Acute infectious diarrhoea and gastroenteritis

At a glance

• Acute diarrhoea is 3 or more loose stools a day for under 14 days. Persistent is 14 to 30 days, chronic over 30 days. Persistent symptoms shift the odds towards parasites and non-infective causes.
• Most episodes are viral and self-limiting. Norovirus is the commonest cause in adults and drives outbreaks in aged care and cruise ships.
• The clinical tasks are rehydration, deciding who to test, and deciding who gets antibiotics. Most people need neither tests nor antibiotics.
• Bloody diarrhoea changes the plan: test, think about STEC before giving antibiotics, and consider a first presentation of inflammatory bowel disease.

Causes

Pattern	Organisms	Clues
Preformed toxin	Staphylococcus aureus, Bacillus cereus (emetic)	Vomiting 1 to 6 hours after a meal; several people affected
Toxin formed in gut	Clostridium perfringens, B. cereus (diarrhoeal)	Watery diarrhoea 8 to 16 hours after reheated meat or stews
Viral	Norovirus, rotavirus, adenovirus, sapovirus	Vomiting prominent, outbreaks, resolves in 2 to 3 days
Inflammatory bacterial	Campylobacter, non-typhoidal Salmonella, Shigella, STEC, Yersinia	Fever, blood, tenesmus; poultry, eggs, undercooked meat
Seafood and water	Vibrio parahaemolyticus, Aeromonas	Raw shellfish, fresh or brackish water
Healthcare	Clostridioides difficile	Antibiotics in the past 3 months, hospital or aged care
Parasites	Giardia, Cryptosporidium, Entamoeba histolytica, Cyclospora	Over 7 days, travel, swimming pools, childcare, men who have sex with men

• Campylobacter is the most commonly notified bacterial gastroenteritis in Australia, and Australia's Salmonella rates are among the highest in the developed world.
• Shigella in Australia now spreads mostly through sex between men, and extensively drug-resistant (XDR) strains resistant to azithromycin, ciprofloxacin and ceftriaxone have caused outbreaks since 2022. Susceptibility testing decides treatment.
• Non-infective causes to keep in mind: new drugs (metformin, magnesium, PPIs, immune checkpoint inhibitors), IBD, ischaemic colitis in older people, thyrotoxicosis, overflow from faecal impaction.

Focused history

• Onset and incubation: hours suggests toxin; 1 to 3 days suggests virus or bacteria; over a week suggests parasites.
• Stool: volume, blood, mucus, frequency, nocturnal stools.
• Exposures: food and who else is unwell, travel (where and when), animals and farms, untreated water, swimming pools, childcare, aged care.
• Antibiotics or admission in the past 3 months: C. difficile.
• Sexual history: Shigella, and in men with proctitis, gonorrhoea, chlamydia (including LGV), syphilis and HSV.
• Host: immunosuppression, HIV, pregnancy (Listeria), vascular grafts or prosthetic valves (Salmonella seeding).
• Occupation: food handler, healthcare worker, childcare. This drives exclusion rules.

Focused examination

• Hydration: postural BP and pulse, mucous membranes, urine output, mental state.
• Abdomen: peritonism or distension (toxic megacolon in C. difficile or colitis), right iliac fossa tenderness (Yersinia mimicking appendicitis).
• Systemic features: rash, jaundice, joint swelling (reactive arthritis after Campylobacter, Salmonella, Shigella or Yersinia).

Red flags

• Bloody diarrhoea, especially without fever: STEC.
• Fever with sepsis, or a returned traveller with fever: think enteric fever and malaria before gastroenteritis.
• Pallor, petechiae, falling urine output 5 to 10 days into a bloody diarrhoeal illness: haemolytic uraemic syndrome.
• Abdominal distension with reduced stool output in C. difficile: ileus or megacolon.
• Age over 70, immunocompromise, severe dehydration or AKI.

Investigations

Who to test

Test only when the result would change management (Therapeutic Guidelines 2025):

• severe or bloody diarrhoea
• diarrhoea lasting more than 5 days
• immunocompromise
• moderate illness in a high-risk person: over 70, third trimester of pregnancy, significant comorbidity
• recent antibiotics or admission (C. difficile), an outbreak, or a public health reason (food handler, childcare worker, aged care)

Uncomplicated watery diarrhoea for a day or two doesn't need a stool test.

Multiplex PCR panels

• Most Australian laboratories now run multiplex PCR on faeces for common bacteria (Campylobacter, Salmonella, Shigella, STEC toxin genes, Yersinia), parasites and sometimes viruses.
• Strengths: faster and more sensitive than culture.
• Limits:
  • No susceptibility result, so labs reflex to culture for Salmonella, Shigella and Campylobacter.
  • DNA from non-viable organisms stays detectable for weeks; don't repeat PCR as a test of cure.
  • Detection isn't proof of disease. PCR picks up small amounts of organism carried without illness, so multiple targets often come back, and C. difficile and Blastocystis can be colonisers. Don't treat a positive result if the patient is already improving or another cause fits better.
• Pitfall: a positive C. difficile PCR in someone with fewer than 3 unformed stools a day, or on laxatives, is likely colonisation. Laboratories use two steps (GDH or PCR, then toxin assay); a toxin-positive result supports true infection.

Faecal parasites

• PCR for Giardia, Cryptosporidium, Entamoeba histolytica and Dientamoeba fragilis has replaced microscopy in most labs.
• Microscopy for ova, cysts and parasites is still needed for helminths and parasites not on the panel. Ask for it after travel or with eosinophilia; several samples on different days raise the yield.
• Strongyloides: use serology. Stool microscopy misses most cases. Test before steroids or other immunosuppression in anyone from an endemic area, including many remote Aboriginal and Torres Strait Islander communities, and treat with ivermectin.

Other tests

• Blood cultures if febrile or septic (Salmonella, including enteric fever in travellers).
• UEC, FBC in moderate to severe illness; FBC, film, LDH and creatinine if STEC is found.
• Imaging for peritonism or suspected megacolon (CT abdomen).
• Flexible sigmoidoscopy for persistent bloody diarrhoea with negative stool tests, or to look for CMV colitis in immunosuppressed patients.

Management

Rehydration

• Oral rehydration solution is first line for most adults. IV fluids for shock, AKI, ongoing vomiting or altered mental state.
• Loperamide is reasonable for watery diarrhoea without fever or blood. Avoid it in dysentery, suspected STEC and C. difficile.

Antibiotics

Most infective diarrhoea doesn't need antibiotics. Give them when:

• the illness is severe or the patient is septic, febrile with dysentery, immunocompromised or frail
• Shigella is confirmed (shortens illness and transmission)
• enteric fever, cholera or invasive Salmonella is suspected
• Giardia or another treatable parasite is found (tinidazole 2 g orally as a single dose for Giardia)

Empirical choice for adults (Therapeutic Guidelines): azithromycin 500 mg orally daily for 3 days, with ciprofloxacin 500 mg 12-hourly for 3 days as the alternative. Campylobacter acquired in Asia is often fluoroquinolone-resistant. Tailor once the organism and susceptibilities are known.

Travellers' diarrhoea: TG 2025 no longer treats mild or moderate travellers' diarrhoea with antibiotics. A standby course to carry is only for travellers at high risk of complications going where healthcare is hard to reach.

Don't give antibiotics for:

• STEC: antibiotics increase toxin release and the risk of HUS
• uncomplicated non-typhoidal Salmonella in a healthy adult: no faster recovery, longer carriage
• Pitfall: treating bloody diarrhoea empirically before stool results in a well, afebrile patient. That is exactly the STEC picture.

Clostridioides difficile

The 2025 ASID guideline replaced the 2016 Australasian guidance.

Situation	Treatment
First episode, non-severe or severe	Oral vancomycin 125 mg 6-hourly for 10 days
High recurrence risk (age over 65, immunosuppression, recurrence)	Fidaxomicin if accessible. ASID 2025 keeps vancomycin first line, unlike IDSA and ESCMID advice; fidaxomicin isn't PBS-listed, so access and cost limit its use
First recurrence	Fidaxomicin, or a vancomycin taper and pulse
Two or more recurrences	Faecal microbiota transplant
Non-severe, oral vancomycin unobtainable	Oral metronidazole, as a fallback only
Fulminant (shock, ileus, megacolon)	Oral or nasogastric vancomycin at higher dose plus IV metronidazole, rectal vancomycin if ileus; early surgical review

• Severe: white cells 15 x 10^9/L or more, or creatinine over 133 µmol/L (IDSA/SHEA threshold; ASID 2016 used a rise of more than 50% above baseline).
• Stop the precipitating antibiotic if you can, and stop unnecessary PPIs.
• Contact precautions and soap-and-water hand washing: alcohol rub doesn't kill spores.

Complications

• Haemolytic uraemic syndrome: microangiopathic haemolytic anaemia, thrombocytopenia and AKI, usually 5 to 10 days after STEC onset. Supportive care, often dialysis. Older adults can develop a TTP-like picture.
• Reactive arthritis 1 to 4 weeks after Campylobacter, Salmonella, Shigella or Yersinia.
• Guillain-Barré syndrome after Campylobacter.
• Post-infectious IBS in about 1 in 10.
• Endovascular Salmonella infection (infected aneurysm or graft) in older adults with bacteraemia.

Public health

• Notifiable in all states and territories: Salmonella, Shigella, STEC, HUS, typhoid and paratyphoid, cholera, Listeria, cryptosporidiosis, hepatitis A, and Campylobacter (NSW added it in 2017, last of the jurisdictions). Outbreaks of norovirus in institutions are notifiable as outbreaks.
• Exclusion: food handlers, healthcare and childcare workers stay off work until 48 hours after symptoms stop. Shigella, STEC and typhoid may need negative clearance stools.

Pitfalls

• Fever and diarrhoea after travel to a malarious area is malaria until films are negative.
• Antibiotics for STEC raise HUS risk. Wait for the stool result if the patient is well.
• A positive PCR isn't a reason to treat by itself, particularly C. difficile without diarrhoea or Blastocystis.
• Repeat PCR as test of cure gives false positives for weeks.
• Steroids without Strongyloides serology in at-risk people can cause fatal hyperinfection.
• Metronidazole as first-line treatment for C. difficile is outdated in Australia since the 2025 ASID guideline. It remains a fallback for non-severe disease when oral vancomycin can't be obtained.