The gastrointestinal microbiology laboratory investigates stool for a range of bacterial pathogens (Salmonella, Shigella, Campylobacter, STEC/E. coli O157, Clostridioides difficile, Yersinia, Vibrio), parasites (Giardia, Cryptosporidium, Entamoeba histolytica), and viruses (norovirus, rotavirus) using targeted culture and molecular methods.
Who Should Have a Stool Culture and When?
Stool culture is indicated when: diarrhoea is severe (profuse, bloody, or associated with high fever), diarrhoea persists for more than 3 to 5 days, a specific public health need exists (food handler, outbreak investigation, returned traveller with a compatible history, immunocompromised patient), or when STEC/Shiga toxin-producing E. coli is suspected (bloody diarrhoea without fever: "haemorrhagic colitis," particularly in children, where antibiotic treatment is potentially harmful).
Stool culture has low yield in community diarrhoea: approximately 5 per cent of unselected stool samples from community diarrhoea yield a recognised bacterial pathogen. In well-selected patients (clinically indicated investigation), yield is higher but rarely above 20 to 30 per cent.
Inpatient diarrhoea developing more than 3 days after admission is very unlikely to be caused by standard GI pathogens (Campylobacter, Salmonella) and more likely to be CDI, laxatives, or non-infectious. Most laboratories apply a "3-day rule": stool samples for routine culture are not processed from inpatients who have been admitted for more than 3 days unless the clinical context suggests an infectious cause (recent travel, immunocompromised, outbreak).
Key GI Pathogens and Their Laboratory Investigation
Campylobacter jejuni and C. coli: the most common bacterial cause of acute gastroenteritis in the UK and most high-income countries, with approximately 55,000 confirmed cases per year in England and Wales (and an estimated true incidence of 500,000 or more per year). Infection causes crampy abdominal pain, profuse watery diarrhoea that may become bloody, fever, and myalgia. Source: poultry (especially undercooked chicken), unpasteurised milk, contaminated water. Incubation: 1 to 7 days.
Laboratory detection: selective culture on modified Charcoal Cefoperazone Deoxycholate Agar (CCDA) under microaerophilic conditions (5 per cent O2, 10 per cent CO2, 85 per cent N2) at 42 degrees Celsius for 48 hours. Campylobacter is uniquely thermophilic at 42 degrees Celsius (above most commensal gut flora growth) and microaerophilic. Multiplex PCR panels from stool have replaced culture in many laboratories as the primary detection method. Treatment: most cases self-limiting. Ciprofloxacin resistance is over 50 per cent in most European countries (due to widespread quinolone use in poultry farming). Azithromycin is the preferred antibiotic when treatment is indicated.
Salmonella species: Approximately 9,000 confirmed cases per year in England and Wales. Non-typhoidal Salmonella (S. Typhimurium, S. Enteritidis) causes self-limiting gastroenteritis. S. Typhi and S. Paratyphi cause typhoid/enteric fever: systemic illness requiring treatment. Culture on selective and differential media (XLDHA — xylose lysine deoxycholate agar; MacConkey showing pale lactose-non-fermenting colonies) with subculture and serological confirmation (Kauffmann-White O and H antigen determination). Notifiable pathogen: all confirmed cases must be reported to public health authorities.
STEC (Shiga toxin-producing E. coli): including E. coli O157:H7 and non-O157 STEC. Causes bloody diarrhoea ("haemorrhagic colitis") without fever in typical cases. Dangerous complication: haemolytic uraemic syndrome (HUS) in approximately 5 to 10 per cent of cases, particularly in young children: microangiopathic haemolytic anaemia, thrombocytopenia, and acute kidney injury. Crucially: antibiotics (particularly quinolones) increase HUS risk by causing lysis of E. coli and release of phage-encoded Shiga toxin — antibiotics are therefore contraindicated in suspected STEC.
Laboratory detection: Shiga toxin EIA or PCR from stool (detecting both stx1 and stx2 genes), and E. coli O157 culture on sorbitol-MacConkey agar (O157:H7 does not ferment sorbitol, appearing as pale colonies while most E. coli are sorbitol-positive and pink). Molecular methods (PCR) are increasingly replacing culture as the primary detection method.
Shigella species: Notifiable. Infective dose very low (10 to 100 organisms). Causes dysentery: painful bloody diarrhoea with mucus, tenesmus, and fever. Four species: S. dysenteriae (most severe, produces Shiga toxin), S. sonnei (most common in UK), S. flexneri, S. boydii. Culture on XLD and DCA agar (non-lactose-fermenting pale colonies, H2S-negative, non-motile). Multi-drug resistance (quinolone, ampicillin, trimethoprim resistance) increasingly common. Azithromycin or ciprofloxacin (if susceptible) for treatment when indicated.
Clostridioides difficile: covered in detail in Topic 37. Two-step GDH/toxin EIA or NAAT diagnostic algorithm. Not a standard "stool culture" pathogen: specific CDI diagnostic testing is ordered separately.
Parasitic GI Infections
Giardia intestinalis (lamblia): the most common intestinal parasite in the UK. Causes chronic or subacute watery, foul-smelling diarrhoea with bloating, flatulence, and weight loss after travel to areas with contaminated water supplies (hikers, "beaver fever"). Diagnosis: stool enzyme immunoassay (EIA) for Giardia antigen or PCR (replacing microscopy for ova and cysts in most UK laboratories). Treat with metronidazole or tinidazole.
Cryptosporidium: a coccidian parasite causing self-limiting profuse watery diarrhoea in immunocompetent hosts, but prolonged and life-threatening in severely immunocompromised (HIV with CD4 below 200). Detection by Cryptosporidium antigen EIA or auramine staining of stool (Cryptosporidium oocysts are strongly auramine-positive). Notifiable pathogen. No reliable anti-cryptosporidial treatment exists for severe immunosuppression cases other than immune reconstitution (ART for HIV).
Entamoeba histolytica: causes amoebiasis: bloody diarrhoea (amoebic dysentery) or amoebic liver abscess in returned travellers and in endemic areas (South Asia, West Africa). Distinguished from non-pathogenic Entamoeba dispar (morphologically identical on microscopy) only by antigen EIA or PCR. Treatment: metronidazole followed by luminal agent (diloxanide furoate) to eradicate cyst carriage.
Frequently Asked Questions
When should a stool culture be requested?
Stool culture is indicated for: diarrhoea lasting more than 3 to 5 days, bloody diarrhoea (especially if STEC or Shigella is suspected), severe illness with high fever, diarrhoea in immunocompromised patients, suspected foodborne illness outbreak, travel-associated diarrhoea with persistent or severe symptoms, and diarrhoea in food handlers or healthcare workers with patient contact.
Why is antibiotic treatment contraindicated in STEC infection?
In Shiga toxin-producing E. coli (STEC, including O157:H7) infection, antibiotics (particularly quinolones, trimethoprim) cause bacterial lysis and release of phage-encoded Shiga toxin from lysed bacteria, increasing systemic Shiga toxin levels and the risk of haemolytic uraemic syndrome (HUS). Large clinical studies and meta-analyses confirm that antibiotics in STEC increase HUS risk by 5 to 17-fold. Antibiotics are contraindicated in suspected or confirmed STEC.
What is haemolytic uraemic syndrome (HUS)?
HUS is a microangiopathic complication of STEC infection characterised by: haemolytic anaemia (microangiopathic, with schistocytes on blood film), thrombocytopenia, and acute kidney injury (often requiring dialysis). It occurs in approximately 5 to 10 per cent of STEC-infected children. Shiga toxin binds to Gb3 receptors on renal glomerular endothelial cells and intestinal cells, causing direct toxicity and thrombotic microangiopathy. Treatment is supportive.
What is the 3-day rule in stool culture?
Most hospital-acquired diarrhoea occurring more than 3 days after admission is not caused by standard enteric pathogens (Campylobacter, Salmonella, Shigella). Applying the 3-day rule, laboratories generally decline to process routine stool cultures from patients who have been in hospital for more than 3 days, unless specific exceptions apply (immunocompromised, suspected outbreak, confirmed infection on admission). CDI testing is excluded from the 3-day rule as CDI develops in hospitalised patients.
What is campylobacteriosis and how is it treated?
Campylobacteriosis is infection with Campylobacter jejuni or C. coli, causing crampy abdominal pain, bloody or watery diarrhoea, and fever. Most cases are self-limiting over 5 to 7 days. Treatment with antibiotics is indicated for: severe illness, prolonged disease, immunocompromised patients, and bacteraemia. Azithromycin is the preferred first-line antibiotic because ciprofloxacin resistance exceeds 50 per cent in UK and European Campylobacter isolates.
What is Giardia and how is it diagnosed?
Giardia intestinalis is a flagellated protozoan parasite that causes chronic diarrhoea with bloating and flatulence after ingestion of contaminated water or food. Diagnosis is by stool antigen EIA or PCR (replacing traditional microscopy for cysts). Treatment is metronidazole (400 mg three times daily for 5 days) or tinidazole (single 2 g dose).
What organisms are included in multiplex GI PCR panels?
Modern multiplex GI PCR panels (e.g., BioFire GI Panel, Luminex xTAG GPP) simultaneously detect 10 to 20 GI pathogens from a single stool sample: Salmonella, Shigella, Campylobacter, STEC/Shiga toxin, C. difficile toxin genes, Yersinia, Vibrio, EIEC, norovirus GI and GII, rotavirus, sapovirus, astrovirus, Giardia, Cryptosporidium, Entamoeba histolytica, and Cyclospora. These panels dramatically improve diagnostic sensitivity over culture-based methods but require careful interpretation as clinical significance of all positive results varies.
What is the difference between Entamoeba histolytica and E. dispar?
E. histolytica and E. dispar are morphologically identical cysts and trophozoites that cannot be distinguished by standard microscopy. E. histolytica is pathogenic (causes amoebic dysentery and liver abscess). E. dispar is non-pathogenic and does not require treatment. Differentiation requires antigen EIA or PCR. Traditional reporting as "Entamoeba histolytica/dispar" without species differentiation is clinically misleading.
Why does Campylobacter culture require special conditions?
Campylobacter is microaerophilic (grows at 5 per cent O2, 10 per cent CO2), thermophilic (optimal growth at 42 degrees Celsius rather than 37 degrees Celsius), and fastidious. Routine stool culture at 37 degrees Celsius in aerobic conditions does not support Campylobacter growth. Selective CCDA agar (inhibiting most other GI flora) incubated at 42 degrees Celsius under microaerophilic conditions is required.
What is norovirus and how is it diagnosed?
Norovirus is the most common cause of infectious gastroenteritis in healthcare settings and communities worldwide, causing epidemic vomiting and diarrhoea outbreaks. It is non-culturable by standard methods and is detected by RT-PCR from stool. It has a very low infectious dose (approximately 18 viral particles). Control in healthcare settings requires strict contact precautions, ward closure, chlorine-based environmental disinfection, and exclusion of symptomatic staff for 48 hours after symptom resolution.