2 Clinical need and practice

The problem addressed

2.1 The integrated multiplex polymerase chain reaction (PCR) tests, xTAG Gastrointestinal Pathogen Panel, FilmArray GI Panel and the Faecal Pathogens B assay, are intended to simultaneously detect and identify pathogens that cause gastroenteritis. The tests are designed to analyse multiple viral, parasitic and bacterial nucleic acids (DNA or RNA) directly from stool samples and produce results within a shorter timeframe than traditional microbiology techniques, which can involve multiple tests and culture of organisms.

2.2 Using the tests may allow earlier targeted treatment for people with suspected gastroenteritis, and reduce the length of antibiotic treatment when non-bacterial causes are identified. In addition, the shorter turnaround times of the tests may result in more efficient use of isolation facilities and allow people to have treatment in open bays when infectious pathogens are not present.

2.3 Other standard tests may be used in conjunction with the integrated multiplex PCR tests to confirm Clostridium difficile as the cause of infection, because it is the toxin produced by the pathogen that results in gastrointestinal disease rather than the presence of the pathogen itself; PCR can detect the presence of the toxin gene but cannot confirm that the gene is expressed and consequently, that toxin has been produced. Supplementary testing may also be needed for bacterial targets to meet Public Health England's mandatory reporting requirements or to provide information on antimicrobial susceptibility.

2.4 The purpose of this assessment is to evaluate the clinical and cost effectiveness of using the xTAG Gastrointestinal Pathogen Panel, the FilmArray GI Panel and the Faecal Pathogens B assay for identifying gastrointestinal pathogens in stool samples from patients in the NHS.

The condition

2.5 Gastroenteritis is a common, transient disorder that is usually caused by infection with viruses, bacteria or parasites. The second study of infectious intestinal disease in the community (IID2; 2011) estimated that around 25% of people in the UK have a gastrointestinal infection each year. Gastroenteritis is characterised by acute onset of diarrhoea with or without vomiting. Depending on the cause of the infection, the symptoms can take a few hours to a few days to develop. The IID2 study found that the most commonly identified pathogens in stool samples in the UK were norovirus, sapovirus, Campylobacter and rotavirus. People taking, or who have recently taken, antibiotics can get antibiotic-associated diarrhoea, a condition often caused by Clostridium difficile or less often by Clostridium perfringens, Staphylococcus aureus, Klebsiella oxytoca or Salmonella species.

2.6 If bacterial gastroenteritis is identified, gastrointestinal symptoms can be caused by toxins produced by the bacteria rather than by the bacteria themselves. When symptoms are caused by toxins, the onset is usually rapid (less than 12 hours) and is typically caused by Staphylococcus aureus, Bacillus cereus or Clostridium perfringens. Some bacteria are able to cause serious illness, for example, infections with Escherichia coli O157 can result in haemolytic uraemic syndrome and renal failure.

2.7 Diarrhoea may have non-infectious causes such as inflammatory bowel disease, and so it is important to be able to identify or exclude infectious causes of gastroenteritis in people presenting to health services with diarrhoea or vomiting. Differential diagnoses for gastroenteritis include non-gastrointestinal infections (for example, pneumonia, urinary tract infection or HIV), irritable bowel syndrome, inflammatory bowel disease, coeliac disease, side effects of medicines, endocrinopathy (for example, diabetes or hyperthyroidism) and secretory tumours.

The diagnostics and care pathways


2.8 Gastroenteritis is usually diagnosed based on clinical features alone. Although diarrhoea is common in people who are in hospital, it is estimated that less than 2% of people in the UK consult their GP for an episode of infectious intestinal disease (IID2 2011). The main symptom of gastrointestinal infection is diarrhoea, but other symptoms can include nausea, sudden onset of vomiting, blood or mucus in the stool, or systemic features such as fever or malaise. Occasionally, diagnostic investigations are needed to confirm that an infection is present or to determine the causative pathogen. The NICE clinical knowledge summary on gastroenteritis recommends that stool samples for microbiological diagnosis are taken when there is:

  • persistent diarrhoea

  • blood or pus in the stool

  • a history of diarrhoea or vomiting, and the patient is systemically unwell

  • a history of recent hospitalisation or

  • a history of antibiotic therapy.

2.9 If parasitic infections are suspected, the NICE clinical knowledge summary on gastroenteritis recommends that 3 samples are sent for testing, 2 to 3 days apart because ova, cysts and parasites are shed intermittently. Hospitals may follow the 3‑day rules when deciding whether to send stool samples from inpatients to the microbiology laboratory, but testing for Clostridium difficile should be done as soon as infective diarrhoea is suspected.


2.10 Infectious gastroenteritis is usually self-limiting and treatment is not needed. However, if symptoms are severe, medicines may be needed. Symptoms are often most severe in older people or younger children, or in people who are immunocompromised. Treatment for gastroenteritis may include anti-diarrhoeal medicines such as loperamide and anti-emetic medications such as metoclopramide to control symptoms, depending on the causative pathogen. Anti-diarrhoeal medicine is not recommended if a person has blood or mucus in the stools or a high fever, and confirmed or suspected Escherichia coli O157, Shigella or Clostridium difficile infection. Antibiotics are not appropriate if the diarrhoea is of unknown pathology. If the causative pathogen has been microbiologically confirmed, antibiotics may be recommended for amoebiasis (Entamoeba histolytica), Campylobacteriosis (Campylobacter), giardiasis (Giardia intestinalis), Shigellosis (Shigella) and Clostridium difficile infection.

2.11 Admission to hospital may be needed if a person is vomiting and cannot retain fluids, or if shock or severe dehydration are suspected. Other factors influencing a clinical decision to recommend hospital admission include the age of the person or any comorbidities that may place them at a greater risk of complications, fever, bloody diarrhoea or abdominal pain and tenderness, or if diarrhoea has lasted more than 10 days.

Infection control

2.12 Isolation and barrier nursing, essential aspects of infection prevention and control, are used to stop infections spreading to other patients or staff, and to protect people who are immunocompromised from getting an infection while in hospital (reverse barrier nursing). Isolation involves caring for a person in a single room or side room of a ward. People with suspected infectious diarrhoea and vomiting are usually nursed in isolation or barrier nursed until negative microbiology results are available or they have been symptom-free for 48 hours. People in isolation will be asked to remain in the room and not enter other areas of the ward or hospital until they have been advised otherwise by members of a hospital infection control team. If side rooms are not available, barrier nursing may be done on the main ward, with extra precautions, for example, staff wearing protective clothing (such as gloves, apron and mask), to prevent the spread of an infection. Cohort nursing (nursing in the same bay) may also be used for several patients who have the same infection, for example, infection with Clostridium difficile. When infection control measures are advised for a person, some non-urgent procedures (for example, endoscopy), may be postponed until the infection has resolved.

2.13 Communicable infections for which isolation or barrier nursing is needed are not restricted to gastrointestinal infections such as Clostridium difficile and norovirus, and include colonisation or infection with methicillin resistant Staphylococcus aureus and multidrug-resistant gram-negative bacteria, such as extended spectrum beta-lactamases and carbapenamase producers. It seems that these bacteria are becoming more common and are increasing pressure on existing isolation facilities. Also, these bacteria are currently detected using culture-based screening because PCR technologies do not give information on a pathogen's likely resistance to antimicrobial therapies.

2.14 When infectious gastroenteritis is suspected in the community, people are often advised to stay away from work or, in the case of children, from schools and nursery. Advice is also given on reducing the risk of transmission, particularly if infection with highly transmissible pathogens such as norovirus or Shigella is suspected. Infectious gastroenteritis can have implications for people in certain professions, such as food handlers and healthcare workers. Food handlers are typically advised to stay at home until 48 hours after symptoms have resolved; however, people with infections due to certain pathogens, including Salmonellatyphi or paratyphi, and Escherichia coli O157, may need negative microbiology results before they can return to work. Sometimes, the detection of suspected food-borne pathogens may result in public health teams investigating the outbreak.

  • National Institute for Health and Care Excellence (NICE)