Diseases

E. coli

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Control Tools

  • Diagnostics availability

  • Commercial diagnostic kits available worldwide

    Many kits are available for detection and identification of VTEC. Some are specific for human infections, other are specifically developed for food analyses. See also section [Main means for prevention, detection and control].

    GAP:

    Generally, need for  better detection assays for non-O157.

  • Commercial diagnostic kits available in Europe

    Kits are available in Europe.

  • 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 EU. A PCR-based technical specification for the detection of the main non-O157 serogroups in food is in the process to be approved by ISO. These methods can be adapted for the analysis of animal faeces. LAMP assays are now available for E. coli.

    GAPS

      • An internationally accepted standard for detection of O157 and VTEC in (animal) faeces and 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.
      • ISO and CEN are mainly operating at the EU level, what about non-European countries?
      • Development of methods in the OIE framework.
      • Pen-side tests
      • Diagnostic method(s) described by International, European or National standards

        The immuno-magnetic concentration-based method ISO16654 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 is in the process to be approved by ISO. The OIE Terrestrial Animal Health Code and an EFSA guideline for monitoring of VTEC in animals published in 2009 describe how to adapt these methods to animal faeces. See also section [Main means for prevention, detection and control] and [Diagnostic kits validated by National or Internation Standards]. LAMP assays are now available for VTEC – Detection in 15 minutes.

      • Commercial potential for diagnostic kits in Europe

        Many diagnostic kits already available for the detection of VTEC O157, VT production and vtx genes. Tests targeting the main non-O157 pathogenic serogroups are urgently required. ELISA based tests are less sensitive than culture/PCR but faster.

        GAPS:

          • Find new unique genetic markers that can identify highly pathogenic VTEC.
          • Multi-target, DNA based screening of enrichment broths are hampered by the fact the identified markers may not be present in the same bacterial strain. E.g. eae is widespread in other bacteria than VTEC.
          • Development of Arrays, Identibac  nano arrays.
          • Development of NGS platforms.
          • Development of LAMP assays and lateral flow assays.
          • DIVA tests required and/or available

            Not applicable presently, although a vaccine is available now.

            GAP:

            If attenuated vaccines are developed, the vaccine strains must be discriminated from the field strains.

            Only commercial vaccines are based on secreted proteins.

          • Opportunities for new developments

            Easy and rapid tests targeting the main non-O157 pathogenic serogroups are urgently required.

            GAP:

            This represents a critical gap.

            • Array platforms, new media through testing isolates in phenotypic assays such as the Biolog?
            • Development of standard methods for non-O157 in foods.
          • Vaccines availability

          • Commercial vaccines availability (globally)

            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.

            GAPS:

              • Who will pay for the vaccine?
              • Will it protect against other VTEC
              • Use of NGS to inform on the development of rapid assays such as LAMP.
              • Commercial vaccines authorised in Europe

                None for VTEC. Available for colibacillosis. Bioniche vaccine available for O157?

              • Marker vaccines available worldwide

                None.

              • Marker vaccines authorised in Europe

                None.

              • Effectiveness of vaccines / Main shortcomings of current vaccines

                The efficacy of the available vaccines against VTEC O157 has still to be fully evaluated. The efficacy against other VTEC serotypes is unknown.

                GAPS:

                In general, more research is required. We don’t know enough about colonization and mucosal immunity to an otherwise commensal organism to understand which aspects of colonization would be best targeted.

              • Commercial potential for vaccines in Europe

                Since cattle are asymptomatic there is little demand from farmers. Vaccination of feedlot calves could be required by companies purchasing the meat. In Member States where selling raw milk is allowed, the involved dairy farms would have a strong interest in vaccination.

                GAPS: 

                  • Who would pay for the vaccine?
                  • Define public health strategies.
                  •  How would the vaccine be administered? Frequency?
                  • 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.

                    GMO E. coli vaccine for poultry recently launched by ZOETIS?

                    GAPS:

                      • Possibility of knockout live vaccine strains?
                      • Regulatory testing for approval of biological products in animals is usually based on efficacy to prevent manifestation of disease. As VTEC do not cause disease, different parameters, such as prevention of colonisation, have to be used, and regulatory agencies have less experience with these.
                      • Commercial feasibility (e.g manufacturing)

                        Feasible to produce but depends on demand.

                      • Opportunity for barrier protection

                        Herd vaccination would be practical in an attempt to reduce infection 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.

                        GAP:

                        Investigate whether vaccination of cattle prior to slaughter is a way to reduce the influx of VTEC into the abattoir.

                      • Opportunity for new developments

                         The development of vaccines against non-O157 or the evaluation of the efficacy of the existing O157 vaccines against the main non-O157 pathogenic serogroups (some of the components can be in common with other serogroups).

                      • Pharmaceutical availability

                      • Current therapy (curative and preventive)

                        In humans, antibiotic therapy is not recommended. Only supportive therapies.

                        No therapy for animals.

                      • Future therapy

                        For reducing colonization and carriage in animals:

                        • Multivalent vaccines
                        • Probiotics
                        • Bacteriophages

                        GAPS:

                          • Pre-biotics, modulation of the gut flora.
                          • Synbiotic, 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 VTEC infection in humans and the need to reduce infection in cattle.

                          • Regulatory and/or policy challenges to approval

                            None.

                          • Commercial feasibility (e.g manufacturing)

                            None.

                          • Opportunities for new developments

                            Development of probiotics for preventing or reducing animal colonization.

                          • New developments for diagnostic tests

                          • Requirements for diagnostics development

                            Rapid tests to identify cattle infected with pathogenic VTEC.

                            Tests for the detection of the main non-O157 serogroups pathogenic to humans in food and animals.

                            Time and costs should be contained.

                            GAPS:

                            • Development of testing strategies.
                            • Knowledge of virulence factors or other gene sequences which differentiate pathogenic and non-pathogenic VTEC. 
                          • Time to develop new or improved diagnostics

                            Depending on when a new candidate vaccine could 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.

                            American data on O157 vaccination in feed lot cattle: there is a prompt immunological reaction, and a decrease in the shedding is also observed. The effects of the vaccines ceases after 2-3 months.

                          • 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 needed. Once validated, a commercial company willing to market the test will be needed.

                            GAP:

                            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.

                             

                          • Research requirements for new or improved diagnostics

                          • Increase knowledge on pathogenesis and involved virulence factors.
                          • Better understanding of VTEC genomics. 
                          • Increased knowledge on immune response.
                          • GAPS:

                              • Increased knowledge about colonization factors in healthy animals. Why VTEC in ruminants and not e.g. pigs.
                              • Better understanding of gut microbial ecology.
                              • Use of metagenomic studies to improve our understanding of why some animals are more susceptible than others?
                              • See also section [Requirements for diagnostics development]
                              • 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 VTEC serogroups).

                                GAPS:

                                See section [Requirements for diagnostic development].

                              • Time to develop new or improved vaccines

                                Depending on when a new candidate vaccine could 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.

                                American data on O157 vaccinaiton in feed loot cattle: there is a prompt immunological reaction, and a decrese in the shedding is also observed. The effects of the vaccines ceases after 2-3 months.

                                GAPS:

                                • How about topical rectal applications?
                                • Investigate whether vaccination of cattle prior to slaughter is a way to reduce the influx of VTEC into the abattoir.
                                • Rapid pen-side tests at the abattoir? LAMP/Lateral flow?
                              • 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 wells as the evaluation of the results. Since there is no disease, these will be expressed by measuring the VTEC shedding.

                              • Research requirements for new or improved vaccines

                                Increased knowledge on the colonization of cattle gut by VTEC.

                                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 VTEC colonization.

                                Development of bacteriophages which have a wide spectrum of specificity for pathogenic VTEC serotypes, and which are active in vivo in the gut.

                                GAPS:

                                Prebiotics, probiotics, synbiotics, phytochemicals topicals, vaccines? Bedding treatments 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 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.

                              • Research requirements for new or improved pharmaceuticals

                                Increase research on the effects of probiotics against VTEC colonization.

                                GAPS:

                                Prebiotics, probiotics, synbiotics, phytochemicals, vaccines and topicals.

                              Disease details

                              • Description and characteristics

                              • Pathogen

                                Escherichia coli is a Gram negative bacterium which is normally inhabitant of the gastrointestinal tract of humans and animals. Most E. coli strains are harmless commensals, however certain strains produce potent toxins and are known as verocytotoxin (Shiga toxin)-producing E. coli (VTEC/STEC/EHEC). VTEC are zoonotic pathogens, which cause severe clinical disease in humans.  Ruminants are considered the primary reservoir for VTEC, with cattle playing the largest role.

                                Strains of E. coli 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 VTEC, with O157:H7 as the serotype most commonly associated from severe human disease. Importantly, non-zoonotic VTEC have been identified as diseases causing organisms in pigs and chickens.

                                GAPS: 

                                  • More accurately understand VTEC evolution and biology.
                                  • Establish a definition of Highly Pathogenic (HP) -VTEC: identify the minimal virulence factors (genes and inducers thereof) required for causing diseases in humans.
                                  • Define the role of “non-LEE” effectors.
                                  • 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 VTEC O157 and other pathogenic clones (e.g. O26 VT2+) 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.
                                  • Variability of the disease

                                    VTEC 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 strains 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 strains are frequent in Europe, even if they have been less frequently associated with HUS. In 2011 a non-LEE positive E. coli O104 was associated with one of the largest outbreaks of human VTEC infection.

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

                                    In the case of VTEC O157, infected cattle show no clinical signs. Cattle are the main reservoir, but VTEC are common in other ruminants sheep, goats, water buffalo and wild ruminants) and have also been isolated from other species, including pigs, horses, dogs, chicken, pigeon and wild birds. 

                                    GAPS:

                                      • Why is disease so variable, and what are the factors influencing this?
                                      • Prevalence of disease due to VTEC is not well known in many countries, especially developing countries VTEC diagnosis is difficult and there is a lack of easy, inexpensive detection tests.
                                      • Specific diagnostics for the non-O157 serotypes mainly associated with disease.
                                      • What is the role of companion animals in VTEC transmission.
                                      • What is the role of soil as a reservoir?
                                      • How do VTEC interact with plants and inanimate surfaces?
                                      • Stability of the agent/pathogen in the environment

                                        VTEC 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 rate survival 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.

                                        GAP:

                                        • How do VTEC survive in the soil?
                                        • How do VTEC survive in water?
                                        • What is the role of manure in the maintenance of VTEC in the farm environment?
                                      • Species involved

                                      • Animal infected/carrier/disease

                                        Ruminants, particularly cattle, are the principal reservoir although many other species can be colonised with VTEC, including wild-life. VTEC are not important animal pathogens: some strains can cause colibacillosis in young calves and strains producing a porcine variant of VT cause the oedema disease in pigs and some strains are associated with swollen head syndrome in poultry. Ruminants harbour VTEC 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 colonisation in cattle, but not other species.

                                        GAPS:

                                          • Better definition of the wild-life reservoirs.
                                          • Better definition of the role of pet animals.
                                          • Is there a special genetic background in animals which can be associated with infection status?
                                          • More information on immunity in animals.
                                          • Human infected/disease

                                            VTEC 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.
                                              • Do humans play a role as a potential reservoir for sorbitol fermenting VTEC O157 and some VTEC non-O157 pathogenic clones?
                                              • Do humans play a role in the dissemination of non-O157 VTEC?
                                              • Why does the disease primarily affect children?
                                              • 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

                                                VTEC are not vector-borne pathogens. However, VTEC 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. VTEC may also be transferred from on species to another by flies.

                                                GAP:

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

                                                Ruminants and particularly cattle are the main reservoirs for VTEC. VTEC O157 and O26 are particularly associated with bovine reservoirs. The organism survives well in the environment.

                                                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 wild-life? Role of companion animals?
                                                  • Description of infection & disease in natural hosts

                                                  • Transmissibility

                                                    In ruminants, VTEC has a very low infectious dose and it 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).

                                                    The infection 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 etc.),  water, direct contact with animals, environmental spread (e.g. swimming in polluted water), human to human transmission.
                                                      • Role of vegetables: 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 VTEC?
                                                      • More research on the role of poultry is required.
                                                      • Research on why VTEC are mainly present in ruminants. VTEC can experimentally be established in pigs, but pigs are not affected/colonized by VTEC in the real world. Or perhaps pigs are a source like described in Chile?
                                                      • Pathogenic life cycle stages

                                                        Not applicable.

                                                      • Signs/Morbidity

                                                        Most VTEC infections in animals are asymptomatic, but some animals can excrete large numbers of organisms in their faeces. Other VTEC serotypes may cause disease with clinical signs in animals (see point 2.1), including dogs. Some evidence to suggest HUS in dogs?

                                                        GAP:

                                                        More information regarding clinical signs in companion animals.

                                                      • Incubation period

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

                                                        GAP:

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

                                                        No mortality reported in ruminants with VTEC O157

                                                      • Shedding kinetic patterns

                                                        Data are available for VTEC O157 only, and mainly in cattle. The shedding pattern is usually intermittent, in general much more intense in the warm season. 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 colonized for longer periods. These “super shedders” might play a major role in maintaining and spreading the infection and could represent the main target of control plans.

                                                        GAPS:

                                                          • Research in the dynamics of infection in animals.
                                                          • What factors determine and influence supper shedding (e.g. their genetic background).
                                                          • Tools and markers for the identification of super shedders.
                                                          • Knowledge of intestinal colonisation sites and shedding patterns for non-O157.
                                                          • Are there super shedders for VTEC non-O157?
                                                          • How does colonisation with non-O157 influence O157 colonisation.
                                                          • Mechanism of pathogenicity

                                                            VT/ST production is the main virulence factor. The strains that have been consistently associated with HUS usually produce the VT2 variant of the toxin and posses the intimin-coding eae gene, associated with the attaching/effacing (AE) mechanism of intestinal adhesion. AE lesions are also observed at recto-anal junction in cattle and could explain how some animals are colonized more intensely (super-shedders).

                                                            GAPS:

                                                              • More information on VT genetic variation and expression and research on the diseases potential of the different toxin variants.
                                                              • Knowledge of pathogenicity of intimin-negative VTEC associated with disease in humans.
                                                              • Role of the subtilase cytotoxins.
                                                              • 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 VTEC infection is poorly known 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 VTEC 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).
                                                                  • HUS: how important are the cases associated with non-O157 infections.
                                                                  • 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.).

                                                                    GAPS:

                                                                    • How about developing countries?
                                                                    • Children immune-compromised?
                                                                    • Contamination of vegetables via ruminant faeces.
                                                                    • Risk associated with seeds and rice.
                                                                  • Symptoms described in humans

                                                                    VTEC 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 clinical signs?
                                                                      • Prevalence of asymptomatic shedding in humans.
                                                                      • Long term sequelae of VTEC infection and after HUS
                                                                      • Timeliness of lab confirmation of VTEC infection
                                                                      • Estimated level of under-reporting in humans

                                                                        In most countries, high level of underreporting, especially for the uncomplicated cases, since the patients do not seek medical attention. Many clinical laboratories do not look for VTEC. Other laboratories only use methods that are specific for O157 and are unable to identify the presence of other VTEC serotypes.

                                                                        GAPS:

                                                                        • Need for better tools to diagnose all VTEC.
                                                                        • Need for better awareness of General Practitioners to recognize patients with symptoms consistent with VTEC infection. 
                                                                      • Likelihood of spread in humans

                                                                        Humans can acquire the infection by different ways. 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.
                                                                        • Possible role of humans as a potential reservoir for sorbitol fermenting VTEC O157 and some VTEC non-O157 pathogenic clones? 
                                                                      • Impact on animal welfare and biodiversity

                                                                      • Both disease and prevention/control measures related

                                                                        None.

                                                                        GAP: VTEC 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)

                                                                        No.

                                                                        GAP:

                                                                        Have some zoo animals 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 object 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?).
                                                                          • 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 VTEC serotypes among countries due to a true difference in the epidemiology or is it due to different sensitivities of the surveillance systems in place?

                                                                             

                                                                          • 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 VTEC sero-pathotypes

                                                                          • Seasonality

                                                                            There is a seasonal trend for colonisation of cattle in the summer and this is reflected in the peak incidence of disease in the human population which also occurs in the summer months. However, cattle may become colonized at any time of the year or under diverse environmental conditions.

                                                                            There may be seasonal outbreaks when pastured cattle die during drought and subsequent heavy rains result in contamination of surface waters, as occurred in southern Africa.

                                                                            GAPS:

                                                                              • More information on epidemiology required, especially on pathogenic non-O157 in animals.
                                                                              • Understanding what modulates the seasonality of infection in cattle is critical for designing control strategies.
                                                                              • 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.

                                                                                GAPS:

                                                                                Speed of spread? How fast?

                                                                                 

                                                                              • Transboundary potential of the disease

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

                                                                                GAP:

                                                                                Refine trade, try to develop production system that reduce animal transport.

                                                                              • Seasonal cycle linked to climate

                                                                                As stated above, there is a summer peak in both the prevalence of cattle colonization and the incidence of human disease. However, animal and human infections can occur any time of the year. See above.

                                                                                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 increased apparent prevalence) or a true increase in prevalence. 
                                                                              • Distribution of disease or vector linked to climate

                                                                                No.

                                                                              • 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.

                                                                                GAP:

                                                                                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)

                                                                                No.

                                                                              • Route of Transmission

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

                                                                                See section [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 [Transmissibility]
                                                                              • Conditions that favour spread

                                                                                The presence of VTEC O157 in a farm may not depend on poor) hygiene and management, which conversely have an important role in the following steps of the food chain for transmission to humans.

                                                                                GAPS:

                                                                                • Inter and intra farm spread: here is a critical gap in knowledge on 1) how he 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, feed.
                                                                              • Detection and Immune response to infection

                                                                              • Mechanism of host response

                                                                                The immune response varies. In humans, VTEC 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-VT antibodies.

                                                                                GAPS:

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

                                                                                    GAP:

                                                                                    Other specific / protective surface antigens should be identified and could 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 among 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 VTEC 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

                                                                                        To control the spread within the farm:

                                                                                        • Use of probiotics may help.
                                                                                        • Bacteriophages to control infections are under development
                                                                                        • Vaccine (see below)

                                                                                        GAPS:

                                                                                        • Need to understand how probiotics provide protection.
                                                                                        • Better understand immune response and vaccination.
                                                                                        • Increased research on phage therapy, including bio-safety issues and the dynamics of phage resistance.
                                                                                      • Diagnostic tools

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

                                                                                        Human infections: methods should aim at identifying any VTEC in peoples with disease, to know if changes in the serotypes causing disease occur over time. Good tools are available:

                                                                                        • VTEC isolation and identification (DNA based)
                                                                                        • Detection of free VT in faeces (Vero cells, immunologically based kits – available commercially)
                                                                                        • Serologic diagnosis (detection of LPS antibodies)
                                                                                        Food and animal faeces: VTEC 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 VTEC O157. Efforts are presently made for developing PCR-based methods to detect the other pathogenic serogroups (O26, O103, O111, O145, O104).

                                                                                        GAPS:

                                                                                          • Possible use of arrays combining targets in pathogenic VTEC, 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 VTEC.
                                                                                          • Vaccines

                                                                                            Experimental vaccines to contrast the colonization of cattle with VTEC 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 complicated by the possibility of promoting antibiotic resistant organisms. Use of antimicrobial growth promoters is not effective and may increase VTEC O157 excretion (these are now banned in the EU).

                                                                                            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.  Currently under regulatory approval process in the US.

                                                                                            In humans, antimicrobial therapy is controversial and may be contraindicated due to a possible increase in the release of VT in the gut.

                                                                                            GAPS:

                                                                                            • Could we use antimicrobials in ruminants? Topical applications?
                                                                                            • Research on possible tools to block toxin production by VTEC strains in the human gut. 
                                                                                          • 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.
                                                                                          • Border/trade/movement control sufficient for control

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

                                                                                            Movement of VTEC strains, cultures and positive samples across borders is very restricted for some countries. Movement of cultures by air transport is restricted, as VTEC are considered Category A by IATA. Movement of foods such as meat may require negative testing for entry into some countries.
                                                                                          • Prevention tools

                                                                                            Hygiene and good practice at:

                                                                                            • Appropriate handling of manure and slurry, to reduce the levels of VTEC 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)
                                                                                            • Water chlorination (or just focus on water quality)
                                                                                            • Personal hygiene following animal contact.

                                                                                            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. 
                                                                                          • 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. Some regions have active surveillance programs.

                                                                                            GAPS:

                                                                                            • More surveillance activities are required.
                                                                                            • Improve diagnostic procedures and diagnostic availability.
                                                                                            • Evaluation of the use of sentinel animals.
                                                                                            • Need of harmonization of surveillance activities in animals and humans, including molecular typing.
                                                                                            • Risk communication to consumers. 
                                                                                          • Past experiences on success (and failures) of prevention, control, eradication in regions outside Europe

                                                                                              Prevention of infection in livestock is difficult. Irradiation of foods is the only assured way to remove/eliminate the pathogen from products, but 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 VTEC from cattle faeces.

                                                                                                GAPS:

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

                                                                                                    Surveys are expensive, and testing cannot ensure food safety as re-infection 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.

                                                                                                    GAP:

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

                                                                                                  • Disease information from the OIE

                                                                                                  • Disease notifiable to the OIE

                                                                                                    Reporting not required as there is no disease in animals. Human outbreaks and sporadic cases are reported through surveillance systems (e.g., CDC in the US and ECDC in the EU). Contaminated food and feed are reported in the RASFF managed by the EU Commission.

                                                                                                    GAP:

                                                                                                    Link of surveillance data from animals and humans at the same time and geographic area

                                                                                                  • OIE disease card available

                                                                                                    No

                                                                                                  • OIE Terrestrial Animal Health Code

                                                                                                    No

                                                                                                  • Socio-economic impact

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

                                                                                                    VTEC infections are probably a worldwide problem. However, systematic collection of information occurs only in industrialized areas (see section [Reported incidence in humans]).

                                                                                                    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:

                                                                                                      • Evaluation of the efficacy of the surveillance systems in place in the different countries.
                                                                                                      • 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 hospitalized, especially children and elderly people. HUS is major public health concern in many countries. In the acute phase it often requires prolonged hospitalization and dialysis, and can result in acquired chronic renal failure. Consequently, the costs medical treatment are substantial. Estimated cost per illness in the US is $6,506 (2008) USD.

                                                                                                        GAP:

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

                                                                                                      • Direct impact (a) on production

                                                                                                        None.

                                                                                                      • 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. The more recent spinach outbreak has caused a crisis of the consumption of this produce.

                                                                                                        Petting zoos and dairy or other farms receiving tourists are tested for O157 and may be shut down when it is detected, in certain countries.
                                                                                                      • Trade implications

                                                                                                      • Impact on international trade/exports from the EU

                                                                                                        No specific international standards for control of VTEC. 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.).

                                                                                                        GAPS:

                                                                                                        • 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. 
                                                                                                      • Main perceived facilitators for effective prevention and control

                                                                                                        Better knowledge of the mechanisms of the pathogenesis of infection in humans and of colonization in livestock.

                                                                                                        GAPS:

                                                                                                        • Understanding within the herd prevalence drivers (Season? Other factors?)
                                                                                                        • Understanding between herd dissemination mechanisms.
                                                                                                        • More effective vaccines with a larger spectrum of activity, including serotypes other than O157. 

                                                                                                      Risk

                                                                                                      • Risks for animals are unlikely, but the appearance of new VTEC organisms which can cause disease in animals is possible. The emergence of new serotypes causing disease in humans must be verified through constant surveillance activities, until they become evident and or predominant.

                                                                                                        GAP:

                                                                                                        Possible emergence of multiple antibiotic resistance and its role in favouring the spread of clones in animal reservoirs

                                                                                                         

                                                                                                      Main critical gaps

                                                                                                      • Human infections

                                                                                                        • Identification of the minimal set of virulence genes/factors (“virulome”) required for causing severe disease in humans.
                                                                                                        • Better diagnostic methods for the identification of human VTEC infections.
                                                                                                        • Better surveillance systems, with inclusion of VTEC non-O157 and definition of the serotypes/clones associated with severe diseases (HUS and bloody diarrea).
                                                                                                        • Estimation of the burden of VTEC infections, including costs, in the population; at present, it is available only for a few countries.
                                                                                                        • Estimation of the possible role of humans as a reservoir for sorbitol fermenting VTEC O157 and some VTEC non-O157 (eg, O26 VT2+ve) pathogenic clones?
                                                                                                        • Research on VT genetic variation and expression and on the diseases potential of the different toxin variants; mechanisms of VT blood transportation during HUS.

                                                                                                         Animal infections

                                                                                                        • In general, to extend the knowledge gained on VTEC O157 to the main pathogenic VTEC non-O157 serogroups.
                                                                                                        • Better understanding of colonisation and persistence of VTEC O157 and non-O157 in ruminants.
                                                                                                        • Better understanding of the biology of the “super shedder” phenomenon and of the role of these subjects in the infection cycles.
                                                                                                        • Better understanding of the immune response in animals, particularly to bacterial structures that could represent vaccine components.
                                                                                                        • Reseach on inter- and intra-farm spread of VTEC: how he organism is spread between one farm to the other, and how animals are exposed within a single farm. Better understanding of the environmental survival.
                                                                                                        • Research on the use of probiotics and phage therapy to prevent colonization.
                                                                                                        • Modelling the cost/benefit of control measures in term of reduction of the burden of VTEC infections in humans.

                                                                                                         Food control

                                                                                                        • Easy and rapid tests targeting the main VTEC non-O157 pathogenic serogroups are required. VTEC that are presumably poorly virulent to humans are abundant in animals and food, so the methods should be targeted to the serogroups/clones most associated with human disease.
                                                                                                        • Role of vegetables: studies on the interaction between bacteria and plant organisms and models for crop contamination via manure and/or irrigation.

                                                                                                      Conclusion

                                                                                                      • Surveillance systems must provide updated information on the VTEC 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 colonization 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 phenomic databases for VTEC

                                                                                                      Sources of information

                                                                                                      • Expert group composition

                                                                                                        Expert group members are included where permission has been given

                                                                                                         

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

                                                                                                        Gad Frankel - Imperial College, UK

                                                                                                        Christian Menge - Friedrich Loeffler Institut, Germany

                                                                                                      • Reviewed by

                                                                                                        Project Management Board.

                                                                                                      • Date of submission by expert group

                                                                                                        10th of March 2015