Gastrointestinal infections: guidance, data and analysis

The characteristics, diagnosis, management and epidemiology of gastrointestinal infections.

Infectious intestinal diseases affect 1 in 5 people in the UK each year and symptoms are not confined to diarrhoea and vomiting.

Public Health England (PHE) monitors trends in infection and outbreaks, drawing on data from:

  • PHE reference laboratories
  • the national laboratory reporting scheme
  • consultants in communicable disease control (CCDCs)
  • environmental health officers (EHOs)
  • microbiologists

For trends in zoonotic infection in humans and animals, see Zoonoses in the UK.

Update during coronavirus (COVID-19) pandemic:

Gastrointestinal infections cause an estimated 17 million cases in the UK each year. Bacterial gastroenteritis is particularly common in summer months and outbreaks of zoonotic infections, such as campylobacteriosis, salmonellosis and Shiga toxin-producing E. coli (STEC) occur every year.

Although a vast majority of cases of gastroenteritis cause self- limiting diarrhoea, symptoms such as fever and diarrhoea can be mistaken for COVID-19. Certain gastrointestinal infections like STEC can cause serious complications such as haemolytic uraemic syndrome (HUS), and Listeria monocytogenes infections can be fatal in severely immunocompromised patients.

During the coronavirus (COVID-19) pandemic, the UK Government advice to stay at home and social distancing strategies have changed patterns of shopping, cooking and food consumption in the population. It is therefore important to be highly vigilant of complicated cases of gastroenteritis in the coming months.


Gastrointestinal bacteria reference unit (GBRU) is the reference laboratory for a range of gastrointestinal pathogens.

During COVID-19 the following critical services will continue:

  1. Detection of STEC from stool specimens and confirmation of STEC isolates using PCR.

  2. Detection of Clostridium botulinum and botulinum toxin from food, stool, serum and tissues.

  3. Confirmation of identity and typing of Salmonella, Shigella, STEC and Listeria spp using whole genome sequencing.

Clinicians and laboratories are advised to continue submitting isolates and appropriate clinical samples to the GBRU for detection, identification and typing of bacterial pathogens.




Published 1 July 2014
Last updated 22 April 2020 + show all updates
  1. Added guidance about gastrointestinal infections and GBRU reference and diagnostic services during the COVID-19 pandemic.

  2. Added: 'Gastrointestinal infections: guidance for public health management'.

  3. Added 'Shiga toxin- producing Escherichia coli (STEC): public health management and questionnaire' in 'Management' section.

  4. Added 'Shigellosis: public health management and questionnaire'.

  5. Added 'Amoebiasis: public health operational guidelines' under management section.

  6. Added new section for surveillance.

  7. First published.