Faecal testing for infectious diarrhoea

Faecal testing for patients with diarrhoea is only indicated when the results will inform management – most patients do not require antimicrobial therapy. Indications for faecal testing for infectious diarrhoea are listed in Indications for faecal testing for infectious diarrhoea. When faecal testing is indicated, a stool sample should be assessed using multiplex polymerase chain reaction (PCR) testing panels and/or faecal culture including tests for Salmonella, Campylobacter and Shigella species. Faecal testing for other specific pathogens may be indicated in some patients; see Indications for specific faecal pathogen testing for infectious diarrhoea.

Multiplex PCR testing panels that include targets for viral, bacterial and protozoal pathogens are widely available for the assessment of infectious diarrhoea; included pathogens vary between laboratories. Interpretation of test results requires consideration of the clinical context, because these tests detect potential pathogens that may not be viable or the causative organism(s)Riddle, 2016Shane, 2017.

Traditional faecal microbiological testing (eg microscopy, bacterial culture, antigen testing) continues to have an important role in the assessment of infectious diarrhoea, despite the relatively low yield in comparison to multiplex PCR testing. A positive culture result is highly likely to be diagnostic, and the resulting bacterial isolates enable antimicrobial susceptibility testing and epidemiological assessment.

Table 1. Indications for faecal testing for infectious diarrhoea

[NB1]

DuPont, 2014Riddle, 2016Shane, 2017White, 2019

Collect a stool sample for faecal testing for patients with:

  • bloody stools
  • severe diarrhoea
  • moderate diarrhoea who are at increased risk of complications and where the result is likely to inform management, including patients
    • older than 70 years with frailty
    • younger than 3 months
    • in the third trimester of pregnancy
    • with comorbidities such as suboptimally managed heart failure
  • significant immune compromise (eg advanced HIV infection, solid organ or bone marrow transplant recipients)
  • symptoms that do not improve after 5 days of rehydration and other supportive measures.

Consider faecal testing for patients with any of the following clinical features:

  • fever (38°C or higher)
  • tachycardia
  • leucocytosis
  • severe abdominal pain
  • high-volume diarrhoea with hypovolaemia.
Note:

NB1: When faecal testing is indicated, a stool sample should be assessed using multiplex polymerase chain reaction (PCR) testing panels and/or faecal culture including tests for Salmonella, Campylobacter and Shigella species.

Table 2. Indications for specific faecal pathogen testing for infectious diarrhoea

DuPont, 2014McDonald, 2018Shane, 2017

Patient group

Recommended tests

patients older than 2 years who have used an antibiotic or stayed in a healthcare setting in the past 90 days [NB1]

Clostridioides difficile (formerly known as Clostridium difficile)

patients with significant immune compromise (eg advanced HIV infection, solid organ or bone marrow transplant recipients) [NB2]

consider testing for:

situations of public health importance (eg an outbreak, in residential aged-care facilities or food handlers)

perform testing as directed by the local public health authority

gay, bisexual and other men who have sex with men, and transgender women [NB1]

consider testing other people engaging in receptive anal sex who report a new sexual partner [NB1]

consider testing for:

for patients engaging in receptive anal sex who also have symptoms of distal proctitis (eg anal pain, discharge, tenesmus) test for:

  • Neisseria gonorrhoeae
  • Chlamydia trachomatis (including the LGV serovar)
  • Treponema pallidum (syphilis)
  • HSV
  • monkeypox virus

patients with abdominal symptoms (eg abdominal pain, diarrhoea) lasting longer than 2 weeks [NB2]

test for gastrointestinal protozoal parasites [NB3], for example:

Note:

CMV = cytomegalovirus; HIV = human immunodeficiency virus; HSV = herpes simplex virus; LGV = lymphogranuloma venereum

NB1: Faecal testing (standard and specific) is only indicated for patients who meet the criteria in Indications for faecal testing for infectious diarrhoea.

NB2: For these patient groups, specific faecal testing may be considered in addition to standard faecal testing irrespective of diarrhoea severity.

NB3: Do not test for protozoal parasites unless abdominal symptoms are present; nonspecific symptoms (eg fatigue) are not an indication for testing.

If an organism is identified, see: