Diarrhea, Bacterial Evaluation


Indications for Testing

  • Bloody diarrhea, diarrhea >3 days, prolonged diarrhea with history of travel

Laboratory Testing

  • CBC – nonspecific; however, if leukocytosis is present, suggests bacterial etiology
  • Stool studies
    • Stool culture – preferred test for suspected bacterial diarrhea evaluation (most useful if diarrhea lasts ≥3 days or is bloody)
      • Should include E. coli Shiga-like toxin by EIA (antigen)
    • Campylobacter antigen by immunochromatography
    • Consider ova and parasite exam and Giardia EIA and/or Clostridium difficile testing, if patient has defined risk factors (history of travel or residence in endemic area, exposure history, immunocompromised state, or high pretest probability for parasitic infection)
    • If HIV or otherwise immunocompromised – also consider Cryptosporidium, Microsporidia, Isospora
    • If no improvement in 3-5 days – consider repeating stool studies and performing a colonoscopy
  • Blood culture – most useful for Salmonella (typhoid fever)
  • Joint fluid examination – if patient has arthritis and there is concern for sepsis in reactive arthritis
    • Culture – negative in reactive arthritis
    • Cell count – a few hundred to 60,000/mL WBCs in reactive arthritis
    • ANA, RF – negative in reactive arthritis

Differential Diagnosis

Clinical Background

Etiology of diarrhea may be infectious or noninfectious presenting with acute (<7 days) or chronic (>7 days) symptoms. Campylobacter, Salmonella, Escherichia, Shigella, Yersinia, Vibrio, and Aeromonas species are the most common causes of bacterial diarrhea. Parasites are an infrequent or rare cause of acute diarrhea, but a more common cause of chronic diarrhea.

  • Acute diarrhea (acute gastroenteritis) – duration 1-7 days
    • Frequently infectious
    • May be foodborne, waterborne, or outbreak-associated
    • Most commonly caused by viruses and occasionally bacteria
    • Testing for gastrointestinal parasites generally not recommended for acute diarrheal episodes
  • Chronic diarrhea – duration >7 days, often longer
    • More commonly noninfectious
    • Testing for parasites should be considered

Most Common Causes of Chronic Diarrhea

Campylobacter species


  • Incidence – Campylobacter jejuni is the leading cause of bacterial gastroenteritis worldwide
  • Age – affects all age groups with peak incidence in children <5 years
  • Occurrence – Campylobacter-caused diarrheal cases are sporadic, but most occur in the spring and fall 
    • Associated with incorrect food handling practices, consumption of poorly cooked poultry or raw milk, contact with pets, travel
    • Outbreaks most often associated with raw milk and contaminated water


  • Campylobacter spp are motile, gram-negative curved, or spiral-shaped bacilli with fastidious growth requirements (microaerophilic)

Clinical Presentation

  • Campylobacter gastroenteritis ranges from asymptomatic infection to severe inflammatory diarrhea
  • Onset of symptoms occurs 2-5 days after ingestion of contaminated food or water
  • Symptoms – generally last 7-10 days
    • Abdominal pain
    • Watery stools containing blood and mucous
    • Fever
    • Nausea or vomiting
  • Complications


  • Antimicrobial and supportive care
Salmonella species


  • Incidence
    • 70% of U.S. cases are related to international travel
      • Remaining 30% of cases are from large, sporadic outbreaks
  • Transmission
    • Undercooked or uncooked foods, contact with infected animals
      • Associated foods include raw meat and vegetables, poultry, eggs, milk, salad dressing, shrimp, and peanut butter
    • Nonsymptomatic individuals can transmit disease to others
    • Incubation period is 3-21 days


  • Salmonella are motile gram-negative bacilli of the Enterobacteriaceae family
    • >2,400 serotypes
    • Etiologic agent of typhoid fever

Clinical Presentation

  • Typhoid fever
    • Prodrome of chills, headache, sore throat, fever, anorexia, cough
    • Progresses to rash (rose spots), epistaxis, diarrhea, relative bradycardia
    • 90% have positive blood cultures in week 1; drops to 50% by week 3
    • Complications
      • Late complications found in untreated adults, including intestinal perforation and gastrointestinal hemorrhage
      • Rare complications include pancreatitis, hepatic and splenic abscesses, endocarditis, pericarditis, orchitis, meningitis, parotitis, osteomyelitis
      • Up to 5% of infected individuals develop chronic carrier state
        • Usually occurs in patients with gall bladder disease or gastric carcinomas
      • Fatality rate is 10%
  • Enteritis
    • Onset of symptoms 6-48 hours after exposure; typically with resolves after 1-2 days
      • Fever, headache
      • Intestinal symptoms – diarrhea (watery), abdominal pain


  • Antimicrobial therapy in conjunction with supportive care
  • Mild symptomatic disease does not require antibiotic therapy
Escherichia coli


  • Incidence – the very young and elderly have greatest complications
  • Transmission
    • Person-to-person contact is a source of outbreak in daycare facilities and nursing homes
    • Outbreaks from consumption of undercooked meats and unwashed produce


  • E. coli is a gram-negative bacillus of the Enterobacteriaceae family
  • Shiga toxin-producing strains (eg, E. coli 0157:H7) cause hemorrhagic colitis and HUS
    • Also referred to as Shiga-like, toxin-producing E. coli or verotoxin-producing E. coli
  • Other types include enteropathogenic, enterotoxigenic, enteroinvasive, enteroaggregative, and diffusely adherent

Clinical Presentation

  • Watery diarrhea turning to bloody diarrhea
  • Abdominal pain
  • Symptoms usually resolve within 8 days
  • HUS – fever, renal dysfunction and hemolytic anemia, thrombocytopenia
    • Most frequent in children <15 years and adults >65 years


  • Supportive or antibiotics
    • Antibiotic usage in Shiga-like toxin-producing isolates is controversial due to potentially increased risk of developing HUS
  • Disease is usually self-limiting; treatment efficacy not well established
Shigella species


  • Incidence – prevalent worldwide distribution
    • Common in countries with poor sanitation
    • Accounts for <10% of reported outbreaks of foodborne illness in the U.S.
  • Transmission – fecal-oral route; no nonhuman hosts
    • Higher risk groups – daycare personnel and clients, nursing home residents, and male homosexuals


  • Shigella are gram-negative, nonmotile bacilli of the Enterobacteriaceae family
    • Agent of bacillary dysentery
    • 4 species – S. dysenteriae, S. flexneri, S. boydii, S. sonnei
  • Some strains produce enterotoxin and Shiga toxin

Clinical Presentation

  • Diarrhea (frequently bloody); may contain mucous or pus
  • Fever
  • Abdominal pain, cramps
  • Dysentery (10-30 stools/day)
  • Onset of symptoms 12-50 hours after exposure
  • Associated with Reiter syndrome (arthritis, uveitis, urethritis)
  • Complications
    • Reactive arthritis (increased risk of development if individual is positive for HLA-B27 allele)
    • HUS (usually S. dysenteriae type 1)


  • Antimicrobial and supportive care for moderate to severe infections
Yersinia species


  • Age – most often in young children
  • Transmission – soil, water, animals, food


  • Yersinia spp are gram-negative coccobacillary organisms of the Enterobacteriaceae family
    • 3 species most commonly isolated from humans – Y. pseudotuberculosis, Y. pestis, Y. enterocolitica
      • Y. pseudotuberculosis and Y. pestis are uncommon causes of gastrointestinal disease
      • Y. enterocolitica can be found in meats (eg, beef, pork), oysters, fish, and unpasteurized milk

Clinical Presentation

  • Onset of symptoms 24-48 hours after ingestion of contaminated food or drink
  • Infection manifests in gastrointestinal tract causing symptoms of diarrhea (loose, watery, or bloody stools), abdominal pain, and fever
    • Infections with Y. enterocolitica and Y. pseudotuberculosis can be asymptomatic, mild, or severe, with infection resolving within a few weeks (with or without use of antibiotics)
    • Yersinia infections are known for mimicking appendicitis
  • Complications include reactive arthritis which can manifest 1-4 weeks post-infection (increased risk of development if individual is positive for HLA-B27 allele)
    • Occurs in about 2-3% of cases
    • The most commonly affected joints are knees and ankles, but other joints such as toes, fingers and wrists can be involved
    • In most cases, 2-4 joints become involved sequentially and asymmetrically over a period of a few days to 2 weeks
    • Joint fluid is sterile
    • Chronic joint disease or ankylosing spondylitis occurs rarely
    • In two-thirds of cases, acute arthritis persists for 1-4 months
    • Reiter syndrome (arthritis, uveitis, and urethritis) occurs in 5% of cases
    • Less common nonsuppurative sequelae of Y. enterocolitica infections include reactive uveitis, iritis, conjunctivitis, glomerulonephritis, urethritis, HUS 


Antimicrobial-based in conjunction with supportive care

Vibrio species


  • Incidence
    • Several pandemics of Vibrio cholerae infection have occurred; no major outbreaks in U.S. since 1911
    • V. vulnificus outbreak reported in New Orleans after hurricane Katrina; usually several lethal cases annually in Florida, typically in summer months
  • Transmission
    • Ingestion of contaminated seafood or through open wounds in sea water


  • Vibrio are motile gram-negative bacilli of the Vibrionaceae family
  • Species that may cause gastroenteritis (with decreasing frequency) – V. parahaemolyticus, V. cholerae, V. vulnificus
  • Some strains produce enterotoxin and Shiga toxin
  • V. parahaemolyticus is the leading cause of bacterial diarrhea associated with foods such as seafood, crab, shrimp, lobster
  • V. vulnificus is the leading cause of death in the U.S. related to seafood consumption 
    • Fatalities are typically due to septicemia – more common in patients with hepatic disease

Clinical Presentation

  • Healthy individuals typically have onset of symptoms within 16 hours of ingestion of contaminated seafood
  • Watery diarrhea, abdominal pain, cramps, vomiting
  • Immunocompromised individuals and patients with cirrhosis may present with primary septicemia
    • Associated with >50% mortality
  • No associated long-term complications


  • Antimicrobial and supportive
Aeromonas species


  • Incidence
    • Causes sporadic cases of gastroenteritis
    • No associated known outbreaks
    • Most commonly affects children and immunocompromised adults
  • Transmission – ingestion of raw or undercooked seafood and meat


  • Motile gram-negative bacilli
  • Found in fresh and brackish waters
  • Species associated with enteritis are A. hydrophilia, A. caviae, A. veronii

Clinical Presentation

  • Diarrhea varies from watery to mucous with blood, abdominal pain, fever
  • Immunocompromised individuals may develop septicemia


  • Antimicrobial and supportive

Indications for Laboratory Testing

  • 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
Test Name and Number Recommended Use Limitations Follow Up
CBC with Platelet Count and Automated Differential 0040003
Method: Automated Cell Count/Differential

Nonspecific, may be helpful in differentiation of bacterial from nonbacterial infections

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

Preferred test for suspected bacterial diarrhea evaluation (most useful if diarrhea lasts ≥3 days or is bloody)

Cultures include Salmonella, Shigella, Campylobacter, and E. coli 0157, as well as EIA for Shiga-like toxin from E. coli

Campylobacter Antigen 0058002
Method: Qualitative Immunochromatography

Use in cases of reactive arthritis and Guillain-Barré syndrome following a history of diarrhea

Assay cannot differentiate between C. jejuni and C. coli

Assay will cross-react with C. upsaliensis

Data on detection of other Campylobacter spp is not available

Stool Culture, Campylobacter 0060135
Method: Culture/Identification

Diagnose Campylobacter-associated diarrhea in patients with appropriate exposure history or risk factors

Stool Culture, Yersinia 0060137
Method: Culture/Identification

Diagnose Yersinia-associated diarrhea in patients with appropriate exposure history or risk factors

Stool Culture, Vibrio 0060136
Method: Culture/Identification

Diagnose Vibrio-associated diarrhea in patients with appropriate exposure history or risk factors

Giardia Antigen by EIA 0060048
Method: Qualitative Enzyme Immunoassay

Test for persistent diarrhea (≥7 days) or known risk factors

Diagnose Giardia duodenalis (synonyms Giardia lamblia, Giardia intestinalis) as etiology of diarrheal disease

Rapid (24-hour) turnaround

Most sensitive method for detection of Giardia

Will not detect parasites other than G. duodenalis

Testing of second specimen may be indicated if first specimen is negative and clinical suspicion is high

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

If parasite infection is suspected as cause of persistent diarrhea (>5 to 7 days), specific pathogen testing is recommended (eg, Giardia antigen by EIA)

Do not order for patients who develop diarrhea during a prolonged hospitalization

Ova may not be detectable in early disease

Less sensitive than stool antigen tests for Giardia duodenalis, Cryptosporidium spp, or Entamoeba histolytica with persistent diarrhea

In patients with negative O & P and persistent diarrhea, follow up negative stool antigen EIA result for Giardia duodenalis (synonyms: Giardia intestinalis, Giardia lamblia), Cryptosporidium spp, or Entamoeba histolytica

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

Additional Tests Available
Click the plus sign to expand the table of additional tests.
Test Name and NumberComments
Campylobacter jejuni Antibody, IgG 0098841
Method: Semi-Quantitative Indirect Fluorescent Antibody
Lactoferrin, Fecal by ELISA 0061164
Method: Qualitative Enzyme-Linked Immunosorbent Assay

May be used for monitoring inflammatory bowel disease (IBD) activity and predicting relapse

May assist in differentiating IBD from functional disorders of the intestinal tract, such as irritable bowel syndrome (IBS)

Do not use to diagnose inflammatory bowel disease (IBD) or irritable bowel syndrome (IBS)

Salmonella typhi and paratyphi Antibodies 2010798
Method: Qualitative Immunoblot

Detects antibodies directed against 5 Salmonella typhi and paratyphi antigens: O Type D; O Type Vi; H Type A; H Type B; or H Type D

E. coli Shiga-like Toxin by EIA 0060047
Method: Qualitative Enzyme Immunoassay

Identifies presence of E. coli Shiga-like toxin; however, test will not determine specific serotypes of E. coli

Yersinia enterocolitica Antibodies, IgA, IgG, and IgM by Immunoblot 0051241
Method: Qualitative Immunoblot
Yersinia enterocolitica Antibody, IgG by Immunoblot 0051229
Method: Qualitative Immunoblot
Yersinia enterocolitica Antibody, IgM by Immunoblot 0051172
Method: Qualitative Immunoblot
Yersinia enterocolitica Antibody, IgA by Immunoblot 0051228
Method: Qualitative Immunoblot
Yersinia enterocolitica Antibodies, IgA and IgG by Immunoblot 0051230
Method: Qualitative Immunoblot
Parasitology Stain by Modified Acid-Fast 0060046
Method: Qualitative Concentration/Stain
Microsporidia Stain by Modified Trichrome 0060050
Method: Qualitative Stain