Diarrhea may be infectious or noninfectious and presents with acute (<14 days) or persistent (>14 days) symptoms. Community-acquired disease is most common. Viruses (norovirus predominates) are the most common cause of acute infectious diarrhea in community dwellers. Bacterial diarrhea represents only 1-5% of diarrhea cases and is often associated with clustering of cases or outbreaks. Clostridium difficile cases, while often nosocomially acquired, are increasing in community dwellers. Parasites are an infrequent or rare cause of acute diarrhea and tend to be sporadic in nature except in at-risk populations (eg, returned travelers, immunocompromised individuals).

  • Diagnosis
  • Algorithms
  • Background
  • Lab Tests
  • References
  • Related Topics
  • Videos

Indications for Testing

  • Symptoms
    • Persistent or chronic diarrhea
    • Bloody diarrhea
    • Diarrhea in association with systemic illness
  • Patient history
    • Immunocompromised status
    • Returned traveler
    • Hospitalized patient
  • Outbreak identification

Laboratory Testing

  • Differential Diagnosis


    Risk Factors

    • Immunocompromised status
      • HIV,  primary immunodeficiency
        • Most common organisms include viruses, C. difficile, Campylobacter jejuniSalmonella spp, E. coli, Giardia, Cryptosporidium spp, and microsporidia
      • Transplantation (solid organ and stem cell)
        • Usually noninfectious
        • Infectious diarrhea most commonly caused by viruses (norovirus predominates), C. difficile, and microsporidia
    • Advanced age (>65 years)
      • Salmonella spp and Shigella spp may require treatment, so identification is important
    • Comorbid illnesses (eg, chronic heartliver, or kidney disease; diabetes mellitus)
      • Increased risk of complications (eg, sepsis)
    • Institutional residency
      • Norovirus
    • Daycare setting
      • Norovirus
      • Giardia
      • Cryptosporidium spp
      • Salmonella spp

    Clinical Presentation

    • Community acquired
      • Acute diarrhea (acute gastroenteritis)
        • Duration – 1-14 days
        • Transmission – foodborne, waterborne, or outbreak associated
        • Most commonly caused by viruses and occasionally bacteria
      • Persistent diarrhea
        • Duration – >14 days, often longer
        • Often noninfectious
        • Testing for parasites may be considered
        • Persistent diarrhea may lead to malabsorption following an infectious diarrhea
    • Hospital acquired
      • Presentation may be similar to community-acquired disease
      • Most commonly caused by viruses
      • Rule out bacterial agent C. difficile if patient history is correct

    Organisms Associated with Diarrhea (CDC, 2014)

    Tests generally appear in the order most useful for common clinical situations. Click on number for test-specific information in the ARUP Laboratory Test Directory.

    Gastrointestinal Viral Panel by PCR 2013577
    Method: Qualitative Polymerase Chain Reaction

    Norovirus, Groups 1 and 2 by PCR 2014546
    Method: Qualitative Reverse Transcription Polymerase Chain Reaction

    Rotavirus Antigen by EIA 0065088
    Method: Qualitative Enzyme Immunoassay

    Rotavirus and Adenovirus 40-41 Antigens 0065067
    Method: Qualitative Enzyme Immunoassay

    Adenovirus 40-41 Antigens by EIA 0065066
    Method: Qualitative Enzyme Immunoassay

    Stool Culture and E. coli Shiga-like Toxin by EIA 0060134
    Method: Culture/Identification


    If an isolate requires testing for Shiga-like toxin (eg, STEC), refer to E. coli Shiga-like toxin by EIA

    Gastrointestinal Bacterial Panel by PCR 2012678
    Method: Qualitative Polymerase Chain Reaction


    A negative result does not rule out the presence of PCR inhibitors in the patient specimen or test-specific nucleic acid in concentrations below the level of detection by this test

    Gastrointestinal Parasite and Microsporidia by PCR 2011660
    Method: Qualitative Polymerase Chain Reaction

    Clostridium difficile toxin B gene (tcdB) by PCR 2002838
    Method: Qualitative Polymerase Chain Reaction

    Gastrointestinal Parasite Panel by PCR 2011150
    Method: Qualitative Polymerase Chain Reaction

    Giardia Antigen by EIA 0060048
    Method: Qualitative Enzyme Immunoassay

    Cryptosporidium Antigen by EIA 0060045
    Method: Qualitative Enzyme Immunoassay

    Parasitology Stain by Modified Acid-Fast 0060046
    Method: Qualitative Concentration/Stain

    Microsporidia by PCR 2011626
    Method: Qualitative Polymerase Chain Reaction


    The nucleic acid from E. intestinalis, E. hellem, and E. cuniculi will be detected by this test but cannot be differentiated

    A negative result does not rule out the presence of PCR inhibitors in the patient specimen or test-specific nucleic acid in concentrations below the level of detection by this test

    Microsporidia Stain by Modified Trichrome 0060050
    Method: Qualitative Stain

    Entamoeba histolytica Antigen, EIA 0058001
    Method: Qualitative Enzyme Immunoassay

    Ova and Parasite Exam, Fecal (Immunocompromised or Travel History) 2002272
    Method: Qualitative Concentration/Trichrome Stain/Microscopy


    Due to the various shedding cycles of many parasites, 3 separate stool specimens collected over a 10-day period are recommended for ova and parasite examination

    A single negative result does not rule out the possibility of a parasitic infection

    Stool antigen testing is the optimal test method for determining the parasitic presence of Giardia, Cryptosporidium spp, or Entamoeba histolytica

    Does not specifically detect CryptosporidiumCyclosporaCystoisospora, or microsporidia


    For Cryptosporidium, refer to the Cryptosporidium antigen by EIA test; for Cyclospora and Cystoisospora, refer to parasitology stain by modified acid-fast; for microsporidia, refer to microsporidia stain


    Farthing M, Salam MA, Lindberg G, Dite P, Khalif I, Salazar-Lindo E, Ramakrishna BS, Goh K, Thomson A, Khan AG, Krabshuis J, LeMair A, WGO. Acute diarrhea in adults and children: a global perspective. J Clin Gastroenterol. 2013; 47(1): 12-20. PubMed

    Foodborne Diseases Active Surveillance Network (FoodNet). Centers for Disease Control and Prevention. Atlanta, GA [Last updated: Nov 2016; Accessed: Dec 2016]

    Guerrant RL, Van Gilder T, Steiner TS, Thielman NM, Slutsker L, Tauxe RV, Hennessy T, Griffin PM, DuPont H, Sack RB, Tarr P, Neill M, Nachamkin I, Reller LB, Osterholm MT, Bennish ML, Pickering LK, Infectious Diseases Society of America. Practice guidelines for the management of infectious diarrhea. Clin Infect Dis. 2001; 32(3): 331-51. PubMed

    Manatsathit S, DuPont HL, Farthing M, Kositchaiwat C, Leelakusolvong S, Ramakrishna BS, Sabra A, Speelman P, Surangsrirat S, Working Party of the Program Committ of the Bangkok World Congress of Gastroenterology 2002. Guideline for the management of acute diarrhea in adults. J Gastroenterol Hepatol. 2002; 17 Suppl: S54-71. PubMed

    Riddle MS, DuPont HL, Connor BA. ACG Clinical Guideline: Diagnosis, Treatment, and Prevention of Acute Diarrheal Infections in Adults. Am J Gastroenterol. 2016; 111(5): 602-22. PubMed

    U.S. Department of Health and Human Services, Centers for Disease Control and Prevention. Manual for the Surveillance of Vaccine-Preventable Diseases. Centers for Disease Control and Prevention. Atlanta, GA [Last updated: Apr 2016; Accessed: Aug 2017]

    General References

    Barr W, Smith A. Acute diarrhea. Am Fam Physician. 2014; 89(3): 180-9. PubMed

    Bernstein DI. Rotavirus overview. Pediatr Infect Dis J. 2009; 28(3 Suppl): S50-3. PubMed

    Calderaro A, Gorrini C, Montecchini S, Peruzzi S, Piccolo G, Rossi S, Gargiulo F, Manca N, Dettori G, Chezzi C. Evaluation of a real-time polymerase chain reaction assay for the laboratory diagnosis of giardiasis. Diagn Microbiol Infect Dis. 2010; 66(3): 261-7. PubMed

    DuPont HL. Clinical practice. Bacterial diarrhea. N Engl J Med. 2009; 361(16): 1560-9. PubMed

    Glass RI, Parashar UD, Estes MK. Norovirus gastroenteritis. N Engl J Med. 2009; 361(18): 1776-85. PubMed

    Graves NS. Acute gastroenteritis. Prim Care. 2013; 40(3): 727-41. PubMed

    Grimwood K, Forbes DA. Acute and persistent diarrhea. Pediatr Clin North Am. 2009; 56(6): 1343-61. PubMed

    Hill DR, Ryan ET. Management of travellers' diarrhoea. BMJ. 2008; 337: a1746. PubMed

    Hunt JM. Shiga toxin-producing Escherichia coli (STEC). Clin Lab Med. 2010; 30(1): 21-45. PubMed

    Khan MA, Bass DM. Viral infections: new and emerging. Curr Opin Gastroenterol. 2010; 26(1): 26-30. PubMed

    Mathis A, Weber R, Deplazes P. Zoonotic potential of the microsporidia. Clin Microbiol Rev. 2005; 18(3): 423-45. PubMed

    Mead PS, Slutsker L, Dietz V, McCaig LF, Bresee JS, Shapiro C, Griffin PM, Tauxe RV. Food-related illness and death in the United States. Emerg Infect Dis. 1999; 5(5): 607-25. PubMed

    Patel MM, Hall AJ, Vinjé J, Parashar UD. Noroviruses: a comprehensive review. J Clin Virol. 2009; 44(1): 1-8. PubMed

    Pawlowski SW, Warren CA, Guerrant R. Diagnosis and treatment of acute or persistent diarrhea. Gastroenterology. 2009; 136(6): 1874-86. PubMed

    Pierce KK, Kirkpatrick BD. Update on human infections caused by intestinal protozoa. Curr Opin Gastroenterol. 2009; 25(1): 12-7. PubMed

    Recommendations for Diagnosis of Shiga Toxin–Producing Escherichia coli Infections by Clinical Laboratories. October 16, 2009, Vol. 58, No. RR-12. Centers for Disease Control and Prevention. Atlanta, GA [Published: Oct 2009; Accessed: Jan 2017]

    Steffen R, Hill DR, DuPont HL. Traveler's diarrhea: a clinical review. JAMA. 2015; 313(1): 71-80. PubMed

    References from the ARUP Institute for Clinical and Experimental Pathology®

    Beal SG, Couturier MR, Gander RM, Doern CD. Diagnostic Algorithm for the Diagnosis of Pediatric Parasitic Gastroenteritis. J Clin Lab Anal. 2016; 30(2): 155-60. PubMed

    Couturier BA, Hale DC, Couturier MR. Association of Campylobacter upsaliensis with persistent bloody diarrhea. J Clin Microbiol. 2012; 50(11): 3792-4. PubMed

    Couturier BA, Jensen R, Arias N, Heffron M, Gubler E, Case K, Gowans J, Couturier MR. Clinical and Analytical Evaluation of a Single-Vial Stool Collection Device with Formalin-Free Fixative for Improved Processing and Comprehensive Detection of Gastrointestinal Parasites J Clin Microbiol. 2015; 53(8): 2539-48. PubMed

    Hymas W, Atkinson A, Stevenson J, Hillyard D. Use of modified oligonucleotides to compensate for sequence polymorphisms in the real-time detection of norovirus. J Virol Methods. 2007; 142(1-2): 10-4. PubMed

    Khot PD, Fisher MA. Novel approach for differentiating Shigella species and Escherichia coli by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol. 2013; 51(11): 3711-6. PubMed

    Rawlins ML, Gerstner C, Hill HR, Litwin CM. Evaluation of a western blot method for the detection of Yersinia antibodies: evidence of serological cross-reactivity between Yersinia outer membrane proteins and Borrelia burgdorferi. Clin Diagn Lab Immunol. 2005; 12(11): 1269-74. PubMed

    Rossi A, Couturier MR. The Brief Case: Cryptosporidiosis in a Severely Immunocompromised HIV Patient. J Clin Microbiol. 2016; 54(9): 2219-21. PubMed

    Shakespeare WA, Davie D, Tonnerre C, Rubin MA, Strong M, Petti CA. Nalidixic acid-resistant Salmonella enterica serotype Typhi presenting as a primary psoas abscess: case report and review of the literature. J Clin Microbiol. 2005; 43(2): 996-8. PubMed

    Medical Reviewers

    Content Reviewed: 
    April 2017

    Last Update: October 2017