in Higher-Income Countries

Purpose of Review

We present a review of the likely consequences of climate change for foodborne pathogens and associated human illness in higher-income countries.

Recent Findings

The relationships between climate and food are complex and hence the impacts of climate change uncertain. This makes it difficult to know which foodborne pathogens will be most affected, what the specific effects will be, and on what timescales changes might occur. Hence, a focus upon current capacity and adaptation potential against foodborne pathogens is essential. We highlight a number of developments that may enhance preparedness for climate change. These include the following:

Adoption of novel surveillance methods, such as syndromic methods, to speed up detection and increase the fidelity of intervention in foodborne outbreaks

Genotype-based approaches to surveillance of food pathogens to enhance spatiotemporal resolution in tracing and tracking of illness

Ever increasing integration of plant, animal and human surveillance systems, One Health, to maximise potential for identifying threats

Increased commitment to cross-border (global) information initiatives (including big data)

Improved clarity regarding the governance of complex societal issues such as the conflict between food safety and food waste

Strong user-centric (social) communications strategies to engage diverse stakeholder groups

Summary

The impact of climate change upon foodborne pathogens and associated illness is uncertain. This emphasises the need to enhance current capacity and adaptation potential against foodborne illness. A range of developments are explored in this paper to enhance preparedness.

High frequency of hybrid Escherichia coli strains with combined Intestinal Pathogenic Escherichia coli (IPEC) and Extraintestinal Pathogenic Escherichia coli (ExPEC) virulence factors isolated from human faecal samples

BACKGROUND

Classification of pathogenic Escherichia coli (E. coli) has traditionally relied on detecting specific virulence associated genes (VAGs) or combinations thereof. For E. coli isolated from faecal samples, the presence of specific genes associated with different intestinal pathogenic pathovars will determine their classification and further course of action. However, the E. coli genome is not a static entity, and hybrid strains are emerging that cross the pathovar definitions. Hybrid strains may show gene contents previously associated with several distinct pathovars making the correct diagnostic classification difficult. We extended the analysis of routinely submitted faecal isolates to include known virulence associated genes that are usually not examined in faecal isolates to detect the frequency of possible hybrid strains.

METHODS

From September 2012 to February 2013, 168 faecal isolates of E. coli routinely submitted to the Norwegian Institute of Public Health (NIPH) from clinical microbiological laboratories throughout Norway were analysed for 33 VAGs using multiplex-PCR, including factors associated with extraintestinal pathogenic E. coli (ExPEC) strains. The strains were further typed by Multiple Locus Variable-Number Tandem-Repeat Analysis (MLVA), and the phylogenetic grouping was determined. One isolate from the study was selected for whole genome sequencing (WGS) with a combination of Oxford Nanopore's MinION and Illumina's MiSeq.

RESULTS

The analysis showed a surprisingly high number of strains carrying ExPEC associated VAGs and strains carrying a combination of both intestinal pathogenic E. coli (IPEC) and ExPEC VAGs. In particular, 93.5% (101/108) of isolates classified as belonging to an IPEC pathovar additionally carried ExPEC VAGs. WGS analysis of a selected hybrid strain revealed that it could, with present classification criteria, be classified as belonging to all of the Enteropathogenic Escherichia coli (EPEC), Uropathogenic Escherichia coli (UPEC), Neonatal meningitis Escherichia coli (NMEC) and Avian pathogenic Escherichia coli (APEC) pathovars.

CONCLUSION

Hybrid ExPEC/IPEC E. coli strains were found at a very high frequency in faecal samples and were in fact the predominant species present. A sequenced hybrid isolate was confirmed to be a cross-pathovar strain possessing recognised hallmarks of several pathovars, and a genome heavily influenced by horizontal gene transfer.

Comparative Genomics and Characterization of the Late Promoter pR' from Shiga Toxin Prophages in Escherichia coli

Shiga-toxin producing Escherichia coli (STEC) causes human illness ranging from mild diarrhea to death. The bacteriophage encoded stx genes are located in the late transcription region, downstream of the antiterminator Q. The transcription of the stx genes is directly under the control of the late promoter pR’, thus the sequence diversity of the region between Q and stx, here termed the pR’ region, may affect Stx toxin production. Here, we compared the gene structure of the pR’ region and the stx subtypes of nineteen STECs. The sequence alignment and phylogenetic analysis suggested that the pR’ region tends to be more heterogeneous than the promoter itself, even if the prophages harbor the same stx subtype. Furthermore, we established and validated transcriptional fusions of the pR’ region to the DsRed reporter gene using mitomycin C (MMC) induction. Finally, these constructs were transformed into native and non-native strains and examined with flow cytometry. The results showed that induction levels changed when pR’ regions were placed under different regulatory systems. Moreover, not every stx gene could be induced in its native host bacteria. In addition to the functional genes, the diversity of the pR’ region plays an important role in determining the level of toxin induction.

Phenotypic characterization and whole genome analysis of extended-spectrum beta-lactamase-producing bacteria isolated from dogs in Germany

Asymptomatic colonization with extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae has been described for humans, various mammal species, and birds. Here, antimicrobial resistant bacteria were recovered from dog feces originating in Germany, Kosovo, Afghanistan, Croatia, and Ukraine, with a subset of mostly E. coli isolates obtained from a longitudinal collection over twelve months. In vitro antimicrobial resistance testing revealed various patterns of resistance against single or all investigated beta-lactam antibiotics, with none of the 101 isolates resistant against two tested carbapenem antibiotics. Whole genome sequence analysis revealed bacteria species-specific patterns for 23 antimicrobial resistance coding DNA sequences (CDS) that were unapparent from the in vitro analysis alone. Phylogenetic analysis of single nucleotide polymorphisms (SNP) revealed clonal bacterial isolates originating from different dogs, suggesting transmission between dogs in the same community. However, individual resistant E. coli clones were not detected over a period longer than seven days. Multi locus sequence typing (MLST) of 85 E. coli isolates revealed 31 different sequence types (ST) with an accumulation of ST744 (n = 9), ST10 (n = 8), and ST648 (n = 6), although the world-wide hospital-associated CTX-M beta-lactamase producing ST131 was not detected. Neither the antimicrobial resistance CDSs patterns nor the phylogenetic analysis revealed an epidemiological correlation among the longitudinal isolates collected from a period longer than seven days. No genetic linkage could be associated with the geographic origin of isolates. In conclusion, healthy dogs frequently carry ESBL-producing bacteria, independent to prior treatment, which may be transmitted between individual dogs of the same community. Otherwise, these antimicrobial resistant bacteria share few commonalities, making their presence eerily unpredictable.

Effect of chlorine on cultivability of Shiga toxin producing Escherichia coli (STEC) and β-lactamase genes carrying E. coli and Pseudomonas aeruginosa

The worldwide spread of toxin-producing and multi-drug resistant bacteria in water, food and the environment is considered a major threat to human health. Drinking water quality is controlled by inspection of fecal indicators presence whereby viable contaminants will be efficiently reduced by chlorination which is a common process for disinfection. However, the all-out efficiency is arguable, because bacterial regrowth has been documented after disinfection. In this study, we investigated the stability of Shiga toxin producing Escherichia coli (STEC) and β-lactamase expressing E. coli and Pseudomonas aeruginosa isolates, both equipped with multiple or single β-lactamase resistance genes. The aim of the study was to analyze the efficiency of chlorine (Cl₂) disinfection against shigatoxigenic or β-lactamase producing bacteria. Cl₂ reacts with the bacterial cells after first contact. Counts of antibiotic resistant E. coli were lower after short than upon extended Cl₂ treatment. P. aeruginosa counts decreased moderately upon 15-60 min treatment with 1.2 mg Cl₂/l, while cells adapted to tap water were not cultivable anymore. We assume that the bacterial physiology changed to a temporary non-cultivatable state at first Cl₂ contact followed by resuscitation of some cells at later stages. STEC viability went down continuously at low Cl₂ concentrations and these toxigenic E. coli isolates exhibited slightly increased stability to Cl₂ treatment compared with non-toxigenic E. coli. Controlling the efficiency of disinfection, realistic counts of cultivatable cells are achieved after extended Cl₂ action.