Stool Culture and Enteric Pathogen Testing

Stool testing for enteric pathogens finds the bacterial, viral and protozoal causes of acute and persistent diarrhoea. Bacterial culture grows organisms on selective media (Salmonella, Shigella, Campylobacter, Escherichia coli O157 and others) and allows antibiotic susceptibility testing. Molecular multiplex panels detect the nucleic acid of 10 to 25 bacteria, viruses and parasites in one run in about one hour. Antigen assays detect norovirus, rotavirus, adenovirus, Giardia and Cryptosporidium.

The test is used to identify the cause of severe, prolonged, bloody or outbreak related diarrhoea, to direct treatment where antibiotics are indicated, and to support public health notification. Most acute diarrhoea is viral and self-limiting, and testing is not needed.

Diarrhoeal disease is the third leading cause of death in children under 5 years, with about 500 000 deaths a year, mostly in low income countries. Norovirus is the commonest cause of acute gastroenteritis in adults, and Campylobacter the commonest bacterial cause in many countries. In travellers, enterotoxigenic Escherichia coli is the leading pathogen.

Indications. Bloody diarrhoea, fever with diarrhoea, severe dehydration, diarrhoea over 7 days, recent hospital admission or antibiotic use (for Clostridioides difficile), immunocompromise, suspected outbreak or food handler, returned traveller, and suspected haemolytic uraemic syndrome. Routine testing in mild acute diarrhoea is not indicated.

Specimen. Fresh liquid or soft stool, 2 to 5 mL or a walnut sized portion, collected in a clean leak proof container, avoiding urine and water. Transport to the laboratory within 2 hours, or place in a transport medium (Cary-Blair for bacterial culture). Rectal swab is acceptable in infants. Do not use stool from a bedpan with disinfectant. Formed stool is rejected for culture unless the clinical details justify it.

Culture. Normal flora includes Escherichia coli, Bacteroides, Enterococcus and others and is not reported. A positive result names the pathogen with susceptibilities. A negative culture means no growth of the pathogens sought and does not exclude viral or parasitic infection.

Common pathogens and findings.

• Salmonella (non-typhoidal): fever, diarrhoea and cramps 6 to 72 hours after exposure. Antibiotics are not given in mild disease and are used in infants, the elderly and the immunocompromised, and for bacteraemia.
• Shigella: dysentery with blood and mucus, fever and tenesmus after a low infective dose. Treatment shortens illness and reduces spread.
• Campylobacter jejuni: bloody diarrhoea, abdominal pain and fever, with Guillain-Barré syndrome as a late complication.
• Shiga toxin producing Escherichia coli (STEC, O157:H7): bloody diarrhoea without fever, with haemolytic uraemic syndrome in 5 to 10%, especially children. Antibiotics increase this risk and are avoided.
• Enterotoxigenic Escherichia coli: watery traveller's diarrhoea.
• Vibrio cholerae: profuse rice water stool and rapid dehydration, with fluid replacement as the main treatment.
• Yersinia enterocolitica: terminal ileitis mimicking appendicitis.
• Norovirus and rotavirus: vomiting and watery diarrhoea, self-limiting, with outbreaks in institutions.
• Giardia, Cryptosporidium and Cyclospora: persistent watery diarrhoea.
• Entamoeba histolytica: dysentery and liver abscess.

Molecular panels. Positive predictive value is high, but detection of nucleic acid does not prove disease, since asymptomatic carriage and prolonged shedding occur. Co-detections (two or more pathogens) happen in up to 10 to 20%, and clinical judgement decides which is responsible. Culture is still needed for susceptibilities and public health typing.

Antimicrobial susceptibility. Resistance to fluoroquinolones in Campylobacter, Salmonella and Shigella is common in many regions, and extended spectrum beta lactamase and carbapenem resistance are emerging. Treatment follows susceptibility.

Critical values and findings needing immediate action.

• STEC or Shiga toxin detected: notify, avoid antimotility drugs and antibiotics, monitor creatinine, platelets and haemoglobin for haemolytic uraemic syndrome.
• Vibrio cholerae, Salmonella Typhi or Paratyphi, Shigella dysenteriae: notifiable, with isolation and public health action.
• Bloody diarrhoea with fever and shock, or toxic megacolon.
• Positive Clostridioides difficile or any pathogen in a patient on a ward with an outbreak.
• A positive culture in a food handler, healthcare worker or childcare worker.

Interferences and pitfalls.

• Delay in transport reduces the yield, especially for Shigella and Campylobacter, which are fragile.
• Antibiotics before sampling reduce culture yield.
• Testing three stools on separate days is no longer routine, and one good sample is enough for most pathogens. Parasitic examination needs separate requests.
• Routine culture does not look for Clostridioides difficile, Giardia or Cryptosporidium, which need specific tests.
• Hospital onset diarrhoea after 3 days of admission is mostly not bacterial, and Clostridioides difficile is tested first.
• Molecular tests can remain positive for weeks after recovery, and test of cure is not needed.
• Over diagnosis of carriage leads to unnecessary antibiotics.
• Rectal swabs are poor for parasites and viruses.

Special groups.

• Children under 5 years: rotavirus, norovirus, adenovirus and Shigella predominate, and rehydration is the priority.
• Older adults and immunocompromised patients: invasive Salmonella and Campylobacter, Cryptosporidium and cytomegalovirus colitis.
• Pregnancy: Listeria infection is considered in febrile gastroenteritis.
• Returned travellers: add protozoa and helminths, typhoid and cholera depending on the region.
• Regions: HIV-associated diarrhoea includes Cryptosporidium, Cystoisospora and microsporidia, and cholera outbreaks occur in areas with poor sanitation.

Follow up tests. Full blood count with film, urea, creatinine and electrolytes, blood cultures when febrile, Clostridioides difficile testing, stool for ova and parasites, Giardia and Cryptosporidium antigen, faecal calprotectin, Shiga toxin gene testing, serotyping at the reference laboratory, antibiotic susceptibilities, and HIV test where indicated.