Public health management of Shiga toxin-producing Escherichia coli (STEC) infection
Scottish Health Protection Network (SHPN) guidance

Overview

This guidance has been developed for use in Scotland through the Scottish Health Protection Network (SHPN).

It was developed using agreed SHPN methods. A full methods statement is available.

You can download a version for printing but please regularly check the most recent version of the guidance available online is being referred to.

This guidance is primarily non-statutory. This means it is not a legal requirement to implement the recommendations made.

Where the guidance references a legal requirement – for example in relation to the Public Health etc. (Scotland) Act 2008 – this is made clear.

The guidance does not replace or override any legislative or statutory requirements.

This national guidance should be used as the primary reference document. This will promote consistency and minimise unnecessary variation in professional practice across Scotland. However, it does not replace individual expert judgement or local response arrangements.

Any comments or suggested improvements can be sent to the PHS Guidance Team at phs.guidance@phs.scot

Intended audience

This guidance is for all professionals involved in the health protection or public health response to Shiga toxin-producing E. coli (STEC) cases and outbreaks.

This includes:

• health protection teams
• environmental health departments
• microbiologists
• epidemiologists

What the guidance covers

In scope

The guidance covers:

• O157 STEC
• non-O157 STEC
• Shiga toxin-negative (stx-negative) O157

It includes information on:

• case and contact definitions for use by public health professionals
• recommended public health actions for cases and contacts
• outbreak identification and response

This guidance replaces the 2018 SHPN guidance for the public health management of Escherichia coli O157 and other Shiga toxin-producing E. coli (STEC) infections.

Out of scope

This guidance does not address clinical management of STEC patients.

The focus of this guidance is on STEC isolated from faecal sample testing.

This does not cover other E. coli from other sample sites causing no gastrointestinal infections, for example bacteraemia and urinary tract infections.

Background

STEC are a group of bacteria which can cause gastrointestinal illness in humans.

Symptoms of STEC infection range from asymptomatic infection to mild non-bloody diarrhoea, through to bloody diarrhoea, abdominal pain and occasionally fever.

STEC infections can be fatal. Other serious outcomes of infection can include haemolytic uraemic syndrome (HUS) which has been shown to be a major cause of acute renal failure in children in Scotland.

Incubation period

For public health management purposes, the incubation period of STEC ranges from 6 hours to 10 days though 2 to 4 days is most common. Occasionally it has been recorded as long as 14 days.

This variation means it can be difficult to distinguish co-primary cases with longer incubation periods from secondary cases with shorter ones.

14 days should be used as the incubation period for the purposes of public health action (for example, when collecting data about food history).

Infectious period

For public health management purposes, the infectious period of STEC is defined as being from the onset of gastrointestinal symptoms until 48 hours symptom free.

For higher risk cases, precautions are maintained until microbiological clearance is confirmed.

Further details about higher risk cases and contacts are available in the guidance.

Epidemiology

Although large foodborne outbreaks occur in Scotland, sporadic infection predominates.

In Scotland, E. coli O157 is the most commonly detected STEC serogroup. It has a low infectious dose so is more likely to cause secondary spread and large outbreaks.

Asymptomatic carriage can also occur.

On average 40% of diagnosed STEC cases are hospitalised as a result of their infection each year and around 10% of cases develop HUS which can result in severe illness and death.

Scotland has a higher proportion of STEC than other UK countries which reinforces the need for the continued and comprehensive application of the wide range of existing control measures embedded in food safety and guidance in Scotland.

Find out more about the latest epidemiology for Scotland.

Sources of infection

Investigators of STEC cases and clusters should be aware of the very wide range of potential sources of infection, with newly documented sources regularly published.

Bovine meat and related products, milk and dairy products, private water supplies and fruit and vegetables are the main sources of STEC infections in Europe.

We have provided some examples of sources of infection in this section. These should not be treated as exhaustive.

Food sources

STEC is derived from the ruminant gut.

Although cases of human illness are often associated with beef, a variety of other foods have been implicated in infections and outbreaks.

These other foods can become contaminated through a variety of means, such as from irrigation of crops with contaminated water or from process failures, such as inadequate pasteurisation.  

Non-food sources

Published reports of STEC outbreaks suggest the following activities increase the likelihood of:

• person to person spread
• transmission from animal to human

Case definitions

STEC refers to both:

• Shiga toxin gene (stx)-positive E. coli O157
• non-O157 Shiga-toxin producing E. coli

The following definitions are recommended for determining the public health management of cases.

For information on stx-negative E. coli O157, go to the stx-negative E. coli O157 section.

All cases should also be classified as being at higher or lower risk of transmission to others. For more information, go to the section on higher and lower risk cases and contacts.

Probable case

A probable case is a person with either:

• gastrointestinal symptoms and an epidemiological link to a confirmed case

or

• significant clinical illness consistent with STEC infection, such as haemolytic uraemic syndrome (HUS) or acute bloody diarrhoea, with or without an epidemiological link to a confirmed case

or

• a positive E. coli O157 latex agglutination test on single non-sorbitol fermenting (NSF) colonies but awaiting biochemical identification
  
  • results may be referred to as 'provisional' or 'presumptive' positives by laboratories at this point
  • refer to local laboratory culture diagnosis for more details on these tests

Confirmed case

A confirmed case is a person with either:

• a positive E. coli O157 latex agglutination test on single NSF colonies and biochemical confirmation
  • refer to local laboratory culture diagnosis for more details on these tests

or

• PCR positive for Shiga toxin genes (stx), regardless of culture result or presence/absence of rfbO157, consistent with the presence of STEC
  • positive for rfbO157 but negative for stx should be followed up as per stx-negative E. coli O157
  • refer to local laboratory PCR diagnosis for public health actions when PCR positive for stx genes and negative culture results

Contact definition

The following contact definitions are recommended to identify people who are more likely to have been infected.

All identified contacts should also be classified as higher or lower risk of transmission to others. For definitions of these go to the section on higher and lower risk cases and contacts.

For the purposes of public health follow-up, a contact is anyone who meets one or more of the definitions below, during the case’s infectious period.

Shared exposure

A shared exposure is when multiple people have been exposed to a known source of infection or highly suspected source of infection.

For example, individuals who do not meet the above contact definitions but have consumed the same food or drink, or have been part of the same group trip to a petting farm, that was known or highly suspected to infect the case.

People with a shared exposure are not contacts, as the case was not symptomatic when they shared the exposure to the known or highly suspected source of infection.

Extending public health action to individuals with a shared exposure can be considered through a risk assessment by the local HPT.

The extent of the public health action will be determined by the risk assessment. It may result in managing those with a shared exposure as contacts.

Symptomatic contact

Any contact with GI symptoms, for example loose stools, is a probable case, as set out in the case definitions section.

Action required

Probable cases should submit a stool sample to their GP.

While waiting for the test result, probable cases should follow the same advice as a confirmed case.

Negative results

Probable cases with negative tests become 'discarded cases'. These should be managed as contacts.

If they develop new symptoms, or symptoms worsen – for example, blood in the stool - they should seek medical advice.

Higher and lower risk cases and contacts

All cases and contacts should be classified as being at 'higher risk' or 'lower risk' of transmission.

This classification informs the appropriate approach to public health action, follow-up, and testing requirements.

All cases and contacts who are not in the higher risk groups, are classified as lower risk of transmission.

The risk of transmission is based on both the:

• risk of transmission to those who are more vulnerable to infection (the young, elderly or immunosuppressed)
• risk of transmission to many people.

Those who fall into the following groups should be classified as higher risk of transmission:

Infection virulence

The infection virulence (risk of severe disease following infection) can be used to inform risk assessments for STEC cases and contacts.

Infection virulence details may not be available for all cases at diagnosis but should be used when they become available.  

Factors to consider should include the following.

Severity of symptoms

Cases (or their contacts) with severe symptoms, for example those requiring hospitalisation or with haemolytic uraemic syndrome (HUS).

Serogroups associated with more severe disease (higher virulence)

Cases identified with stx-positive O157 or O26. These are associated with more severe disease.

Stx-positive serogroups known to be associated with current or previous outbreaks.

Genes associated with more severe disease

Where no stx identified

Isolates with a negative stx result are considered lower virulence and public health action is not required, aside from completion of the enhanced surveillance form.

Further advice

Further advice on the virulence profile of individual isolates is available from the Scottish E. coli O157/STEC Reference Laboratory (SERL).

Public health actions

STEC infection can cause severe disease.

Public health response to an STEC case must start on the day of notification. Complete the risk assessment and begin relevant public heath actions within 24 hours of notification at the latest.

The key to public health action for STEC is detailed risk assessment to identify the:

• likely source of infection
• likelihood of further cases
• measures required to remove or mitigate risks

Notification

This section of the guidance relates to a legal duty.

Section 13 of the Public Health etc. (Scotland) Act 2008 places a duty on medical practitioners to notify the HPT of any suspected:

• clinical syndrome due to E. coli O157 infection
• haemolytic uraemic syndrome (HUS)

Section 16 of the Public Health etc. (Scotland) Act 2008 places a duty on registered medical laboratories to notify the HPT of any identified:

• verocytotoxin-producing E.coli (VTEC)

These duties should be interpreted to include any E. coli non-O157 infection. Also, VTEC should be read as STEC.

Timing of notification

It is advised that all STEC and HUS notification should be considered urgent, for the purposes of the Public Health etc. (Scotland) Act 2008.

HPTs should have clear arrangements in place to receive urgent notification of all identified STEC related disease and infection from laboratories and medical practitioners including out of hours.

Public health response to an STEC case must start on the day of notification. As a minimum, the risk assessment should be completed. Subsequent public heath actions should be initiated within 24 hours of notification.

Stx-negative E. coli O157

Where diagnostic and reference laboratories use GI-PCR testing to detect rfbO157 and stx genes, it is likely that stx-negative E. coli O157 will be detected.

The majority of stx negative E. coli O157 strains isolated and typed in Scotland are serotypes other than E. coli O157:H7 (for example O157:H16 or O157:H39).

These are associated with less severe disease than E. coli O157:H7 and are likely to be enteropathogenic E. coli (EPEC) which have never carried stx genes.

An STEC enhanced surveillance form is required for stx-negative E. coli O157 to allow for national surveillance.

For more information go to the surveillance section.

No further public health action is to be taken when stx-negative E. coli O157 are detected. Stx-negative E. coli O157 can be managed in line with other gastrointestinal pathogens.

If public health action has started before the stx profile was known this action can now be stood down or reversed.

For example, if high risk contacts of a stx-negative E. coli O157 case are not attending work, school or childcare while they await clearance testing, these restrictions can be lifted.

SERL will no longer isolate an organism from faecal samples where the presence of stx-negative E. coli O157 is indicated.

If a high suspicion of STEC infection remains, for example in the presence of severe symptoms, discuss follow up testing with SERL.

Surveillance

Enhanced surveillance questionnaires should be completed for all cases:

• who are E.coli O157 or STEC positive (including stx-negative E.coli O157 cases)
• where E. coli O157 or STEC is clinically suspected and test results are awaited 

Download the STEC surveillance form.

Risk assessment

The investigation should begin with the collection of the information necessary to make the risk assessment.

The PHS enhanced surveillance form must be used to ensure complete collection of this information about every case.

The information may come from the case, contacts, or others.

Key areas to consider during the risk assessment include the following.

Other activities, day trips or hobbies – such as hillwalking or rural sports – which may bring the individual into close contact with animal faeces, should also be considered.

The risk assessment should also include gathering of details of all contacts, including sufficient information to assess if they fall into the higher risk groups (see section on higher and lower risk cases and contacts).

Further investigations to identify or confirm the source may be necessary.

Find out more information on foodborne sources in the Food Standards Scotland foodborne guidance.

Risk assessment of cases

Where risk assessment is required to inform public health action, this should consider the:

• infection virulence (risk of severe disease)
• risk of onward transmission from the case

More detail on the infection virulence can be found in the section on infection virulence.

The risk of onward transmission should be classified as per the section on higher and lower risk cases and contacts.

Control measures

Actions to mitigate the risk and prevent onward transmission should be taken working with environmental health officers (EHOs) and other agencies as appropriate.

Actions should be proportionate to the risk.

Cases and contacts should be provided with information and advice on reducing the risk of further spread.

Advice should be given both verbally and in writing.

Hand hygiene

Good infection-control practice, in particular hand hygiene, is key.

Stress the importance of:

• washing hands with liquid soap and running warm water, as well as drying thoroughly with a separate towel, every time after using the toilet, before food preparation, and before eating
• Washing hands after any activity where faecal contamination is a possibility, for example:
  • handling of soiled linen
  • contact with animals
  • before and after assisting younger children with toileting, including nappy changing

Other control measures

Until 48 hours after symptoms stop, individuals should not:

• prepare food for others
• share towels
• go swimming or share baths
• have sexual contact

Environmental cleaning should pay attention to:

• toilets and surrounding areas
• food preparation areas
• other hard surfaces such as sinks, taps and door handles

Food businesses should discuss their needs with the local environmental health department.

Additional resources are available from Food Standards Scotland:

• food handlers fitness to work guidance
• testing for pathogens guidance

Case and contact follow-up and testing

Public health actions should commence immediately for all probable and confirmed cases.

Cases and contacts, and their carers if applicable, should be provided with hygiene advice. For details of who is in the higher and lower risk of transmission groups see the section on higher and lower risk cases and contacts.

Lower risk cases and contacts

Lower risk cases

Lower risk cases do not require case clearance testing.

They should be advised that after 48 hours symptom free they can return to any work, school or childcare.

There is up-to-date information about Escherichia coli (E. coli) on NHS inform.

Lower risk contacts

Lower risk contacts do not require testing before attending work, childcare or school.

They should be advised to be vigilant for symptoms.

If they develop symptoms they are classed as 'probable cases' and should:

• not attend work, school or childcare
• seek medical advice
• submit a stool sample to their GP
• contact the HPT

Higher risk cases and contacts

Cases in the higher risk of transmission groups should complete case clearance testing to demonstrate they are no longer infectious before returning to work, childcare or school.

All cases and contacts who are awaiting testing should be told to refrain from attending work, nursery, childcare or school (as relevant), until test results show they are not infected.

This applies to:

• probable cases
• cases awaiting clearance
• contacts in higher risk of transmission groups awaiting testing

If there are concerns about compliance, then the health board Competent Person should consider using powers under the Public Health etc. (Scotland) Act 2008.

When using these powers, consider imposing the least restrictive order necessary to protect public health.

This may include redeployment or changed duties away from the high-risk duties.

When using exclusion or restriction orders it is vital to follow the guidance published by the Scottish Government including ensuring the individual is aware of their rights to claim for loss of income.

Review exclusion and restriction orders regularly, every 3 weeks at the most.

Case clearance testing

Case clearance testing should not begin until the case is 48 hours symptom free.

Where an original diagnosis of STEC is made at the local diagnostic laboratory (either by culture or by PCR) then clearance should also be conducted locally.

If the original diagnosis was made at SERL, then clearance should be conducted at SERL.

If results are negative on 2 consecutive clearance samples taken at least 24 hours apart, no further testing is required.

If a case still tests positive after six weeks of testing, contact SERL to discuss further testing options.

Contact testing

Contacts in the higher risk of transmission groups should demonstrate they are not infected through contact testing before returning to work, childcare or school.

Detected at local diagnostic laboratory

If the case (who the contact was with) was detected at the local diagnostic laboratory (either by culture or PCR), the contact faecal sample must be tested at the local diagnostic laboratory.

Detected at SERL

If the case (who the contact was with) was detected at SERL, the contact faecal sample must be tested at SERL.

Actions

If the contact is culture negative for STEC on 2 consecutive samples taken at least 24 hours apart, no further testing is required.

If a contact sample tests positive locally, local isolation of E. coli O157 (if indicated) must be attempted, and an isolate forwarded to SERL for confirmation of identity and typing.

If a person with gastrointestinal symptoms and an epidemiological link to a confirmed case tests negative locally but there is still a high clinical suspicion of STEC:

• HPTs may wish to discuss further testing with SERL
• SERL will continue to assist with isolation of non-O157 STEC from cases detected locally

Minimising burden on households requiring multiple clearance tests

Where a household (or other grouping) requires multiple people to be tested, a strategy for the timing of case clearance testing and contact testing samples should be agreed following discussion between cases, contacts and HPTs.

The goal should be to balance the burden on individuals against the risk of onward transmission to vulnerable people.

Theoretically if samples are taken from the close contact whilst the index case is still infectious, later cross infection may be missed.

However, the use of good personal hygiene and environmental cleaning would make transmission between competent adults very unlikely.

Early clearance testing

Cross-infection is less likely with those who work:

• with food
• in clinical or social care

The nature of their work means they should have greater understanding of, and compliance to, necessary hygiene measures.

Therefore, clearance sampling for these contacts could potentially begin at the same time as the case, after appropriate risk assessment.

Delaying clearance testing

For other contacts, consideration should be given to delaying the start of clearance sampling, especially if either case or contact is aged 5 or under, or unable to perform adequate personal hygiene.

Practical implications of household testing

Attention should be paid by HPTs to the practical implications of household testing including:

• the provision of an ample supply of sample pots
• clear instructions on the submission of samples
• advance notice to diagnostic laboratories of the sample arrival

Household testing for cases with HUS

In cases of HUS, detecting the organism in an infected household contact’s stool can help:

• confirm diagnosis of STEC-associated HUS and avoid unnecessary treatment for atypical HUS (a rare complement dysregulation disorder not related to STEC)
• guide further investigations and management
• identify sources of transmission within the household
• contain further person-to-person transmission

Therefore, HPTs may wish to consider offering testing to all household contacts of HUS cases, including those not in higher risk groups. This decision should be made in collaboration with clinical teams where relevant.

Household contacts who submit samples do not need to stay away from work, school or childcare while awaiting results or if testing positive for STEC if the following applies.

They both:

• have no symptoms

and

• are not in a higher risk group

Any contacts of a case of HUS who test positive or develop symptoms should be managed as confirmed or probable cases respectively.

 

Prolonged shedding

Individuals, especially young children, can continue to shed E. coli STEC in the stool for some time after the symptomatic infection has passed.

It is important that cases and/or parents and carers are aware that clearance can be a lengthy process.

In some individuals, shedding can continue for a significantly longer time than the expected range.

In these cases, it is appropriate to review the risk assessment, including any restrictions that have been placed on the individual.

The public health benefit of any continued exclusion needs to be balanced against the potential harm from prolonged periods away from work or educational settings.

Further risk assessment and consideration of alternative control measures (such as supervised hand washing), if necessary, should occur for these cases.

The timing of review will depend on the individual circumstances of the case.

Around six to eight weeks after notification is likely to be reasonable.

In chronic shedding, reduction in the frequency of sampling should be considered.

Where shedding continues for many months, consideration should be given to referral to the local infectious diseases team and discussion with PHS GIZ Team and SERL.

Clusters and outbreaks

Cluster or outbreak investigation and management

Outbreaks should be managed in line with management of public health incidents: guidance on the roles and responsibilities of NHS-led incident management teams.

Foodborne outbreaks

Where an incident management team (IMT) undertakes an investigation of a potentially foodborne STEC outbreak, guidance on the management of outbreaks of foodborne illness in Scotland should be followed.

This guidance includes advice on:

• roles and responsibilities during a foodborne investigation
• the use of trawling questionnaires
• analytical epidemiology
• food chain investigations, including:
  • the seizure or detention of implicated products
  • inspection of premises
• laboratory investigation, including the use of whole genome sequencing (WGS)
• communications

Outbreaks in populations at highest risk of severe disease

Outbreaks of STEC in populations at the highest risk of severe disease – for example, those aged under 5 or the very elderly – can be challenging to manage due to the:

• higher risk of person-to-person transmission
• higher proportion of cases and contacts that may require exclusion

All child cases attending nursery will be classified as higher risk of transmission due to their age and will require exclusion and further testing.

Many of the staff will also be classed as higher risk contacts due to:

• their role
• having carried out nappy changing or assisted toileting with the case(s)

Widening the contact definition

During an outbreak investigation in a population at the highest risk of severe disease – for example, those aged five or under or the very elderly – an IMT may also decide to widen the contact definition.

The widened contact group should be clearly defined and kept as small as possible. For instance, this could mean close friends of the case, or staff who worked closely with the case.

It is not recommended to widen the contact definition without a suspicion of person-to-person transmission or shared exposure. Asymptomatic testing of the whole population in a setting (for example, an entire nursery class) is not recommended. 

Once defined and identified, contacts in this wider group should be treated as other contacts and follow the advice in case and contact follow up and testing.

All contacts in the higher risk of transmission groups should demonstrate they are not infected through contact testing before returning to work, childcare or school.

Refer to case and contact follow up and testing for advice:

• if an asymptomatic contact tests positive as they are now a case
• on managing symptomatic contacts as they are now a probable case

Reassess any contacts who have completed their follow up and returned to the setting but then develop symptoms.

Temporary closure may be required:

• where large numbers of staff or children are required to be absent
• if a reduction in staff means that the business cannot operate safely
• if the IMT have public health or IPC concerns about the nursery

These decisions should always be made in partnership with relevant agencies, for example, the education authority or Care Inspectorate.

Additional guidance aimed at the staff of children and young people settings is available in the health protection in children and young people settings, including education guidance.

Outbreaks linked to animal visitor attractions

Attractions that bring about closer interactions with humans and farm or other animals have been associated with significant STEC outbreaks.

Review possible exposure routes and any shortcomings in hygiene measures. Put measures in place to address any issues identified.

This may result in:

• taking action to reduce possible contact between the public and animal faeces
• limiting or stopping all public access (particularly younger children) to the animals
• considering whether to close the whole facility

HPT and EHD joint visits may also be considered.

For more information, refer to:

Laboratory testing

Local and reference laboratory roles

Local laboratory testing

Confirmation of diagnosis of STEC infection by diagnostic (local) laboratories is by:

• culture of STEC from faecal samples

and/or

• detection of stx or rfbO157 by PCR from faecal samples

See local laboratory culture diagnosis for details of the laboratory tests. 

Refe​rence laboratory testing

Visit the Scottish E. coli O157/STEC Reference Laboratory website for detailed guidance, including how to submit and transport samples.

 As part of the Reference Laboratory Scope of Service, SERL provide:

• confirmation of identity and relevant typing (including virulence gene detection and whole genome sequencing) of submitted isolates and organisms isolated at SERL from submitted faeces 
• confirmation of local positive GI-PCR result and isolation of a viable organism from locally detected PCR positive faeces submitted from routine diagnostic labs from which it has not been possible to locally culture an organism 
• isolation of a viable organism from submitted faeces testing positive by SERL faecal screening PCR - see the reference laboratory diagnosis by PCR section
• outbreak detection
• provision of advice to clinicians, public health and epidemiology colleagues at NHS board level and national level  

In addition to human isolates, SERL accepts isolates of STEC known or thought to be linked to clinical cases of infection, from:

• food
• water
• environmental
• veterinary sources

These should be by prior arrangement by telephone.

Isolates related to outbreak investigations are routinely processed by SERL and will be prioritised along with human isolates.

Local laboratory culture diagnosis

Diagnostic laboratories routinely test all submitted faecal specimens for the presence of non-sorbitol fermenting (NSF) E. coli O157.

Local culture confirmation of E. coli O157 at the diagnostic laboratory takes 24 to 48 hours from receipt of the sample.

Steps for obtaining culture result

In general, culture confirmation of E. coli O157 follows these steps.

Communicating culture results

Clinical and public health management the diagnostic laboratory result.

Diagnostic laboratories should inform the clinician and the HPT immediately of a presumptive positive E. coli O157, pending full identification of the organism as E. coli.

For more information on the requirements for communicating results, see the notification section.

Written or electronic notification of the result is issued within three days.

Sending to SERL

If the patient has haemolytic uraemic syndrome (HUS), the local diagnostic laboratory should provide a faecal sample to SERL as soon as practical (on the day of receipt or the next business day) for SERL faecal screening PCR. This SERL testing should proceed in parallel with any local testing.

E. coli O157 isolates should be sent to SERL for final confirmation of identity and typing.

All culture negative samples that fulfil the criteria set out in reference laboratory diagnosis by PCR section should be tested by PCR locally or at SERL.

If gastrointestinal PCR (GI-PCR) is not available locally, SERL offer a faecal screening PCR service.

See the reference laboratory diagnosis by PCR section.

Local laboratory PCR diagnosis

Some local laboratories undertake PCR testing for STEC using GI-PCR.

For the purposes of public health management, a person with positive GI-PCR is a confirmed case.

See the case definitions section.

A person with a positive GI-PCR test but a negative culture result should also be classed as a confirmed case.

However, the HPT should assess the need for public health action based on:

• epidemiology
• clinical picture

If there is doubt over the PCR test result, based on the clinical and epidemiological information, advice can be sought from SERL.

Interpreting PCR Results 

Contact SERL for advice on interpreting PCR for STEC.

If local PCR testing is negative but the patient has symptoms indicative of an STEC infection, the faecal sample should be forwarded to SERL for further testing, if cases fulfil the criteria highlighted in the reference laboratory section.

Some STEC, for example, those carrying the stx2f variant, are not detected by certain commercial GI-PCR platforms.

Communicating PCR results

Positive PCR results should be immediately reported to the local clinician and HPT if local laboratories are using GI-PCR to detect the presence of:

• E. coli O157

and/or

• STEC

See the notification section for more information on the requirements for communicating results.

Isolation of E. coli O157 and STEC from PCR positive faeces

If the presence of stx-positive E. coli O157 is indicated from the PCR result, local diagnostic labs must attempt to locally culture E. coli O157.

It is important that culture facilities are retained by diagnostic laboratories when molecular screening tests are introduced.

If culture is successful, the cultured organism must be submitted to SERL for confirmation of identity and further typing.

The PCR positive faeces must be submitted to SERL for further investigation without delay if:

• the E. coli O157 culture is unsuccessful
• only stx genes are detected in the faecal sample, indicating the potential presence of non-O157 STEC

The isolation of non-O157 STEC from faeces is not straightforward. Although every effort will be made to isolate a viable organism, this may not be possible in all cases.

SERL data has shown that up to 25% of stool samples testing positive for stx genes fail to yield a STEC organism on culture.

In instances where it has not been possible to isolate an organism, reports will state the PCR results and a comment 'not confirmed by culture'.

No further tests will be performed on this sample.

Refer to the previous PCR section for advice on how this links to the necessary public health actions.

SERL will no longer isolate an organism from faecal samples where the presence of stx negative E. coli O157 is indicated.

Refer to shiga toxin negative E. coli O157 section for public health management advice.

Reference laboratory PCR diagnosis

For those labs without GI-PCR capability, SERL offers a faecal screening PCR service to detect:

• stx variants
  • stx1a
  • stx1c
  • stx1d
  • stx2a-g
• rfbO157

This service does not differentiate between the stx variants detected.

This is no longer a funded reference laboratory test. Local health boards will be charged for each faecal screening PCR conducted at SERL. 

Submit faecal samples to SERL for faecal screening PCR in the following instances:  

• from cases of HUS or suspected HUS, irrespective of other enteric pathogens present (direct urgent referral, pending local culture)
• faecal samples fulfilling the following criteria where local PCR is not available:
• cases of bloody diarrhoea in whom culture has failed to yield a pathogen
• symptomatic contacts of E. coli O157/STEC infection in whom conventional laboratory testing has failed to yield a pathogen
• outbreak-associated symptomatic cases in whom conventional laboratory testing has failed to identify a pathogen
• if determined by local HPT or IMT, outbreak associated asymptomatic individuals in whom conventional laboratory testing has failed to identify a pathogen
• if there remains a high clinical suspicion of STEC infection as determined by local clinical teams despite negative results from local testing

Positive PCR results will be telephoned, immediately, to the referring diagnostic laboratory and a preliminary report issued.

Reference laboratory whole genome sequencing

Whole genome sequencing (WGS) is conducted by SERL on all isolates of STEC.

It provides genetic information that may help inform risk assessment for public health purposes.

It advises on:

• E. coli serotype
• stx variant subtype
• presence of virulence genes, for example, eae and aggR

WGS is also a valuable tool in:

• assessing the relatedness of strains
• indicating clusters
• identifying outbreaks of infection

Communicating reference laboratory results

Reference laboratory reports are issued electronically to the clinician identified on the request form.

Submitted isolates (detected locally)

An interim report confirming the identity of the organism and including PCR results (rfbO157, stx1, stx2) will be issued within five working days of receipt.

A final report, including serotype and stx subtype, will be issued following WGS in 10 to 14 working days.

Submitted faeces testing negative by PCR at SERL

A single final report will be issued within 3 to 5 working days of receipt.

Submitted faeces testing positive by PCR at SERL

SERL will alert referring diagnostic laboratories by telephone or email if a faecal sample from a new or unknown case tests positive by SERL faecal PCR.

A preliminary electronic report will be issued to the referring laboratory following the telephoned or emailed communication. This will detail what genes have been detected in the sample. For example, rfbO157, stx1, stx2.

A final report will be issued once an organism has been isolated and WGS completed (10 to 14 working days). This will include serotype and stx variant subtype.

If it has not been possible to isolate an organism then the final report will confirm the PCR results and state 'not confirmed by culture'. No further work will be conducted on this sample.

Guidance for faecal sample submission to reference laboratory

The faecal sample most likely to test positive is the one taken closest to the episode of infection.

Only a single sample should be submitted per patient, multiple samples from the same patient on the same day will not be accepted.

If it is not possible to take a faecal sample, rectal swabs may be submitted following discussion with SERL. 

For contact details and guidance around the types of bloody diarrhoeal samples to be submitted to SERL, please refer to the Scottish E. coli O157/STEC Reference Laboratory website.

Health protection and health inequalities

What are health inequalities?

Health inequalities are unjust and avoidable differences in people’s health across the population and between specific population groups.

While undertaking health protection for STEC we may unintentionally worsen health inequalities.

Requesting individuals to stay away from their usual place of work, care, or learning to reduce the risk to others should always take into account the potential harms alongside the benefits of preventing infectious disease.

Harms can include:

• reduced educational or childcare opportunities
• carers’ absence from work with consequent reduced income
• other family costs

To mitigate these harms, ensure individuals are aware of their rights to claim for loss of income for themselves or as a carer for a child who cannot attend school or childcare.

Health inequalities and poverty

Those who live in poverty are more likely to:

• suffer acute infections
• be disabled or suffering long term ill health, or live in a household with long term ill health
• lack the opportunities for knowledge and means to reduce risk of illness
• take longer to recover from illness

They may also be less likely to be able to comply with public health advice – for example staying away from a workplace setting due to illness – because of financial pressures, unstable employment or differential sick leave policies.

Financial pressures may also make it more difficult for individuals to submit clearance samples due to, for example:

• lower rates of car ownership
• challenges with public transport
• challenges with time away from work

The households in which they live are also more likely to be over-crowded, further exacerbating the risk of infection and transmission to others.

Recognising and mitigating inequality

Accounting for differences between people when applying health protection measures is a legal obligation under the Public Sector Equality Duty (2011).

Each situation should be considered on a case-by-case basis.

Examples

These are some examples of how health protection professionals can recognise and mitigate inequality arising from health protection measures.

Claims for loss of income

When using powers under the Public Health etc. (Scotland) Act, it is vital to ensure the individual is aware of their rights to claim for loss of income for themselves or as a carer for a child who cannot attend school or childcare.

If individuals have shift working or zero hours contracts, they may need to provide evidence of average income to be able to claim funds.

Some cases and contacts may have challenges in claiming funds for loss of earnings due to, for example, lower literacy levels or digital exclusion, and may require support to help them to claim.

Translations and Easy Read versions

Ensure relevant translation of any communications for individuals or workplaces about STEC and public health actions (for example, hygiene measures) are available in suitable languages.

This includes Easy Read versions to account for differing levels of literacy.

Support and encouragement

Consider ways in which individuals can be supported and encouraged to report illness and keep themselves or their children away from the setting when unwell without being penalised.

HPTs may need to have supportive conversations with employers to encourage compliance.

Safeguarding concerns

Check if there are any concerns about safeguarding, wellbeing or other concerns in relation to children being excluded or asked to stay away from a setting due to STEC.

Learning opportunities

Work with education settings to ensure that children who are asked to stay away from school for any period of time due to an infection risk are not disadvantaged by considering what appropriate learning opportunities can be made available.

Education colleagues should use existing guidance on Getting it right for every child (GIRFEC) to guide decision making.

Information for cases and contacts

Information for the public

NHS inform provides up to date information on Escherichia coli (E. coli).

Patient information leaflets

Patient information leaflets are available for individuals with STEC infection as well those that have been identified as contacts.

Guidance development method

Guidance development process

Method

This guidance was developed in line with the SHPN evidence-based guideline method.

Guidance Development Group (GDG)

A multidisciplinary Guidance Development Group (GDG) was convened to produce this guidance.

The GDG had representation from:

• NHS health protection teams
• NHS diagnostic laboratories
• Scottish E. coli Reference Laboratory
• Local authority environmental health
• Public Health Scotland
• Scottish Government

Each GDG member has submitted a conflict-of-interest form, and no conflicts were declared.

Evidence base

Key questions

The GDG agreed key questions (KQs) to address in this guidance update. These are available in Table 1.

The GDG identified sources of evidence that would be used to address each KQ. Evidence sources to inform KQs ranged from:

• undertaking a review of the literature
• novel data analysis and associated reports
• expert opinion from GDG members

Search strategy

The GDG agreed that a systematic evidence review should be undertaken to inform KQ1 and KQ7.

Three databases (Medline, Embase and Scopus) were searched for terms related to STEC, VTEC or EHEC, Shiga toxins and other virulence genes, shedding, clearance, testing, exclusion and contacts. Full search terms are available by emailing phs.guidance@phs.scot

Papers were included if:

• they were in English
• the population was human and from the global north or other comparable countries to Scotland
• studies were published since 2017
• the study covered more than one case

Single case reports and animal/in vitro studies were excluded

Review of literature

Title and abstract as well as full text screening was carried out by two reviewers and conflicts resolved by discussion. Data was extracted in Covidence by one reviewer and checked by a second reviewer. Critical appraisal of included studies was not completed due to time limitations.

To supplement published literature, abstracts from the 11th international symposium on Shiga Toxin (Verocytotoxin) Producing Escherichia coli Infections (VTEC Banff 2023) were read by one reviewer and relevant information for KQ1 and KQ7 extracted into a table.

STEC public health guidance from other countries and regions was identified from the reference list for the UKHSA STEC guidance, and from studies included in the systematic review. There was no systematic search for these guidance documents. Guidance was read by a single reviewer and relevant content extracted and collated in a table.

Evidence identified

77 studies were included in the evidence review for key questions 1 and 7 (see table 1), as well as 16 Banff abstracts and 13 pieces of guidance (including Scotland). A narrative synthesis for the findings from the evidence review was produced. This will be published on the PHS website soon.

Other sources of evidence, including novel analysis, were presented at GDG meetings. Expert opinion was also sought during GDG meetings or via email.

A Considered Judgement (CJ) Form A was also produced to summarise the key findings for each KQ. CJ Form A also provided an overview of the quality and quantity of evidence that was identified. 

Evidence to recommendation

CJ Form A and the narrative synthesis were shared with the GDG for their consideration.

A CJ Form B was also developed which included draft guidance recommendations for the GDG to discuss.

The GDG met twice to consider and discuss the evidence gathered for each KQ, and to update the draft recommendations. The evidence base, benefits / harms and feasibility were all considered when agreeing recommendations.

The CJ Form B underwent five rounds of revision before the GDG agreed on the final recommendations. This was achieved through informal consensus.

Drafting the guidance

The guidance was drafted using the final recommendations in the CJ Form B.

The co-chairs of the GDG have approved the consultation version.

Consultation

The guidance and the Equality Impact Assessment (EQIA) were circulated for consultation with stakeholders. The consultation took place in August 2023 and was open for four weeks.

The consultation responses were reviewed by the GDG. Both the guidance and EQIA were updated accordingly.

Approval and review

The guidance has been endorsed by the SHPN GIZ Topic Group and the SHPN Guidance Group. PHS have approved this guidance.

In line with the SHPN method the guidance will be reviewed at least every three years from its publication date.

Equality Impact Assessment

An equality impact assessment (EQIA) was undertaken to consider any unintended or differential impact or risks arising from implementing the recommendations in the guidance.

For example, how the guidance might:

• affect children differently to adults
• be different for people living with different levels of deprivation

Where variable impacts were identified by the GDG or the consultation, the GDG considered the rationale for these and adapted the guidance to mitigate or minimise unfair differences.

Download the EQIA

Audit criteria

Audit criteria are clearly defined, measurable, explicit statements, which are used to assess the quality of public health practice.

These have been specifically designed to audit the application of the STEC public health guidance. The criteria outlined on this page are proposed as the key auditable elements.

Health protection teams (HPTs) can develop and incorporate their own audit criteria to assess local pathways for STEC, including aspects beyond those outlined in the guidance.

HPTs can share any summary learning from their audit on the use of this guidance to the PHS Guidance Team. Please email phs.guidance@phs.scot

Auditing the application of this guidance is not mandatory.

Infection virulence

Notification

Surveillance

Control measures

Higher and lower risk cases and contacts

Higher risk cases and contacts

Prolonged shedding

Glossary