Testing for pathogens

How to make sure you protect consumers from infection with Shiga toxin-producing E. coli (STEC).

This information will help you develop your Food Safety Management System (FSMS) and Hazard Analysis and Critical Control Point (HACCP) plan in relation to STEC.

As a food business you must ensure the food you supply is safe. This information explains what you should do to protect consumers when microbiological testing shows that STEC is present in food.

Enforcement authorities must carry out official checks to ensure that businesses are applying appropriate controls to meet this obligation.

This information will:

  • encourage a consistent response to test results from food businesses and enforcement authorities so that public health is protected
  • help food businesses meet their legal obligation to provide safe food

What is STEC?

Shiga toxin-producing Escherichia coli (STEC) is a pathogen that can cause severe illness. It contains Shiga toxin producing genes, also known as stx, and testing regimes for STEC are based on detection of this gene.

There are different types of STEC:

STEC O157:H7 currently accounts for the majority of cases in the UK, although non-O157 STECs are also capable of causing severe disease. A wide range of different non-O157 STECs have been isolated from cases of human illness in the UK, and based on current evidence, any STEC is considered to be potentially pathogenic.

Identifying the risk

As a first step, you should consider if there is an STEC risk associated with the food you produce.  As an example, STEC has been detected in a range of different foods including:

  • Beef and other meats
  • Milk and dairy products
  • Leafy vegetables/salads
  • Fruits
  • Sprouts and sprouted seeds
  • Herbs & spices
  • Uncooked flour including dough

When the presence of STEC could be a hazard in your product, you must consider it in your FSMS or HACCP plan.

Sampling and testing for STEC

Sampling and testing is one of the ways of demonstrating that your FSMS or HACCP procedures are effective (validated) and working properly (verified).  Enforcing authorities (including local authorities Food Standards Scotland and Food Standards Agency in the rest of the UK) may also carry out investigative sampling as part of their official control activities.  This information will help you to interpret the results of the testing you carry out.

  • Profile 1 - Ready-to-eat (RTE) foods and foods intended to be consumed less than thoroughly cooked. The presence of any STEC in ready-to-eat food is unacceptable and should always be considered a serious risk to public health.
  • Profile 2 - Foods intended to be consumed following further processing that will remove the STEC risk, for example by achieving a 6-log reduction of harmful bacteria (including STEC).

Reduction in the level of contamination with harmful bacteria is often expressed in scientific terms as log (short for logarithm) reductions. A 1 log reduction is a ten-fold or 90% reduction in bacteria. A 6-log reduction is equivalent to killing 99.9999% of the bacteria initially present.

Initial PCR test

A test known as polymerase chain reaction (PCR) is used to screen food for Shiga toxin genes (stx1 and stx2).

The result of the PCR test will indicate whether STEC is absent in the sample or whether further tests are needed.

Negative PCR test result

  • No actions will normally be required. You should continue to apply your normal controls, sampling and testing regimes as laid down in your FSMS/HACCP plan.

Positive PCR test result

  • This is known as a presumptive positive result which indicates that the stx gene is present, and therefore that an STEC may also be present. 

Our risk assessment shows it is not possible to determine the public health risk based on the presence of stx genes alone i.e. on a presumptive positive result. This is because the stx genes can be detected in the absence of viable (live) E. coli cells, they may be present in other organisms that would not cause harm, or as free DNA that is not inside the cell of a bacteria. Further (confirmatory) tests are required to determine whether STEC is present in the food.

In most circumstances, a presumptive positive result would not require risk management action. However, the food business or enforcing authority may decide to take action at this stage, where the risk assessment suggests that interventions, such as removing the food from the market are necessary to protect public health. This would be based on additional information such as evidence of a breakdown in food safety management or a link to an outbreak, which indicates that contamination may have occurred.

Confirmatory test

Confirmatory tests are carried out following a presumptive positive result to determine whether STEC is present. These require the culture and isolation of E. coli colonies containing stx genes.

Negative confirmatory result:

  • You are not required to take action on negative confirmatory results provided there is no additional evidence that the food may be unsafe.

Positive confirmatory result:

  • If the presence of an E. coli colony containing stx genes is confirmed, the appropriate actions will vary according to the food profile.


Profile 1 – Ready-to-eat foods

When STEC is confirmed in a batch of Profile 1 food this indicates a serious risk to public health. You should consult your enforcing authority on appropriate risk management action.  Affected batches and other batches or products which may have been contaminated are considered unsafe for human consumption and therefore must be removed from the market

If the food is still within the control of the FBO (and has not reached retail level), food may be re-directed for further processing if it is rendered safe for its intended use. Where this approach is used it must be:

  • included in the business’s FSMS
  • agreed with the enforcement authority as providing a sufficient level of public health protection

Profile 2 – Foods intended to be consumed following further processing method capable of eliminating STEC

Risk assessment shows it can be reasonably assumed that the risk presented by STEC-contaminated Profile 2 food products will be controlled by normal hygienic practices and conditions of use of the food by the food handler or consumer (e.g. by thorough cooking).

You should document the risk management response to detection of STEC in your FSMS. It would be expected that you’d discuss these responses with enforcement authorities during routine official checks

You must pass information to other businesses along the supply chain, or to the final consumer. This must provide all the mandatory food information elements including instructions which may be necessary to ensure the food is handled, stored, processed (e.g. cooked) and consumed safely.

In situations where this information is not provided, there may be a risk that contaminated food is consumed without cooking or other treatment that would remove the STEC risk. Therefore, the affected product should be treated according to food Profile 1.

Businesses supplying caterers, particularly those catering vulnerable groups should always ensure that such caterers are aware of the potential risks associated with their products.

Export requirements

Businesses wishing to export will need to meet the requirements of the receiving country.  Those controls may be different to those applied within the UK due to different approaches to controlling food safety. Where a decision is made to divert products to the domestic market, you must take account of UK food authority advice and handle the product accordingly.

About this information

In developing this guidance, FSS and FSA have consulted with UK public health bodies, enforcement and industry stakeholders. This information has been made with reference to expert scientific opinion of EFSA, the Food and Agriculture Organisation of the United Nations and World Health Organisation; and the UK Advisory Committee on the Microbiological Safety of Food.

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