Stool tests: culture, calprotectin and FIT

A stool test is only as useful as the question behind it. The laboratory can report five broad categories of result, and each tells you something different:

• Is there a pathogen? Bacterial stool culture and nucleic-acid (polymerase chain reaction, PCR) panels look for infective organisms in diarrhoea.
• Is there toxin-producing Clostridioides difficile? Because this bug can colonise without causing disease, testing combines several complementary methods.
• Are there parasites? Microscopy for ova and parasites, together with targeted antigen or molecular tests for Giardia, Cryptosporidium and (separately) Helicobacter pylori.
• Is there intestinal inflammation? Faecal calprotectin is a neutrophil protein released when the mucosa is inflamed.
• Is there bleeding or defective digestion? A faecal immunochemical test (FIT) detects human haemoglobin, while faecal elastase, faecal fat, reducing substances and the stool osmotic gap describe how well macronutrients are being digested and absorbed.

The first thing to decide is whether testing is needed at all. Most acute diarrhoea in an otherwise healthy adult is viral and self-limiting; routine stool testing changes management in only a minority of cases. Reserve testing for people with red flags, immunocompromise, recent travel, severe or prolonged illness, bloody stool, older age with antibiotic exposure, or public-health concerns such as suspected outbreaks. ^[2] Where antibiotics are justified, collect the specimen first, because antimicrobial drugs reduce culture yield. ^[2]

In chronic diarrhoea the work-up is different. The goal is to separate organic disease (inflammatory bowel disease, microscopic colitis, coeliac disease, malignancy, malabsorption) from a functional bowel disorder. Non-invasive stool tests are done in primary care before referral: coeliac serology, faecal calprotectin, and, where appropriate, FIT and faecal elastase. ^[1]

This page covers the meaning, ranges and patterns of all of these results, followed by three illustrative sample reports and their step-by-step interpretation.

Several bodies shape the recommendations quoted on this page:

• NICE: NICE guideline NG199 (Clostridioides difficile infection: antimicrobial prescribing, 2021) for CDI prescribing context ^[7]; NICE guideline NG12 (suspected cancer: recognition and referral, published 2015 and last updated 15 April 2026) for FIT urgent-referral thresholds in symptomatic adults. ^[6]
• IDSA/SHEA: the 2017 update of the clinical practice guidelines for Clostridioides difficile infection (referenced in the 2026 narrative review, Barriers-to-Diagnosis article) underpins the multistep CDI testing approach. ^[2].
• ECCO: the European Crohn's and Colitis Organisation's imaging and monitoring recommendations treat faecal calprotectin as part of the biomarker triad (with endoscopy and imaging) used to judge mucosal inflammation in inflammatory bowel disease. ^[4]
• WHO: the clinical case-management approach to acute diarrhoea prioritises assessing dehydration, continuing feeding and giving zinc; routine laboratory testing is not a standard part of care for straightforward watery diarrhoea.

A stool culture tries to grow the enteric bacteria that cause diarrhoea. A routine panel looks for Salmonella, Shigella and Campylobacter, and extended panels add Yersinia, Vibrio, Shiga-toxin producing Escherichia coli and Aeromonas depending on local policy. A negative routine culture does not exclude viral or toxin-mediated disease, so the clinical picture still decides.

A multiplex PCR panel detects the DNA or RNA of bacteria (and often viruses and parasites) directly. It is fast and sensitive, and it can detect organisms that are difficult to culture. Two cautions follow. First, molecular detection says a virulence gene is present; it cannot separate colonisation, carriage or dead organisms from active infection. Second, a positive screen does not yield an isolate, so if antimicrobial susceptibility or typing matters, reflex culture should be considered. ^[2]

Practical points:

• Stool should be fresh and well formed, and sent before antibiotics are started.
• Usually one sample is enough for a routine bacterial screen; repeated sets are reserved for suspected parasites or when the first result does not match the illness.
• Routine follow-up stool testing is unnecessary once the patient is well; clearance testing is driven by public-health rules, not by clinical recovery. ^[2]

C. difficile requires more than one test, because roughly 5 to 15 percent of healthy adults carry a toxigenic strain without disease. The aim of the algorithm is to detect the organism while avoiding over-diagnosis of colonisation. ^[2]

• Glutamate dehydrogenase (GDH) antigen is a sensitive screen for the presence of C. difficile (toxigenic or non-toxigenic).
• Toxin A/B enzyme immunoassay (EIA) is specific for active toxin in the stool.
• Nucleic-acid amplification test (NAAT, PCR) detects the toxin B gene and is very sensitive.

One common multistep approach is: GDH antigen plus toxin EIA together, with a NAAT to resolve discordant results. ^[2] The 2017 IDSA/SHEA guideline recommends including a stool toxin test in a multistep algorithm, especially where institutions do not have agreed submission criteria. ^[2]

Diagnostic stewardship matters as much as the test. Testing should generally be limited to patients with new-onset, unexplained diarrhoea (usually at least 3 unformed stools in 24 hours) and should not be repeated within 7 days during the same episode, nor used as a test of cure. ^[2]

An ova-and-parasite (O&P) examination looks by microscopy for protozoan cysts/trophozoites and helminth eggs or larvae. It is best used when there is a clinical reason to suspect parasitic infection (travel, residence in or immigration from an endemic area, persistent diarrhoea, day-care exposure, or eosinophilia). Routine O&P in acute, uncomplicated watery diarrhoea has a very low yield; repeat specimens on separate days may be needed if shedding is intermittent. Antigen detection methods, and now molecular panels, are the more sensitive way to detect Giardia and Cryptosporidium.

• Giardia and Cryptosporidium stool-antigen tests and PCR panels are preferred over microscopy where they are available.
• Helicobacter pylori stool antigen test (SAT) detects H. pylori antigen in faeces and can both diagnose active infection and confirm eradication. Monoclonal assays are the preferred format, because they perform more consistently than older polyclonal tests. ^[5] Antigen recovery can be impaired by watery stool, delayed processing or unsuitable storage, and proton-pump inhibitors, antibiotics or bismuth cause false-negative results if taken recently. ^[5]

Calprotectin is a calcium- and zinc-binding protein that makes up most of the cytosolic protein of neutrophils. When the intestinal mucosa is inflamed, neutrophils move into the lumen and calprotectin is shed into the stool. It is a sensitive marker of mucosal inflammation.

Its main job in primary care is to separate inflammatory bowel disease (Crohn's disease, ulcerative colitis) from irritable bowel syndrome (IBS): IBS is a disorder of gut-brain interaction without mucosal inflammation. Calprotectin is also used to monitor mucosal inflammation in known IBD, to predict relapse, and to triage patients toward endoscopy. ^{[1] [4]}

A low/normal calprotectin makes significant colonic inflammation unlikely; a raised value is not specific for IBD, because colonic infection, diverticular or microscopic colitis, colorectal neoplasia, NSAID enteropathy and other inflammatory states can also raise it. Calprotectin is a triage tool, not a diagnosis.

FIT uses antibodies to detect the globin portion of human haemoglobin in faeces. Because the antibody is species-specific, diet and most medicines do not cause false positivity (an advantage over the older guaiac-based test). A positive FIT means lower-gastrointestinal blood loss above the sensitivity of the assay. It is used in bowel-cancer screening programmes and in primary care to guide referral in people with symptoms. ^{[1] [6]}

Faecal elastase-1 is secreted by the pancreas and survives intestinal transit; it is 5 to 6 times more concentrated in stool than in duodenal juice, and stable in the stool for up to a week at room temperature. It is now the preferred non-invasive test of pancreatic exocrine insufficiency, replacing chymotrypsin and the 3-day faecal fat test; enzymatic and breath tests are the alternatives. ^{[1] [8]}

• Faecal fat: historically measured on a 3-day collection with the patient eating 100 g fat per day; an excretion of more than 7 percent of ingested fat indicated fat malabsorption. The test is laborious, unpleasant and no longer performed in most UK laboratories; steatocrit, a breath test or faecal elastase are preferred. ^[8]
• Reducing substances in the stool (applied to the watery fraction with reagent strips or Benedict's method) are positive when unabsorbed sugars reach the colon; they point to carbohydrate (for example lactose) malabsorption, most often in children.
• Stool osmotic gap separates osmotic from secretory diarrhoea. Watery stool is centrifuged; the supernatant sodium and potassium are measured and the gap calculated as 290 minus 2 times the sum of stool sodium and potassium. A low gap (less than 50 mOsm/kg) suggests secretory diarrhoea; a high gap (more than 100 mOsm/kg) suggests osmotic diarrhoea. ^[3]

Reference ranges are not universal. They vary by laboratory, age, sex, method, population and iodine/supplement use. Read every result against the interval printed on the report your laboratory actually issued.

A plain note: ranges differ by laboratory, age, sex, population and method, so the laboratory's own range always wins. An assay change can move a patient across the cut-off without any clinical change.

Named combinations and what each should make you think:

• Low calprotectin (less than 50) with normal screening bloods and typical IBS symptoms in an adult younger than 40 supports a functional bowel disorder; endoscopy is usually unnecessary. ^[1]
• Calprotectin 50 or more, or a markedly raised value, suggests organic inflammatory disease. It separates the patient from IBS and pushes the work-up toward colonoscopy, cross-sectional imaging and specialist review. It is not, by itself, a diagnosis. ^{[1] [4]}
• Secretory watery diarrhoea is characterised by a stool osmotic gap below 50 mOsm per kilogram, often large-volume stools that continue when fasting, and sometimes nocturnal symptoms; think toxin-mediated gastroenteritis or bacterial enterotoxins. ^[3]
• Osmotic watery diarrhoea carries a gap above 100 mOsm per kilogram and often a positive reducing-substance test; think carbohydrate or fat malabsorption, disaccharidase deficiency, osmotic laxatives or overfeeding of carbohydrate in infants. ^[3]
• Steatorrhoea with a low faecal elastase and more than 7 percent fat excretion points to exocrine pancreatic insufficiency. ^[8]
• Loose stools after antibiotics, a positive GDH screen with a positive toxin test (or a GDH-positive, toxin-negative sample with a positive NAAT in a symptomatic patient) defines the C. difficile testing picture. Treat colonisation differently from infection by using symptoms, severity markers and discordant-test follow-up. ^[2]
• Chronic diarrhoea with positive Giardia or Cryptosporidium antigen and an osmotic gap (often without high calprotectin) is the classic parasitic pattern.
• A positive FIT (at least 10 micrograms haemoglobin per gram of faeces in a symptomatic adult) triggers the suspected-cancer referral pathway, even after a previously negative screening sample. ^[6]
• Raised calprotectin with a positive FIT in the same patient needs two explanations pursued in parallel: inflammation and occult bleeding both require colonoscopy.
• Dyspepsia or epigastric symptoms with a positive monoclonal H. pylori stool antigen supports active H. pylori infection; repeat the same monoclonal test as a test of cure at least 4 weeks after completion of eradication therapy and after stopping the proton-pump inhibitor. ^[5]

Every sheet below is an illustrative sample invented for teaching. None of it is a real patient or a real laboratory report. The values are not claims and need no citation; every range, threshold and rule used in the interpretation is cited.

Sample sheet 1 (normal adult male, 34 years, asymptomatic). Illustrative sample only.

Step-by-step interpretation:

1. Stool culture shows no bacterial enteric pathogens, and no parasites are seen. ^[1]
2. C. difficile GDH screening is negative, so no further C. difficile testing is needed in a healthy adult without diarrhoea. ^[2]
3. Calprotectin 28 is below 50, making significant mucosal inflammation unlikely. ^[1]
4. FIT is negative (human haemoglobin below 10) and faecal fat is 4 percent, within the accepted 7 percent for a 100 g fat diet. ^{[6] [8]}
5. Faecal elastase sits inside the laboratory's interval; faecal fat, osmotic gap (35, below 50) and reducing substances are all normal. ^{[8] [3]}
6. Every listed marker is normal, so there is no infection, inflammation, bleeding, carbohydrate malabsorption, secretory diarrhoea or pancreatic exocrine failure in this sample.

Conclusion: this is a normal stool panel in an asymptomatic adult; no infection, inflammation, bleeding or malabsorption is evident, and no further action or monitoring is required beyond routine. ^{[1] [2]}

Sample sheet 2 (78-year-old woman, watery diarrhoea for 5 days after 3 days of co-amoxiclav; low-grade fever and mild leukocytosis). Illustrative sample only.

Step-by-step interpretation:

1. The patient has new-onset diarrhoea with a clear antibiotic exposure; testing of this quality is indicated. ^[2]
2. The negative toxin EIA and positive NAAT form a discordant result: C. difficile is present and carriage is likely, and active infection must be judged clinically. ^[2]
3. The raised calprotectin fits a toxin-mediated mucosal inflammation and is not explained by IBS. ^[1]
4. The negative routine culture makes ordinary bacterial enteritis less likely. ^[2]
5. Repeat testing within 7 days during the same episode would add no information. ^[2]
6. Severity should now be assessed with clinical and laboratory criteria before treatment is chosen, because NAAT-positive/toxin-negative patients often have milder disease markers than toxin-positive patients. ^[2]

Conclusion: this picture is consistent with Clostridioides difficile infection rather than asymptomatic colonisation, and the patient should be treated according to current IDSA/SHEA recommendations (fidaxomicin preferred when available, oral vancomycin as an effective alternative) with clinical reassessment, not with another stool test. ^{[2] [7]}

Sample sheet 3 (5-year-old child with 6 weeks of bloating, foul-smelling watery stools and 2 years of low weight; history of calf contact). Illustrative sample only.

Step-by-step interpretation:

1. Giardia trophozoites and a positive Giardia antigen confirm giardiasis; Cryptosporidium and H. pylori are absent on this sample. ^[5]
2. Calprotectin 38 is below 50, so gross mucosal inflammation from IBD is unlikely; an IBD work-up is not needed on this result. ^[1]
3. The osmotic gap of 165 (above 100) points to osmotic diarrhoea, and the positive reducing substances indicate malabsorbed fermentable carbohydrate. ^[3]
4. Excretion of 24 percent of dietary fat, above the 7 percent upper limit of normal, demonstrates fat malabsorption. ^[8]
5. Faecal elastase 110 is below the laboratory's stated interval, so pancreatic exocrine insufficiency is the likely explanation for the steatorrhoea. ^{[1] [8]}
6. The diarrhoea therefore has two mechanisms running together: a treatable parasitic infection (giardiasis) and fat (and carbohydrate) malabsorption.

Conclusion: this child has giardiasis with secondary osmotic diarrhoea and exocrine pancreatic insufficiency causing fat malabsorption, and should be treated according to local guidance and reassessed for nutritional status and growth. ^{[3] [8]}

• Testing acute, self-limiting watery diarrhoea in a healthy person rarely changes management. Start with red flags, not panels. ^[2]
• Antibiotics before collection lower yield for all culture-based methods; if a sample cannot be sent promptly, store and send according to the laboratory's instructions.
• One test is not the disease. A NAAT that detects the toxigenic gene does not prove active CDI; it can be a coloniser. Read it with symptoms, toxin testing and severity, not in isolation. ^[2]
• Do not test of cure. Repeating CDI testing after recovery, or within 7 days in the same episode, wastes money and can prompt unnecessary treatment. ^[2]
• Calprotectin is sensitive, not specific. Infection, diverticular or microscopic colitis, NSAID enteropathy, colorectal cancer and even vigorous exercise can raise it; it can fall with proximal small-bowel disease that does not reach the colon. ^[1]
• Calprotectin does not behave like CRP. A water-bowel hurry from an irritable colon is not inflammation; confirm the clinical picture, and if it stays raised, proceed to colonoscopy rather than repeating it indefinitely.
• FIT cannot localise the bleed. A positive FIT says blood was present and that colonoscopy is needed; it does not say where. A negative FIT does not prove there is no cancer or polyp, particularly if present intermittently. ^[6]
• FIT is for human haemoglobin. Diet, alcohol or vitamin C do not produce false positivity (unlike guaiac), but it misses right-sided or non-bleeding lesions. ^[1]
• Stool electrolytes must be measured on watery stool. Formed stool gives a misleading osmotic gap; this test is not useful once the stool dries or is collected on a swab.
• Reducing substances spoil quickly. Test fresh watery stool; delay changes the result and a negative test does not exclude all carbohydrate losses.
• Faecal fat has largely been retired. If you still order 3-day fat, check your local laboratory policy; most now prefer elastase, steatocrit or a breath test. ^[8]
• SAT false negatives follow proton-pump inhibitors, antibiotics or bismuth, and poor collection or storage. Document these clearly before sending a Helicobacter stool antigen and repeat testing as a test of cure only after the correct washout. ^[5]
• Reference ranges move. A new calibrator or a new assay can shift a patient across the cut-off without a clinical change; the older result and the new one may not be comparable.

• Stool tests answer five different questions: pathogen, CDI, parasite, inflammation (calprotectin), bleeding or digestion (FIT, elastase, fat, reducing substances, osmotic gap).
• Routine bacterial stool culture looks for Salmonella, Shigella and Campylobacter; multiplex PCR is broader and faster, but cannot separate infection from colonisation or provide an isolate. ^[2]
• Where antibiotics are justified, collect the specimen first to protect culture yield. ^[2]
• C. difficile needs a multistep algorithm: GDH screen, toxin A/B EIA, and NAAT only to resolve discordance. ^[2]
• Never test for C. difficile as a test of cure, repeat within 7 days in the same episode, or use NAAT alone as proof of disease. ^[2]
• Calprotectin below 50 micrograms per gram makes significant mucosal inflammation (IBD) unlikely and supports an IBS diagnosis in the young, otherwise healthy. ^[1]
• Calprotectin of 50 or more is not specific to IBD; it triages the patient toward colonoscopy and specialist review. ^{[1] [4]}
• FIT detects human haemoglobin with species-specific antibodies and is not affected by diet; at least 10 micrograms per gram of faeces in a symptomatic adult triggers the suspected-cancer pathway. ^[6]
• Faecal elastase is the preferred non-invasive test of pancreatic exocrine insufficiency; steatorrhoea with a low value is the classic pancreatic pattern. ^{[1] [8]}
• A 100 g fat diet with excretion above 7 percent of ingested fat confirms fat malabsorption; quantitative 3-day collection is now largely superseded. ^[8]
• The stool osmotic gap (290 minus 2 times stool sodium plus potassium) is low (below 50 mOsm per kg) in secretory and high (above 100) in osmotic diarrhoea. ^[3]
• Reducing substances point to carbohydrate malabsorption, especially in children, and must be tested on fresh watery stool.
• H. pylori stool antigen is best done with a monoclonal assay and repeated after the right washout interval as a test of cure. ^[5]
• Giardiasis and cryptosporidiosis are detected better by antigen or PCR than by microscopy, and typically present with osmotic diarrhoea and a rock-normal calprotectin.
• Every range varies by laboratory, age, sex, method and population; the laboratory's printed interval always wins.