E. coli

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Control Tools

  • Diagnostics availability

  • Commercial diagnostic kits available worldwide

    • Numerous kits are available for the detection and identification of STEC. Some are specific for human infection and animal colonisation, whilst others are focused on food and environmental sample analyses.
    • A number of culture media have been developed for O157 and Non-O157 STEC.
    • The use of paired selective media has been successfully used in some diagnostic laboratories.

    List of commercially available kits (Diagnostics for Animals)

    GAPS :

    • Generally, there is a need for better detection assays for non-O157 STEC, non-clinical sample preparation and for rapid phylotyping.
    • Understanding what level of carriage/shedding poses a risk.
    • Sensitive and specific, pen-side/point of care tests should be available worldwide.
  • Diagnostic kits validated by International, European or National Standards

    • Several kits for the detection of E. coli O157 in food have been validated against accepted reference culture methods, i.e. the ISO 16654 method in the EU.
    • A PCR-based technical specification for the detection of the main non-O157 serogroups in food including milk has been validated and approved by ISO. These methods can be adapted for the analysis of animal faeces. LAMP and RPA assays are now available in research laboratories for a number of E. coli serotypes.
    • Animal faeces are included in the field of application of ISO TS 13136 for STEC detection in food.

    GAPS :

    • An internationally accepted standard for the detection of O157 and STEC in all environmental samples is needed. This could be used to validate alternative methods. ISO/CEN are currently trying to broaden their mandate, so their methods can be used for non-food matrices.
    • Test required for food matrices, such as salad.
    • ISO and CEN are mainly operating at the EU level, what about non-European countries.
    • Development of methods in the OIE (WOAH) framework.
    • A number of patient-side / pen-side tests are under development for E. coli including AI assisted result interpretation.
  • Diagnostic method(s) described by International, European or National standards

    • The immuno-magnetic concentration-based ISO16654 method for E. coli O157 in food. Commercial kits validated against this method. For the detection of the main non-O157 serogroups in food, a PCR-based technical specification ISO TS 13136 has been approved. The OIE Terrestrial Animal Health Code and an EFSA guideline for monitoring of STEC in animals published in 2009 describes how to adapt these methods to animal faeces.
    • LAMP assays are now available for STEC – Detection in 15 minutes.

    GAPS :

    Additional IMS methods for less frequently isolated STEC are urgently required. IMS for E. coli O80 is needed as it becomes an important serogroup of clinical significance in Europe.

  • Commercial potential for diagnostic kits in Europe

    • Many diagnostic kits already available for the detection of STEC O157, ST production and vtx/stx genes.
    • Tests targeting the main non-O157 pathogenic serogroups are urgently required.
    • ELISA based tests are less sensitive than culture/PCR, but faster.
    • Loop Mediated-Isothermal Amplification (LAMP) based tests have been developed that can detect STEC less than 15 minutes, but these are not commercially available.

    GAPS :

    • Find new unique genetic markers that can identify highly pathogenic STEC (Stx subtypes are such markers (EFSA 2020).
    • Multi-target, DNA based screening of enrichment broths are hampered by the fact the identified markers may not be present in the same bacterial isolate. e.g., eae is widespread in other bacteria.
    • Identification of new biomarkers for the rapid screening of pathogenic STEC (stx- and eae- positive strains) in food commodities is required.
    • Development of NGS platforms.
    • Direct sequencing – Nanopore.
    • Development of LAMP assays linked to lateral flow assays.
  • DIVA tests required and/or available

    • Not applicable presently, although a vaccine for ruminants is available.
    • Commercial vaccines are currently based on a selection of secreted proteins; differentiation of the immune response possible in theory based on antigens (proteinaceous or LPS) not included in the vaccine.
    • If applied in a control scheme similar to that, e.g., for Salmonella, DIVA compatibility of the vaccine may be dispensable.

    GAPS :

    • If attenuated vaccines are developed, these must not be able to produce wild-type Shiga-toxin for biosafety reasons.
    • The vaccine strains must at least be discriminated from field strains by the truncation or complete deletion of the stx gene or by the lack of verocytotoxic activity.
  • Vaccines availability

  • Commercial vaccines availability (globally)

    • A vaccine directed against Type III secreted proteins has obtained licensing approval from a number of countries.
    • Another product which targets bacterial surface proteins and protein receptors involved in iron uptake has obtained a conditional approval by the U.S. Department of Agriculture.
    • A number of vaccine candidates are currently under validation for different species.

    GAPS :

    • Who will pay for the vaccine.
    • Will it protect against other STEC.
  • Marker vaccines available worldwide


  • Effectiveness of vaccines / Main shortcomings of current vaccines

    • The efficacy of the available vaccines against different sub-types of STEC O157 still needs to be fully evaluated. The efficacy against other STEC serotypes is unknown.
    • Efficacy in other species to be evaluated.

    GAPS :

    In general, more research is required. We don’t know enough about colonisation and mucosal immunity to an otherwise commensal organism, to understand which aspects of colonisation would be best targeted, although targeting the T3SS and ST seems logical.

  • Commercial potential for vaccines in Europe

    • Since cattle and other ruminants are asymptomatic there is little demand from farmers. Vaccination of feedlot calves could be required by companies purchasing the meat.
    • In Member States where the sale of raw milk is permitted, dairy farms (and small ruminant) may have a stronger interest in vaccination.
    • On farm production of dairy (including raw milk cheese) and selling in on-farm shops is increasingly deployed by family-owned farms (cattle, goat, and sheep farms). Demand on the rise for control measures at primary production level to mitigate intrusion of STEC in the production line.

    GAPS :

    • Who would pay for the vaccine,
    • Define public health strategies.
    • How would the vaccine be administered.
    • Frequency of vaccination.
    • What species should be vaccinated.
  • Regulatory and/or policy challenges to approval

    • Use of genetically modified vaccines might be problematic in some countries. The field trials may need specific regulation regarding the release of GMOs into the environment.
    • A number of other GMO vaccines are licensed for use in animals.

    GAPS :

    • Possibility of live attenuated vaccine strains.
    • Regulatory testing for approval of biological products in animals is usually based on efficacy to prevent manifestation of disease but, Salmonella vaccines for poultry may be used as showcase for alternate routes.
    • As STEC do not cause disease in cattle, different parameters, such as prevention of colonisation/shedding, have to be used, and regulatory agencies have less experience with these.
  • Commercial feasibility (e.g manufacturing)

    • Feasible of production?
    • Viability depends on demand and who would cover the cost.

    GAPS :

    The cost of the vaccine needs to be low to encourage uptake.

  • Opportunity for barrier protection

    • Herd vaccination would be practical in an attempt to reduce colonisation in cattle.
    • Vaccination certification (rather than extensive testing for faecal excretion of O157 and negative certification of animals, which controversial) could be used to protect against (trade?) barriers.

    GAPS :

    • Investigate whether vaccination of cattle prior to slaughter is a way to reduce the influx of STEC into the abattoir.
    • Non-O157 need to be considered.
    • Other reservoir animals need to be considered.
  • Pharmaceutical availability

  • Current therapy (curative and preventive)

    • In humans, antibiotic therapy is not recommended. Only supportive therapies.
    • Eculizumab treatment used in certain HUS cases to reduce the risk of neurological symptoms
    • No therapy for asymptomatic carrier animals, although decolonisation of the rectal anal junction is an option.
    • Identification and isolation of super shedder animals.

    GAPS :

    Alternatives to antibiotics urgently required. Possible alternatives for use in animals:

    • Phytochemicals
    • Novel compounds that interfere with colonisation
    • Novel antimicrobials
    • Probiotics
    • Phage therapy
    • Modulation of the gut microflora
    • Passive vaccination – Plantibodies.
    • Association of certain antibiotic classes (e.g. fosphomicin) with other molecules (e.g. zidovudine).
  • Future therapy

    For reducing colonisation and carriage in animals:

    • Multivalent vaccines
    • Probiotics
    • Bacteriophages
    • Phytochemicals

    GAPS :

    Possible alternatives for use in animals:

    • Probiotics, modulation of the gut flora
    • Prebiotics, modulation of the gut flora.
    • Synbiotic, modulation of the gut flora.
    • Postbiotic, modulation of the gut flora.
    • Non antibiotic therapeutics?
    • Specially designed fusion proteins for vaccination.
    • The use of phages should be further explored.
  • Commercial potential for pharmaceuticals in Europe

    Limited potential, and dependant on policies in relation to STEC infection in humans, and the need to reduce colonisation in cattle and other reservoir animals.

    GAPS :

    Better scientific evidence for alternative therapies is urgently required.

  • Regulatory and/or policy challenges to approval


  • Commercial feasibility (e.g manufacturing)


  • New developments for diagnostic tests

  • Requirements for diagnostics development

    • Rapid tests to identify ruminants infected with pathogenic STEC.
    • Tests for the detection of the main non-O157 serogroups pathogenic to humans in food and animals.
    • Time to undertake test and associated costs must be kept as low as possible.

    GAPS :

    • Development of testing strategies.
    • Knowledge of virulence factors or other gene sequences which differentiate virulent and less virulent STEC.
    • Knowledge of virulence factors or other gene sequences which differentiate non-O157 STEC.
    • Use of NGS to inform on the development of rapid assays such as LAMP.
  • Time to develop new or improved diagnostics

    When the principles are defined, the development of tests is generally faster and less expensive than that of vaccines.

  • Cost of developing new or improved diagnostics and their validation

    • The development and validation of new tests is resource demanding (time consuming and labour intensive).
    • The costs cannot be specified as they will depend on the nature of the test, the cost of reagents and of reading or processing machines, if required.
    • Once validated, a commercial company willing to market the test will be required.

    GAPS :

    • If there is a framework for the development of diagnostic kits and a need for tests, then this almost automatically drive companies to market new methods. The validation of alternative tests is then the responsibility of the respective company.
    • Commercial companies can help undertake the validation studies.
  • Research requirements for new or improved diagnostics

    • Increase knowledge on pathogenesis and involved virulence factors.
    • Better understanding of STEC genomics and evolution (especially in relation to the emergence of hybrid isolates).
    • Increased knowledge on immune response.
    • Microflora studies.

    GAPS :

    • Increased knowledge about colonisation factors in healthy animals. Why is STEC generally more prevalent in ruminants?
    • Better understanding of gut microbial ecology.
    • Use of metagenomic studies to improve our understanding of colonisation sites and dynamics.
  • Technology to determine virus freedom in animals

    Not applicable.

  • New developments for vaccines

  • Requirements for vaccines development / main characteristics for improved vaccines

    Serotype independent (targeted against bacterial factors common to the main pathogenic STEC serogroups).

  • Time to develop new or improved vaccines

    • Depending on when a new candidate vaccine might be identified the timescale could be 5-10 years. This will involve development of clinical trials and licensing. Potential vaccines need to be identified and subjected to initial trials. The time to commercial availability will depend on the outcome of these trials.
    • Experimental data on O157 vaccination in feed lot cattle: there is a prompt immunological response, and a decrease in shedding is also observed. Order of “protection” was poorly reproducibly under field conditions in North American feedlots.

    GAPS :

    • Topical rectal applications?
    • A number of experimental vaccines are undergoing validation – Need to consider boosters to.
    • Investigate whether vaccination of cattle prior to slaughter is a way to reduce the influx of STEC into the abattoir.
  • Cost of developing new or improved vaccines and their validation

    • Expensive, with the need to develop and undertake all the relevant tests to provide data to enable the product to be authorised.
    • Field trials will be difficult, as will the evaluation of the results. Since there is no disease, efficacy will be assessed by measuring STEC shedding in the faeces.

    GAPS :

    Evaluation of the influence of vaccines on the normal flora are essential.

  • Research requirements for new or improved vaccines

    Increased knowledge on the colonisation of cattle and humans by STEC.

    GAPS :

    Increased knowledge on genotype and phenotype, emergence of new pathotypes and evolutionary pressures.

  • New developments for pharmaceuticals

  • Requirements for pharmaceuticals development

    • Probiotics effective against STEC colonisation.
    • Development of bacteriophages which have a wide spectrum of specificity for pathogenic STEC serotypes, and which are active in vivo in the gut.

    GAPS :

    Possible alternatives for use in animals:

    • Prebiotics, probiotics, synbiotics, postbiotics, phytochemicals topicals, vaccines? Photocorms, bedding treatments, anti-infective compounds that block pathogenesis and colonisation etc.
  • Time to develop new or improved pharmaceuticals

    Time to develop would depend on the product and the trials necessary to validate the efficacy and safety. Commercial production would then take further time. Five to ten years seems a realistic timeframe.

    GAPS :

    Five to 10 years seems a realistic timeframe.

  • Cost of developing new or improved pharmaceuticals and their validation

    Difficult to assess as it will depend on the product and the trials necessary to validate and license.

    GAPS :

    Difficult to assess as it will depend on the product and the trials necessary to validate and license.

  • Research requirements for new or improved pharmaceuticals

    Increase research on the effects of probiotics and other novel interventions against STEC colonisation and ST production in humans.

    GAPS :

    Possible alternatives for use in animals:

    • Prebiotics, probiotics, synbiotics, postbiotics, phytochemicals, vaccines and topicals etc.

Disease details

  • Description and characteristics

  • Pathogen

    Escherichia coli is a Gram-negative bacterium which is a normal inhabitant of the gastrointestinal tract of humans and animals.

    Most E. coli isolates are harmless commensals, however certain isolates produce potent toxins and are known as Shiga toxin-producing E. coli (VTEC/STEC/EHEC).

    STEC are zoonotic pathogens, which cause severe clinical disease in humans. Ruminants are considered the primary reservoir for STEC, with cattle identified as the primary reservoir.

    STEC are classified into serotypes based on their somatic “O” and flagella “H” antigens. More than 100 different serotypes of E. coli have been identified as STEC, with O157:H7 the most commonly associated with severe human disease.

    Regionally, non-O157 isolates may dominate as human pathogens.

    Importantly, non-zoonotic STEC have been identified as disease-causing organisms in pigs and poultry.

    GAPS :

    • More accurately understand STEC evolution and biology.
    • Establish a definition of Highly virulent (HV) -STEC: identify the minimal virulence factors (genes and inducers thereof) required for causing diseases in humans.
    • Country specific regulations for priority-STEC ?
    • Define the role of “non-LEE” effectors in colonisation and persistence.
    • Tests which may identify non-O157 STEC which are more likely to be associated with disease (e.g., presence of certain virulence genes).
    • Understand if sorbitol fermenting STEC O157 and other pathogenic clones (e.g., O26 ST2+) have a real zoonotic origin.
    • Understand the role of Shiga toxin in persistence.
    • Understand the pathobiology of Super shedders.
    • Explore the dynamics of horizontal gene transfer and AMR.
    • Understand how phylotype influence colonisation/persistence.
    • Understand how metabolic diversity contributes to colonisation/persistence.
    • Understand how STEC influence the gut microflora.
  • Variability of the disease

    STEC can cause a wide spectrum of disease in humans, ranging from mild uncomplicated diarrhoea to severe bloody diarrhoea and haemolytic uraemic syndrome (HUS), a potentially life-threatening condition which is mainly observed in children. The isolates that are most frequently associated with HUS usually harbour the intimin gene (eae), associated with the attaching/effacing mechanism of intestinal adhesion, and belong to a restricted number of serogroups: O157, O26, O101, O111, O145, O121. In addition, eae-negative O91 isolates are frequent in Europe, even if they have been less frequently associated with HUS. In 2011 a LEE negative E. coli O104 was associated with one of the largest outbreaks of human STEC infection.

    STEC are not important animal pathogens: However, some isolates can cause colibacillosis in young calves and isolates producing a porcine variant of the ST cause the oedema disease in pigs. Furthermore, some isolates are associated with swollen head syndrome in poultry.

    Infected adult cattle show no clinical signs. Cattle are the main reservoir, but STEC are common in other ruminants like sheep, goats, water buffalo and wild ruminants) and have also been isolated from other species, including pigs, horses, new world camelids, dogs, chicken, pigeon and wild birds and rodents.

    GAPS :

    • Why is the human disease so variable, and what are the factors influencing this?
    • Prevalence of disease due to STEC is not well known in many countries, especially developing countries STEC diagnosis is difficult and there is a lack of easy, inexpensive detection tests.
    • Specific diagnostics for the non-O157 serotypes mainly associated with disease (O80 is emerging in Europe).
    • What is the role of companion animals in STEC transmission.
    • Further evidence that non-O157 cause a different spectrum of disease
    • What is the role of soil as a reservoir?
    • How do STEC interact with plants and inanimate surfaces?
    • What is the role of wildlife (wild ruminants, rodents) reservoirs?
    • What are the pathogenic mechanisms of LEE-negative STEC causing severe disease?
  • Stability of the agent/pathogen in the environment

    STEC can survive in the environment for extended periods of time. Reports suggest that the organism can survive for more than 90 days in soil. In water, the survival rate is inversely proportional to the temperature and general environmental conditions. Long-term (months to years) survival is reported in manure. The organism also survives in many food products, including highly acidic foods and flour.

    GAPS :

    • How do STEC survive in the soil?
    • How do STEC survive in water?
    • STEC survival in food?
    • What is the role of manure in the maintenance of STEC in the farm environment?
    • How does climate change influence environmental survival.
  • Species involved

  • Animal infected/carrier/disease

    Ruminants, particularly cattle, are the principal reservoir although many other species can be colonised with STEC, including wildlife. STEC are not important animal pathogens: some isolates can cause colibacillosis in young calves and isolates producing a porcine variant of ST cause the oedema disease in pigs and some isolates are associated with swollen head syndrome in poultry. Ruminants harbour STEC O157 and other serotypes without displaying any evidence of disease. However, microscopic changes (attaching and effacing lesions) can be observed in the intestinal tract of many animal species. The recto-anal junction appears to be the main site of O157 colonisation in cattle, but not always in other species.

    GAPS :

    • Better definition of the wildlife reservoirs.
    • Better definition of the role of pet animals?
    • Is there a special genetic background in animals which can be associated with colonisation/infection status?
    • More information on immunity in animals is required.
    • More information regarding the resident microflora at the site of colonisation.
  • Human infected/disease

    STEC can cause a wide spectrum of disease in humans, ranging from asymptomatic carriage to mild uncomplicated diarrhoea, severe bloody diarrhoea and, in children, HUS, HC and TCP.

    GAPS :

    • More information on asymptomatic carriage is required.
    • Relative weighting of contamination from direct ingestion of food/water vs subsequent human-human transmission.
    • Do humans play a role as a potential reservoir for sorbitol fermenting STEC O157 and some STEC non-O157 pathogenic clones?
    • Do humans play a role in the dissemination of non-O157 STEC?
    • Why does the disease primarily affect children and the elderly?
    • Is there a particular genetic predisposition in humans associated with specific disease outcome, namely HUS?
    • The role of past exposure and acquired immunity in relation to disease manifestation are unknown.
  • Vector cyclical/non-cyclical

    STEC are not vector-borne pathogens. However, STEC can be recovered from many different domestic and wild animal species (horses, dogs, flies, rodents), presumably a result of transient infection from ruminant or environmental sources. These animals may act as vehicles of infection to humans. STEC may also be transferred from on species to another by flies.

    GAPS :

    • How about soil dwelling organisms? Earthworms etc.
    • More information on flies as reservoirs required.
  • Reservoir (animal, environment)

    • Ruminants and particularly cattle are the main reservoirs for STEC. STEC O157 and O26 are particularly associated with bovine reservoirs. The organism survives well in the environment.
    • Wildlife may also be important reservoirs.

    GAPS :

    • Lack of knowledge of the role of other species as reservoirs for O157 and non-O157.
    • Lack of knowledge regarding environmental survival.
    • Prevalence in wildlife?
    • Role of companion animals?
    • Role of Protozoa in the persistence in soil/water?
  • Description of infection & disease in natural hosts

  • Transmissibility

    In ruminants, STEC is transmitted via the faecal-oral route. It can spread within the farm by direct contact, contamination of water, feed, environment, and by other animals such as flies and birds. Contamination of feed troughs and ropes can also occur through the saliva. Inter-herd transmission may occur by animal movements, but also via other animals, such as birds and fomites (trucks, equipment).

    STEC can be transmitted to humans with a low infectious dose, and person-to-person transmission does occur. Routes of transmission include ingestion of contaminated foods of animal origin, especially beef and dairy products, water and vegetables contaminated with farm slurry, direct contact with live animals or contaminated animal products (e.g., handling ground beef in the kitchen). Contacts with a contaminated environment (soil, swimming in lakes or pools) also represent a risk.

    GAPS :

    Research on the relative importance of the different routes of transmission:

    • Foods (beef, dairy, fresh produce, flour etc.).
    • Potable water.
    • Direct contact with animals.
    • Environmental spread (e.g., swimming in polluted water).
    • Human to human transmission.
    • Role of vegetables/flour: interaction between bacteria and plant organisms.
    • Role of birds in local and long-distance transmission.
    • Role of fish in transmission, e.g., in Africa.
    • Role of exotic pet trade in the dissemination of STEC?
    • More research on the role of poultry is required.
    • Research on why STEC are mainly present in ruminants. STEC can experimentally be established in pigs, but pigs are not affected/colonised by STEC in the field in many parts of the world except Argentina, where carriage in pigs seems to play a major role.
  • Pathogenic life cycle stages

    Not applicable.

  • Signs/Morbidity

    STEC colonisation in animals is generally asymptomatic, but some animals can excrete large numbers of organisms in their faeces. Other STEC serotypes may cause disease with clinical signs in animals, including dogs, pigs and poultry.

    There is some evidence to suggest HUS occurs in dogs.

    GAPS :

    More information regarding clinical signs in companion animals.

  • Incubation period

    Between 1 and 7 days (typically 2-3) in humans. Not known in animals.

    GAPS :

    • How about non-O157 STEC?
    • How is the incubation period influenced by immunity?
  • Mortality

    No mortality reported in ruminants or other species with STEC O157 or other zoonotic isolates.

  • Shedding kinetic patterns

    The shedding pattern in cattle is usually intermittent, in general much more intense in the warm season. As far as O157 is concerned, most animals excrete 102-103 CFU/g of the faeces. However, a few animals, defined as “super shedders” can excrete 104-105 CFU/g of the faeces, and can remain colonised for longer periods. These “super shedders” might play a major role in maintaining and spreading STEC and could represent the main target of control plans.

    GAPS :

    • Research on the dynamics of colonisation in animals.
    • What factors determine and influence the phenomenon of super shedding (e.g., their genetic background).
    • Distinction between “super shedders” and (transient) “super shedding events” urgently required to better understand the respective impact on epidemiology and to identify intervention options
    • Tools and markers for the identification of super shedding.
    • Knowledge of intestinal colonisation sites and shedding patterns for non-O157.
    • Is there super shedding for STEC non-O157?
    • How does colonisation with non-O157 influence O157 colonisation.
  • Mechanism of pathogenicity

    VT/ST production is the main virulence factor. The isolates that have been consistently associated with HUS usually produce the ST2 variant of the toxin and possess the intimin-coding eae gene, associated with the attaching/effacing (AE) mechanism of intestinal adhesion.

    AE lesions are also observed at the recto-anal junction in cattle and could explain how some animals are colonised more intensely (super shedders).

    GAPS :

    • More information on ST genetic variation and expression and research on the disease potential of the different toxin variants.
    • Knowledge of pathogenicity of intimin-negative STEC associated with disease in humans.
    • Broader studies relating to pathogenesis are required.
    • Hybrid STEC isolates.
    • ST genetic location in context of functional phage influencing ST production levels (how does this vary over ST type?).
    • Machine Learning approaches for designing biomarkers that target priority STEC: Identify factors which by their presence or absence, provide a predictive model for the virulence potential of a STEC isolate.
  • Zoonotic potential

  • Reported incidence in humans

    Surveillance systems are in place in industrialized areas such as Europe, North America, Japan, and Australia. Data are also available for South America, especially Argentina. In the US, the incidence is estimated to be around 100,000 cases per year. The epidemiology of STEC is poorly understood in developing countries. Large community outbreaks associated with ingestion of contaminated food or water are frequently reported. However, most cases are sporadic. Many affected people do not seek medical attention and faecal samples are rarely examined. In most clinical laboratories the methods used for detection are specifically targeted to STEC O157. This means that the presence of the other serotypes often remains undiagnosed.

    GAPS :

    • Better reporting of human infections.
    • Better definition of monitoring (just counting cases) and surveillance (counting cases and in addition intervene) systems.
    • Improved diagnostics approach.
    • Special focus on cases with severe diseases (HUS).
    • Common case definition.
  • Risk of occurence in humans, populations at risk, specific risk factors

    Food at risk includes undercooked ground beef, unpasteurised milk and dairy products made of minimally heat-treated milk, fresh produce (vegetables), and potable water. Infection can be acquired by direct or indirect contact with animals especially cattle, or through contact with water or soil contaminated with ruminants’ faeces. Inter-human transmission frequently occurs (kindergarten outbreaks, etc.).

    Flour has emerged as a food item of concern recently, with the source of contamination unknown.

    GAPS :

    • How about developing countries
    • Children immunocompromised
    • Contamination of vegetables via ruminant faeces
    • Seeds
    • Rice
    • Wheat flour
    • Other vegetables
    • Raw milk and associated products.
    • Contamination of crops through the use of biosolids and reclaimed water.
  • Symptoms described in humans

    STEC can cause a wide spectrum of disease in humans, ranging from mild uncomplicated diarrhoea to severe bloody diarrhoea and, in children, the haemolytic uremic syndrome (HUS). The disease affects all ages with the young and elderly more likely to develop severe illness.

    GAPS :

    • What are the less overt/common clinical signs?
    • Prevalence of asymptomatic shedding in humans.
    • Long term sequelae of STEC infection and after HUS.
    • Timeliness of lab confirmation of STEC infection.
    • Prevalence of eae positive non-STEC isolates in the general population.
  • Likelihood of spread in humans

    As stated above, humans can acquire the infection through a number of different routes. Infection can also spread from person to person due to the low infectious dose, even in settings with acceptable levels of personal hygiene.

    GAPS :

    • Human to human spread.
    • Risk factors for human-human infection?
    • Possible role of humans as a potential reservoir for sorbitol fermenting STEC O157 and some STEC non-O157 pathogenic pathotypes.
  • Impact on animal welfare and biodiversity

  • Both disease and prevention/control measures related


    GAPS :

    STEC could have an impact on biodiversity, as they may have selective advantage in ruminant host gut and thereby reduce Enterobacteriaceae diversity.

  • Endangered wild species affected or not (estimation for Europe / worldwide)


    GAPS :

    Some zoo animals have been affected.

  • Slaughter necessity according to EU rules or other regions

    Not at present.

    A “stamping out” approach could be considered if the role of super shedder animals was confirmed and reliable and feasible methods for the identification of such animals becomes available. However, this option is the subject of debate, since the multiple hosts and the environmental persistence of the organisms could make the “eradication” policy un-effective.

    GAPS :

    • Evaluation of the effectiveness of a super shedder stamping out policy (development of models of in-farm transmission and feasibility studies).
    • Who would compensate the losses due to stamping out?
    • Influence of animal genetics on shedding rate.
  • Geographical distribution and spread

  • Current occurence/distribution

    Worldwide, but there is some evidence that there is variability in the geographic distribution of serotypes involved in human infections.

    GAPS :

    Is the variability in the distribution of STEC serotypes among countries due to a true difference in the epidemiology or is it due to different sensitivities of the surveillance systems in place? A country specific regulation for priority STEC ?

  • Epizootic/endemic- if epidemic frequency of outbreaks

    In animals, endemic. Not Epizootic as animals are carriers.

    In humans, endemic (most cases are sporadic) with frequent outbreaks.

    GAPS :

    • Knowledge of the geographic distribution of the different STEC sero-pathotypes.
    • Source attribution in regions where sporadic cases in humans occur with increased frequencies. These sometimes coincide with cattle-dense areas but source and/or transmission route remains obscure.
  • Speed of spatial spread during an outbreak

    In humans, outbreaks can be associated with foods that are widely distributed to many persons and spread over very large geographical areas.

    Primary epidemiological curve due to food source followed by a second curve mainly driven by human-to-human transmission in large outbreaks.

    GAPS :

    Speed of spread?

  • Transboundary potential of the disease

    Spread via animals, movement of animals and export of contaminated foods, e.g., frozen beef, fruits, vegetables.

    Clean animals prior to slaughter.

    In the abattoir - tie of rectum post euthanasia.

  • Route of Transmission

  • Usual mode of transmission (introduction, means of spread)

    See section “Description of Colonisation/ infection & disease in natural hosts > Transmissibility”.

    GAPS :

    • Better understanding of specific risk factors for sporadic vs epidemic cases
    • Role of human asymptomatic carriers.
    • Role of rodents or birds.
  • Occasional mode of transmission

    See section “Description of Colonisation/ infection & disease in natural hosts > Transmissibility”.

  • Conditions that favour spread

    The presence of STEC on a farm may not be associated with poor hygiene and management, which conversely have an important role in the following steps of the food chain for transmission to humans.

    STEC isolates from cattle show different degrees of adaptation to the host versus the environment in terms of metabolism and biofilm formation.

    GAPS :

    • Inter and intra farm spread of individual isolates: here is a critical gap in knowledge on 1) how the organism is spread between one farm to the other and 2) how animals are exposed within a single farm. This framework provides two complementary approaches to mitigation design.
    • Specific: role of wet litter, breed of animal, stocking density, stress levels, feed etc.
    • Role of different STEC phenotypes in driving epidemiology on farm and at the environment-farm and animal-human interfaces not yet understood.
  • Detection and Immune response to infection

  • Mechanism of host response

    The immune response varies. In humans, STEC colonisation/infection results in the production of antibodies against the toxin, intimin and other factors involved in adhesion, and the O serogroup-specific LPS antigen. The immune response in animals has been less investigated: cattle develop anti-O157 antibodies, but rarely anti-ST antibodies. Anti-ST1 antibodies are more frequent than anti-ST2. Young cattle, even though colonised by STEC from the first weeks of life onwards, only develop anti-ST titres at an age of 2 years, i.e., close to giving birth to the next generation.

    GAPS :

    • Immune response in animals, particularly to bacterial structures involved in colonisation (flagella, intimin, exported proteins, non-LEE encoded effectors) and could represent vaccine components.
    • Influence of host metabolism in the gut on ruminant colonisation.
    • Influence of STEC metabolism on colonisation.
  • Immunological basis of diagnosis

    LPS-antibodies detection is used for diagnosis of human infections.Serology is not used for diagnosis in animals.Anti-O157 antibodies cross-react with Yersinia and Brucella LPS.

    GAPS :

    Other specific / protective surface antigens should be identified and could be used in diagnostics.

  • Main means of prevention, detection and control

  • Sanitary measures

    Although many sanitary interventions have been proposed, none have proven to significantly impact O157 carriage in cattle. High cattle density on farms is associated with increased O157 prevalence.

    GAPS :

    • For farm visitors, public education, even on basic procedures such as hand washing.
    • Better knowledge of the general ecology of STEC with investigation on so far unknown habitats / host.
    • Development of indicators for cost efficiency of the measures.
    • Influence of milking hygiene and equipment on milk contamination.
  • Mechanical and biological control

    Control the spread within the farm.

    Use of probiotics may help.

    Bacteriophages to control colonisation/infection are under development.

    Vaccine (see below).

    Cleaning animals at the abattoir to avoid hide contamination.

    GAPS :

    • Need to understand how probiotics provide protection.
    • Better understand the immune response and vaccination.
    • Increased research on phage therapy, including biosafety issues and the dynamics of phage resistance.
  • Prevention through breeding

    Some breeds may be more susceptible.

    GAPS :

    More research into breed susceptibility required to determine if breed influences susceptibility.

  • Diagnostic tools

    In general, the laboratory tools for STEC O157 detection are adequate, while those for STEC Non-O157 detection are poor.

    Human infections: methods should aim at identifying any STEC in peoples with disease, to understand if changes in the serotypes causing disease, occur over time.

    STEC isolation and identification (DNA based).

    Detection of free ST in faeces (Vero cells, immunologically based kits – available commercially)

    Serologic diagnosis (detection of LPS antibodies).

    Food and animal faeces : STEC that are presumably poorly virulent to humans are abundant, so the methods should be targeted to the serogroups most associated with human disease. Good tools (cultural, molecular, immuno-detection) are available for the detection/isolation of STEC O157. Efforts are ongoing for the development of PCR/LAMP-based methods to detect the other pathogenic serogroups (e.g. O26, O103, O111, O145, O104).

    GAPS :

    • Possible use of arrays combining targets in pathogenic STEC, mainly virulence genes.
    • Development of effective (cheap, easy and fast) diagnostic tools to identify these types,
    • New diagnostic media.
    • What are the bacterial numbers of non-O157 serotypes in the intestine of carrier animals.
    • Is enrichment required to detect them and are the enrichment conditions the same for each of the serotypes.
    • Determine human risk (disposition) of foods contaminated with non-O157 STEC.
  • Vaccines

    Experimental vaccines to control the colonisation of cattle with STEC O157 have been developed, but their efficacy is still controversial.

    A vaccine directed against type III secreted proteins has obtained licensing approval from the Canadian Food Inspection Agency. Another product which targets bacterial surface proteins and protein receptors involved in iron uptake. has recently obtained a conditional approval by the U.S. Department of Agriculture.

  • Therapeutics

    In cattle, neomycin administration is effective at eliminating most O157 in cattle, but its use is unacceptable because of the possibility of promoting antibiotic resistant organisms.

    Use of antimicrobial growth promoters is not effective and may increase STEC O157 excretion (these are now banned in the EU and many other countries).

    Administration of sodium chlorate immediately pre-harvest is effective at reducing many Gram-negative facultative anaerobes (including E. coli O157) from the gastrointestinal tract of ruminants.

    In humans, antimicrobial therapy is controversial and may be contraindicated due to a possible increase in the release of ST in the gut. During human outbreaks, testing the isolates incriminated for response to antimicrobials in terms of ST production and release has impacted on antibiotic stewardship recommendations in time.

    GAPS :

    • Could antimicrobials be used in ruminants? Topical applications?
    • Research on possible tools to block toxin production by STEC isolates in the human gut.
    • Alternatives to antibiotics (phage etc.).
  • Biosecurity measures effective as a preventive measure

    The low infective dose for humans requires care in handling animals.

    Good food hygiene is essential to prevent zoonotic transmission.

    Also, care is required in handling cultures and samples in the laboratory and during transport between laboratories and countries.

    GAPS :

    • Foot dips, clean ropes, good manure management.
    • Feeding and water supply.
    • Changes in farm management, e.g., separation of animals.
    • Procedures of animal husbandry which would mitigate the risk of contamination of environment (e.g., correct manure management) and products.
    • Risk communication to consumers.
    • Hygiene concepts for visitors to farms including petting zoos mandatory but not known or strictly applied on many premises.
  • Border/trade/movement control sufficient for control

    None in place for animals, as carrier animals may be intermittent excretors of STEC.

    Movement of STEC isolates, cultures and positive samples across borders is very restricted for some countries. Movement of cultures by air transport is restricted, as STEC are considered Category A by IATA.

    Movement of foods such as meat may require negative testing for entry into some countries.

  • Prevention tools

    Appropriate handling of manure and slurry, to reduce the levels of STEC in the environment.

    The abattoir, to reduce the carcass contamination rate.

    Trimming, washing and steam pasteurization of carcasses.

    Processing and retail, to reduce food contamination rate.

    Consumer sanitation and hygiene to prevent cross-contamination and adequate cooking of foods.

    Good Agricultural Practices in vegetable production (water quality, manure application, worker hygiene, sanitation).

    Implementation of Risk assessments.

    Water chlorination (or just focus on water quality).

    Personal hygiene following animal contact. Hygiene concepts for visitors to farms including petting zoos and respective counter-measures (disinfection dispensers etc.) mandatory.

    GAPS :

    • Influence of slaughter practice: transport, lairage, clean animals, isolation of rectum and faeces etc.
    • Effects of different feeding and water supply strategies.
    • Effects of prebiotics on the intestinal contents of animals.
    • Consumer education.
    • Better risk assessments for non O157 STEC.
  • Surveillance

    Passive? surveillance in animals, through examination of faecal samples collected on farm or during surveys at the abattoir.

    Surveillance of human infections to promptly detect outbreaks and to follow the trend of serotypes and virulotypes. Some regions have active surveillance programs.


    Practical approaches for the implementation of intervention measures against STEC carriage and shedding in animals are required.If counter-measures with acceptable cost-benefit profiles become available:

    • More surveillance activities are required.
    • Improve diagnostic procedures and diagnostic availability.
    • Evaluation of the use of sentinel animals.
    • Need of harmonisation of surveillance activities in animals and humans, including molecular typing.
    • Refinement of the current surveillance activities is recommended.
  • Past experiences on success (and failures) of prevention, control, eradication in regions outside Europe

    Prevention of colonisation in livestock is difficult. Irradiation of foods is the only assured way to remove/eliminate the pathogen from products, but it may present social acceptance challenges.

    Probiotics are used widely in the US.

    Livestock vaccination attempts and phage therapy are still in the experimental stages.

    Most efforts have been made on ensuring that food and water are not contaminated with STEC from cattle faeces.

    GAPS :

    • Removal of super shedders.
    • Ensure animals receive colostrum (evidence to suggest colostrum deprivation increases O157 colonisation).
    • Role of pre-disposing colonisation (BIV, Cryptosporidium etc.).
  • Costs of above measures

    Surveys are expensive, and testing cannot ensure food safety as re-infection/colonisation occurs readily.

    An effective pre-harvest intervention could be cost-effective, even if cost-effectiveness is difficult to evaluate, as there is no disease in animals to measure.

    Contamination may be sporadically located on hides or carcasses, and prevention will be critical.

    It must be considered that any intervention will likely increase the cost of production to the farmer.

    GAPS :

    Modelling the cost/benefit of control measures in term of reduction of the burden of STEC infections in humans.

  • Disease information from the WOAH

  • Disease notifiable to the WOAH


  • WOAH disease card available


  • WOAH Terrestrial Animal Health Code


  • Socio-economic impact

  • Zoonosis: impact on affected individuals and/or aggregated DALY figures

    Most affected people recover in 5 to 10 days. However, long term sequelae may occur in children with HUS, who may develop chronic renal failure.

    GAPS :

    • Better definition of HUS rate and socio-economic costs.
    • Long term sequelae studies.
  • Zoonosis: cost of treatment and control of the disease in humans

    Cases of severe disease are often hospitalised, especially children and elderly people. HUS is major public health concern in many countries. In the acute phase it often requires prolonged hospitalisation and dialysis, and can result in acquired chronic renal failure and the need for kidney transplantation. Consequently, the costs of medical treatment are substantial.

    GAPS :

    Estimation of the burden of STEC infections, including costs, in population is only available for a few countries.

  • Direct impact (a) on production


  • Direct impact (b) cost of private and public control measures

    Surveys on farms and at abattoir are expensive, as well as the tests performed on food both as official controls or own checks.

  • Indirect impact

    The large outbreaks have had serious consequences on the agri-food industry. In the US, fast food operations had a crisis after the outbreaks occurring between the end of the 1980s and the 1990s. Other outbreaks (spinach, seeds) have resulted in reduced consumption of the respective produce.

    In certain countries, petting zoos and dairy or other farms receiving visitors are tested for O157 and may be shut down when it is detected.

  • Trade implications

  • Impact on international trade/exports from the EU

    No specific international standards for control of STEC. No mention in the OIE Terrestrial Animal Health Code.

  • Impact on EU intra-community trade

    As for other foodborne pathogens.

  • Impact on national trade

    As for other foodborne pathogens.

  • Main perceived obstacles for effective prevention and control

    Many reservoir hosts, many routes of transmission, the persistence of environmental contamination represent the primary obstacles for control. E. coli are dynamic organisms which are continuously evolving. Vaccination, if effective, is currently restricted to VTEC O157.

    Socio-economic problems related with interventions:

    • costs to farmers and disagreement as to who should bear the cost: farmers, food industry, consumers public support.
    • consumer acceptance of interventions (irradiation, GMOs, phages, etc.).


    • The potential of vaccines in the control of VTEC (all the pathogenic serotypes) should be further evaluated.
    • Research on phages as a control tool.
    • Lack of awareness of farmers about the risks for public health associated with VTEC.
    • Lack of awareness of consumers the risks associated with VTEC.
  • Links to climate

    Seasonal cycle linked to climate

    There is a summer peak in both the prevalence of cattle colonisation and the incidence of human disease. However, animal and human colonisation/infection can occur any time of the year.

    GAPS :

    • Is this true worldwide?
    • Need to better define if seasonality is a change in magnitude of shedding (and therefore increased sensitivity of detection, hence increase prevalence) or a true increase in prevalence.
  • Distribution of disease or vector linked to climate

    Houseflies are implicated in transmission in animal barns.

    GAPS :

    Does climate change and shifts in insect populations and higher insect burden in livestock husbandry, especially in temperate zones, affect transmission probabilities of zoonotic pathogens incl. STEC in livestock production and to humans?

  • Outbreaks linked to extreme weather

    Heavy rainfall may facilitate sewage systems overflow and the spread of ruminant manure in the environment and may also affect the efficiency of drinking water filtration systems. Some important waterborne outbreaks have occurred after heavy rainfalls. Muddy conditions in livestock pens may increase prevalence and subsequent increase in carcass contamination at harvest.

    GAPS :

    Impact of global warming/more extreme weather (precipitation, temperature, flooding etc.).

  • Sensitivity of disease or vectors to the effects of global climate change (climate/environment/land use)

    Houseflies are implicated in transmission in animal barns.

  • Main perceived facilitators for effective prevention and control

    Better funding.

    Risk assessments for non-O157 STEC.

    Government support.

    Retailer support.Support from pharmaceutical companies.

Global challenges

  • Antimicrobial resistance (AMR)

  • Mechanism of action

    Multiple – ampicillin, neomycin, tetracycline, streptomycin, kanamycin, trimethoprim, chloramphenicol, spectinomycin and sulphonamides.

    GAPS :

    Better comparative genomic studies to understand the distribution of AMR genes in STEC.

  • Conditions that reduce need for antimicrobials

    Antibiotics are not used to treat STEC infections in humans.

    GAPS :

    Reducing the use of antibiotics in animals through the use of alternatives and better antibiotic stewardship will reduce the prevalence of AMR in STEC.

  • Alternatives to antimicrobials

    Multiple alternatives available.

    GAPS :

    Alternatives need to be validated in a clinical setting.

  • Impact of AMR on disease control

    Antibiotics are contraindication in human infections. However, some STEC infections in animals may be untreatable due to AMR.

    GAPS :

    Need more studies to understand the prevalence of AMR in disease causing STEC in animals.

  • Established links with AMR in humans

    AMR STEC isolates from animals may be transmitted to humans.

    GAPS :

    A better understanding of the epidemiology of AMR in STEC is required. A better understanding of how AMR influences STEC fitness is also required.

  • Digital health

  • Precision technologies available/needed

    Use of AI for the prediction and detection of STEC on farms. AI could also be used to model Super-shedders.

    GAPS :

    More research into how AI can be used to detect and control STEC is required.

  • Data requirements

    Good databases available.

    GAPS :

    Better shared databases required.

  • Data availability

    Most data is accessible.

    GAPS :

    Open access to sequences and metadata.

  • Data standardisation

    Only some data is standardised.

    GAPS :

    Use of standardised databases.

  • Climate change

  • Role of disease control for climate adaptation

    Changes in climate may result in different geographical distribution of STEC in reservoir hosts.

    GAPS :

    More research into the influence of climate on STEC prevalence is required.

  • Effect of disease (control) on resource use

    • Vaccination of reservoir hosts can be costly.
    • Investigation of disease outbreaks in humans can be costly.

    GAPS :

    • More funding for scanning surveillance required.
    • Link between climate and STEC colonisation/infection.
  • Effect of disease (control) on emissions and pollution (greenhouse gases, phosphate, nitrate, …)

    • Controls that modulate the gut flora may also result in benefits regarding gas emissions.
    • Production of interventions requires careful though regarding the environment and sustainability.

    GAPS :

    • Consider novel sustainable feed sources for ruminants that may reduce STEC colonisation.
    • More research into the sustainable and environmentally friendly production of interventions such as vaccines.
  • Preparedness

  • Syndromic surveillance

    Only applicable to humans as zoonotic STEC do not generally cause clinical disease in animals.

  • Diagnostic platforms

    LAMP and direct sequencing assays available.

    GAPS :

    Validation of LAMP assays urgently required – More widespread use of direct sequencing.

  • Mathematical modelling

    A number of studies have been conducted using mathematic modelling to study STEC dynamics in reservoir hosts.

    GAPS :

    More funding for mathematical modelling required.

  • Intervention platforms

    Vaccines are available, but of limited efficacy to mitigate STEC shedding.

    GAPS :

    More research into novel vaccines and their integration in to-be-developed control strategies at farm level required.

  • Communication strategies

    Good communication strategies have been used to educate the public about STEC on petting farms and in raw meeting, but more could be done.

    GAPS :

    Better social media communication channels and linkage to large EU/US consortia such as the OHEJP.

Main critical gaps

  • Better data on STEC prevalence.

    Urgent need for novel interventions.

    Better understanding of the role of the microflora on STEC colonisation.

    Urgent need for better diagnostics.

    Better understanding of the immune response to non-O157 STEC required.


  • Surveillance systems must provide updated information on the STEC serogroups causing human infections. These will represent the targets for control activities in animals and food.A better knowledge of the mechanisms of the pathogenesis of infection in humans and of colonisation in livestock is required to identify the most suitable targets for diagnostics and vaccines.

    GAPS :

    • Need more info on genetics/phenotype and environmental survival.
    • Need of better surveillance and data on human infections.
    • Need of better risk communication strategies to consumers.
    • Need for better genomic and phenomics data bases for STEC.

Sources of information

  • Expert group composition

    Roberto La Ragione - University of Surrey, UK - [Leader]

    Andrew Roe - University of Glasgow, UK

    Stefano Morabito - ISS, Italy

    Jenny Ritchie - University of Surrey, UK

    Christian Menge – FLI, Germany

  • Date of submission by expert group

    December 2022