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Laboratory Investigation of Infectious Diarrhoea

Key messages & Introduction
    Diarrhoea | Infectious diarrhoea
Sending specimens to the laboratory
    Faecal culture | Giardia & Crypto | Ova & cysts | Viral causes | C. difficile
    Listeria | Clinical information | Sample collection
Notifiable diseases
Appendices:    Appendix 1 | Appendix 2 | Appendix 3 | Appendix 4

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Key messages

  • Laboratory investigations are not routinely required for most patients with acute diarrhoea
  • If laboratory testing is indicated, a single stool specimen for faecal culture is usually appropriate
  • Giardia and cryptosporidium require a single faecal sample and should only be requested if there are risk factors
  • Testing for “ova and parasites” is rarely indicated
  • Notification to the Medical Officer of Health is required if the case may be part of an outbreak

Tests to request for specific risk factors

Risk factors What boxes to tick Notes
Giardia Crypto Ova and cysts C. difficile  
Diarrhoea, no risk factors No tests Manage
Food handler
< 5 years of age Tick       Consider Rotavirus but testing is not routinely required
Child care attendance
Tick Tick      
Rural Tick Tick      
Raw seafood Tick       Provide clinical details to lab
Bloody diarrhoea Tick       Provide clinical details to lab
Recent antibiotics or
Recent hospitalisation       Tick  
Age > 70 years Tick     Tick  
Immunocompromised Tick Tick Tick    
Overseas travel,
Tick Tick Tick    
Persistent diarrhoea Tick Tick Tick    


Infectious diarrhoea is the most common type of diarrhoea worldwide. It is the leading cause of childhood death in undeveloped countries. In New Zealand very few people die of diarrhoeal illnesses and most of these are elderly. The New Zealand Food Safety Authority has recently reported an estimated 6.5 million cases of vomiting and diarrhoea each year in New Zealand, and approximately 5 million lost working days each year due to gastrointestinal illness.1

The occurrence of diarrhoeal illnesses is estimated as being between 1.2 to 1.9 illnesses per person per year, with the highest rates for children under three years.2 It is difficult to determine the numbers of cases of infectious diarrhoea in New Zealand because many people never seek medical attention or are not investigated. However, in 2006 over 20 000 cases of infectious diarrhoea were reported.3 The most common causes of notifiable diarrhoeal infection in New Zealand are Campylobacter, Salmonella, and Giardia. For number of cases reported in 2005 and 2006, see Appendix 1.


Defining Diarrhoea

Diarrhoea is a change in bowel habit for the individual that results in substantially more frequent and looser stools. It is the consistency of the stools rather than the number that is important. For example, passing formed stools frequently is not diarrhoea.

A number of more precise definitions of diarrhoea are often used in research and hospital settings, but this degree of precision is not usually required in primary care. Infectious diarrhoea is often accompanied by symptoms of nausea, vomiting or abdominal cramps.

Diarrhoea may be defined as acute if the duration of symptoms is less than 14 days, persistent if it has lasted for more than 14 days, and chronic when symptoms have been present for more than four weeks.4

Differential diagnosis

Whilst the most likely cause of acute diarrhoea in general practice is acute gastrointestinal infection, the challenge is to identify those with other causes.


  1. Gastrointestinal infection
  2. An associated symptom of an acute systemic infection/illness
  3. Drugs/diet
  4. Gastrointestinal conditions - acute abdomen e.g. appendicitis, inflammatory bowel disease, malabsorption, tumour
  5. Others as clinical picture dictate e.g. thyrotoxicosis.

Infectious diarrhoea

Table 1: Causes of acute infectious diarrhoea in New Zealand
  • Campylobacter
  • Salmonella
  • Clostridium difficile
  • Yersenia
  • Shigella
  • E coli 0157*
  • Vibro
  • Norovirus
  • Rotavirus
  • Enteric adenoviruses
  • Giardia
  • Cryptosporidium
*E. coli 0157 = one of the verotoxin producing E. coli

Causes of acute infectious diarrhoea in New Zealand

Causes of acute infectious diarrhoea are listed in Table 1. The prevalence of different infectious agents varies throughout the world. In New Zealand the most commonly diagnosed, in order of occurrence, are Campylobacter, Rotavirus, Salmonella and Giardia. A summary of the clinically important causes of infectious diarrhoea is provided in Appendix 2.

Clinical details

As for any condition, the clinical details provide the information required for deciding the path of further management. For people with acute diarrhoea, it is important to determine the severity of their condition, identify if a pathogen may be causative, and to check the physical status of the person.

History: assessing severity

  • Frequency and duration of diarrhoea or vomiting
     Possible threats to adequate hydration
  • Characteristics of the diarrhoea, blood or mucus
     Bloody diarrhoea suggests bacterial cause
  • Any other symptoms, in particular abdominal pain, fever or systemically unwell
     If systemically unwell may have a bacterial infection
  • Recent fluid intake and urine output
     Hydration status
  • Medication taken
  • General medical history/social support
  • Medical conditions such as immunosuppressive medications, AIDS, gastrectomy
     Predispose to infectious diarrhoea
  • Pregnant women who may infect newborn if still excreting enteric pathogen at the time of delivery
     May benefit from specific antibiotics

History: identifying pathogen

To identify infections that could be specifically treated with an antibiotic, avoid spread to others and identify any food source that could be a public health risk. Identification of any of the factors listed below may suggest one of the causative agents listed:

  • Changes to normal diet, in particular food from different sources, alternative water sources, consumption of unsafe foods such as raw or under-cooked meat and unpasteurised milk (E. coli, Salmonella sp., Campylobacter sp.) and raw seafood (Vibro sp.).
  • Travel to a developing area (wide range)
  • Unwell patient contacts; household, sexual or occupational (Shigella sp., E. coli, Salmonella sp., Campylobacter sp., Giardia sp.)
  • Recent hospitalisation or use of antibiotics (Clostridium difficile)
  • Swimming in fresh water lake, river or swimming pools (E. coli, Salmonella sp., Campylobacter sp., Cryptosporidium)
  • Recent visit to farm, petting zoo or contact with pets with diarrhoea (E. coli, Salmonella sp., Campylobacter sp., Cryptosporidium)

Physical examination

  • Vital signs/abdominal examination/other examination as indicated
  • Determine the hydration status* of patient and exclude other causes

* The most useful symptoms/signs are a combination of dry mucus membranes, absence of tears, low urine output and hypotension, however clinical determination of hydration status is inaccurate.

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